From 588042b69abf8e60bcc950b24c283933c7dd422f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 8 Jun 2005 13:41:35 +0000
Subject: [PATCH] Formatted source

---
 src/MCview/Atom.java                               |   79 +-
 src/MCview/Bond.java                               |  120 +-
 src/MCview/MCMatrix.java                           |  251 +-
 src/MCview/PDBChain.java                           |  431 +--
 src/MCview/PDBfile.java                            |  223 +-
 src/MCview/Residue.java                            |   36 +-
 src/MCview/Zsort.java                              |   74 +-
 src/MCview/myAtom.java                             |   79 +-
 src/MCview/rotCanvas.java                          | 1129 ++++----
 src/ext/vamsas/JPredWS.java                        |   30 +-
 src/ext/vamsas/JPredWSService.java                 |   26 +-
 src/ext/vamsas/JPredWSServiceLocator.java          |  270 +-
 src/ext/vamsas/JpredResult.java                    |  298 +-
 src/ext/vamsas/JpredSoapBindingStub.java           |  674 +++--
 src/ext/vamsas/Msfalignment.java                   |  295 +-
 src/ext/vamsas/MuscleWS.java                       |   31 +-
 src/ext/vamsas/MuscleWSService.java                |   27 +-
 src/ext/vamsas/MuscleWSServiceLocator.java         |  271 +-
 src/ext/vamsas/MuscleWSSoapBindingStub.java        |  696 ++---
 src/ext/vamsas/Result.java                         |  784 ++---
 src/ext/vamsas/Secstructpred.java                  |  232 +-
 src/ext/vamsas/Sequence.java                       |  295 +-
 src/jalview/analysis/AAFrequency.java              |  571 ++--
 src/jalview/analysis/AlignSeq.java                 |  944 +++---
 src/jalview/analysis/AlignmentSorter.java          |  497 ++--
 src/jalview/analysis/AlignmentUtil.java            |  326 +--
 src/jalview/analysis/CompareAlignments.java        |  197 +-
 src/jalview/analysis/Conservation.java             |  716 ++---
 src/jalview/analysis/NJTree.java                   | 1188 ++++----
 src/jalview/analysis/PCA.java                      |  321 ++-
 src/jalview/analysis/SeqsetUtils.java              |  209 +-
 src/jalview/analysis/SequenceIdMatcher.java        |  239 +-
 src/jalview/appletgui/APopupMenu.java              |  173 +-
 src/jalview/appletgui/AlignFrame.java              |  704 +++--
 src/jalview/appletgui/AlignViewport.java           |  491 ++--
 src/jalview/appletgui/AlignmentPanel.java          |  421 +--
 src/jalview/appletgui/AnnotationLabels.java        |  156 +-
 src/jalview/appletgui/AnnotationPanel.java         |  579 ++--
 src/jalview/appletgui/ColumnSelection.java         |   98 +-
 src/jalview/appletgui/CutAndPasteTransfer.java     |   62 +-
 src/jalview/appletgui/FeatureRenderer.java         |   89 +-
 src/jalview/appletgui/Finder.java                  |  272 +-
 src/jalview/appletgui/FontChooser.java             |   98 +-
 src/jalview/appletgui/IdCanvas.java                |  230 +-
 src/jalview/appletgui/IdPanel.java                 |  214 +-
 src/jalview/appletgui/IdwidthAdjuster.java         |   96 +-
 src/jalview/appletgui/OverviewPanel.java           |  241 +-
 src/jalview/appletgui/PCAPanel.java                |   90 +-
 src/jalview/appletgui/PaintRefresher.java          |   60 +-
 src/jalview/appletgui/PairwiseAlignPanel.java      |  138 +-
 src/jalview/appletgui/RedundancyPanel.java         |  148 +-
 src/jalview/appletgui/RotatableCanvas.java         |  491 ++--
 src/jalview/appletgui/ScalePanel.java              |  144 +-
 src/jalview/appletgui/SeqCanvas.java               |  474 +--
 src/jalview/appletgui/SeqPanel.java                |  722 +++--
 src/jalview/appletgui/SequenceRenderer.java        |  220 +-
 src/jalview/appletgui/SliderPanel.java             |  217 +-
 src/jalview/appletgui/TreeCanvas.java              |  568 ++--
 src/jalview/appletgui/TreePanel.java               |  186 +-
 src/jalview/appletgui/UserDefinedColours.java      |  227 +-
 src/jalview/bin/Cache.java                         |  151 +-
 src/jalview/bin/Jalview.java                       |  248 +-
 src/jalview/bin/JalviewLite.java                   |  220 +-
 src/jalview/binding/Alignment.java                 |  115 +-
 src/jalview/binding/Annotation.java                |  218 +-
 src/jalview/binding/AnnotationElement.java         |  177 +-
 src/jalview/binding/Colour.java                    |  115 +-
 src/jalview/binding/JGroup.java                    |  398 ++-
 src/jalview/binding/JSeq.java                      |  193 +-
 src/jalview/binding/JalviewModel.java              |  129 +-
 src/jalview/binding/JalviewModelSequence.java      |  359 +--
 src/jalview/binding/JalviewModelSequence2.java     |  171 +-
 src/jalview/binding/JalviewModelSequence2Item.java |  118 +-
 src/jalview/binding/JalviewUserColours.java        |  158 +-
 src/jalview/binding/JalviewUserColoursItem.java    |   53 +-
 src/jalview/binding/Residue.java                   |  127 +-
 src/jalview/binding/Sequence.java                  |   91 +-
 src/jalview/binding/SequenceSet.java               |  261 +-
 src/jalview/binding/SequenceType.java              |  127 +-
 src/jalview/binding/UserColour.java                |  128 +-
 src/jalview/binding/UserColourScheme.java          |   90 +-
 src/jalview/binding/UserColours.java               |  116 +-
 src/jalview/binding/VAMSAS.java                    |  300 +-
 src/jalview/binding/VamsasModel.java               |   91 +-
 src/jalview/binding/Viewport.java                  |  722 +++--
 src/jalview/datamodel/Alignment.java               |  876 +++---
 src/jalview/datamodel/AlignmentAnnotation.java     |  204 +-
 src/jalview/datamodel/AlignmentI.java              |  118 +-
 src/jalview/datamodel/AlignmentOrder.java          |  191 +-
 src/jalview/datamodel/Annotation.java              |   55 +-
 src/jalview/datamodel/BinaryNode.java              |  309 +-
 src/jalview/datamodel/BinarySequence.java          |  160 +-
 src/jalview/datamodel/HistoryItem.java             |   76 +-
 src/jalview/datamodel/Sequence.java                |  437 +--
 src/jalview/datamodel/SequenceFeature.java         |  141 +-
 src/jalview/datamodel/SequenceGroup.java           |  484 ++--
 src/jalview/datamodel/SequenceI.java               |   63 +-
 src/jalview/datamodel/SequenceNode.java            |  108 +-
 src/jalview/datamodel/SequencePoint.java           |   23 +-
 src/jalview/datamodel/SuperGroup.java              |  159 +-
 src/jalview/gui/AlignFrame.java                    | 3018 +++++++++++---------
 src/jalview/gui/AlignViewport.java                 |  590 ++--
 src/jalview/gui/AlignmentPanel.java                |  805 +++---
 src/jalview/gui/AnnotationLabels.java              |  362 ++-
 src/jalview/gui/AnnotationPanel.java               |  828 +++---
 src/jalview/gui/ColumnSelection.java               |  102 +-
 src/jalview/gui/CutAndPasteTransfer.java           |  245 +-
 src/jalview/gui/Desktop.java                       |  683 +++--
 src/jalview/gui/FeatureRenderer.java               |  101 +-
 src/jalview/gui/Finder.java                        |  327 ++-
 src/jalview/gui/FontChooser.java                   |  131 +-
 src/jalview/gui/IdCanvas.java                      |  247 +-
 src/jalview/gui/IdPanel.java                       |  258 +-
 src/jalview/gui/IdwidthAdjuster.java               |  108 +-
 src/jalview/gui/Jalview2XML.java                   |  761 ++---
 src/jalview/gui/OverviewPanel.java                 |  278 +-
 src/jalview/gui/PCAPanel.java                      |  111 +-
 src/jalview/gui/PaintRefresher.java                |   64 +-
 src/jalview/gui/PairwiseAlignPanel.java            |  170 +-
 src/jalview/gui/PopupMenu.java                     |  283 +-
 src/jalview/gui/Preferences.java                   |  379 ++-
 src/jalview/gui/RedundancyPanel.java               |   85 +-
 src/jalview/gui/RotatableCanvas.java               |  597 ++--
 src/jalview/gui/ScalePanel.java                    |  174 +-
 src/jalview/gui/SeqCanvas.java                     |  582 ++--
 src/jalview/gui/SeqPanel.java                      |  731 +++--
 src/jalview/gui/SequenceRenderer.java              |  237 +-
 src/jalview/gui/SliderPanel.java                   |  300 +-
 src/jalview/gui/SplashScreen.java                  |  113 +-
 src/jalview/gui/TreeCanvas.java                    |  661 +++--
 src/jalview/gui/TreePanel.java                     |  366 ++-
 src/jalview/gui/UserDefinedColours.java            |  304 +-
 src/jalview/gui/WebserviceInfo.java                |  160 +-
 src/jalview/io/AlignFile.java                      |  165 +-
 src/jalview/io/BLCFile.java                        |  280 +-
 src/jalview/io/ClustalFile.java                    |  315 +-
 src/jalview/io/EBIFetchClient.java                 |  262 +-
 src/jalview/io/FastaFile.java                      |  291 +-
 src/jalview/io/FileParse.java                      |   66 +-
 src/jalview/io/FormatAdapter.java                  |  156 +-
 src/jalview/io/HTMLOutput.java                     |  399 +--
 src/jalview/io/IdentifyFile.java                   |  143 +-
 src/jalview/io/JPredFile.java                      |  555 ++--
 src/jalview/io/JalviewFileChooser.java             |  701 ++---
 src/jalview/io/JalviewFileFilter.java              |  228 +-
 src/jalview/io/JalviewFileView.java                |  139 +-
 src/jalview/io/MSFfile.java                        |  440 +--
 src/jalview/io/NewickFile.java                     | 1032 ++++---
 src/jalview/io/PIRFile.java                        |  210 +-
 src/jalview/io/PfamFile.java                       |  267 +-
 src/jalview/io/PileUpfile.java                     |  489 ++--
 src/jalview/io/SequenceFeatureFetcher.java         |  680 ++---
 src/jalview/io/WSWUBlastClient.java                |  322 ++-
 src/jalview/jbappletgui/GAlignFrame.java           | 1762 +++++-------
 src/jalview/jbappletgui/GAlignmentPanel.java       |  146 +-
 src/jalview/jbappletgui/GCutAndPasteTransfer.java  |  110 +-
 src/jalview/jbappletgui/GFinder.java               |  185 +-
 src/jalview/jbappletgui/GFontChooser.java          |  230 +-
 src/jalview/jbappletgui/GPCAPanel.java             |  147 +-
 src/jalview/jbappletgui/GPairwiseAlignPanel.java   |   71 +-
 src/jalview/jbappletgui/GSliderPanel.java          |  187 +-
 src/jalview/jbappletgui/GTreePanel.java            |  208 +-
 src/jalview/jbappletgui/GUserDefinedColours.java   |  337 +--
 src/jalview/jbgui/GAlignFrame.java                 | 2102 ++++++--------
 src/jalview/jbgui/GAlignmentPanel.java             |  175 +-
 src/jalview/jbgui/GCutAndPasteTransfer.java        |  219 +-
 src/jalview/jbgui/GDesktop.java                    |  329 +--
 src/jalview/jbgui/GFinder.java                     |  190 +-
 src/jalview/jbgui/GFontChooser.java                |  267 +-
 src/jalview/jbgui/GPCAPanel.java                   |  180 +-
 src/jalview/jbgui/GPairwiseAlignPanel.java         |  100 +-
 src/jalview/jbgui/GPreferences.java                |  376 ++-
 src/jalview/jbgui/GSliderPanel.java                |  237 +-
 src/jalview/jbgui/GTreePanel.java                  |  331 +--
 src/jalview/jbgui/GUserDefinedColours.java         |  188 +-
 src/jalview/jbgui/GWebserviceInfo.java             |  160 +-
 src/jalview/math/Matrix.java                       | 1057 +++----
 src/jalview/math/RotatableMatrix.java              |  417 +--
 src/jalview/schemes/Blosum62ColourScheme.java      |   77 +-
 src/jalview/schemes/BuriedColourScheme.java        |   16 +-
 src/jalview/schemes/ClustalxColourScheme.java      |  458 ++-
 src/jalview/schemes/ColourSchemeI.java             |   14 +-
 src/jalview/schemes/ColourSchemeProperty.java      |  338 ++-
 src/jalview/schemes/Consensus.java                 |   73 +-
 src/jalview/schemes/ConservationColourScheme.java  |  140 +-
 src/jalview/schemes/HelixColourScheme.java         |   17 +-
 src/jalview/schemes/HydrophobicColourScheme.java   |   16 +-
 src/jalview/schemes/NucleotideColourScheme.java    |   51 +-
 src/jalview/schemes/PIDColourScheme.java           |   54 +-
 src/jalview/schemes/ResidueColourScheme.java       |   68 +-
 src/jalview/schemes/ResidueProperties.java         | 2110 +++++++-------
 src/jalview/schemes/ScoreColourScheme.java         |   66 +-
 src/jalview/schemes/StrandColourScheme.java        |   18 +-
 src/jalview/schemes/TaylorColourScheme.java        |    9 +-
 src/jalview/schemes/TurnColourScheme.java          |   17 +-
 src/jalview/schemes/UserColourScheme.java          |   19 +-
 src/jalview/schemes/ZappoColourScheme.java         |    8 +-
 src/jalview/util/BrowserLauncher.java              | 1264 ++++----
 src/jalview/util/Comparison.java                   |  297 +-
 src/jalview/util/Format.java                       | 1151 ++++----
 src/jalview/util/QuickSort.java                    |  153 +-
 src/jalview/ws/JPredClient.java                    |  729 +++--
 src/jalview/ws/MsaWSClient.java                    |  694 ++---
 src/jalview/ws/MsaWServices.java                   |   63 +-
 src/jalview/ws/WSClient.java                       |   46 +-
 src/jalview/ws/WSClientI.java                      |   17 +-
 src/vamsas/objects/simple/Alignment.java           |  271 +-
 src/vamsas/objects/simple/Alignment_Helper.java    |  117 +-
 src/vamsas/objects/simple/MsaResult.java           |  151 +-
 src/vamsas/objects/simple/MsaResult_Helper.java    |   95 +-
 src/vamsas/objects/simple/Object.java              |   92 +-
 src/vamsas/objects/simple/Object_Helper.java       |   83 +-
 src/vamsas/objects/simple/Result.java              |  582 ++--
 src/vamsas/objects/simple/Result_Helper.java       |  205 +-
 src/vamsas/objects/simple/Sequence.java            |  201 +-
 src/vamsas/objects/simple/SequenceSet.java         |  166 +-
 src/vamsas/objects/simple/SequenceSet_Helper.java  |   95 +-
 src/vamsas/objects/simple/Sequence_Helper.java     |  106 +-
 src/vamsas/objects/simple/WsJobId.java             |  193 +-
 src/vamsas/objects/simple/WsJobId_Helper.java      |  106 +-
 220 files changed, 35766 insertions(+), 33140 deletions(-)

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index b3a8fdb..0aaf040 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -16,56 +16,57 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
-import java.util.*;
+
 import java.awt.*;
 
-public class Atom {
-  double x;
-  double y;
-  double z;
-  int number;
-  String name;
-  String resName;
-  int resNumber;
-  int type;
-  Color color;
-  String chain;
+import java.util.*;
 
-  public Atom(StringTokenizer str) {
-    this.number  = (new Integer(str.nextToken())).intValue();
-    this.name    = str.nextToken();
-    this.resName = str.nextToken();
 
-    String tmpstr = new String();
+public class Atom {
+    double x;
+    double y;
+    double z;
+    int number;
+    String name;
+    String resName;
+    int resNumber;
+    int type;
+    Color color;
+    String chain;
 
-    try {
-      tmpstr = str.nextToken();
+    public Atom(StringTokenizer str) {
+        this.number = (new Integer(str.nextToken())).intValue();
+        this.name = str.nextToken();
+        this.resName = str.nextToken();
 
-      this.resNumber = (new Integer(tmpstr).intValue());
-      this.chain     = "A";
-      this.color     = Color.green;
+        String tmpstr = new String();
 
-    } catch(NumberFormatException e) {
-      this.chain = tmpstr;
+        try {
+            tmpstr = str.nextToken();
 
-      if (tmpstr.equals("A")) {
-        this.color = new Color((float)Math.random(),(float)Math.random(),(float)Math.random());
-      } else {
-        this.color = Color.red;
-      }
-      this.resNumber = (new Integer(str.nextToken()).intValue());
-    }
+            this.resNumber = (new Integer(tmpstr).intValue());
+            this.chain = "A";
+            this.color = Color.green;
+        } catch (NumberFormatException e) {
+            this.chain = tmpstr;
 
-    this.x = (double)(new Double(str.nextToken()).floatValue());
-    this.y = (double)(new Double(str.nextToken()).floatValue());
-    this.z = (double)(new Double(str.nextToken()).floatValue());
+            if (tmpstr.equals("A")) {
+                this.color = new Color((float) Math.random(),
+                        (float) Math.random(), (float) Math.random());
+            } else {
+                this.color = Color.red;
+            }
 
-  }
+            this.resNumber = (new Integer(str.nextToken()).intValue());
+        }
 
-  public void setColor(Color col) {
-    this.color = col;
-  }
+        this.x = (double) (new Double(str.nextToken()).floatValue());
+        this.y = (double) (new Double(str.nextToken()).floatValue());
+        this.z = (double) (new Double(str.nextToken()).floatValue());
+    }
 
+    public void setColor(Color col) {
+        this.color = col;
+    }
 }
diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index c84152a..17f66bb 100755
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -16,69 +16,69 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
 
 import java.awt.*;
 
-public class Bond {
-
-  float start[];
-  float end[];
-
-  Color startCol;
-  Color endCol;
-
-  public myAtom at1;
-  public myAtom at2;
-
-  public Bond(float[] start, float[] end, myAtom at1, myAtom at2) {
-    this.start    = start;
-    this.end      = end;
-    this.startCol = at1.color;
-    this.endCol   = at2.color;
-    this.at1      = at1;
-    this.at2      = at2;
-  }
-  public Bond(Bond bond) {
-    this.start    = new float[3];
-
-    this.start[0] = bond.start[0];
-    this.start[1] = bond.start[1];
-    this.start[2] = bond.start[2];
-
-    this.end    = new float[3];
 
-    this.end[0] = bond.end[0];
-    this.end[1] = bond.end[1];
-    this.end[2] = bond.end[2];
-
-    this.startCol = bond.startCol;
-    this.endCol   = bond.endCol;
-  }
-
-  public void print() {
-    System.out.println("Start " + start[0] + " "+ start[1] + " " + start[2]);
-    System.out.println("End   " + end[0] + " "+ end[1] + " " + end[2]);
-  }
-
-  public float length() {
-    float len = (end[0] - start[0])*(end[0] - start[0]) +
-                (end[1] - start[1])*(end[1] - start[1]) +
-                (end[2] - start[2])*(end[2] - start[2]);
-
-    len = (float)(Math.sqrt(len));
-
-    return len;
-  }
-  public void translate(float x, float y, float z) {
-    start[0] = (start[0] + x);
-    end[0]   = (end[0] + x);
-
-    start[1] = (start[1] + y);
-    end[1]   = (end[1] + y);
-
-    start[2] = (start[2] + z);
-    end[2]   = (end[2] + z);
-  }
+public class Bond {
+    float[] start;
+    float[] end;
+    Color startCol;
+    Color endCol;
+    public myAtom at1;
+    public myAtom at2;
+
+    public Bond(float[] start, float[] end, myAtom at1, myAtom at2) {
+        this.start = start;
+        this.end = end;
+        this.startCol = at1.color;
+        this.endCol = at2.color;
+        this.at1 = at1;
+        this.at2 = at2;
+    }
+
+    public Bond(Bond bond) {
+        this.start = new float[3];
+
+        this.start[0] = bond.start[0];
+        this.start[1] = bond.start[1];
+        this.start[2] = bond.start[2];
+
+        this.end = new float[3];
+
+        this.end[0] = bond.end[0];
+        this.end[1] = bond.end[1];
+        this.end[2] = bond.end[2];
+
+        this.startCol = bond.startCol;
+        this.endCol = bond.endCol;
+    }
+
+    public void print() {
+        System.out.println("Start " + start[0] + " " + start[1] + " " +
+            start[2]);
+        System.out.println("End   " + end[0] + " " + end[1] + " " + end[2]);
+    }
+
+    public float length() {
+        float len = ((end[0] - start[0]) * (end[0] - start[0])) +
+            ((end[1] - start[1]) * (end[1] - start[1])) +
+            ((end[2] - start[2]) * (end[2] - start[2]));
+
+        len = (float) (Math.sqrt(len));
+
+        return len;
+    }
+
+    public void translate(float x, float y, float z) {
+        start[0] = (start[0] + x);
+        end[0] = (end[0] + x);
+
+        start[1] = (start[1] + y);
+        end[1] = (end[1] + y);
+
+        start[2] = (start[2] + z);
+        end[2] = (end[2] + z);
+    }
 }
diff --git a/src/MCview/MCMatrix.java b/src/MCview/MCMatrix.java
index 31af9d4..2effba6 100755
--- a/src/MCview/MCMatrix.java
+++ b/src/MCview/MCMatrix.java
@@ -16,147 +16,146 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
 
 public class MCMatrix {
-  float matrix[][];
-  float tmp[][];
-
-  float mycos;
-  float mysin;
-  float myconst = (float)(Math.PI/180);
-
-  public MCMatrix(int rows, int cols) {
-    matrix = new float[rows][cols];
-    tmp    = new float[rows][cols];
-  }
-
-  public void addElement(int i, int j, float value) {
-    matrix[i][j] = value;
-  }
-
-  public void print() {
-    System.out.println(matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);
-    System.out.println(matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);
-    System.out.println(matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);
-  }
-
-  public void rotatex(float degrees) {
-    mycos = (float)(Math.cos(degrees*myconst));
-    mysin = (float)(Math.sin(degrees*myconst));
-
-    tmp[0][0] = 1;
-    tmp[0][1] = 0;
-    tmp[0][2] = 0;
-    tmp[1][0] = 0;
-    tmp[1][1] = mycos;
-    tmp[1][2] = mysin;
-    tmp[2][0] = 0;
-    tmp[2][1] = -mysin;
-    tmp[2][2] = mycos;
-    preMultiply(tmp);
-  }
-
-  public void rotatez(float degrees) {
-    mycos = (float)(Math.cos(degrees*myconst));
-    mysin = (float)(Math.sin(degrees*myconst));
-
-    tmp[0][0] = mycos;
-    tmp[0][1] = -mysin;
-    tmp[0][2] = 0;
-    tmp[1][0] = mysin;
-    tmp[1][1] = mycos;
-    tmp[1][2] = 0;
-    tmp[2][0] = 0;
-    tmp[2][1] = 0;
-    tmp[2][2] = 1;
-
-    preMultiply(tmp);
-  }
-
-  public void rotatey(float degrees) {
-    mycos = (float)(Math.cos(degrees*myconst));
-    mysin = (float)(Math.sin(degrees*myconst));
-
-    tmp[0][0] = mycos;
-    tmp[0][1] = 0;
-    tmp[0][2] = -mysin;
-    tmp[1][0] = 0;
-    tmp[1][1] = 1;
-    tmp[1][2] = 0;
-    tmp[2][0] = mysin;
-    tmp[2][1] = 0;
-    tmp[2][2] = mycos;
-
-    preMultiply(tmp);
-  }
-
-  public float[] vectorMultiply(float[] vect) {
-    float temp[] = new float[3];
-
-    temp[0] = vect[0];
-    temp[1] = vect[1];
-    temp[2] = vect[2];
-
-    for (int i = 0; i < 3; i++) {
-      temp[i] = (float)matrix[i][0]*vect[0] + (float)matrix[i][1]*vect[1] +(float)matrix[i][2]*vect[2];
+    float[][] matrix;
+    float[][] tmp;
+    float mycos;
+    float mysin;
+    float myconst = (float) (Math.PI / 180);
+
+    public MCMatrix(int rows, int cols) {
+        matrix = new float[rows][cols];
+        tmp = new float[rows][cols];
     }
 
-    vect[0] = temp[0];
-    vect[1] = temp[1];
-    vect[2] = temp[2];
+    public void addElement(int i, int j, float value) {
+        matrix[i][j] = value;
+    }
 
-    return vect;
-  }
+    public void print() {
+        System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +
+            matrix[0][2]);
+        System.out.println(matrix[1][0] + " " + matrix[1][1] + " " +
+            matrix[1][2]);
+        System.out.println(matrix[2][0] + " " + matrix[2][1] + " " +
+            matrix[2][2]);
+    }
 
-  public void preMultiply(float mat[][]) {
-    float tmp[][]  = new float[3][3];
+    public void rotatex(float degrees) {
+        mycos = (float) (Math.cos(degrees * myconst));
+        mysin = (float) (Math.sin(degrees * myconst));
+
+        tmp[0][0] = 1;
+        tmp[0][1] = 0;
+        tmp[0][2] = 0;
+        tmp[1][0] = 0;
+        tmp[1][1] = mycos;
+        tmp[1][2] = mysin;
+        tmp[2][0] = 0;
+        tmp[2][1] = -mysin;
+        tmp[2][2] = mycos;
+        preMultiply(tmp);
+    }
 
-    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];
-      }
+    public void rotatez(float degrees) {
+        mycos = (float) (Math.cos(degrees * myconst));
+        mysin = (float) (Math.sin(degrees * myconst));
+
+        tmp[0][0] = mycos;
+        tmp[0][1] = -mysin;
+        tmp[0][2] = 0;
+        tmp[1][0] = mysin;
+        tmp[1][1] = mycos;
+        tmp[1][2] = 0;
+        tmp[2][0] = 0;
+        tmp[2][1] = 0;
+        tmp[2][2] = 1;
+
+        preMultiply(tmp);
     }
 
-    for (int i = 0; i < 3 ; i++) {
-      for (int j = 0; j < 3; j++ ) {
-        matrix[i][j] = tmp[i][j];
-      }
+    public void rotatey(float degrees) {
+        mycos = (float) (Math.cos(degrees * myconst));
+        mysin = (float) (Math.sin(degrees * myconst));
+
+        tmp[0][0] = mycos;
+        tmp[0][1] = 0;
+        tmp[0][2] = -mysin;
+        tmp[1][0] = 0;
+        tmp[1][1] = 1;
+        tmp[1][2] = 0;
+        tmp[2][0] = mysin;
+        tmp[2][1] = 0;
+        tmp[2][2] = mycos;
+
+        preMultiply(tmp);
     }
-  }
 
-  public void postMultiply(float mat[][]) {
-    float tmp[][]  = new float[3][3];
+    public float[] vectorMultiply(float[] vect) {
+        float[] temp = new float[3];
+
+        temp[0] = vect[0];
+        temp[1] = vect[1];
+        temp[2] = vect[2];
+
+        for (int i = 0; i < 3; i++) {
+            temp[i] = ((float) matrix[i][0] * vect[0]) +
+                ((float) matrix[i][1] * vect[1]) +
+                ((float) matrix[i][2] * vect[2]);
+        }
 
-    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];
-      }
+        vect[0] = temp[0];
+        vect[1] = temp[1];
+        vect[2] = temp[2];
+
+        return vect;
     }
 
-    for (int i = 0; i < 3 ; i++) {
-      for (int j = 0; j < 3; j++ ) {
-        matrix[i][j] = tmp[i][j];
-      }
+    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++) {
+                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++) {
+                matrix[i][j] = tmp[i][j];
+            }
+        }
     }
-  }
-
-  public void setIdentity() {
-    matrix[0][0] = 1;
-    matrix[1][1] = 1;
-    matrix[2][2] = 1;
-    matrix[0][1] = 0;
-    matrix[0][2] = 0;
-    matrix[1][0] = 0;
-    matrix[1][2] = 0;
-    matrix[2][0] = 0;
-    matrix[2][1] = 0;
-  }
-}
 
+    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++) {
+                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++) {
+                matrix[i][j] = tmp[i][j];
+            }
+        }
+    }
 
+    public void setIdentity() {
+        matrix[0][0] = 1;
+        matrix[1][1] = 1;
+        matrix[2][2] = 1;
+        matrix[0][1] = 0;
+        matrix[0][2] = 0;
+        matrix[1][0] = 0;
+        matrix[1][2] = 0;
+        matrix[2][0] = 0;
+        matrix[2][1] = 0;
+    }
+}
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index fdb74bd..4bfe255 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -16,253 +16,268 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
 
 import jalview.datamodel.*;
+
 import jalview.schemes.ResidueProperties;
 
 import java.awt.*;
+
 import java.util.*;
 
 
 public class PDBChain {
+    public String id;
+    public Vector bonds = new Vector();
+    public Vector atoms = new Vector();
+    public Vector residues = new Vector();
+    public int offset;
+    public Sequence sequence;
+    public boolean isVisible = false;
+    public int pdbstart = 0;
+    public int pdbend = 0;
+    public int seqstart = 0;
+    public int seqend = 0;
+
+    //public DrawableSequence ds;
+    public PDBChain(String id) {
+        this.id = id;
+    }
 
-  public String id;
-  public Vector bonds = new Vector();
-  public Vector atoms = new Vector();
-  public Vector residues = new Vector();
-  public int offset;
-
-  public Sequence sequence;
-  public boolean isVisible = false;
-
-  public int pdbstart=0, pdbend=0, seqstart=0, seqend=0;
-
-  //public DrawableSequence ds;
-
-  public PDBChain(String id) {
-    this.id = id;
-  }
-
+    public String print() {
+        String tmp = "";
 
-  public String print() {
-    String tmp = "";
-    for (int i=0; i < bonds.size() ;i++) {
-      tmp = tmp + ((Bond)bonds.elementAt(i)).at1.resName + " " + ((Bond)bonds.elementAt(i)).at1.resNumber +" " + offset+ "\n";
-    }
-    return tmp;
-  }
-  public void makeCaBondList() {
-    for (int i = 0; i < (residues.size() - 1) ; i++) {
-      Residue tmpres = (Residue)residues.elementAt(i);
-      Residue tmpres2 = (Residue)residues.elementAt(i+1);
-      myAtom at1 = tmpres.findAtom("CA");
-      myAtom at2 = tmpres2.findAtom("CA");
-      if ((at1 != null) && (at2 != null)) {
-        if (at1.chain.equals(at2.chain)) {
-          makeBond(at1,at2);
-        }
-      }
-    }
-  }
-
-  public void makeBond(myAtom at1, myAtom at2) {
-    float[] start = new float[3];
-    float[] end = new float[3];
-
-    start[0] = at1.x;
-    start[1] = at1.y;
-    start[2] = at1.z;
-
-    end[0] = at2.x;
-    end[1] = at2.y;
-    end[2] = at2.z;
-
-    bonds.addElement(new Bond(start, end, at1,at2));
-  }
-
-  public void makeResidueList() {
-    int count = 0;
-    String seq = "";
-    for (int i = 0; i < atoms.size(); i++) {
-
-      myAtom tmp = (myAtom)atoms.elementAt(i);
-      String resName = tmp.resName;
-      int resNumber = tmp.resNumber;
-      int res = resNumber;
-
-      if (i ==0) {
-        offset = resNumber;
-      }
-      Vector resAtoms = new Vector();
-
-      resAtoms.addElement((myAtom)atoms.elementAt(i));
-      i++;
-      resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
-
-      //Add atoms to a vector while the residue number
-      //remains the same
-      while ((resNumber == res) && (i < atoms.size())) {
-
-        resAtoms.addElement((myAtom)atoms.elementAt(i));
-        i++;
-        if (i < atoms.size()) {
-          resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
-        } else {
-          resNumber++;
+        for (int i = 0; i < bonds.size(); i++) {
+            tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " " +
+                ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset +
+                "\n";
         }
-      }
-
-      //We need this to keep in step with the outer for i = loop
-      i--;
-
-      //Make a new Residue object with the new atoms vector
-      residues.addElement(new Residue(resAtoms, resNumber - 1,count));
-      count++;
-      Residue tmpres = (Residue)residues.lastElement();
-      myAtom tmpat = (myAtom)tmpres.atoms.elementAt(0);
-
-      // Keep totting up the sequence
-      if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
-        System.err.println("PDBReader:Null aa3Hash for " + tmpat.resName);
-      } else {
-        String tmpres2 =
-          ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()];
-        seq = seq + tmpres2;
-      }
-      //      System.out.println(tmpat.resName + " " + tmpres2);
+
+        return tmp;
     }
-    sequence = new Sequence("PDB_seq",seq,1,seq.length());
-    System.out.println("PDB Sequence is :\nSequence = " + seq);
-    System.out.println("No of residues = " +residues.size());
-  }
-
-  public void setChargeColours() {
-    for (int i = 0; i < bonds.size(); i++) {
-      try {
-        Bond b = (Bond)bonds.elementAt(i);
-
-        if (b.at1.resName.toUpperCase().equals("ASP") || b.at1.resName.toUpperCase().equals("GLU")) {
-          b.startCol = Color.red;
-        } else if (b.at1.resName.toUpperCase().equals("LYS") || b.at1.resName.toUpperCase().equals("ARG")) {
-          b.startCol = Color.blue;
-        } else if (b.at1.resName.toUpperCase().equals("CYS")) {
-          b.startCol = Color.yellow;
-        } else {
-          int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
-          b.startCol = Color.lightGray;
-        }
-        if (b.at2.resName.toUpperCase().equals("ASP") || b.at2.resName.toUpperCase().equals("GLU")) {
-          b.endCol = Color.red;
-        } else if (b.at2.resName.toUpperCase().equals("LYS") || b.at2.resName.toUpperCase().equals("ARG")) {
-          b.endCol = Color.blue;
-        } else if (b.at2.resName.toUpperCase().equals("CYS")) {
-          b.endCol = Color.yellow;
-        } else {
-          int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
-          b.endCol = Color.lightGray;
+
+    public void makeCaBondList() {
+        for (int i = 0; i < (residues.size() - 1); i++) {
+            Residue tmpres = (Residue) residues.elementAt(i);
+            Residue tmpres2 = (Residue) residues.elementAt(i + 1);
+            myAtom at1 = tmpres.findAtom("CA");
+            myAtom at2 = tmpres2.findAtom("CA");
+
+            if ((at1 != null) && (at2 != null)) {
+                if (at1.chain.equals(at2.chain)) {
+                    makeBond(at1, at2);
+                }
+            }
         }
-      } catch (Exception e) {
-        Bond b = (Bond)bonds.elementAt(i);
-        b.startCol = Color.gray;
-        b.endCol = Color.gray;
-      }
     }
-  }
 
-  public void setHydrophobicityColours() {
-    float hydmin = (float)ResidueProperties.getHydmin();
-    float hydmax = (float)ResidueProperties.getHydmax();
-    double[] hyd  = ResidueProperties.getHyd();
+    public void makeBond(myAtom at1, myAtom at2) {
+        float[] start = new float[3];
+        float[] end = new float[3];
 
-    Hashtable AA3Hash = ResidueProperties.getAA3Hash();
+        start[0] = at1.x;
+        start[1] = at1.y;
+        start[2] = at1.z;
 
-    for (int i = 0; i < bonds.size(); i++) {
-      try {
-        Bond b = (Bond)bonds.elementAt(i);
+        end[0] = at2.x;
+        end[1] = at2.y;
+        end[2] = at2.z;
 
-        int   atno = ((Integer)AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
-        float red  = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
+        bonds.addElement(new Bond(start, end, at1, at2));
+    }
 
-        if (red > (float)1.0) {
-          red = (float)1.0;
-        }
-        if (red < (float)0.0) {
-          red = (float)0.0;
+    public void makeResidueList() {
+        int count = 0;
+        String seq = "";
+
+        for (int i = 0; i < atoms.size(); i++) {
+            myAtom tmp = (myAtom) atoms.elementAt(i);
+            String resName = tmp.resName;
+            int resNumber = tmp.resNumber;
+            int res = resNumber;
+
+            if (i == 0) {
+                offset = resNumber;
+            }
+
+            Vector resAtoms = new Vector();
+
+            resAtoms.addElement((myAtom) atoms.elementAt(i));
+            i++;
+            resNumber = ((myAtom) atoms.elementAt(i)).resNumber;
+
+            //Add atoms to a vector while the residue number
+            //remains the same
+            while ((resNumber == res) && (i < atoms.size())) {
+                resAtoms.addElement((myAtom) atoms.elementAt(i));
+                i++;
+
+                if (i < atoms.size()) {
+                    resNumber = ((myAtom) atoms.elementAt(i)).resNumber;
+                } else {
+                    resNumber++;
+                }
+            }
+
+            //We need this to keep in step with the outer for i = loop
+            i--;
+
+            //Make a new Residue object with the new atoms vector
+            residues.addElement(new Residue(resAtoms, resNumber - 1, count));
+            count++;
+
+            Residue tmpres = (Residue) residues.lastElement();
+            myAtom tmpat = (myAtom) tmpres.atoms.elementAt(0);
+
+            // Keep totting up the sequence
+            if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
+                System.err.println("PDBReader:Null aa3Hash for " +
+                    tmpat.resName);
+            } else {
+                String tmpres2 = ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
+                                                                                  .get(tmpat.resName)).intValue()];
+                seq = seq + tmpres2;
+            }
+
+            //      System.out.println(tmpat.resName + " " + tmpres2);
         }
 
-        b.startCol = new Color(red,(float)0.0,(float)1.0-red);
-        atno = ((Integer)AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
-
-        red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
+        sequence = new Sequence("PDB_seq", seq, 1, seq.length());
+        System.out.println("PDB Sequence is :\nSequence = " + seq);
+        System.out.println("No of residues = " + residues.size());
+    }
 
-        if (red > (float)1.0) {
-          red = (float)1.0;
+    public void setChargeColours() {
+        for (int i = 0; i < bonds.size(); i++) {
+            try {
+                Bond b = (Bond) bonds.elementAt(i);
+
+                if (b.at1.resName.toUpperCase().equals("ASP") ||
+                        b.at1.resName.toUpperCase().equals("GLU")) {
+                    b.startCol = Color.red;
+                } else if (b.at1.resName.toUpperCase().equals("LYS") ||
+                        b.at1.resName.toUpperCase().equals("ARG")) {
+                    b.startCol = Color.blue;
+                } else if (b.at1.resName.toUpperCase().equals("CYS")) {
+                    b.startCol = Color.yellow;
+                } else {
+                    int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
+                    b.startCol = Color.lightGray;
+                }
+
+                if (b.at2.resName.toUpperCase().equals("ASP") ||
+                        b.at2.resName.toUpperCase().equals("GLU")) {
+                    b.endCol = Color.red;
+                } else if (b.at2.resName.toUpperCase().equals("LYS") ||
+                        b.at2.resName.toUpperCase().equals("ARG")) {
+                    b.endCol = Color.blue;
+                } else if (b.at2.resName.toUpperCase().equals("CYS")) {
+                    b.endCol = Color.yellow;
+                } else {
+                    int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
+                    b.endCol = Color.lightGray;
+                }
+            } catch (Exception e) {
+                Bond b = (Bond) bonds.elementAt(i);
+                b.startCol = Color.gray;
+                b.endCol = Color.gray;
+            }
         }
-        if (red < (float)0.0) {
-          red = (float)0.0;
-        }
-
-        b.endCol = new Color(red,(float)0.2,(float)1.0-red);
-      } catch (Exception e) {
-        Bond b = (Bond)bonds.elementAt(i);
-        b.startCol = Color.gray;
-        b.endCol = Color.gray;
-      }
     }
-  }
-
 
-  public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
-jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
+    public void setHydrophobicityColours() {
+        float hydmin = (float) ResidueProperties.getHydmin();
+        float hydmax = (float) ResidueProperties.getHydmax();
+        double[] hyd = ResidueProperties.getHyd();
 
+        Hashtable AA3Hash = ResidueProperties.getAA3Hash();
 
-    for (int i = 0; i < bonds.size(); i++) {
-      Bond tmp = (Bond)bonds.elementAt(i);
-      try {
+        for (int i = 0; i < bonds.size(); i++) {
+            try {
+                Bond b = (Bond) bonds.elementAt(i);
 
-        if (tmp.at1.resNumber >= (offset + pdbstart - 1) && tmp.at1.resNumber <= (offset + pdbend - 1)) {
+                int atno = ((Integer) AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
+                float red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
 
-          int pos   = seqstart + (tmp.at1.resNumber - pdbstart - offset) ;
-          int index = seq.findIndex(pos);
+                if (red > (float) 1.0) {
+                    red = (float) 1.0;
+                }
 
+                if (red < (float) 0.0) {
+                    red = (float) 0.0;
+                }
 
-          tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
+                b.startCol = new Color(red, (float) 0.0, (float) 1.0 - red);
+                atno = ((Integer) AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
 
-        } else {
-          tmp.startCol = Color.gray;
-        }
+                red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
 
-        if (tmp.at2.resNumber >= (offset + pdbstart -1) && tmp.at2.resNumber <= (pdbend+offset-1)) {
+                if (red > (float) 1.0) {
+                    red = (float) 1.0;
+                }
 
-          int pos    = seqstart + (tmp.at2.resNumber - pdbstart-offset);
-          int index  = seq.findIndex(pos);
+                if (red < (float) 0.0) {
+                    red = (float) 0.0;
+                }
 
-          tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
+                b.endCol = new Color(red, (float) 0.2, (float) 1.0 - red);
+            } catch (Exception e) {
+                Bond b = (Bond) bonds.elementAt(i);
+                b.startCol = Color.gray;
+                b.endCol = Color.gray;
+            }
+        }
+    }
 
-        } else {
-          tmp.endCol = Color.gray;
+    public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
+        jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
+
+        for (int i = 0; i < bonds.size(); i++) {
+            Bond tmp = (Bond) bonds.elementAt(i);
+
+            try {
+                if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&
+                        (tmp.at1.resNumber <= ((offset + pdbend) - 1))) {
+                    int pos = seqstart +
+                        (tmp.at1.resNumber - pdbstart - offset);
+                    int index = seq.findIndex(pos);
+
+                    tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),
+                            seq, index);
+                } else {
+                    tmp.startCol = Color.gray;
+                }
+
+                if ((tmp.at2.resNumber >= ((offset + pdbstart) - 1)) &&
+                        (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {
+                    int pos = seqstart +
+                        (tmp.at2.resNumber - pdbstart - offset);
+                    int index = seq.findIndex(pos);
+
+                    tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),
+                            seq, index);
+                } else {
+                    tmp.endCol = Color.gray;
+                }
+            } catch (Exception e) {
+                tmp.startCol = Color.lightGray;
+                tmp.endCol = Color.lightGray;
+            }
         }
-      } catch (Exception e) {
-        tmp.startCol = Color.lightGray;
-        tmp.endCol = Color.lightGray;
-      }
     }
-  }
-
-  public void setChainColours() {
-    for (int i = 0; i < bonds.size(); i++) {
-      Bond tmp = (Bond)bonds.elementAt(i);
-      try {
-        tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
-        tmp.endCol   = (Color) ResidueProperties.getChainColours().get(id);
-      } catch (Exception e) {
-        tmp.startCol = Color.lightGray;
-        tmp.endCol   = Color.lightGray;
-      }
+
+    public void setChainColours() {
+        for (int i = 0; i < bonds.size(); i++) {
+            Bond tmp = (Bond) bonds.elementAt(i);
+
+            try {
+                tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
+                tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);
+            } catch (Exception e) {
+                tmp.startCol = Color.lightGray;
+                tmp.endCol = Color.lightGray;
+            }
+        }
     }
-  }
 }
-
-
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 1937a8f..71d8c11 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -16,149 +16,150 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
 
 import jalview.datamodel.*;
+
 import java.io.*;
+
 import java.net.*;
+
 import java.util.*;
 
 
 public class PDBfile extends jalview.io.FileParse {
+    public Vector chains = new Vector();
+    Vector lineArray = new Vector();
 
-  public Vector chains = new Vector();
+    public PDBfile(String[] lines) {
+        for (int i = 0; i < lines.length; i++)
+            lineArray.addElement(lines[i]);
 
-  Vector lineArray = new Vector();
-
-  public PDBfile(String [] lines)
-  {
-    for(int i=0; i<lines.length; i++)
-      lineArray.addElement(lines[i]);
+        noLines = lineArray.size();
+        parse();
+    }
 
-    noLines = lineArray.size();
-    parse();
-  }
+    public PDBfile(String inFile, String inType) throws IOException {
+        super(inFile, inType);
 
-  public PDBfile(String inFile, String inType) throws IOException {
+        String line;
+        this.lineArray = new Vector();
 
-    super(inFile,inType);
+        BufferedReader dataIn;
 
-    String line;
-    this.lineArray = new Vector();
-    BufferedReader dataIn;
+        if (inType.equals("File")) {
+            dataIn = new BufferedReader(new FileReader(inFile));
+        }
+        else {
+            URL url = new URL(inFile);
+            this.fileSize = 0;
+            dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+        }
 
-    if (inType.equals("File"))
-      dataIn =  new BufferedReader(new FileReader( inFile ));
+        while ((line = dataIn.readLine()) != null) {
+            lineArray.addElement(line);
+        }
 
-    else
-    {
-      URL url = new URL(inFile);
-      this.fileSize = 0;
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    }
+        noLines = lineArray.size();
 
-    while ((line = dataIn.readLine()) != null) {
-      lineArray.addElement(line);
+        parse();
     }
-    noLines = lineArray.size();
 
-    parse();
+    public void parse() {
+        for (int i = 0; i < lineArray.size(); i++) {
+            StringTokenizer str = new StringTokenizer(lineArray.elementAt(i)
+                                                               .toString());
+
+            if (str.hasMoreTokens()) {
+                String inStr = str.nextToken();
+
+                if (inStr.indexOf("ATOM") != -1) {
+                    try {
+                        myAtom tmpatom = new myAtom(str);
+
+                        if (findChain(tmpatom.chain) != null) {
+                            //   System.out.println("Adding to chain " + tmpatom.chain);
+                            findChain(tmpatom.chain).atoms.addElement(tmpatom);
+                        } else {
+                            //  System.out.println("Making chain " + tmpatom.chain);
+                            PDBChain tmpchain = new PDBChain(tmpatom.chain);
+                            chains.addElement(tmpchain);
+                            tmpchain.atoms.addElement(tmpatom);
+                        }
+                    } catch (NumberFormatException e) {
+                        System.err.println("Caught" + e);
+                        System.err.println("Record not added to PDB model:" +
+                            lineArray.elementAt(i).toString());
+                    }
+                }
+            }
+        }
 
-}
+        makeResidueList();
+        makeCaBondList();
 
+        //    for (int i=0; i < chains.size() ; i++) {
+        //  String pog = ((PDBChain)chains.elementAt(i)).print();
+        //  System.out.println(pog);
+        // }
+    }
 
-  public void parse() {
-
-    for (int i = 0; i < lineArray.size(); i++) {
-      StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
-      if (str.hasMoreTokens()) {
-        String inStr = str.nextToken();
-
-        if (inStr.indexOf("ATOM") != -1) {
-          try {
-            myAtom tmpatom = new myAtom(str);
-            if (findChain(tmpatom.chain) != null) {
-           //   System.out.println("Adding to chain " + tmpatom.chain);
-              findChain(tmpatom.chain).atoms.addElement(tmpatom);
-            } else {
-            //  System.out.println("Making chain " + tmpatom.chain);
-              PDBChain tmpchain = new PDBChain(tmpatom.chain);
-              chains.addElement(tmpchain);
-              tmpchain.atoms.addElement(tmpatom);
-            }
-          } catch(NumberFormatException e) {
-            System.err.println("Caught" +  e);
-            System.err.println("Record not added to PDB model:"+lineArray.elementAt(i).toString());
-          }
+    public void makeResidueList() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).makeResidueList();
         }
-      }
-    }
-    makeResidueList();
-    makeCaBondList();
-    //    for (int i=0; i < chains.size() ; i++) {
-    //  String pog = ((PDBChain)chains.elementAt(i)).print();
-    //  System.out.println(pog);
-    // }
-  }
-
-  public void makeResidueList() {
-    for (int i=0; i < chains.size() ; i++) {
-      ((PDBChain)chains.elementAt(i)).makeResidueList();
     }
-  }
-  public void makeCaBondList() {
-    for (int i=0; i < chains.size() ; i++) {
-      ((PDBChain)chains.elementAt(i)).makeCaBondList();
-    }
-  }
-
-  public PDBChain findChain(String id) {
-    for (int i=0; i < chains.size(); i++) {
-      // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
-      if (((PDBChain)chains.elementAt(i)).id.equals(id)) {
-        return (PDBChain)chains.elementAt(i);
-      }
+
+    public void makeCaBondList() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).makeCaBondList();
+        }
     }
-    return null;
-  }
 
+    public PDBChain findChain(String id) {
+        for (int i = 0; i < chains.size(); i++) {
+            // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
+            if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
+                return (PDBChain) chains.elementAt(i);
+            }
+        }
 
-  public void setChargeColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChargeColours();
+        return null;
     }
-  }
 
-  public void setHydrophobicityColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();
-    }
-  }
-
-  public void colourBySequence(Sequence seq) {
-//SMJS TODO
-//    int max = seq.maxchain;
-//    if (seq.maxchain != -1) {
-//      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
-//    }
-  }
-
-  public void setChainColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChainColours();
+    public void setChargeColours() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setChargeColours();
+        }
     }
-  }
-  public static void main(String[] args) {
-    try {
-      PDBfile pdb = new PDBfile("enkp1.pdb","File");
-    } catch(IOException e) {
-      System.out.println(e);
-      e.printStackTrace();
-      System.exit(0);
+
+    public void setHydrophobicityColours() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setHydrophobicityColours();
+        }
     }
-  }
-}
 
+    public void colourBySequence(Sequence seq) {
+        //SMJS TODO
+        //    int max = seq.maxchain;
+        //    if (seq.maxchain != -1) {
+        //      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
+        //    }
+    }
 
+    public void setChainColours() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setChainColours();
+        }
+    }
 
+    public static void main(String[] args) {
+        try {
+            PDBfile pdb = new PDBfile("enkp1.pdb", "File");
+        } catch (IOException e) {
+            System.out.println(e);
+            e.printStackTrace();
+            System.exit(0);
+        }
+    }
+}
diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java
index 998e388..b01d982 100755
--- a/src/MCview/Residue.java
+++ b/src/MCview/Residue.java
@@ -16,32 +16,30 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
 
 import java.util.*;
 
 
 public class Residue {
-  Vector atoms = new Vector();
-
-  int number;
-  int count;
-  int seqnumber;
-
-  public Residue(Vector atoms, int number, int count) {
-    this.atoms  = atoms;
-    this.number = number;
-    this.count  = count;
-  }
+    Vector atoms = new Vector();
+    int number;
+    int count;
+    int seqnumber;
+
+    public Residue(Vector atoms, int number, int count) {
+        this.atoms = atoms;
+        this.number = number;
+        this.count = count;
+    }
 
-  public myAtom findAtom(String name) {
+    public myAtom findAtom(String name) {
+        for (int i = 0; i < atoms.size(); i++) {
+            if (((myAtom) atoms.elementAt(i)).name.equals(name)) {
+                return (myAtom) atoms.elementAt(i);
+            }
+        }
 
-    for (int i = 0; i < atoms.size(); i++) {
-      if (((myAtom)atoms.elementAt(i)).name.equals(name)) {
-        return (myAtom)atoms.elementAt(i);
-      }
+        return null;
     }
-    return null;
-  }
 }
diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index 215f753..322fd2a 100755
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -16,54 +16,48 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
 
 import java.util.*;
 
-public class Zsort {
-
-  public static void Zsort(Vector bonds) {
-
-    sort(bonds,0,bonds.size()-1);
-  }
-
-
-
-  public static void sort(Vector bonds,int p, int r) {
-    int q;
 
-    if (p < r) {
-      q = partition(bonds,p,r);
-      sort(bonds,p,q);
-      sort(bonds,q+1,r);
+public class Zsort {
+    public static void Zsort(Vector bonds) {
+        sort(bonds, 0, bonds.size() - 1);
     }
-  }
-
-  private static int partition(Vector bonds, int p, int r) {
-    float x = ((Bond)bonds.elementAt(p)).start[2];
-    int i = p-1;
-    int j = r+1;
 
-    while(true) {
-      do {
-        j = j-1;
-      }	while (j >= 0  && ((Bond)bonds.elementAt(j)).start[2] > x);
+    public static void sort(Vector bonds, int p, int r) {
+        int q;
 
-      do {
-        i = i+1;
-      } while (i < bonds.size() && ((Bond)bonds.elementAt(i)).start[2] < x);
+        if (p < r) {
+            q = partition(bonds, p, r);
+            sort(bonds, p, q);
+            sort(bonds, q + 1, r);
+        }
+    }
 
-      if ( i < j) {
-        Bond tmp = (Bond)bonds.elementAt(i);
-        bonds.setElementAt(bonds.elementAt(j),i);
-        bonds.setElementAt(tmp,j);
-      } else {
-        return j;
-      }
+    private static int partition(Vector bonds, int p, int r) {
+        float x = ((Bond) bonds.elementAt(p)).start[2];
+        int i = p - 1;
+        int j = r + 1;
+
+        while (true) {
+            do {
+                j = j - 1;
+            } while ((j >= 0) && (((Bond) bonds.elementAt(j)).start[2] > x));
+
+            do {
+                i = i + 1;
+            } while ((i < bonds.size()) &&
+                    (((Bond) bonds.elementAt(i)).start[2] < x));
+
+            if (i < j) {
+                Bond tmp = (Bond) bonds.elementAt(i);
+                bonds.setElementAt(bonds.elementAt(j), i);
+                bonds.setElementAt(tmp, j);
+            } else {
+                return j;
+            }
+        }
     }
-  }
 }
-
-
-
diff --git a/src/MCview/myAtom.java b/src/MCview/myAtom.java
index 27a4b08..75dec37 100755
--- a/src/MCview/myAtom.java
+++ b/src/MCview/myAtom.java
@@ -16,59 +16,56 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
 
-import java.util.*;
 import java.awt.*;
 
-public class myAtom {
-  float x;
-  float y;
-  float z;
-
-  public int     number;
-  public String  name;
-  public String  resName;
-  public int     resNumber;
-  public int     type;
-  public Color   color;
-  public String  chain;
-  public boolean isSelected = false;
+import java.util.*;
 
-  public myAtom(StringTokenizer str) {
 
-    this.number  = (new Integer(str.nextToken())).intValue();
-    this.name    = str.nextToken();
-    this.resName = str.nextToken();
+public class myAtom {
+    float x;
+    float y;
+    float z;
+    public int number;
+    public String name;
+    public String resName;
+    public int resNumber;
+    public int type;
+    public Color color;
+    public String chain;
+    public boolean isSelected = false;
 
-    String tmpstr = new String();
+    public myAtom(StringTokenizer str) {
+        this.number = (new Integer(str.nextToken())).intValue();
+        this.name = str.nextToken();
+        this.resName = str.nextToken();
 
-    try {
-      tmpstr         = str.nextToken();
-      this.resNumber = (new Integer(tmpstr).intValue());
-      this.chain     = "A";
-      this.color     = Color.lightGray;
+        String tmpstr = new String();
 
-    } catch(NumberFormatException e) {
-      this.chain = tmpstr;
+        try {
+            tmpstr = str.nextToken();
+            this.resNumber = (new Integer(tmpstr).intValue());
+            this.chain = "A";
+            this.color = Color.lightGray;
+        } catch (NumberFormatException e) {
+            this.chain = tmpstr;
 
-      if (tmpstr.equals("A")) {
-        this.color = Color.lightGray;
+            if (tmpstr.equals("A")) {
+                this.color = Color.lightGray;
+            } else {
+                this.color = Color.red;
+            }
 
-      } else {
-        this.color = Color.red;
-      }
+            this.resNumber = (new Integer(str.nextToken()).intValue());
+        }
 
-      this.resNumber = (new Integer(str.nextToken()).intValue());
+        this.x = (float) (new Float(str.nextToken()).floatValue());
+        this.y = (float) (new Float(str.nextToken()).floatValue());
+        this.z = (float) (new Float(str.nextToken()).floatValue());
     }
 
-    this.x = (float)(new Float(str.nextToken()).floatValue());
-    this.y = (float)(new Float(str.nextToken()).floatValue());
-    this.z = (float)(new Float(str.nextToken()).floatValue());
-  }
-
-  public void setColor(Color col) {
-    this.color = col;
-  }
+    public void setColor(Color col) {
+        this.color = col;
+    }
 }
diff --git a/src/MCview/rotCanvas.java b/src/MCview/rotCanvas.java
index a165129..154e7e6 100755
--- a/src/MCview/rotCanvas.java
+++ b/src/MCview/rotCanvas.java
@@ -16,709 +16,712 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package MCview;
-// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.*;
-import java.awt.event.*;
-import java.util.*;
-import java.io.*;
-import javax.swing.*;
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.*;
-
-public class rotCanvas extends JPanel implements KeyListener,
-                                                 MouseListener,
-                                                 MouseMotionListener {
-  MCMatrix  idmat  = new MCMatrix(3,3);
-  MCMatrix  objmat = new MCMatrix(3,3);
-
-  boolean redrawneeded =true;
-
-  int omx = 0;
-  int mx = 0;
-  int omy = 0;
-  int my = 0;
-
-  public PDBfile pdb;
-
-  int bsize;
-
-  Image img;
-  Graphics ig;
 
-  Dimension prefsize;
-
-  float centre[] = new float[3];
-  float width[]  = new float[3];
+import jalview.analysis.AlignSeq;
 
-  float maxwidth;
-  float scale;
+import jalview.datamodel.*;
 
-  String inStr;
-  String inType;
+// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
+import java.awt.*;
+import java.awt.event.*;
 
-  boolean depthcue   = true;
-  boolean wire       = false;
-  boolean bymolecule = false;
-  boolean zbuffer    = true;
+import java.io.*;
 
-  boolean dragging;
+import java.util.*;
 
-  int xstart;
-  int xend;
-  int ystart;
-  int yend;
-  int xmid;
-  int ymid;
+import javax.swing.*;
 
-  Font font = new Font("Helvetica",Font.PLAIN,10);
 
-  public rotCanvas(PDBfile pdb, Sequence sequence, jalview.gui.AlignViewport av) throws IOException {
+public class rotCanvas extends JPanel implements KeyListener, MouseListener,
+    MouseMotionListener {
+    MCMatrix idmat = new MCMatrix(3, 3);
+    MCMatrix objmat = new MCMatrix(3, 3);
+    boolean redrawneeded = true;
+    int omx = 0;
+    int mx = 0;
+    int omy = 0;
+    int my = 0;
+    public PDBfile pdb;
+    int bsize;
+    Image img;
+    Graphics ig;
+    Dimension prefsize;
+    float[] centre = new float[3];
+    float[] width = new float[3];
+    float maxwidth;
+    float scale;
+    String inStr;
+    String inType;
+    boolean depthcue = true;
+    boolean wire = false;
+    boolean bymolecule = false;
+    boolean zbuffer = true;
+    boolean dragging;
+    int xstart;
+    int xend;
+    int ystart;
+    int yend;
+    int xmid;
+    int ymid;
+    Font font = new Font("Helvetica", Font.PLAIN, 10);
+
+    public rotCanvas(PDBfile pdb, Sequence sequence,
+        jalview.gui.AlignViewport av) throws IOException {
+        int max = -10;
+        int maxchain = -1;
+        int pdbstart = 0;
+        int pdbend = 0;
+        int seqstart = 0;
+        int seqend = 0;
+
+        for (int i = 0; i < pdb.chains.size(); i++) {
+            // Now lets compare the sequences to get
+            // the start and end points.
+            java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(),
+                    ".");
+            String newString = "";
+
+            while (str.hasMoreTokens()) {
+                newString += str.nextToken();
+            }
 
-    int max = -10;
-    int maxchain = -1;
-    int pdbstart=0, pdbend=0,  seqstart =0,  seqend=0;
+            // Align the sequence to the pdb
+            AlignSeq as = new AlignSeq(sequence,
+                    ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
+            as.calcScoreMatrix();
+            as.traceAlignment();
+            as.printAlignment();
+
+            if (as.maxscore > max) {
+                max = as.maxscore;
+                maxchain = i;
+
+                pdbstart = as.seq2start;
+                pdbend = as.seq2end;
+                seqstart = as.seq1start - 1;
+                seqend = as.seq1end - 1;
+            }
 
+            System.out.println("PDB start/end " + pdbstart + " " + pdbend);
+            System.out.println("SEQ start/end " + seqstart + " " + seqend);
+        }
 
-    for (int i=0; i < pdb.chains.size(); i++) {
-      // Now lets compare the sequences to get
-      // the start and end points.
+        ((PDBChain) pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).pdbend = pdbend;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).seqstart = seqstart;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).seqend = seqend;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).colourBySequence(av,
+            sequence);
+
+        this.pdb = pdb;
+        this.prefsize = new Dimension(getWidth(), getHeight());
+
+        //Initialize the matrices to identity
+        for (int i = 0; i < 3; i++) {
+            for (int j = 0; j < 3; j++) {
+                if (i != j) {
+                    idmat.addElement(i, j, 0);
+                    objmat.addElement(i, j, 0);
+                } else {
+                    idmat.addElement(i, j, 1);
+                    objmat.addElement(i, j, 1);
+                }
+            }
+        }
 
-    java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(), ".");
-    String newString = "";
+        addMouseMotionListener(this);
+        addMouseListener(this);
+        addKeyListener(this);
 
-    while (str.hasMoreTokens()) {
-        newString += str.nextToken();
-    }
-      // Align the sequence to the pdb
-      AlignSeq as = new AlignSeq(sequence,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");
-      as.calcScoreMatrix();
-      as.traceAlignment();
-      as.printAlignment();
-
-      if (as.maxscore > max) {
-        max = as.maxscore;
-        maxchain = i;
-
-        pdbstart = as.seq2start;
-        pdbend = as.seq2end;
-        seqstart = as.seq1start  - 1 ;
-        seqend = as.seq1end  -1;
-      }
-
-      System.out.println("PDB start/end " + pdbstart + " " + pdbend);
-      System.out.println("SEQ start/end " + seqstart + " " + seqend);
+        addPDBfile();
+        ToolTipManager.sharedInstance().registerComponent(this);
     }
 
+    public void addPDBfile() {
+        findCentre();
+        findWidth();
 
-    ( (PDBChain)pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;
-    ( (PDBChain)pdb.chains.elementAt(maxchain)).pdbend = pdbend;
-    ( (PDBChain)pdb.chains.elementAt(maxchain)).seqstart = seqstart;
-     ( (PDBChain)pdb.chains.elementAt(maxchain)).seqend = seqend;
-     ( (PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;
-     ( (PDBChain) pdb.chains.elementAt(maxchain)).sequence = sequence;
-     ( (PDBChain)pdb.chains.elementAt(maxchain)).colourBySequence(av, sequence);
+        scale = findScale();
 
+        System.out.println("Scale factor = " + scale);
+    }
 
+    public void deleteBonds() {
+        scale = 0;
+        maxwidth = 0;
 
-    this.pdb      = pdb;
-    this.prefsize = new Dimension( getWidth(), getHeight());
+        width[0] = 0;
+        width[1] = 0;
+        width[2] = 0;
 
-    //Initialize the matrices to identity
+        centre[0] = 0;
+        centre[1] = 0;
+        centre[2] = 0;
 
-    for (int i = 0; i < 3; i++) {
-      for (int j = 0; j < 3 ; j++) {
-        if (i != j) {
-          idmat.addElement(i,j,0);
-          objmat.addElement(i,j,0);
-        } else {
-          idmat.addElement(i,j,1);
-          objmat.addElement(i,j,1);
+        for (int i = 0; i < pdb.chains.size(); i++) {
+            ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
         }
-      }
     }
 
-    addMouseMotionListener(this);
-    addMouseListener(this);
-    addKeyListener(this);
-
-    addPDBfile();
-    ToolTipManager.sharedInstance().registerComponent(this);
-
-  }
+    public void findWidth() {
+        float[] max = new float[3];
+        float[] min = new float[3];
 
-  public void addPDBfile() {
-    findCentre();
-    findWidth();
+        max[0] = (float) -1e30;
+        max[1] = (float) -1e30;
+        max[2] = (float) -1e30;
 
-    scale = findScale();
+        min[0] = (float) 1e30;
+        min[1] = (float) 1e30;
+        min[2] = (float) 1e30;
 
-    System.out.println("Scale factor = " + scale);
-  }
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
+                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-  public void deleteBonds() {
-    scale     = 0;
-    maxwidth  = 0;
+                for (int i = 0; i < bonds.size(); i++) {
+                    Bond tmp = (Bond) bonds.elementAt(i);
 
-    width[0] = 0;
-    width[1] = 0;
-    width[2] = 0;
+                    if (tmp.start[0] >= max[0]) {
+                        max[0] = tmp.start[0];
+                    }
 
-    centre[0] = 0;
-    centre[1] = 0;
-    centre[2] = 0;
+                    if (tmp.start[1] >= max[1]) {
+                        max[1] = tmp.start[1];
+                    }
 
-    for (int i=0; i < pdb.chains.size(); i++) {
-      ((PDBChain)pdb.chains.elementAt(i)).bonds = null;
-    }
-  }
+                    if (tmp.start[2] >= max[2]) {
+                        max[2] = tmp.start[2];
+                    }
 
-  public void findWidth() {
-    float max[] = new float[3];
-    float min[] = new float[3];
+                    if (tmp.start[0] <= min[0]) {
+                        min[0] = tmp.start[0];
+                    }
 
-    max[0] = (float)-1e30;
-    max[1] = (float)-1e30;
-    max[2] = (float)-1e30;
+                    if (tmp.start[1] <= min[1]) {
+                        min[1] = tmp.start[1];
+                    }
 
-    min[0] = (float)1e30;
-    min[1] = (float)1e30;
-    min[2] = (float)1e30;
+                    if (tmp.start[2] <= min[2]) {
+                        min[2] = tmp.start[2];
+                    }
 
-    for (int ii=0; ii < pdb.chains.size(); ii++) {
-      if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
+                    if (tmp.end[0] >= max[0]) {
+                        max[0] = tmp.end[0];
+                    }
 
-        Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
+                    if (tmp.end[1] >= max[1]) {
+                        max[1] = tmp.end[1];
+                    }
 
-        for (int i = 0; i < bonds.size(); i++) {
-          Bond tmp = (Bond)bonds.elementAt(i);
-
-          if (tmp.start[0] >= max[0])
-            max[0] = tmp.start[0];
-          if (tmp.start[1] >= max[1])
-            max[1] = tmp.start[1];
-          if (tmp.start[2] >= max[2])
-            max[2] = tmp.start[2];
-          if (tmp.start[0] <= min[0])
-            min[0] = tmp.start[0];
-          if (tmp.start[1] <= min[1])
-            min[1] = tmp.start[1];
-          if (tmp.start[2] <= min[2])
-            min[2] = tmp.start[2];
-
-          if (tmp.end[0] >= max[0])
-            max[0] = tmp.end[0];
-          if (tmp.end[1] >= max[1])
-            max[1] = tmp.end[1];
-          if (tmp.end[2] >= max[2])
-            max[2] = tmp.end[2];
-          if (tmp.end[0] <= min[0])
-            min[0] = tmp.end[0];
-          if (tmp.end[1] <= min[1])
-            min[1] = tmp.end[1];
-          if (tmp.end[2] <= min[2])
-            min[2] = tmp.end[2];
-        }
-      }
-    }
+                    if (tmp.end[2] >= max[2]) {
+                        max[2] = tmp.end[2];
+                    }
 
-    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]);
+                    if (tmp.end[0] <= min[0]) {
+                        min[0] = tmp.end[0];
+                    }
 
-    width[0] = (float)Math.abs(max[0] - min[0]);
-    width[1] = (float)Math.abs(max[1] - min[1]);
-    width[2] = (float)Math.abs(max[2] - min[2]);
+                    if (tmp.end[1] <= min[1]) {
+                        min[1] = tmp.end[1];
+                    }
 
-    maxwidth = width[0];
+                    if (tmp.end[2] <= min[2]) {
+                        min[2] = tmp.end[2];
+                    }
+                }
+            }
+        }
 
-    if (width[1] > width[0])
-      maxwidth = width[1];
-    if (width[2] > width[1])
-      maxwidth = width[2];
+        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]);
 
-    System.out.println("Maxwidth = " + maxwidth);
-  }
+        width[0] = (float) Math.abs(max[0] - min[0]);
+        width[1] = (float) Math.abs(max[1] - min[1]);
+        width[2] = (float) Math.abs(max[2] - min[2]);
 
-  public float findScale() {
-    int dim, width, height;
+        maxwidth = width[0];
 
-    if ( getWidth() != 0) {
-      width  = getWidth();
-      height = getHeight();
+        if (width[1] > width[0]) {
+            maxwidth = width[1];
+        }
 
-    } else {
-      width  = prefsize.width;
-      height = prefsize.height;
-    }
+        if (width[2] > width[1]) {
+            maxwidth = width[2];
+        }
 
-    if (width < height) {
-      dim = width;
-    } else {
-      dim = height;
+        System.out.println("Maxwidth = " + maxwidth);
     }
 
-    return (float)(dim/(1.5d*maxwidth));
-  }
-
+    public float findScale() {
+        int dim;
+        int width;
+        int height;
 
+        if (getWidth() != 0) {
+            width = getWidth();
+            height = getHeight();
+        } else {
+            width = prefsize.width;
+            height = prefsize.height;
+        }
 
-  public void findCentre() {
-    float xtot = 0;
-    float ytot = 0;
-    float ztot = 0;
+        if (width < height) {
+            dim = width;
+        } else {
+            dim = height;
+        }
 
-    int bsize  = 0;
-    //Find centre coordinate
+        return (float) (dim / (1.5d * maxwidth));
+    }
 
-    for (int ii = 0; ii < pdb.chains.size() ; ii++) {
-      if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
+    public void findCentre() {
+        float xtot = 0;
+        float ytot = 0;
+        float ztot = 0;
 
-        Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
+        int bsize = 0;
 
-        bsize += bonds.size();
+        //Find centre coordinate
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
+                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-        for (int i = 0; i < bonds.size(); i++) {
+                bsize += bonds.size();
 
-          xtot = xtot + ((Bond)bonds.elementAt(i)).start[0] +
-                 ((Bond)bonds.elementAt(i)).end[0];
+                for (int i = 0; i < bonds.size(); i++) {
+                    xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] +
+                        ((Bond) bonds.elementAt(i)).end[0];
 
-          ytot = ytot + ((Bond)bonds.elementAt(i)).start[1] +
-                 ((Bond)bonds.elementAt(i)).end[1];
+                    ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] +
+                        ((Bond) bonds.elementAt(i)).end[1];
 
-          ztot = ztot + ((Bond)bonds.elementAt(i)).start[2] +
-                 ((Bond)bonds.elementAt(i)).end[2];
+                    ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] +
+                        ((Bond) bonds.elementAt(i)).end[2];
+                }
+            }
         }
-      }
+
+        centre[0] = xtot / (2 * (float) bsize);
+        centre[1] = ytot / (2 * (float) bsize);
+        centre[2] = ztot / (2 * (float) bsize);
     }
 
-    centre[0] = xtot / (2 * (float)bsize);
-    centre[1] = ytot / (2 * (float)bsize);
-    centre[2] = ztot / (2 * (float)bsize);
-  }
+    public void paint(Graphics g) {
+        //Only create the image at the beginning -
+        //this saves much memory usage
+        if ((img == null) || (prefsize.width != getWidth()) ||
+                (prefsize.height != getHeight())) {
+            prefsize.width = getWidth();
+            prefsize.height = getHeight();
 
-  public void paint(Graphics g) {
-    //Only create the image at the beginning -
-    //this saves much memory usage
-    if ((img == null) || (prefsize.width != getWidth()) || (prefsize.height != getHeight())) {
-      prefsize.width  = getWidth();
-      prefsize.height = getHeight();
+            scale = findScale();
+            img = createImage(prefsize.width, prefsize.height);
+            ig = img.getGraphics();
 
-      scale = findScale();
-      img   = createImage(prefsize.width,prefsize.height);
-      ig    = img.getGraphics();
+            redrawneeded = true;
+        }
 
-      redrawneeded = true;
-    }
+        if (redrawneeded == true) {
+            drawBackground(ig, Color.black);
+            drawScene(ig);
+            redrawneeded = false;
+        } else {
+            ig = img.getGraphics();
+        }
 
-    if (redrawneeded == true) {
-      drawBackground(ig,Color.black);
-      drawScene(ig);
-      redrawneeded = false;
-    } else {
-      ig = img.getGraphics();
+        g.drawImage(img, 0, 0, this);
     }
 
-    g.drawImage(img,0,0,this);
-  }
+    public void drawBackground(Graphics g, Color col) {
+        g.setColor(col);
+        g.fillRect(0, 0, prefsize.width, prefsize.height);
+    }
 
-  public void drawBackground(Graphics g, Color col) {
-    g.setColor(col);
-    g.fillRect(0,0,prefsize.width,prefsize.height);
-  }
+    public void drawScene(Graphics g) {
+        // Sort the bonds by z coord
+        Vector bonds = new Vector();
 
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
+                Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-  public void drawScene(Graphics g) {
-    // Sort the bonds by z coord
+                for (int i = 0; i < tmp.size(); i++) {
+                    bonds.addElement(tmp.elementAt(i));
+                }
+            }
+        }
 
-    Vector bonds = new Vector();
+        if (zbuffer) {
+            Zsort.Zsort(bonds);
+        }
 
+        for (int i = 0; i < bonds.size(); i++) {
+            Bond tmpBond = (Bond) bonds.elementAt(i);
+
+            xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
+                (getWidth() / 2));
+            ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
+                (getHeight() / 2));
+
+            xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
+                (getWidth() / 2));
+            yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
+                (getHeight() / 2));
+
+            xmid = (xend + xstart) / 2;
+            ymid = (yend + ystart) / 2;
+
+            if (depthcue && !bymolecule) {
+                if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
+                    g.setColor(tmpBond.startCol.darker().darker());
+                    drawLine(g, xstart, ystart, xmid, ymid);
+
+                    g.setColor(tmpBond.endCol.darker().darker());
+                    drawLine(g, xmid, ymid, xend, yend);
+                } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
+                    g.setColor(tmpBond.startCol.darker());
+                    drawLine(g, xstart, ystart, xmid, ymid);
+
+                    g.setColor(tmpBond.endCol.darker());
+                    drawLine(g, xmid, ymid, xend, yend);
+                } else {
+                    g.setColor(tmpBond.startCol);
+                    drawLine(g, xstart, ystart, xmid, ymid);
+
+                    g.setColor(tmpBond.endCol);
+                    drawLine(g, xmid, ymid, xend, yend);
+                }
+            } else if (depthcue && bymolecule) {
+                if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
+                    g.setColor(Color.green.darker().darker());
+                    drawLine(g, xstart, ystart, xend, yend);
+                } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
+                    g.setColor(Color.green.darker());
+                    drawLine(g, xstart, ystart, xend, yend);
+                } else {
+                    g.setColor(Color.green);
+                    drawLine(g, xstart, ystart, xend, yend);
+                }
+            } else if (!depthcue && !bymolecule) {
+                g.setColor(tmpBond.startCol);
+                drawLine(g, xstart, ystart, xmid, ymid);
+                g.setColor(tmpBond.endCol);
+                drawLine(g, xmid, ymid, xend, yend);
+            } else {
+                drawLine(g, xstart, ystart, xend, yend);
+            }
+        }
+    }
 
-    for (int ii = 0; ii < pdb.chains.size() ; ii++) {
-      if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
+    public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
+        if (!wire) {
+            if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) {
+                g.drawLine(x1, y1, x2, y2);
+                g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
+                g.drawLine(x1, y1 - 1, x2, y2 - 1);
+            } else {
+                g.setColor(g.getColor().brighter());
+                g.drawLine(x1, y1, x2, y2);
+                g.drawLine(x1 + 1, y1, x2 + 1, y2);
+                g.drawLine(x1 - 1, y1, x2 - 1, y2);
+            }
+        } else {
+            g.drawLine(x1, y1, x2, y2);
+        }
+    }
 
-        Vector tmp = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
+    public Dimension minimumsize() {
+        return prefsize;
+    }
 
-        for (int i=0; i < tmp.size(); i++) {
-          bonds.addElement(tmp.elementAt(i));
-        }
-      }
+    public Dimension preferredsize() {
+        return prefsize;
     }
 
-    if (zbuffer) {
-      Zsort.Zsort(bonds);
+    public void keyTyped(KeyEvent evt) {
     }
 
-    for (int i = 0; i < bonds.size(); i++) {
-      Bond tmpBond = (Bond)bonds.elementAt(i);
+    public void keyReleased(KeyEvent evt) {
+    }
 
-      xstart = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);
-      ystart = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);
+    public void keyPressed(KeyEvent evt) {
+        int key = evt.getKeyChar();
+
+        if (evt.getKeyCode() == KeyEvent.VK_UP) {
+            scale = (float) (scale * 1.1);
+            redrawneeded = true;
+            repaint();
+        } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {
+            scale = (float) (scale * 0.9);
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'w') {
+            wire = !wire;
+            System.out.println("wireframe " + wire);
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'd') {
+            depthcue = !depthcue;
+            System.out.println("Depth cueing is " + depthcue);
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'm') {
+            bymolecule = !bymolecule;
+            System.out.println("Bymolecule is " + bymolecule);
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'z') {
+            zbuffer = !zbuffer;
+            System.out.println("Z buffering is " + zbuffer);
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'c') {
+            bymolecule = false;
+            pdb.setChainColours();
+            System.out.println("Colouring by chain");
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'h') {
+            bymolecule = false;
+            pdb.setHydrophobicityColours();
+            System.out.println("Colouring by hydrophobicity");
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'q') {
+            bymolecule = false;
+            pdb.setChargeColours();
+            System.out.println("Colouring charges and cysteines");
+            redrawneeded = true;
+            repaint();
+        }
 
-      xend = (int)((tmpBond.end[0] - centre[0])*scale + getWidth()/2);
-      yend = (int)((tmpBond.end[1] - centre[1])*scale + getHeight()/2);
+        return;
+    }
 
-      xmid = (xend+xstart)/2;
-      ymid = (yend+ystart)/2;
+    public void mousePressed(MouseEvent e) {
+        mx = e.getX();
+        my = e.getY();
+        omx = mx;
+        omy = my;
+        dragging = false;
+    }
 
+    public void mouseMoved(MouseEvent e) {
+        myAtom fatom = null;
 
-      if (depthcue && !bymolecule) {
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
 
-        if (tmpBond.start[2] < (centre[2] - maxwidth/6))  {
-          g.setColor(tmpBond.startCol.darker().darker());
-          drawLine(g,xstart,ystart,xmid,ymid);
+            if (chain.isVisible) {
+                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-          g.setColor(tmpBond.endCol.darker().darker());
-          drawLine(g,xmid,ymid,xend,yend);
-        } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {
-          g.setColor(tmpBond.startCol.darker());
-          drawLine(g,xstart,ystart,xmid,ymid);
+                for (int i = 0; i < bonds.size(); i++) {
+                    Bond tmpBond = (Bond) bonds.elementAt(i);
+                    int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
+                        (getWidth() / 2));
 
-          g.setColor(tmpBond.endCol.darker());
-          drawLine(g,xmid,ymid,xend,yend);
-        } else {
-          g.setColor(tmpBond.startCol);
-          drawLine(g,xstart,ystart,xmid,ymid);
+                    if (Math.abs(truex - e.getX()) <= 2) {
+                        int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
+                            (getHeight() / 2));
 
-          g.setColor(tmpBond.endCol);
-          drawLine(g,xmid,ymid,xend,yend);
+                        if (Math.abs(truey - e.getY()) <= 2) {
+                            fatom = tmpBond.at1;
+                        }
+                    }
+                }
+            }
         }
-      } else if (depthcue && bymolecule) {
-        if (tmpBond.start[2] < (centre[2] - maxwidth/6))  {
-          g.setColor(Color.green.darker().darker());
-          drawLine(g,xstart,ystart,xend,yend);
-
-        } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {
-          g.setColor(Color.green.darker());
-          drawLine(g,xstart,ystart,xend,yend);
 
+        if (fatom != null) {
+            this.setToolTipText(fatom.resName);
         } else {
-          g.setColor(Color.green);
-          drawLine(g,xstart,ystart,xend,yend);
-
+            this.setToolTipText(null);
         }
-      } else if (!depthcue && !bymolecule) {
-        g.setColor(tmpBond.startCol);
-        drawLine(g,xstart,ystart,xmid,ymid);
-        g.setColor(tmpBond.endCol);
-        drawLine(g,xmid,ymid,xend,yend);
-
-      } else {
-        drawLine(g,xstart,ystart,xend,yend);
-      }
     }
-  }
 
-  public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
-    if (!wire) {
-
-      if (((float)Math.abs(y2-y1)/(float)Math.abs(x2-x1)) < 0.5) {
-
-        g.drawLine(x1,y1,x2,y2);
-        g.drawLine(x1+1,y1+1,x2+1,y2+1);
-        g.drawLine(x1,y1-1,x2,y2-1);
-      } else {
-        g.setColor(g.getColor().brighter());
-        g.drawLine(x1,y1,x2,y2);
-        g.drawLine(x1+1,y1,x2+1,y2);
-        g.drawLine(x1-1,y1,x2-1,y2);
+    public void mouseClicked(MouseEvent e) {
+    }
 
-      }
-    } else {
-      g.drawLine(x1,y1,x2,y2);
+    public void mouseEntered(MouseEvent e) {
     }
-  }
-
-  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) {
-    int key = evt.getKeyChar();
-
-    if (evt.getKeyCode() == KeyEvent.VK_UP) {
-      scale        = (float)(scale * 1.1);
-      redrawneeded = true;
-      repaint();
-
-    } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {
-      scale        = (float)(scale * 0.9);
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'w') {
-
-      wire = !wire;
-      System.out.println("wireframe " + wire);
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'd') {
-      depthcue = !depthcue;
-      System.out.println("Depth cueing is " + depthcue);
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'm') {
-      bymolecule = !bymolecule;
-      System.out.println("Bymolecule is " + bymolecule);
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'z') {
-      zbuffer = !zbuffer;
-      System.out.println("Z buffering is " + zbuffer);
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'c') {
-      bymolecule = false;
-      pdb.setChainColours();
-      System.out.println("Colouring by chain");
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'h') {
-      bymolecule = false;
-      pdb.setHydrophobicityColours();
-      System.out.println("Colouring by hydrophobicity");
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'q') {
-      bymolecule = false;
-      pdb.setChargeColours();
-      System.out.println("Colouring charges and cysteines");
-      redrawneeded = true;
-      repaint();
 
+    public void mouseExited(MouseEvent e) {
     }
-    return;
-  }
 
-  public void mousePressed(MouseEvent e)
-  {
+    public void mouseDragged(MouseEvent evt) {
+        int x = evt.getX();
+        int y = evt.getY();
+        mx = x;
+        my = y;
 
-      mx = e.getX();
-      my = e.getY();
-      omx = mx;
-      omy = my;
-      dragging = false;
-}
+        MCMatrix objmat = new MCMatrix(3, 3);
+        objmat.setIdentity();
 
-  public void mouseMoved(MouseEvent e)
-  {
-    myAtom fatom = null;
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
-    {
-
-      PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
-      if (chain.isVisible)
-      {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
-        for (int i = 0; i < bonds.size(); i++)
-        {
-          Bond tmpBond = (Bond) bonds.elementAt(i);
-          int truex = (int) ( (tmpBond.start[0] - centre[0]) * scale +
-                             getWidth() / 2);
-          if (Math.abs(truex - e.getX()) <= 2)
-          {
-            int truey = (int) ( (tmpBond.start[1] - centre[1]) * scale +
-                               getHeight() / 2);
-            if (Math.abs(truey - e.getY()) <= 2)
-              fatom = tmpBond.at1;
-          }
+        if ((evt.getModifiers() & Event.META_MASK) != 0) {
+            objmat.rotatez((float) ((mx - omx)));
+        } else {
+            objmat.rotatex((float) ((my - omy)));
+            objmat.rotatey((float) ((omx - mx)));
         }
-      }
-    }
-    if(fatom!=null)
-     {
-       this.setToolTipText(fatom.resName);
-     }
-     else
-        this.setToolTipText(null);
-  }
-
-  public void mouseClicked(MouseEvent e) { }
-  public void mouseEntered(MouseEvent e) { }
-  public void mouseExited(MouseEvent e) { }
-
-  public void mouseDragged(MouseEvent evt) {
-    int x = evt.getX();
-    int y = evt.getY();
-    mx = x;
-    my = y;
-
-    MCMatrix objmat = new MCMatrix(3,3);
-    objmat.setIdentity();
-
-    if ((evt.getModifiers()  & Event.META_MASK) != 0) {
-      objmat.rotatez((float)((mx-omx)));
-    } else {
-      objmat.rotatex((float)((my-omy)));
-      objmat.rotatey((float)((omx-mx)));
-    }
 
-    //Alter the bonds
-    for (int ii = 0; ii < pdb.chains.size() ; ii++) {
-      Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
+        //Alter the bonds
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-      for (int i = 0; i < bonds.size(); i++) {
+            for (int i = 0; i < bonds.size(); i++) {
+                Bond tmpBond = (Bond) bonds.elementAt(i);
 
-        Bond tmpBond = (Bond)bonds.elementAt(i);
+                //Translate the bond so the centre is 0,0,0
+                tmpBond.translate(-centre[0], -centre[1], -centre[2]);
 
-        //Translate the bond so the centre is 0,0,0
-        tmpBond.translate(-centre[0],-centre[1],-centre[2]);
-
-        //Now apply the rotation matrix
-        tmpBond.start = objmat.vectorMultiply(tmpBond.start);
-        tmpBond.end   = objmat.vectorMultiply(tmpBond.end);
-
-        //Now translate back again
-        tmpBond.translate(centre[0],centre[1],centre[2]);
-      }
-    }
+                //Now apply the rotation matrix
+                tmpBond.start = objmat.vectorMultiply(tmpBond.start);
+                tmpBond.end = objmat.vectorMultiply(tmpBond.end);
 
-    objmat = null;
+                //Now translate back again
+                tmpBond.translate(centre[0], centre[1], centre[2]);
+            }
+        }
 
-    omx    = mx;
-    omy    = my;
+        objmat = null;
 
-    redrawneeded = true;
+        omx = mx;
+        omy = my;
 
-    paint(this.getGraphics());
+        redrawneeded = true;
 
-    dragging = true;
-    return;
-  }
+        paint(this.getGraphics());
 
-  public void mouseReleased(MouseEvent evt) {
-    int x = evt.getX();
-    int y = evt.getY();
+        dragging = true;
 
-    if (!dragging) {
-      myAtom tmp = findAtom(x,y);
+        return;
     }
-    drawLabels();
-    return;
-  }
-
-  public void drawLabels() {
-    redrawneeded = true;
-    paint(this.getGraphics());
-
-    for (int ii = 0; ii < pdb.chains.size() ; ii++) {
 
-      PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);
-
-      if (chain.isVisible) {
-
-        Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
-
-        for (int i = 0; i < bonds.size(); i++) {
-          Bond tmpBond = (Bond)bonds.elementAt(i);
-
-          if (tmpBond.at1.isSelected) {
-            labelAtom(img.getGraphics(),tmpBond,1);
-          }
-
-          if (tmpBond.at2.isSelected) {
-            labelAtom(img.getGraphics(),tmpBond,2);
-          }
+    public void mouseReleased(MouseEvent evt) {
+        int x = evt.getX();
+        int y = evt.getY();
 
+        if (!dragging) {
+            myAtom tmp = findAtom(x, y);
         }
-      }
-    }
-
-    this.getGraphics().drawImage(img,0,0,this);
-
-    dragging = false;
-
-  }
-
-  public void labelAtom(Graphics g,Bond b, int n) {
 
-    g.setFont(font);
+        drawLabels();
 
-    if (n ==1) {
-
-      int xstart = (int)((b.start[0] - centre[0])*scale + getWidth()/2);
-      int ystart = (int)((b.start[1] - centre[1])*scale + getHeight()/2);
-
-      g.setColor(Color.red);
-      g.drawString(b.at1.resName + "-" + b.at1.resNumber,xstart,ystart);
+        return;
     }
 
-    if (n ==2) {
+    public void drawLabels() {
+        redrawneeded = true;
+        paint(this.getGraphics());
 
-      int xstart = (int)((b.end[0] - centre[0])*scale + getWidth()/2);
-      int ystart = (int)((b.end[1] - centre[1])*scale + getHeight()/2);
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
 
-      g.setColor(Color.red);
-      g.drawString(b.at2.resName + "-" + b.at2.resNumber,xstart,ystart);
-    }
-  }
+            if (chain.isVisible) {
+                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
+                for (int i = 0; i < bonds.size(); i++) {
+                    Bond tmpBond = (Bond) bonds.elementAt(i);
 
-  public myAtom findAtom(int x, int y) {
-    myAtom fatom = null;
+                    if (tmpBond.at1.isSelected) {
+                        labelAtom(img.getGraphics(), tmpBond, 1);
+                    }
 
-    int foundchain = -1;
+                    if (tmpBond.at2.isSelected) {
+                        labelAtom(img.getGraphics(), tmpBond, 2);
+                    }
+                }
+            }
+        }
 
-    for (int ii = 0; ii < pdb.chains.size() ; ii++) {
+        this.getGraphics().drawImage(img, 0, 0, this);
 
-      PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);
+        dragging = false;
+    }
 
-      if (chain.isVisible) {
+    public void labelAtom(Graphics g, Bond b, int n) {
+        g.setFont(font);
 
-        Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
+        if (n == 1) {
+            int xstart = (int) (((b.start[0] - centre[0]) * scale) +
+                (getWidth() / 2));
+            int ystart = (int) (((b.start[1] - centre[1]) * scale) +
+                (getHeight() / 2));
 
-        for (int i = 0; i < bonds.size(); i++) {
-          Bond tmpBond = (Bond)bonds.elementAt(i);
+            g.setColor(Color.red);
+            g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
+        }
 
-          int truex = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);
+        if (n == 2) {
+            int xstart = (int) (((b.end[0] - centre[0]) * scale) +
+                (getWidth() / 2));
+            int ystart = (int) (((b.end[1] - centre[1]) * scale) +
+                (getHeight() / 2));
 
-          if (Math.abs(truex - x) <= 2) {
+            g.setColor(Color.red);
+            g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
+        }
+    }
 
-            int truey = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);
+    public myAtom findAtom(int x, int y) {
+        myAtom fatom = null;
+
+        int foundchain = -1;
+
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+
+            if (chain.isVisible) {
+                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+
+                for (int i = 0; i < bonds.size(); i++) {
+                    Bond tmpBond = (Bond) bonds.elementAt(i);
+
+                    int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
+                        (getWidth() / 2));
+
+                    if (Math.abs(truex - x) <= 2) {
+                        int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
+                            (getHeight() / 2));
+
+                        if (Math.abs(truey - y) <= 2) {
+                            System.out.println("Found match");
+                            System.out.println(x + " " + y);
+                            System.out.println(truex + " " + truey);
+                            System.out.println(tmpBond.start[0] + " " +
+                                tmpBond.start[1]);
+                            System.out.println("Atom 1 = " +
+                                tmpBond.at1.resName + " " +
+                                tmpBond.at1.resNumber + " " +
+                                tmpBond.at1.chain);
+                            fatom = tmpBond.at1;
+                            fatom.isSelected = !fatom.isSelected;
+                            foundchain = ii;
+                        }
+                    }
+                }
+            }
 
-            if (Math.abs(truey - y) <= 2) {
+            if (fatom != null) //)&& chain.ds != null)
+             {
+                chain = (PDBChain) pdb.chains.elementAt(foundchain);
 
-              System.out.println("Found match");
-              System.out.println(x + " " + y);
-              System.out.println(truex + " " + truey);
-              System.out.println(tmpBond.start[0] + " " + tmpBond.start[1]);
-              System.out.println("Atom 1 = " + tmpBond.at1.resName + " " +
-                                 tmpBond.at1.resNumber + " " + tmpBond.at1.chain);
-              fatom = tmpBond.at1;
-              fatom.isSelected = !fatom.isSelected;
-              foundchain = ii;
+                // SMJS TODO
+                // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;
+                // int pos = chain.ds.findIndex(tmp);
+                // System.out.println("Found seq " + chain.ds.name + " "  + tmp + " " + pos);
             }
-          }
         }
-      }
-
-      if (fatom != null) //)&& chain.ds != null)
-      {
-        chain = (PDBChain)pdb.chains.elementAt(foundchain);
-        // SMJS TODO
-        // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;
-        // int pos = chain.ds.findIndex(tmp);
-        // System.out.println("Found seq " + chain.ds.name + " "  + tmp + " " + pos);
-      }
 
+        return fatom;
     }
-    return fatom;
-  }
-
-  public void update(Graphics g) {
-    paint(g);
-  }
 
+    public void update(Graphics g) {
+        paint(g);
+    }
 }
diff --git a/src/ext/vamsas/JPredWS.java b/src/ext/vamsas/JPredWS.java
index 82e58c2..194272e 100755
--- a/src/ext/vamsas/JPredWS.java
+++ b/src/ext/vamsas/JPredWS.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,13 +22,19 @@
 * 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 ext.vamsas;
-
-public interface JPredWS extends java.rmi.Remote {
-    public java.lang.String predict(ext.vamsas.Sequence in0) throws java.rmi.RemoteException;
-    public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0) throws java.rmi.RemoteException;
-    public ext.vamsas.Secstructpred getpredict(java.lang.String in0) throws java.rmi.RemoteException;
-    public ext.vamsas.JpredResult getresult(java.lang.String in0) throws java.rmi.RemoteException;
-}
+*/
+package ext.vamsas;
+
+public interface JPredWS extends java.rmi.Remote {
+    public java.lang.String predict(ext.vamsas.Sequence in0)
+        throws java.rmi.RemoteException;
+
+    public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0)
+        throws java.rmi.RemoteException;
+
+    public ext.vamsas.Secstructpred getpredict(java.lang.String in0)
+        throws java.rmi.RemoteException;
+
+    public ext.vamsas.JpredResult getresult(java.lang.String in0)
+        throws java.rmi.RemoteException;
+}
diff --git a/src/ext/vamsas/JPredWSService.java b/src/ext/vamsas/JPredWSService.java
index e14c51d..3cb5e5d 100755
--- a/src/ext/vamsas/JPredWSService.java
+++ b/src/ext/vamsas/JPredWSService.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,14 +22,14 @@
 * 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 ext.vamsas;
-
-public interface JPredWSService extends javax.xml.rpc.Service {
-    public java.lang.String getjpredAddress();
-
-    public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException;
-
-    public ext.vamsas.JPredWS getjpred(java.net.URL portAddress) throws javax.xml.rpc.ServiceException;
-}
+*/
+package ext.vamsas;
+
+public interface JPredWSService extends javax.xml.rpc.Service {
+    public java.lang.String getjpredAddress();
+
+    public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException;
+
+    public ext.vamsas.JPredWS getjpred(java.net.URL portAddress)
+        throws javax.xml.rpc.ServiceException;
+}
diff --git a/src/ext/vamsas/JPredWSServiceLocator.java b/src/ext/vamsas/JPredWSServiceLocator.java
index af51043..cb4006d 100755
--- a/src/ext/vamsas/JPredWSServiceLocator.java
+++ b/src/ext/vamsas/JPredWSServiceLocator.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,134 +22,146 @@
 * 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 ext.vamsas;
-
-public class JPredWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.JPredWSService {
-
-    public JPredWSServiceLocator() {
-    }
-
-
-    public JPredWSServiceLocator(org.apache.axis.EngineConfiguration config) {
-        super(config);
-    }
-
-    // Use to get a proxy class for jpred
-    private java.lang.String jpred_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred";
-
-    public java.lang.String getjpredAddress() {
-        return jpred_address;
-    }
-
-    // The WSDD service name defaults to the port name.
-    private java.lang.String jpredWSDDServiceName = "jpred";
-
-    public java.lang.String getjpredWSDDServiceName() {
-        return jpredWSDDServiceName;
-    }
-
-    public void setjpredWSDDServiceName(java.lang.String name) {
-        jpredWSDDServiceName = name;
-    }
-
-    public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException {
-       java.net.URL endpoint;
-        try {
-            endpoint = new java.net.URL(jpred_address);
-        }
-        catch (java.net.MalformedURLException e) {
-            throw new javax.xml.rpc.ServiceException(e);
-        }
-        return getjpred(endpoint);
-    }
-
-    public ext.vamsas.JPredWS getjpred(java.net.URL portAddress) throws javax.xml.rpc.ServiceException {
-        try {
-            ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(portAddress, this);
-            _stub.setPortName(getjpredWSDDServiceName());
-            return _stub;
-        }
-        catch (org.apache.axis.AxisFault e) {
-            return null;
-        }
-    }
-
-    public void setjpredEndpointAddress(java.lang.String address) {
-        jpred_address = address;
-    }
-
+*/
+package ext.vamsas;
+
+public class JPredWSServiceLocator extends org.apache.axis.client.Service
+    implements ext.vamsas.JPredWSService {
+    // Use to get a proxy class for jpred
+    private java.lang.String jpred_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred";
+
+    // The WSDD service name defaults to the port name.
+    private java.lang.String jpredWSDDServiceName = "jpred";
+    private java.util.HashSet ports = null;
+
+    public JPredWSServiceLocator() {
+    }
+
+    public JPredWSServiceLocator(org.apache.axis.EngineConfiguration config) {
+        super(config);
+    }
+
+    public java.lang.String getjpredAddress() {
+        return jpred_address;
+    }
+
+    public java.lang.String getjpredWSDDServiceName() {
+        return jpredWSDDServiceName;
+    }
+
+    public void setjpredWSDDServiceName(java.lang.String name) {
+        jpredWSDDServiceName = name;
+    }
+
+    public ext.vamsas.JPredWS getjpred() throws javax.xml.rpc.ServiceException {
+        java.net.URL endpoint;
+
+        try {
+            endpoint = new java.net.URL(jpred_address);
+        } catch (java.net.MalformedURLException e) {
+            throw new javax.xml.rpc.ServiceException(e);
+        }
+
+        return getjpred(endpoint);
+    }
+
+    public ext.vamsas.JPredWS getjpred(java.net.URL portAddress)
+        throws javax.xml.rpc.ServiceException {
+        try {
+            ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(portAddress,
+                    this);
+            _stub.setPortName(getjpredWSDDServiceName());
+
+            return _stub;
+        } catch (org.apache.axis.AxisFault e) {
+            return null;
+        }
+    }
+
+    public void setjpredEndpointAddress(java.lang.String address) {
+        jpred_address = address;
+    }
+
     /**
-     * For the given interface, get the stub implementation.
-     * If this service has no port for the given interface,
-     * then ServiceException is thrown.
-     */
-    public java.rmi.Remote getPort(Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
-        try {
-            if (ext.vamsas.JPredWS.class.isAssignableFrom(serviceEndpointInterface)) {
-                ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(new java.net.URL(jpred_address), this);
-                _stub.setPortName(getjpredWSDDServiceName());
-                return _stub;
-            }
-        }
-        catch (java.lang.Throwable t) {
-            throw new javax.xml.rpc.ServiceException(t);
-        }
-        throw new javax.xml.rpc.ServiceException("There is no stub implementation for the interface:  " + (serviceEndpointInterface == null ? "null" : serviceEndpointInterface.getName()));
-    }
-
+ * For the given interface, get the stub implementation.
+ * If this service has no port for the given interface,
+ * then ServiceException is thrown.
+ */
+    public java.rmi.Remote getPort(Class serviceEndpointInterface)
+        throws javax.xml.rpc.ServiceException {
+        try {
+            if (ext.vamsas.JPredWS.class.isAssignableFrom(
+                        serviceEndpointInterface)) {
+                ext.vamsas.JpredSoapBindingStub _stub = new ext.vamsas.JpredSoapBindingStub(new java.net.URL(
+                            jpred_address), this);
+                _stub.setPortName(getjpredWSDDServiceName());
+
+                return _stub;
+            }
+        } catch (java.lang.Throwable t) {
+            throw new javax.xml.rpc.ServiceException(t);
+        }
+
+        throw new javax.xml.rpc.ServiceException(
+            "There is no stub implementation for the interface:  " +
+            ((serviceEndpointInterface == null) ? "null"
+                                                : serviceEndpointInterface.getName()));
+    }
+
     /**
-     * For the given interface, get the stub implementation.
-     * If this service has no port for the given interface,
-     * then ServiceException is thrown.
-     */
-    public java.rmi.Remote getPort(javax.xml.namespace.QName portName, Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
-        if (portName == null) {
-            return getPort(serviceEndpointInterface);
-        }
-        java.lang.String inputPortName = portName.getLocalPart();
-        if ("jpred".equals(inputPortName)) {
-            return getjpred();
-        }
-        else  {
-            java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-            ((org.apache.axis.client.Stub) _stub).setPortName(portName);
-            return _stub;
-        }
-    }
-
-    public javax.xml.namespace.QName getServiceName() {
-        return new javax.xml.namespace.QName("vamsas", "JPredWSService");
-    }
-
-    private java.util.HashSet ports = null;
-
-    public java.util.Iterator getPorts() {
-        if (ports == null) {
-            ports = new java.util.HashSet();
-            ports.add(new javax.xml.namespace.QName("vamsas", "jpred"));
-        }
-        return ports.iterator();
-    }
-
+ * For the given interface, get the stub implementation.
+ * If this service has no port for the given interface,
+ * then ServiceException is thrown.
+ */
+    public java.rmi.Remote getPort(javax.xml.namespace.QName portName,
+        Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
+        if (portName == null) {
+            return getPort(serviceEndpointInterface);
+        }
+
+        java.lang.String inputPortName = portName.getLocalPart();
+
+        if ("jpred".equals(inputPortName)) {
+            return getjpred();
+        } else {
+            java.rmi.Remote _stub = getPort(serviceEndpointInterface);
+            ((org.apache.axis.client.Stub) _stub).setPortName(portName);
+
+            return _stub;
+        }
+    }
+
+    public javax.xml.namespace.QName getServiceName() {
+        return new javax.xml.namespace.QName("vamsas", "JPredWSService");
+    }
+
+    public java.util.Iterator getPorts() {
+        if (ports == null) {
+            ports = new java.util.HashSet();
+            ports.add(new javax.xml.namespace.QName("vamsas", "jpred"));
+        }
+
+        return ports.iterator();
+    }
+
     /**
-    * Set the endpoint address for the specified port name.
-    */
-    public void setEndpointAddress(java.lang.String portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
-        if ("jpred".equals(portName)) {
-            setjpredEndpointAddress(address);
-        }
-        else { // Unknown Port Name
-            throw new javax.xml.rpc.ServiceException(" Cannot set Endpoint Address for Unknown Port" + portName);
-        }
-    }
-
+* Set the endpoint address for the specified port name.
+*/
+    public void setEndpointAddress(java.lang.String portName,
+        java.lang.String address) throws javax.xml.rpc.ServiceException {
+        if ("jpred".equals(portName)) {
+            setjpredEndpointAddress(address);
+        } else { // Unknown Port Name
+            throw new javax.xml.rpc.ServiceException(
+                " Cannot set Endpoint Address for Unknown Port" + portName);
+        }
+    }
+
     /**
-    * Set the endpoint address for the specified port name.
-    */
-    public void setEndpointAddress(javax.xml.namespace.QName portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
-        setEndpointAddress(portName.getLocalPart(), address);
-    }
-
-}
+* Set the endpoint address for the specified port name.
+*/
+    public void setEndpointAddress(javax.xml.namespace.QName portName,
+        java.lang.String address) throws javax.xml.rpc.ServiceException {
+        setEndpointAddress(portName.getLocalPart(), address);
+    }
+}
diff --git a/src/ext/vamsas/JpredResult.java b/src/ext/vamsas/JpredResult.java
index 741d3df..e7d089b 100755
--- a/src/ext/vamsas/JpredResult.java
+++ b/src/ext/vamsas/JpredResult.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,150 +22,164 @@
 * 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 ext.vamsas;
-
-public class JpredResult  extends ext.vamsas.Result  implements java.io.Serializable {
-    private java.lang.String aligfile;
-    private java.lang.String predfile;
-
-    public JpredResult() {
-    }
-
-    public JpredResult(
-           java.lang.String aligfile,
-           java.lang.String predfile) {
-           this.aligfile = aligfile;
-           this.predfile = predfile;
-    }
-
-
+*/
+package ext.vamsas;
+
+public class JpredResult extends ext.vamsas.Result
+    implements java.io.Serializable {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(JpredResult.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "JpredResult"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("aligfile");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "aligfile"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("predfile");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "predfile"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    private java.lang.String aligfile;
+    private java.lang.String predfile;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public JpredResult() {
+    }
+
+    public JpredResult(java.lang.String aligfile, java.lang.String predfile) {
+        this.aligfile = aligfile;
+        this.predfile = predfile;
+    }
+
     /**
-     * Gets the aligfile value for this JpredResult.
-     *
-     * @return aligfile
-     */
-    public java.lang.String getAligfile() {
-        return aligfile;
-    }
-
-
+ * Gets the aligfile value for this JpredResult.
+ *
+ * @return aligfile
+ */
+    public java.lang.String getAligfile() {
+        return aligfile;
+    }
+
     /**
-     * Sets the aligfile value for this JpredResult.
-     *
-     * @param aligfile
-     */
-    public void setAligfile(java.lang.String aligfile) {
-        this.aligfile = aligfile;
-    }
-
-
+ * Sets the aligfile value for this JpredResult.
+ *
+ * @param aligfile
+ */
+    public void setAligfile(java.lang.String aligfile) {
+        this.aligfile = aligfile;
+    }
+
     /**
-     * Gets the predfile value for this JpredResult.
-     *
-     * @return predfile
-     */
-    public java.lang.String getPredfile() {
-        return predfile;
-    }
-
-
+ * Gets the predfile value for this JpredResult.
+ *
+ * @return predfile
+ */
+    public java.lang.String getPredfile() {
+        return predfile;
+    }
+
     /**
-     * Sets the predfile value for this JpredResult.
-     *
-     * @param predfile
-     */
-    public void setPredfile(java.lang.String predfile) {
-        this.predfile = predfile;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof JpredResult)) return false;
-        JpredResult other = (JpredResult) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = super.equals(obj) &&
-            ((this.aligfile==null && other.getAligfile()==null) ||
-             (this.aligfile!=null &&
-              this.aligfile.equals(other.getAligfile()))) &&
-            ((this.predfile==null && other.getPredfile()==null) ||
-             (this.predfile!=null &&
-              this.predfile.equals(other.getPredfile())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = super.hashCode();
-        if (getAligfile() != null) {
-            _hashCode += getAligfile().hashCode();
-        }
-        if (getPredfile() != null) {
-            _hashCode += getPredfile().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(JpredResult.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("aligfile");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "aligfile"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("predfile");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "predfile"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+ * Sets the predfile value for this JpredResult.
+ *
+ * @param predfile
+ */
+    public void setPredfile(java.lang.String predfile) {
+        this.predfile = predfile;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof JpredResult)) {
+            return false;
+        }
+
+        JpredResult other = (JpredResult) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = super.equals(obj) &&
+            (((this.aligfile == null) && (other.getAligfile() == null)) ||
+            ((this.aligfile != null) &&
+            this.aligfile.equals(other.getAligfile()))) &&
+            (((this.predfile == null) && (other.getPredfile() == null)) ||
+            ((this.predfile != null) &&
+            this.predfile.equals(other.getPredfile())));
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = super.hashCode();
+
+        if (getAligfile() != null) {
+            _hashCode += getAligfile().hashCode();
+        }
+
+        if (getPredfile() != null) {
+            _hashCode += getPredfile().hashCode();
+        }
+
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java
index d27a582..bed6fa3 100755
--- a/src/ext/vamsas/JpredSoapBindingStub.java
+++ b/src/ext/vamsas/JpredSoapBindingStub.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,308 +22,368 @@
 * 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 ext.vamsas;
-
-public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.JPredWS {
-    private java.util.Vector cachedSerClasses = new java.util.Vector();
-    private java.util.Vector cachedSerQNames = new java.util.Vector();
-    private java.util.Vector cachedSerFactories = new java.util.Vector();
-    private java.util.Vector cachedDeserFactories = new java.util.Vector();
-
-    static org.apache.axis.description.OperationDesc [] _operations;
-
-    static {
-        _operations = new org.apache.axis.description.OperationDesc[4];
-        _initOperationDesc1();
-    }
-
-    private static void _initOperationDesc1(){
-        org.apache.axis.description.OperationDesc oper;
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("predict");
-        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence"), ext.vamsas.Sequence.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        oper.setReturnClass(java.lang.String.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "predictReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
-        oper.setUse(org.apache.axis.constants.Use.LITERAL);
-        _operations[0] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("predictOnMsa");
-        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment"), ext.vamsas.Msfalignment.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        oper.setReturnClass(java.lang.String.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "predictOnMsaReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
-        oper.setUse(org.apache.axis.constants.Use.LITERAL);
-        _operations[1] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("getpredict");
-        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred"));
-        oper.setReturnClass(ext.vamsas.Secstructpred.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "getpredictReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
-        oper.setUse(org.apache.axis.constants.Use.LITERAL);
-        _operations[2] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("getresult");
-        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult"));
-        oper.setReturnClass(ext.vamsas.JpredResult.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("vamsas", "getresultReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
-        oper.setUse(org.apache.axis.constants.Use.LITERAL);
-        _operations[3] = oper;
-
-    }
-
-    public JpredSoapBindingStub() throws org.apache.axis.AxisFault {
-         this(null);
-    }
-
-    public JpredSoapBindingStub(java.net.URL endpointURL, javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-         this(service);
-         super.cachedEndpoint = endpointURL;
-    }
-
-    public JpredSoapBindingStub(javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-        if (service == null) {
-            super.service = new org.apache.axis.client.Service();
-        } else {
-            super.service = service;
-        }
-            java.lang.Class cls;
-            javax.xml.namespace.QName qName;
-            java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
-            java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
-            java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
-            java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
-            java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
-            java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
-            java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
-            java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
-            java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
-            java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
-            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence");
-            cachedSerQNames.add(qName);
-            cls = ext.vamsas.Sequence.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred");
-            cachedSerQNames.add(qName);
-            cls = ext.vamsas.Secstructpred.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment");
-            cachedSerQNames.add(qName);
-            cls = ext.vamsas.Msfalignment.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "JpredResult");
-            cachedSerQNames.add(qName);
-            cls = ext.vamsas.JpredResult.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("http://dataTypes.vamsas", "Result");
-            cachedSerQNames.add(qName);
-            cls = ext.vamsas.Result.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-    }
-
-    protected org.apache.axis.client.Call createCall() throws java.rmi.RemoteException {
-        try {
-            org.apache.axis.client.Call _call =
-                    (org.apache.axis.client.Call) super.service.createCall();
-            if (super.maintainSessionSet) {
-                _call.setMaintainSession(super.maintainSession);
-            }
-            if (super.cachedUsername != null) {
-                _call.setUsername(super.cachedUsername);
-            }
-            if (super.cachedPassword != null) {
-                _call.setPassword(super.cachedPassword);
-            }
-            if (super.cachedEndpoint != null) {
-                _call.setTargetEndpointAddress(super.cachedEndpoint);
-            }
-            if (super.cachedTimeout != null) {
-                _call.setTimeout(super.cachedTimeout);
-            }
-            if (super.cachedPortName != null) {
-                _call.setPortName(super.cachedPortName);
-            }
-            java.util.Enumeration keys = super.cachedProperties.keys();
-            while (keys.hasMoreElements()) {
-                java.lang.String key = (java.lang.String) keys.nextElement();
-                _call.setProperty(key, super.cachedProperties.get(key));
-            }
-            // All the type mapping information is registered
-            // when the first call is made.
-            // The type mapping information is actually registered in
-            // the TypeMappingRegistry of the service, which
-            // is the reason why registration is only needed for the first call.
-            synchronized (this) {
-                if (firstCall()) {
-                    // must set encoding style before registering serializers
-                    _call.setEncodingStyle(null);
-                    for (int i = 0; i < cachedSerFactories.size(); ++i) {
-                        java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
-                        javax.xml.namespace.QName qName =
-                                (javax.xml.namespace.QName) cachedSerQNames.get(i);
-                        java.lang.Class sf = (java.lang.Class)
-                                 cachedSerFactories.get(i);
-                        java.lang.Class df = (java.lang.Class)
-                                 cachedDeserFactories.get(i);
-                        _call.registerTypeMapping(cls, qName, sf, df, false);
-                    }
-                }
-            }
-            return _call;
-        }
-        catch (java.lang.Throwable _t) {
-            throw new org.apache.axis.AxisFault("Failure trying to get the Call object", _t);
-        }
-    }
-
-    public java.lang.String predict(ext.vamsas.Sequence in0) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[0]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setEncodingStyle(null);
-        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
-        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "predict"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (java.lang.String) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp, java.lang.String.class);
-            }
-        }
-    }
-
-    public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[1]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setEncodingStyle(null);
-        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
-        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "predictOnMsa"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (java.lang.String) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp, java.lang.String.class);
-            }
-        }
-    }
-
-    public ext.vamsas.Secstructpred getpredict(java.lang.String in0) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[2]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setEncodingStyle(null);
-        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
-        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getpredict"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (ext.vamsas.Secstructpred) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (ext.vamsas.Secstructpred) org.apache.axis.utils.JavaUtils.convert(_resp, ext.vamsas.Secstructpred.class);
-            }
-        }
-    }
-
-    public ext.vamsas.JpredResult getresult(java.lang.String in0) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[3]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setEncodingStyle(null);
-        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR, Boolean.FALSE);
-        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS, Boolean.FALSE);
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getresult"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {in0});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (ext.vamsas.JpredResult) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (ext.vamsas.JpredResult) org.apache.axis.utils.JavaUtils.convert(_resp, ext.vamsas.JpredResult.class);
-            }
-        }
-    }
-
-}
+*/
+package ext.vamsas;
+
+public class JpredSoapBindingStub extends org.apache.axis.client.Stub
+    implements ext.vamsas.JPredWS {
+    static org.apache.axis.description.OperationDesc[] _operations;
+
+    static {
+        _operations = new org.apache.axis.description.OperationDesc[4];
+        _initOperationDesc1();
+    }
+
+    private java.util.Vector cachedSerClasses = new java.util.Vector();
+    private java.util.Vector cachedSerQNames = new java.util.Vector();
+    private java.util.Vector cachedSerFactories = new java.util.Vector();
+    private java.util.Vector cachedDeserFactories = new java.util.Vector();
+
+    public JpredSoapBindingStub() throws org.apache.axis.AxisFault {
+        this(null);
+    }
+
+    public JpredSoapBindingStub(java.net.URL endpointURL,
+        javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
+        this(service);
+        super.cachedEndpoint = endpointURL;
+    }
+
+    public JpredSoapBindingStub(javax.xml.rpc.Service service)
+        throws org.apache.axis.AxisFault {
+        if (service == null) {
+            super.service = new org.apache.axis.client.Service();
+        } else {
+            super.service = service;
+        }
+
+        java.lang.Class cls;
+        javax.xml.namespace.QName qName;
+        java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
+        java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
+        java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
+        java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
+        java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
+        java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
+        java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
+        java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
+        java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
+        java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+        qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",
+                "Sequence");
+        cachedSerQNames.add(qName);
+        cls = ext.vamsas.Sequence.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",
+                "Secstructpred");
+        cachedSerQNames.add(qName);
+        cls = ext.vamsas.Secstructpred.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",
+                "Msfalignment");
+        cachedSerQNames.add(qName);
+        cls = ext.vamsas.Msfalignment.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",
+                "JpredResult");
+        cachedSerQNames.add(qName);
+        cls = ext.vamsas.JpredResult.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("http://dataTypes.vamsas",
+                "Result");
+        cachedSerQNames.add(qName);
+        cls = ext.vamsas.Result.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+    }
+
+    private static void _initOperationDesc1() {
+        org.apache.axis.description.OperationDesc oper;
+        oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("predict");
+        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"),
+            new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence"),
+            ext.vamsas.Sequence.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        oper.setReturnClass(java.lang.String.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("vamsas",
+                "predictReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+        oper.setUse(org.apache.axis.constants.Use.LITERAL);
+        _operations[0] = oper;
+
+        oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("predictOnMsa");
+        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"),
+            new javax.xml.namespace.QName("http://dataTypes.vamsas",
+                "Msfalignment"), ext.vamsas.Msfalignment.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        oper.setReturnClass(java.lang.String.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("vamsas",
+                "predictOnMsaReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+        oper.setUse(org.apache.axis.constants.Use.LITERAL);
+        _operations[1] = oper;
+
+        oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("getpredict");
+        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"),
+            new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
+                "string"), java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "Secstructpred"));
+        oper.setReturnClass(ext.vamsas.Secstructpred.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("vamsas",
+                "getpredictReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+        oper.setUse(org.apache.axis.constants.Use.LITERAL);
+        _operations[2] = oper;
+
+        oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("getresult");
+        oper.addParameter(new javax.xml.namespace.QName("vamsas", "in0"),
+            new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
+                "string"), java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "JpredResult"));
+        oper.setReturnClass(ext.vamsas.JpredResult.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("vamsas",
+                "getresultReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.WRAPPED);
+        oper.setUse(org.apache.axis.constants.Use.LITERAL);
+        _operations[3] = oper;
+    }
+
+    protected org.apache.axis.client.Call createCall()
+        throws java.rmi.RemoteException {
+        try {
+            org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service.createCall();
+
+            if (super.maintainSessionSet) {
+                _call.setMaintainSession(super.maintainSession);
+            }
+
+            if (super.cachedUsername != null) {
+                _call.setUsername(super.cachedUsername);
+            }
+
+            if (super.cachedPassword != null) {
+                _call.setPassword(super.cachedPassword);
+            }
+
+            if (super.cachedEndpoint != null) {
+                _call.setTargetEndpointAddress(super.cachedEndpoint);
+            }
+
+            if (super.cachedTimeout != null) {
+                _call.setTimeout(super.cachedTimeout);
+            }
+
+            if (super.cachedPortName != null) {
+                _call.setPortName(super.cachedPortName);
+            }
+
+            java.util.Enumeration keys = super.cachedProperties.keys();
+
+            while (keys.hasMoreElements()) {
+                java.lang.String key = (java.lang.String) keys.nextElement();
+                _call.setProperty(key, super.cachedProperties.get(key));
+            }
+
+            // All the type mapping information is registered
+            // when the first call is made.
+            // The type mapping information is actually registered in
+            // the TypeMappingRegistry of the service, which
+            // is the reason why registration is only needed for the first call.
+            synchronized (this) {
+                if (firstCall()) {
+                    // must set encoding style before registering serializers
+                    _call.setEncodingStyle(null);
+
+                    for (int i = 0; i < cachedSerFactories.size(); ++i) {
+                        java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
+                        javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames.get(i);
+                        java.lang.Class sf = (java.lang.Class) cachedSerFactories.get(i);
+                        java.lang.Class df = (java.lang.Class) cachedDeserFactories.get(i);
+                        _call.registerTypeMapping(cls, qName, sf, df, false);
+                    }
+                }
+            }
+
+            return _call;
+        } catch (java.lang.Throwable _t) {
+            throw new org.apache.axis.AxisFault("Failure trying to get the Call object",
+                _t);
+        }
+    }
+
+    public java.lang.String predict(ext.vamsas.Sequence in0)
+        throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[0]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setEncodingStyle(null);
+        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,
+            Boolean.FALSE);
+        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
+            Boolean.FALSE);
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "predict"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { in0 });
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException) _resp;
+        } else {
+            extractAttachments(_call);
+
+            try {
+                return (java.lang.String) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp,
+                    java.lang.String.class);
+            }
+        }
+    }
+
+    public java.lang.String predictOnMsa(ext.vamsas.Msfalignment in0)
+        throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[1]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setEncodingStyle(null);
+        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,
+            Boolean.FALSE);
+        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
+            Boolean.FALSE);
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+                "predictOnMsa"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { in0 });
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException) _resp;
+        } else {
+            extractAttachments(_call);
+
+            try {
+                return (java.lang.String) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(_resp,
+                    java.lang.String.class);
+            }
+        }
+    }
+
+    public ext.vamsas.Secstructpred getpredict(java.lang.String in0)
+        throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[2]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setEncodingStyle(null);
+        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,
+            Boolean.FALSE);
+        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
+            Boolean.FALSE);
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+                "getpredict"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { in0 });
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException) _resp;
+        } else {
+            extractAttachments(_call);
+
+            try {
+                return (ext.vamsas.Secstructpred) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (ext.vamsas.Secstructpred) org.apache.axis.utils.JavaUtils.convert(_resp,
+                    ext.vamsas.Secstructpred.class);
+            }
+        }
+    }
+
+    public ext.vamsas.JpredResult getresult(java.lang.String in0)
+        throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[3]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setEncodingStyle(null);
+        _call.setProperty(org.apache.axis.client.Call.SEND_TYPE_ATTR,
+            Boolean.FALSE);
+        _call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
+            Boolean.FALSE);
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+                "getresult"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { in0 });
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException) _resp;
+        } else {
+            extractAttachments(_call);
+
+            try {
+                return (ext.vamsas.JpredResult) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (ext.vamsas.JpredResult) org.apache.axis.utils.JavaUtils.convert(_resp,
+                    ext.vamsas.JpredResult.class);
+            }
+        }
+    }
+}
diff --git a/src/ext/vamsas/Msfalignment.java b/src/ext/vamsas/Msfalignment.java
index d94e2b9..c9fbf85 100755
--- a/src/ext/vamsas/Msfalignment.java
+++ b/src/ext/vamsas/Msfalignment.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,150 +22,161 @@
 * 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 ext.vamsas;
-
-public class Msfalignment  implements java.io.Serializable {
-    private java.lang.String msf;
-    private java.lang.String notes;
-
-    public Msfalignment() {
-    }
-
-    public Msfalignment(
-           java.lang.String msf,
-           java.lang.String notes) {
-           this.msf = msf;
-           this.notes = notes;
-    }
-
-
+*/
+package ext.vamsas;
+
+public class Msfalignment implements java.io.Serializable {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Msfalignment.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "Msfalignment"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("msf");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "msf"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("notes");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "notes"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    private java.lang.String msf;
+    private java.lang.String notes;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public Msfalignment() {
+    }
+
+    public Msfalignment(java.lang.String msf, java.lang.String notes) {
+        this.msf = msf;
+        this.notes = notes;
+    }
+
     /**
-     * Gets the msf value for this Msfalignment.
-     *
-     * @return msf
-     */
-    public java.lang.String getMsf() {
-        return msf;
-    }
-
-
+ * Gets the msf value for this Msfalignment.
+ *
+ * @return msf
+ */
+    public java.lang.String getMsf() {
+        return msf;
+    }
+
     /**
-     * Sets the msf value for this Msfalignment.
-     *
-     * @param msf
-     */
-    public void setMsf(java.lang.String msf) {
-        this.msf = msf;
-    }
-
-
+ * Sets the msf value for this Msfalignment.
+ *
+ * @param msf
+ */
+    public void setMsf(java.lang.String msf) {
+        this.msf = msf;
+    }
+
     /**
-     * Gets the notes value for this Msfalignment.
-     *
-     * @return notes
-     */
-    public java.lang.String getNotes() {
-        return notes;
-    }
-
-
+ * Gets the notes value for this Msfalignment.
+ *
+ * @return notes
+ */
+    public java.lang.String getNotes() {
+        return notes;
+    }
+
     /**
-     * Sets the notes value for this Msfalignment.
-     *
-     * @param notes
-     */
-    public void setNotes(java.lang.String notes) {
-        this.notes = notes;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Msfalignment)) return false;
-        Msfalignment other = (Msfalignment) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true &&
-            ((this.msf==null && other.getMsf()==null) ||
-             (this.msf!=null &&
-              this.msf.equals(other.getMsf()))) &&
-            ((this.notes==null && other.getNotes()==null) ||
-             (this.notes!=null &&
-              this.notes.equals(other.getNotes())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getMsf() != null) {
-            _hashCode += getMsf().hashCode();
-        }
-        if (getNotes() != null) {
-            _hashCode += getNotes().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Msfalignment.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Msfalignment"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("msf");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "msf"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("notes");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "notes"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+ * Sets the notes value for this Msfalignment.
+ *
+ * @param notes
+ */
+    public void setNotes(java.lang.String notes) {
+        this.notes = notes;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Msfalignment)) {
+            return false;
+        }
+
+        Msfalignment other = (Msfalignment) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = true &&
+            (((this.msf == null) && (other.getMsf() == null)) ||
+            ((this.msf != null) && this.msf.equals(other.getMsf()))) &&
+            (((this.notes == null) && (other.getNotes() == null)) ||
+            ((this.notes != null) && this.notes.equals(other.getNotes())));
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = 1;
+
+        if (getMsf() != null) {
+            _hashCode += getMsf().hashCode();
+        }
+
+        if (getNotes() != null) {
+            _hashCode += getNotes().hashCode();
+        }
+
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/ext/vamsas/MuscleWS.java b/src/ext/vamsas/MuscleWS.java
index 37f851d..ffbe5cb 100755
--- a/src/ext/vamsas/MuscleWS.java
+++ b/src/ext/vamsas/MuscleWS.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,13 +22,20 @@
 * 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 ext.vamsas;
-
-public interface MuscleWS extends java.rmi.Remote {
-    public vamsas.objects.simple.WsJobId align(vamsas.objects.simple.SequenceSet seqSet) throws java.rmi.RemoteException;
-    public vamsas.objects.simple.Alignment getalign(java.lang.String job_id) throws java.rmi.RemoteException;
-    public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id) throws java.rmi.RemoteException;
-    public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId) throws java.rmi.RemoteException;
-}
+*/
+package ext.vamsas;
+
+public interface MuscleWS extends java.rmi.Remote {
+    public vamsas.objects.simple.WsJobId align(
+        vamsas.objects.simple.SequenceSet seqSet)
+        throws java.rmi.RemoteException;
+
+    public vamsas.objects.simple.Alignment getalign(java.lang.String job_id)
+        throws java.rmi.RemoteException;
+
+    public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id)
+        throws java.rmi.RemoteException;
+
+    public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)
+        throws java.rmi.RemoteException;
+}
diff --git a/src/ext/vamsas/MuscleWSService.java b/src/ext/vamsas/MuscleWSService.java
index b1a41cc..ffc4abc 100755
--- a/src/ext/vamsas/MuscleWSService.java
+++ b/src/ext/vamsas/MuscleWSService.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,14 +22,15 @@
 * 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 ext.vamsas;
-
-public interface MuscleWSService extends javax.xml.rpc.Service {
-    public java.lang.String getMuscleWSAddress();
-
-    public ext.vamsas.MuscleWS getMuscleWS() throws javax.xml.rpc.ServiceException;
-
-    public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress) throws javax.xml.rpc.ServiceException;
-}
+*/
+package ext.vamsas;
+
+public interface MuscleWSService extends javax.xml.rpc.Service {
+    public java.lang.String getMuscleWSAddress();
+
+    public ext.vamsas.MuscleWS getMuscleWS()
+        throws javax.xml.rpc.ServiceException;
+
+    public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress)
+        throws javax.xml.rpc.ServiceException;
+}
diff --git a/src/ext/vamsas/MuscleWSServiceLocator.java b/src/ext/vamsas/MuscleWSServiceLocator.java
index fd906cd..96ef074 100755
--- a/src/ext/vamsas/MuscleWSServiceLocator.java
+++ b/src/ext/vamsas/MuscleWSServiceLocator.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,134 +22,147 @@
 * 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 ext.vamsas;
-
-public class MuscleWSServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.MuscleWSService {
-
-    public MuscleWSServiceLocator() {
-    }
-
-
-    public MuscleWSServiceLocator(org.apache.axis.EngineConfiguration config) {
-        super(config);
-    }
-
-    // Use to get a proxy class for MuscleWS
-    private java.lang.String MuscleWS_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/MuscleWS";
-
-    public java.lang.String getMuscleWSAddress() {
-        return MuscleWS_address;
-    }
-
-    // The WSDD service name defaults to the port name.
-    private java.lang.String MuscleWSWSDDServiceName = "MuscleWS";
-
-    public java.lang.String getMuscleWSWSDDServiceName() {
-        return MuscleWSWSDDServiceName;
-    }
-
-    public void setMuscleWSWSDDServiceName(java.lang.String name) {
-        MuscleWSWSDDServiceName = name;
-    }
-
-    public ext.vamsas.MuscleWS getMuscleWS() throws javax.xml.rpc.ServiceException {
-       java.net.URL endpoint;
-        try {
-            endpoint = new java.net.URL(MuscleWS_address);
-        }
-        catch (java.net.MalformedURLException e) {
-            throw new javax.xml.rpc.ServiceException(e);
-        }
-        return getMuscleWS(endpoint);
-    }
-
-    public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress) throws javax.xml.rpc.ServiceException {
-        try {
-            ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(portAddress, this);
-            _stub.setPortName(getMuscleWSWSDDServiceName());
-            return _stub;
-        }
-        catch (org.apache.axis.AxisFault e) {
-            return null;
-        }
-    }
-
-    public void setMuscleWSEndpointAddress(java.lang.String address) {
-        MuscleWS_address = address;
-    }
-
+*/
+package ext.vamsas;
+
+public class MuscleWSServiceLocator extends org.apache.axis.client.Service
+    implements ext.vamsas.MuscleWSService {
+    // Use to get a proxy class for MuscleWS
+    private java.lang.String MuscleWS_address = "http://anaplog.compbio.dundee.ac.uk:8080/axis/services/MuscleWS";
+
+    // The WSDD service name defaults to the port name.
+    private java.lang.String MuscleWSWSDDServiceName = "MuscleWS";
+    private java.util.HashSet ports = null;
+
+    public MuscleWSServiceLocator() {
+    }
+
+    public MuscleWSServiceLocator(org.apache.axis.EngineConfiguration config) {
+        super(config);
+    }
+
+    public java.lang.String getMuscleWSAddress() {
+        return MuscleWS_address;
+    }
+
+    public java.lang.String getMuscleWSWSDDServiceName() {
+        return MuscleWSWSDDServiceName;
+    }
+
+    public void setMuscleWSWSDDServiceName(java.lang.String name) {
+        MuscleWSWSDDServiceName = name;
+    }
+
+    public ext.vamsas.MuscleWS getMuscleWS()
+        throws javax.xml.rpc.ServiceException {
+        java.net.URL endpoint;
+
+        try {
+            endpoint = new java.net.URL(MuscleWS_address);
+        } catch (java.net.MalformedURLException e) {
+            throw new javax.xml.rpc.ServiceException(e);
+        }
+
+        return getMuscleWS(endpoint);
+    }
+
+    public ext.vamsas.MuscleWS getMuscleWS(java.net.URL portAddress)
+        throws javax.xml.rpc.ServiceException {
+        try {
+            ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(portAddress,
+                    this);
+            _stub.setPortName(getMuscleWSWSDDServiceName());
+
+            return _stub;
+        } catch (org.apache.axis.AxisFault e) {
+            return null;
+        }
+    }
+
+    public void setMuscleWSEndpointAddress(java.lang.String address) {
+        MuscleWS_address = address;
+    }
+
     /**
-     * For the given interface, get the stub implementation.
-     * If this service has no port for the given interface,
-     * then ServiceException is thrown.
-     */
-    public java.rmi.Remote getPort(Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
-        try {
-            if (ext.vamsas.MuscleWS.class.isAssignableFrom(serviceEndpointInterface)) {
-                ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(new java.net.URL(MuscleWS_address), this);
-                _stub.setPortName(getMuscleWSWSDDServiceName());
-                return _stub;
-            }
-        }
-        catch (java.lang.Throwable t) {
-            throw new javax.xml.rpc.ServiceException(t);
-        }
-        throw new javax.xml.rpc.ServiceException("There is no stub implementation for the interface:  " + (serviceEndpointInterface == null ? "null" : serviceEndpointInterface.getName()));
-    }
-
+ * For the given interface, get the stub implementation.
+ * If this service has no port for the given interface,
+ * then ServiceException is thrown.
+ */
+    public java.rmi.Remote getPort(Class serviceEndpointInterface)
+        throws javax.xml.rpc.ServiceException {
+        try {
+            if (ext.vamsas.MuscleWS.class.isAssignableFrom(
+                        serviceEndpointInterface)) {
+                ext.vamsas.MuscleWSSoapBindingStub _stub = new ext.vamsas.MuscleWSSoapBindingStub(new java.net.URL(
+                            MuscleWS_address), this);
+                _stub.setPortName(getMuscleWSWSDDServiceName());
+
+                return _stub;
+            }
+        } catch (java.lang.Throwable t) {
+            throw new javax.xml.rpc.ServiceException(t);
+        }
+
+        throw new javax.xml.rpc.ServiceException(
+            "There is no stub implementation for the interface:  " +
+            ((serviceEndpointInterface == null) ? "null"
+                                                : serviceEndpointInterface.getName()));
+    }
+
     /**
-     * For the given interface, get the stub implementation.
-     * If this service has no port for the given interface,
-     * then ServiceException is thrown.
-     */
-    public java.rmi.Remote getPort(javax.xml.namespace.QName portName, Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
-        if (portName == null) {
-            return getPort(serviceEndpointInterface);
-        }
-        java.lang.String inputPortName = portName.getLocalPart();
-        if ("MuscleWS".equals(inputPortName)) {
-            return getMuscleWS();
-        }
-        else  {
-            java.rmi.Remote _stub = getPort(serviceEndpointInterface);
-            ((org.apache.axis.client.Stub) _stub).setPortName(portName);
-            return _stub;
-        }
-    }
-
-    public javax.xml.namespace.QName getServiceName() {
-        return new javax.xml.namespace.QName("vamsas", "MuscleWSService");
-    }
-
-    private java.util.HashSet ports = null;
-
-    public java.util.Iterator getPorts() {
-        if (ports == null) {
-            ports = new java.util.HashSet();
-            ports.add(new javax.xml.namespace.QName("vamsas", "MuscleWS"));
-        }
-        return ports.iterator();
-    }
-
+ * For the given interface, get the stub implementation.
+ * If this service has no port for the given interface,
+ * then ServiceException is thrown.
+ */
+    public java.rmi.Remote getPort(javax.xml.namespace.QName portName,
+        Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
+        if (portName == null) {
+            return getPort(serviceEndpointInterface);
+        }
+
+        java.lang.String inputPortName = portName.getLocalPart();
+
+        if ("MuscleWS".equals(inputPortName)) {
+            return getMuscleWS();
+        } else {
+            java.rmi.Remote _stub = getPort(serviceEndpointInterface);
+            ((org.apache.axis.client.Stub) _stub).setPortName(portName);
+
+            return _stub;
+        }
+    }
+
+    public javax.xml.namespace.QName getServiceName() {
+        return new javax.xml.namespace.QName("vamsas", "MuscleWSService");
+    }
+
+    public java.util.Iterator getPorts() {
+        if (ports == null) {
+            ports = new java.util.HashSet();
+            ports.add(new javax.xml.namespace.QName("vamsas", "MuscleWS"));
+        }
+
+        return ports.iterator();
+    }
+
     /**
-    * Set the endpoint address for the specified port name.
-    */
-    public void setEndpointAddress(java.lang.String portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
-        if ("MuscleWS".equals(portName)) {
-            setMuscleWSEndpointAddress(address);
-        }
-        else { // Unknown Port Name
-            throw new javax.xml.rpc.ServiceException(" Cannot set Endpoint Address for Unknown Port" + portName);
-        }
-    }
-
+* Set the endpoint address for the specified port name.
+*/
+    public void setEndpointAddress(java.lang.String portName,
+        java.lang.String address) throws javax.xml.rpc.ServiceException {
+        if ("MuscleWS".equals(portName)) {
+            setMuscleWSEndpointAddress(address);
+        } else { // Unknown Port Name
+            throw new javax.xml.rpc.ServiceException(
+                " Cannot set Endpoint Address for Unknown Port" + portName);
+        }
+    }
+
     /**
-    * Set the endpoint address for the specified port name.
-    */
-    public void setEndpointAddress(javax.xml.namespace.QName portName, java.lang.String address) throws javax.xml.rpc.ServiceException {
-        setEndpointAddress(portName.getLocalPart(), address);
-    }
-
-}
+* Set the endpoint address for the specified port name.
+*/
+    public void setEndpointAddress(javax.xml.namespace.QName portName,
+        java.lang.String address) throws javax.xml.rpc.ServiceException {
+        setEndpointAddress(portName.getLocalPart(), address);
+    }
+}
diff --git a/src/ext/vamsas/MuscleWSSoapBindingStub.java b/src/ext/vamsas/MuscleWSSoapBindingStub.java
index b2739bd..35e2470 100755
--- a/src/ext/vamsas/MuscleWSSoapBindingStub.java
+++ b/src/ext/vamsas/MuscleWSSoapBindingStub.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,325 +22,373 @@
 * 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 ext.vamsas;
-
-public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.MuscleWS {
-    private java.util.Vector cachedSerClasses = new java.util.Vector();
-    private java.util.Vector cachedSerQNames = new java.util.Vector();
-    private java.util.Vector cachedSerFactories = new java.util.Vector();
-    private java.util.Vector cachedDeserFactories = new java.util.Vector();
-
-    static org.apache.axis.description.OperationDesc [] _operations;
-
-    static {
-        _operations = new org.apache.axis.description.OperationDesc[4];
-        _initOperationDesc1();
-    }
-
-    private static void _initOperationDesc1(){
-        org.apache.axis.description.OperationDesc oper;
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("align");
-        oper.addParameter(new javax.xml.namespace.QName("", "seqSet"), new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"), vamsas.objects.simple.SequenceSet.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
-        oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("", "alignReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[0] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("getalign");
-        oper.addParameter(new javax.xml.namespace.QName("", "job_id"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
-        oper.setReturnClass(vamsas.objects.simple.Alignment.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("", "getalignReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[1] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("getResult");
-        oper.addParameter(new javax.xml.namespace.QName("", "job_id"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "MsaResult"));
-        oper.setReturnClass(vamsas.objects.simple.MsaResult.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("", "getResultReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[2] = oper;
-
-        oper = new org.apache.axis.description.OperationDesc();
-        oper.setName("cancel");
-        oper.addParameter(new javax.xml.namespace.QName("", "jobId"), new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"), java.lang.String.class, org.apache.axis.description.ParameterDesc.IN, false, false);
-        oper.setReturnType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
-        oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
-        oper.setReturnQName(new javax.xml.namespace.QName("", "cancelReturn"));
-        oper.setStyle(org.apache.axis.constants.Style.RPC);
-        oper.setUse(org.apache.axis.constants.Use.ENCODED);
-        _operations[3] = oper;
-
-    }
-
-    public MuscleWSSoapBindingStub() throws org.apache.axis.AxisFault {
-         this(null);
-    }
-
-    public MuscleWSSoapBindingStub(java.net.URL endpointURL, javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-         this(service);
-         super.cachedEndpoint = endpointURL;
-    }
-
-    public MuscleWSSoapBindingStub(javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
-        if (service == null) {
-            super.service = new org.apache.axis.client.Service();
-        } else {
-            super.service = service;
-        }
-            java.lang.Class cls;
-            javax.xml.namespace.QName qName;
-            java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
-            java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
-            java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
-            java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
-            java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
-            java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
-            java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
-            java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
-            java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
-            java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Sequence.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Sequence[].class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(arraysf);
-            cachedDeserFactories.add(arraydf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "MsaResult");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.MsaResult.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.SequenceSet.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("http://simple.objects.vamsas", "Object");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Object.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Alignment.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.WsJobId.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-            qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_xsd_string");
-            cachedSerQNames.add(qName);
-            cls = java.lang.String[].class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(arraysf);
-            cachedDeserFactories.add(arraydf);
-
-            qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
-            cachedSerQNames.add(qName);
-            cls = vamsas.objects.simple.Result.class;
-            cachedSerClasses.add(cls);
-            cachedSerFactories.add(beansf);
-            cachedDeserFactories.add(beandf);
-
-    }
-
-    protected org.apache.axis.client.Call createCall() throws java.rmi.RemoteException {
-        try {
-            org.apache.axis.client.Call _call =
-                    (org.apache.axis.client.Call) super.service.createCall();
-            if (super.maintainSessionSet) {
-                _call.setMaintainSession(super.maintainSession);
-            }
-            if (super.cachedUsername != null) {
-                _call.setUsername(super.cachedUsername);
-            }
-            if (super.cachedPassword != null) {
-                _call.setPassword(super.cachedPassword);
-            }
-            if (super.cachedEndpoint != null) {
-                _call.setTargetEndpointAddress(super.cachedEndpoint);
-            }
-            if (super.cachedTimeout != null) {
-                _call.setTimeout(super.cachedTimeout);
-            }
-            if (super.cachedPortName != null) {
-                _call.setPortName(super.cachedPortName);
-            }
-            java.util.Enumeration keys = super.cachedProperties.keys();
-            while (keys.hasMoreElements()) {
-                java.lang.String key = (java.lang.String) keys.nextElement();
-                _call.setProperty(key, super.cachedProperties.get(key));
-            }
-            // All the type mapping information is registered
-            // when the first call is made.
-            // The type mapping information is actually registered in
-            // the TypeMappingRegistry of the service, which
-            // is the reason why registration is only needed for the first call.
-            synchronized (this) {
-                if (firstCall()) {
-                    // must set encoding style before registering serializers
-                    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-                    _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
-                    for (int i = 0; i < cachedSerFactories.size(); ++i) {
-                        java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
-                        javax.xml.namespace.QName qName =
-                                (javax.xml.namespace.QName) cachedSerQNames.get(i);
-                        java.lang.Class sf = (java.lang.Class)
-                                 cachedSerFactories.get(i);
-                        java.lang.Class df = (java.lang.Class)
-                                 cachedDeserFactories.get(i);
-                        _call.registerTypeMapping(cls, qName, sf, df, false);
-                    }
-                }
-            }
-            return _call;
-        }
-        catch (java.lang.Throwable _t) {
-            throw new org.apache.axis.AxisFault("Failure trying to get the Call object", _t);
-        }
-    }
-
-    public vamsas.objects.simple.WsJobId align(vamsas.objects.simple.SequenceSet seqSet) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[0]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "align"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {seqSet});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (vamsas.objects.simple.WsJobId) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.WsJobId.class);
-            }
-        }
-    }
-
-    public vamsas.objects.simple.Alignment getalign(java.lang.String job_id) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[1]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getalign"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {job_id});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (vamsas.objects.simple.Alignment) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.Alignment) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.Alignment.class);
-            }
-        }
-    }
-
-    public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[2]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "getResult"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {job_id});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (vamsas.objects.simple.MsaResult) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.MsaResult) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.MsaResult.class);
-            }
-        }
-    }
-
-    public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId) throws java.rmi.RemoteException {
-        if (super.cachedEndpoint == null) {
-            throw new org.apache.axis.NoEndPointException();
-        }
-        org.apache.axis.client.Call _call = createCall();
-        _call.setOperation(_operations[3]);
-        _call.setUseSOAPAction(true);
-        _call.setSOAPActionURI("");
-        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
-        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "cancel"));
-
-        setRequestHeaders(_call);
-        setAttachments(_call);
-        java.lang.Object _resp = _call.invoke(new java.lang.Object[] {jobId});
-
-        if (_resp instanceof java.rmi.RemoteException) {
-            throw (java.rmi.RemoteException)_resp;
-        }
-        else {
-            extractAttachments(_call);
-            try {
-                return (vamsas.objects.simple.WsJobId) _resp;
-            } catch (java.lang.Exception _exception) {
-                return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp, vamsas.objects.simple.WsJobId.class);
-            }
-        }
-    }
-
-}
+*/
+package ext.vamsas;
+
+public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub
+    implements ext.vamsas.MuscleWS {
+    static org.apache.axis.description.OperationDesc[] _operations;
+
+    static {
+        _operations = new org.apache.axis.description.OperationDesc[4];
+        _initOperationDesc1();
+    }
+
+    private java.util.Vector cachedSerClasses = new java.util.Vector();
+    private java.util.Vector cachedSerQNames = new java.util.Vector();
+    private java.util.Vector cachedSerFactories = new java.util.Vector();
+    private java.util.Vector cachedDeserFactories = new java.util.Vector();
+
+    public MuscleWSSoapBindingStub() throws org.apache.axis.AxisFault {
+        this(null);
+    }
+
+    public MuscleWSSoapBindingStub(java.net.URL endpointURL,
+        javax.xml.rpc.Service service) throws org.apache.axis.AxisFault {
+        this(service);
+        super.cachedEndpoint = endpointURL;
+    }
+
+    public MuscleWSSoapBindingStub(javax.xml.rpc.Service service)
+        throws org.apache.axis.AxisFault {
+        if (service == null) {
+            super.service = new org.apache.axis.client.Service();
+        } else {
+            super.service = service;
+        }
+
+        java.lang.Class cls;
+        javax.xml.namespace.QName qName;
+        java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
+        java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
+        java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
+        java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
+        java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
+        java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
+        java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
+        java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
+        java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
+        java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+        qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+                "Sequence");
+        cachedSerQNames.add(qName);
+        cls = vamsas.objects.simple.Sequence.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
+        cachedSerQNames.add(qName);
+        cls = vamsas.objects.simple.Sequence[].class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(arraysf);
+        cachedDeserFactories.add(arraydf);
+
+        qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+                "MsaResult");
+        cachedSerQNames.add(qName);
+        cls = vamsas.objects.simple.MsaResult.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+                "SequenceSet");
+        cachedSerQNames.add(qName);
+        cls = vamsas.objects.simple.SequenceSet.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",
+                "Object");
+        cachedSerQNames.add(qName);
+        cls = vamsas.objects.simple.Object.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+                "Alignment");
+        cachedSerQNames.add(qName);
+        cls = vamsas.objects.simple.Alignment.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId");
+        cachedSerQNames.add(qName);
+        cls = vamsas.objects.simple.WsJobId.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+
+        qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_xsd_string");
+        cachedSerQNames.add(qName);
+        cls = java.lang.String[].class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(arraysf);
+        cachedDeserFactories.add(arraydf);
+
+        qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
+        cachedSerQNames.add(qName);
+        cls = vamsas.objects.simple.Result.class;
+        cachedSerClasses.add(cls);
+        cachedSerFactories.add(beansf);
+        cachedDeserFactories.add(beandf);
+    }
+
+    private static void _initOperationDesc1() {
+        org.apache.axis.description.OperationDesc oper;
+        oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("align");
+        oper.addParameter(new javax.xml.namespace.QName("", "seqSet"),
+            new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"),
+            vamsas.objects.simple.SequenceSet.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "WsJobId"));
+        oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("", "alignReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.RPC);
+        oper.setUse(org.apache.axis.constants.Use.ENCODED);
+        _operations[0] = oper;
+
+        oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("getalign");
+        oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
+            new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
+                "string"), java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "Alignment"));
+        oper.setReturnClass(vamsas.objects.simple.Alignment.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("", "getalignReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.RPC);
+        oper.setUse(org.apache.axis.constants.Use.ENCODED);
+        _operations[1] = oper;
+
+        oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("getResult");
+        oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
+            new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
+                "string"), java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "MsaResult"));
+        oper.setReturnClass(vamsas.objects.simple.MsaResult.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("", "getResultReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.RPC);
+        oper.setUse(org.apache.axis.constants.Use.ENCODED);
+        _operations[2] = oper;
+
+        oper = new org.apache.axis.description.OperationDesc();
+        oper.setName("cancel");
+        oper.addParameter(new javax.xml.namespace.QName("", "jobId"),
+            new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema",
+                "string"), java.lang.String.class,
+            org.apache.axis.description.ParameterDesc.IN, false, false);
+        oper.setReturnType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "WsJobId"));
+        oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
+        oper.setReturnQName(new javax.xml.namespace.QName("", "cancelReturn"));
+        oper.setStyle(org.apache.axis.constants.Style.RPC);
+        oper.setUse(org.apache.axis.constants.Use.ENCODED);
+        _operations[3] = oper;
+    }
+
+    protected org.apache.axis.client.Call createCall()
+        throws java.rmi.RemoteException {
+        try {
+            org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service.createCall();
+
+            if (super.maintainSessionSet) {
+                _call.setMaintainSession(super.maintainSession);
+            }
+
+            if (super.cachedUsername != null) {
+                _call.setUsername(super.cachedUsername);
+            }
+
+            if (super.cachedPassword != null) {
+                _call.setPassword(super.cachedPassword);
+            }
+
+            if (super.cachedEndpoint != null) {
+                _call.setTargetEndpointAddress(super.cachedEndpoint);
+            }
+
+            if (super.cachedTimeout != null) {
+                _call.setTimeout(super.cachedTimeout);
+            }
+
+            if (super.cachedPortName != null) {
+                _call.setPortName(super.cachedPortName);
+            }
+
+            java.util.Enumeration keys = super.cachedProperties.keys();
+
+            while (keys.hasMoreElements()) {
+                java.lang.String key = (java.lang.String) keys.nextElement();
+                _call.setProperty(key, super.cachedProperties.get(key));
+            }
+
+            // All the type mapping information is registered
+            // when the first call is made.
+            // The type mapping information is actually registered in
+            // the TypeMappingRegistry of the service, which
+            // is the reason why registration is only needed for the first call.
+            synchronized (this) {
+                if (firstCall()) {
+                    // must set encoding style before registering serializers
+                    _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+                    _call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
+
+                    for (int i = 0; i < cachedSerFactories.size(); ++i) {
+                        java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
+                        javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames.get(i);
+                        java.lang.Class sf = (java.lang.Class) cachedSerFactories.get(i);
+                        java.lang.Class df = (java.lang.Class) cachedDeserFactories.get(i);
+                        _call.registerTypeMapping(cls, qName, sf, df, false);
+                    }
+                }
+            }
+
+            return _call;
+        } catch (java.lang.Throwable _t) {
+            throw new org.apache.axis.AxisFault("Failure trying to get the Call object",
+                _t);
+        }
+    }
+
+    public vamsas.objects.simple.WsJobId align(
+        vamsas.objects.simple.SequenceSet seqSet)
+        throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[0]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "align"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { seqSet });
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException) _resp;
+        } else {
+            extractAttachments(_call);
+
+            try {
+                return (vamsas.objects.simple.WsJobId) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp,
+                    vamsas.objects.simple.WsJobId.class);
+            }
+        }
+    }
+
+    public vamsas.objects.simple.Alignment getalign(java.lang.String job_id)
+        throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[1]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+                "getalign"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { job_id });
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException) _resp;
+        } else {
+            extractAttachments(_call);
+
+            try {
+                return (vamsas.objects.simple.Alignment) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (vamsas.objects.simple.Alignment) org.apache.axis.utils.JavaUtils.convert(_resp,
+                    vamsas.objects.simple.Alignment.class);
+            }
+        }
+    }
+
+    public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id)
+        throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[2]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas",
+                "getResult"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { job_id });
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException) _resp;
+        } else {
+            extractAttachments(_call);
+
+            try {
+                return (vamsas.objects.simple.MsaResult) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (vamsas.objects.simple.MsaResult) org.apache.axis.utils.JavaUtils.convert(_resp,
+                    vamsas.objects.simple.MsaResult.class);
+            }
+        }
+    }
+
+    public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)
+        throws java.rmi.RemoteException {
+        if (super.cachedEndpoint == null) {
+            throw new org.apache.axis.NoEndPointException();
+        }
+
+        org.apache.axis.client.Call _call = createCall();
+        _call.setOperation(_operations[3]);
+        _call.setUseSOAPAction(true);
+        _call.setSOAPActionURI("");
+        _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+        _call.setOperationName(new javax.xml.namespace.QName("vamsas", "cancel"));
+
+        setRequestHeaders(_call);
+        setAttachments(_call);
+
+        java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobId });
+
+        if (_resp instanceof java.rmi.RemoteException) {
+            throw (java.rmi.RemoteException) _resp;
+        } else {
+            extractAttachments(_call);
+
+            try {
+                return (vamsas.objects.simple.WsJobId) _resp;
+            } catch (java.lang.Exception _exception) {
+                return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils.convert(_resp,
+                    vamsas.objects.simple.WsJobId.class);
+            }
+        }
+    }
+}
diff --git a/src/ext/vamsas/Result.java b/src/ext/vamsas/Result.java
index 97d766b..3115fd1 100755
--- a/src/ext/vamsas/Result.java
+++ b/src/ext/vamsas/Result.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,416 +22,420 @@
 * 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 ext.vamsas;
-
-public class Result  implements java.io.Serializable {
-    private boolean broken;
-    private boolean failed;
-    private boolean finished;
-    private boolean invalid;
-    private boolean jobFailed;
-    private boolean queued;
-    private boolean running;
-    private boolean serverError;
-    private int state;
-    private java.lang.String status;
-    private boolean suspended;
-
-    public Result() {
-    }
-
-    public Result(
-           boolean broken,
-           boolean failed,
-           boolean finished,
-           boolean invalid,
-           boolean jobFailed,
-           boolean queued,
-           boolean running,
-           boolean serverError,
-           int state,
-           java.lang.String status,
-           boolean suspended) {
-           this.broken = broken;
-           this.failed = failed;
-           this.finished = finished;
-           this.invalid = invalid;
-           this.jobFailed = jobFailed;
-           this.queued = queued;
-           this.running = running;
-           this.serverError = serverError;
-           this.state = state;
-           this.status = status;
-           this.suspended = suspended;
-    }
-
-
+*/
+package ext.vamsas;
+
+public class Result implements java.io.Serializable {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Result.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "Result"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("broken");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "broken"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("failed");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "failed"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("finished");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "finished"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("invalid");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "invalid"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("jobFailed");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "jobFailed"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("queued");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "queued"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("running");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "running"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("serverError");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "serverError"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("state");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "state"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "int"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("status");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "status"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("suspended");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "suspended"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    private boolean broken;
+    private boolean failed;
+    private boolean finished;
+    private boolean invalid;
+    private boolean jobFailed;
+    private boolean queued;
+    private boolean running;
+    private boolean serverError;
+    private int state;
+    private java.lang.String status;
+    private boolean suspended;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public Result() {
+    }
+
+    public Result(boolean broken, boolean failed, boolean finished,
+        boolean invalid, boolean jobFailed, boolean queued, boolean running,
+        boolean serverError, int state, java.lang.String status,
+        boolean suspended) {
+        this.broken = broken;
+        this.failed = failed;
+        this.finished = finished;
+        this.invalid = invalid;
+        this.jobFailed = jobFailed;
+        this.queued = queued;
+        this.running = running;
+        this.serverError = serverError;
+        this.state = state;
+        this.status = status;
+        this.suspended = suspended;
+    }
+
     /**
-     * Gets the broken value for this Result.
-     *
-     * @return broken
-     */
-    public boolean isBroken() {
-        return broken;
-    }
-
-
+ * Gets the broken value for this Result.
+ *
+ * @return broken
+ */
+    public boolean isBroken() {
+        return broken;
+    }
+
     /**
-     * Sets the broken value for this Result.
-     *
-     * @param broken
-     */
-    public void setBroken(boolean broken) {
-        this.broken = broken;
-    }
-
-
+ * Sets the broken value for this Result.
+ *
+ * @param broken
+ */
+    public void setBroken(boolean broken) {
+        this.broken = broken;
+    }
+
     /**
-     * Gets the failed value for this Result.
-     *
-     * @return failed
-     */
-    public boolean isFailed() {
-        return failed;
-    }
-
-
+ * Gets the failed value for this Result.
+ *
+ * @return failed
+ */
+    public boolean isFailed() {
+        return failed;
+    }
+
     /**
-     * Sets the failed value for this Result.
-     *
-     * @param failed
-     */
-    public void setFailed(boolean failed) {
-        this.failed = failed;
-    }
-
-
+ * Sets the failed value for this Result.
+ *
+ * @param failed
+ */
+    public void setFailed(boolean failed) {
+        this.failed = failed;
+    }
+
     /**
-     * Gets the finished value for this Result.
-     *
-     * @return finished
-     */
-    public boolean isFinished() {
-        return finished;
-    }
-
-
+ * Gets the finished value for this Result.
+ *
+ * @return finished
+ */
+    public boolean isFinished() {
+        return finished;
+    }
+
     /**
-     * Sets the finished value for this Result.
-     *
-     * @param finished
-     */
-    public void setFinished(boolean finished) {
-        this.finished = finished;
-    }
-
-
+ * Sets the finished value for this Result.
+ *
+ * @param finished
+ */
+    public void setFinished(boolean finished) {
+        this.finished = finished;
+    }
+
     /**
-     * Gets the invalid value for this Result.
-     *
-     * @return invalid
-     */
-    public boolean isInvalid() {
-        return invalid;
-    }
-
-
+ * Gets the invalid value for this Result.
+ *
+ * @return invalid
+ */
+    public boolean isInvalid() {
+        return invalid;
+    }
+
     /**
-     * Sets the invalid value for this Result.
-     *
-     * @param invalid
-     */
-    public void setInvalid(boolean invalid) {
-        this.invalid = invalid;
-    }
-
-
+ * Sets the invalid value for this Result.
+ *
+ * @param invalid
+ */
+    public void setInvalid(boolean invalid) {
+        this.invalid = invalid;
+    }
+
     /**
-     * Gets the jobFailed value for this Result.
-     *
-     * @return jobFailed
-     */
-    public boolean isJobFailed() {
-        return jobFailed;
-    }
-
-
+ * Gets the jobFailed value for this Result.
+ *
+ * @return jobFailed
+ */
+    public boolean isJobFailed() {
+        return jobFailed;
+    }
+
     /**
-     * Sets the jobFailed value for this Result.
-     *
-     * @param jobFailed
-     */
-    public void setJobFailed(boolean jobFailed) {
-        this.jobFailed = jobFailed;
-    }
-
-
+ * Sets the jobFailed value for this Result.
+ *
+ * @param jobFailed
+ */
+    public void setJobFailed(boolean jobFailed) {
+        this.jobFailed = jobFailed;
+    }
+
     /**
-     * Gets the queued value for this Result.
-     *
-     * @return queued
-     */
-    public boolean isQueued() {
-        return queued;
-    }
-
-
+ * Gets the queued value for this Result.
+ *
+ * @return queued
+ */
+    public boolean isQueued() {
+        return queued;
+    }
+
     /**
-     * Sets the queued value for this Result.
-     *
-     * @param queued
-     */
-    public void setQueued(boolean queued) {
-        this.queued = queued;
-    }
-
-
+ * Sets the queued value for this Result.
+ *
+ * @param queued
+ */
+    public void setQueued(boolean queued) {
+        this.queued = queued;
+    }
+
     /**
-     * Gets the running value for this Result.
-     *
-     * @return running
-     */
-    public boolean isRunning() {
-        return running;
-    }
-
-
+ * Gets the running value for this Result.
+ *
+ * @return running
+ */
+    public boolean isRunning() {
+        return running;
+    }
+
     /**
-     * Sets the running value for this Result.
-     *
-     * @param running
-     */
-    public void setRunning(boolean running) {
-        this.running = running;
-    }
-
-
+ * Sets the running value for this Result.
+ *
+ * @param running
+ */
+    public void setRunning(boolean running) {
+        this.running = running;
+    }
+
     /**
-     * Gets the serverError value for this Result.
-     *
-     * @return serverError
-     */
-    public boolean isServerError() {
-        return serverError;
-    }
-
-
+ * Gets the serverError value for this Result.
+ *
+ * @return serverError
+ */
+    public boolean isServerError() {
+        return serverError;
+    }
+
     /**
-     * Sets the serverError value for this Result.
-     *
-     * @param serverError
-     */
-    public void setServerError(boolean serverError) {
-        this.serverError = serverError;
-    }
-
-
+ * Sets the serverError value for this Result.
+ *
+ * @param serverError
+ */
+    public void setServerError(boolean serverError) {
+        this.serverError = serverError;
+    }
+
     /**
-     * Gets the state value for this Result.
-     *
-     * @return state
-     */
-    public int getState() {
-        return state;
-    }
-
-
+ * Gets the state value for this Result.
+ *
+ * @return state
+ */
+    public int getState() {
+        return state;
+    }
+
     /**
-     * Sets the state value for this Result.
-     *
-     * @param state
-     */
-    public void setState(int state) {
-        this.state = state;
-    }
-
-
+ * Sets the state value for this Result.
+ *
+ * @param state
+ */
+    public void setState(int state) {
+        this.state = state;
+    }
+
     /**
-     * Gets the status value for this Result.
-     *
-     * @return status
-     */
-    public java.lang.String getStatus() {
-        return status;
-    }
-
-
+ * Gets the status value for this Result.
+ *
+ * @return status
+ */
+    public java.lang.String getStatus() {
+        return status;
+    }
+
     /**
-     * Sets the status value for this Result.
-     *
-     * @param status
-     */
-    public void setStatus(java.lang.String status) {
-        this.status = status;
-    }
-
-
+ * Sets the status value for this Result.
+ *
+ * @param status
+ */
+    public void setStatus(java.lang.String status) {
+        this.status = status;
+    }
+
     /**
-     * Gets the suspended value for this Result.
-     *
-     * @return suspended
-     */
-    public boolean isSuspended() {
-        return suspended;
-    }
-
-
+ * Gets the suspended value for this Result.
+ *
+ * @return suspended
+ */
+    public boolean isSuspended() {
+        return suspended;
+    }
+
     /**
-     * Sets the suspended value for this Result.
-     *
-     * @param suspended
-     */
-    public void setSuspended(boolean suspended) {
-        this.suspended = suspended;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Result)) return false;
-        Result other = (Result) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true &&
-            this.broken == other.isBroken() &&
-            this.failed == other.isFailed() &&
-            this.finished == other.isFinished() &&
-            this.invalid == other.isInvalid() &&
-            this.jobFailed == other.isJobFailed() &&
-            this.queued == other.isQueued() &&
-            this.running == other.isRunning() &&
-            this.serverError == other.isServerError() &&
-            this.state == other.getState() &&
-            ((this.status==null && other.getStatus()==null) ||
-             (this.status!=null &&
-              this.status.equals(other.getStatus()))) &&
-            this.suspended == other.isSuspended();
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += getState();
-        if (getStatus() != null) {
-            _hashCode += getStatus().hashCode();
-        }
-        _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Result.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Result"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("broken");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "broken"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("failed");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "failed"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("finished");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "finished"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("invalid");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "invalid"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("jobFailed");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "jobFailed"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("queued");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "queued"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("running");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "running"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("serverError");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "serverError"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("state");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "state"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("status");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "status"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("suspended");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "suspended"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+ * Sets the suspended value for this Result.
+ *
+ * @param suspended
+ */
+    public void setSuspended(boolean suspended) {
+        this.suspended = suspended;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Result)) {
+            return false;
+        }
+
+        Result other = (Result) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = true && (this.broken == other.isBroken()) &&
+            (this.failed == other.isFailed()) &&
+            (this.finished == other.isFinished()) &&
+            (this.invalid == other.isInvalid()) &&
+            (this.jobFailed == other.isJobFailed()) &&
+            (this.queued == other.isQueued()) &&
+            (this.running == other.isRunning()) &&
+            (this.serverError == other.isServerError()) &&
+            (this.state == other.getState()) &&
+            (((this.status == null) && (other.getStatus() == null)) ||
+            ((this.status != null) && this.status.equals(other.getStatus()))) &&
+            (this.suspended == other.isSuspended());
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = 1;
+        _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += getState();
+
+        if (getStatus() != null) {
+            _hashCode += getStatus().hashCode();
+        }
+
+        _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/ext/vamsas/Secstructpred.java b/src/ext/vamsas/Secstructpred.java
index 290ac3c..d1da9be 100755
--- a/src/ext/vamsas/Secstructpred.java
+++ b/src/ext/vamsas/Secstructpred.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,116 +22,128 @@
 * 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 ext.vamsas;
-
-public class Secstructpred  implements java.io.Serializable {
-    private java.lang.String output;
-
-    public Secstructpred() {
-    }
-
-    public Secstructpred(
-           java.lang.String output) {
-           this.output = output;
-    }
-
-
+*/
+package ext.vamsas;
+
+public class Secstructpred implements java.io.Serializable {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Secstructpred.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "Secstructpred"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("output");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "output"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    private java.lang.String output;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public Secstructpred() {
+    }
+
+    public Secstructpred(java.lang.String output) {
+        this.output = output;
+    }
+
     /**
-     * Gets the output value for this Secstructpred.
-     *
-     * @return output
-     */
-    public java.lang.String getOutput() {
-        return output;
-    }
-
-
+ * Gets the output value for this Secstructpred.
+ *
+ * @return output
+ */
+    public java.lang.String getOutput() {
+        return output;
+    }
+
     /**
-     * Sets the output value for this Secstructpred.
-     *
-     * @param output
-     */
-    public void setOutput(java.lang.String output) {
-        this.output = output;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Secstructpred)) return false;
-        Secstructpred other = (Secstructpred) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true &&
-            ((this.output==null && other.getOutput()==null) ||
-             (this.output!=null &&
-              this.output.equals(other.getOutput())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getOutput() != null) {
-            _hashCode += getOutput().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Secstructpred.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Secstructpred"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("output");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "output"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+ * Sets the output value for this Secstructpred.
+ *
+ * @param output
+ */
+    public void setOutput(java.lang.String output) {
+        this.output = output;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Secstructpred)) {
+            return false;
+        }
+
+        Secstructpred other = (Secstructpred) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = true &&
+            (((this.output == null) && (other.getOutput() == null)) ||
+            ((this.output != null) && this.output.equals(other.getOutput())));
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = 1;
+
+        if (getOutput() != null) {
+            _hashCode += getOutput().hashCode();
+        }
+
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/ext/vamsas/Sequence.java b/src/ext/vamsas/Sequence.java
index c2b9da8..4d73bcf 100755
--- a/src/ext/vamsas/Sequence.java
+++ b/src/ext/vamsas/Sequence.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,150 +22,161 @@
 * 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 ext.vamsas;
-
-public class Sequence  implements java.io.Serializable {
-    private java.lang.String id;
-    private java.lang.String seq;
-
-    public Sequence() {
-    }
-
-    public Sequence(
-           java.lang.String id,
-           java.lang.String seq) {
-           this.id = id;
-           this.seq = seq;
-    }
-
-
+*/
+package ext.vamsas;
+
+public class Sequence implements java.io.Serializable {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Sequence.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "Sequence"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("id");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "id"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("seq");
+        elemField.setXmlName(new javax.xml.namespace.QName(
+                "http://dataTypes.vamsas", "seq"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "string"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
+    private java.lang.String id;
+    private java.lang.String seq;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public Sequence() {
+    }
+
+    public Sequence(java.lang.String id, java.lang.String seq) {
+        this.id = id;
+        this.seq = seq;
+    }
+
     /**
-     * Gets the id value for this Sequence.
-     *
-     * @return id
-     */
-    public java.lang.String getId() {
-        return id;
-    }
-
-
+ * Gets the id value for this Sequence.
+ *
+ * @return id
+ */
+    public java.lang.String getId() {
+        return id;
+    }
+
     /**
-     * Sets the id value for this Sequence.
-     *
-     * @param id
-     */
-    public void setId(java.lang.String id) {
-        this.id = id;
-    }
-
-
+ * Sets the id value for this Sequence.
+ *
+ * @param id
+ */
+    public void setId(java.lang.String id) {
+        this.id = id;
+    }
+
     /**
-     * Gets the seq value for this Sequence.
-     *
-     * @return seq
-     */
-    public java.lang.String getSeq() {
-        return seq;
-    }
-
-
+ * Gets the seq value for this Sequence.
+ *
+ * @return seq
+ */
+    public java.lang.String getSeq() {
+        return seq;
+    }
+
     /**
-     * Sets the seq value for this Sequence.
-     *
-     * @param seq
-     */
-    public void setSeq(java.lang.String seq) {
-        this.seq = seq;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Sequence)) return false;
-        Sequence other = (Sequence) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true &&
-            ((this.id==null && other.getId()==null) ||
-             (this.id!=null &&
-              this.id.equals(other.getId()))) &&
-            ((this.seq==null && other.getSeq()==null) ||
-             (this.seq!=null &&
-              this.seq.equals(other.getSeq())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getId() != null) {
-            _hashCode += getId().hashCode();
-        }
-        if (getSeq() != null) {
-            _hashCode += getSeq().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Sequence.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("http://dataTypes.vamsas", "Sequence"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("id");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "id"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("seq");
-        elemField.setXmlName(new javax.xml.namespace.QName("http://dataTypes.vamsas", "seq"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "string"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+ * Sets the seq value for this Sequence.
+ *
+ * @param seq
+ */
+    public void setSeq(java.lang.String seq) {
+        this.seq = seq;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Sequence)) {
+            return false;
+        }
+
+        Sequence other = (Sequence) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = true &&
+            (((this.id == null) && (other.getId() == null)) ||
+            ((this.id != null) && this.id.equals(other.getId()))) &&
+            (((this.seq == null) && (other.getSeq() == null)) ||
+            ((this.seq != null) && this.seq.equals(other.getSeq())));
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = 1;
+
+        if (getId() != null) {
+            _hashCode += getId().hashCode();
+        }
+
+        if (getSeq() != null) {
+            _hashCode += getSeq().hashCode();
+        }
+
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 02569ef..41c6599 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -16,397 +16,374 @@
 * 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.jbgui.*;
+import jalview.analysis.*;
+
 import jalview.datamodel.*;
+
 import jalview.io.*;
-import jalview.analysis.*;
 
-import java.awt.*;
+import jalview.jbgui.*;
+
 import java.applet.Applet;
-import java.util.*;
-import java.net.*;
+
+import java.awt.*;
+
 import java.io.*;
 
-public class AAFrequency {
+import java.net.*;
 
+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) {
+        Vector result = new Vector();
+
+        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) {
+                    Sequence s = (Sequence) sequences.elementAt(j);
+
+                    if (s.getSequence().length() > i) {
+                        String res = s.getSequence().charAt(i) + "";
+
+                        if (!jalview.util.Comparison.isGap(res.charAt(0))) {
+                            nongap++;
+                        } else {
+                            res = "-"; // we always use this for gaps in the property vectors
+                        }
+
+                        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) {
+                                    maxResidue = res;
+                                } else if (maxResidue.indexOf(res) == -1) {
+                                    maxResidue += res;
+                                }
+
+                                maxCount = count;
+                            }
+
+                            residueHash.put(res, new Integer(count));
+                        } else {
+                            residueHash.put(res, new Integer(1));
+                        }
+                    } else {
+                        if (residueHash.containsKey("-")) {
+                            int count = ((Integer) residueHash.get("-")).intValue();
+                            count++;
+                            residueHash.put("-", new Integer(count));
+                        } else {
+                            residueHash.put("-", new Integer(1));
+                        }
+                    }
+                }
+            }
 
+            residueHash.put("maxCount", new Integer(maxCount));
 
-    public static Vector calculate(Vector sequences,int start,int end) {
-
-    Vector result = new Vector();
-
-    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)
-        {
-          Sequence s = (Sequence)sequences.elementAt(j);
-
-          if (s.getSequence().length() > i)
-          {
-
-            String res = s.getSequence().charAt(i)+"";
-
-            if (!jalview.util.Comparison.isGap(res.charAt(0)))
-              nongap++;
-            else
-              res = "-"; // we always use this for gaps in the property vectors
-
-            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)
-                      maxResidue = res;
-                  else if(maxResidue.indexOf(res)==-1)
-                      maxResidue += res;
-
-                  maxCount = count;
-	      }
-
-              residueHash.put(res,new Integer(count));
+            if (maxCount < 0) {
+                System.out.println("asasa " + maxCount);
             }
-            else
-              residueHash.put(res,new Integer(1));
-
-
-          }
-          else
-          {
-            if (residueHash.containsKey("-"))
-            {
-              int count = ((Integer)residueHash.get("-")).intValue() ;
-              count++;
-              residueHash.put("-",new Integer(count));
-            }
-            else
-              residueHash.put("-",new Integer(1));
 
-          }
+            residueHash.put("maxResidue", maxResidue);
+            residueHash.put("size", new Integer(sequences.size()));
+            residueHash.put("nongap", new Integer(nongap));
+            result.addElement(residueHash);
         }
-      }
-
-      residueHash.put("maxCount",new Integer(maxCount));
-      if(maxCount<0)
-        System.out.println("asasa "+maxCount);
-      residueHash.put("maxResidue", maxResidue);
-      residueHash.put("size", new Integer(sequences.size()));
-      residueHash.put("nongap", new Integer(nongap));
-      result.addElement(residueHash);
-    }
-
-    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();
+        return result;
+    }
 
-	result.addElement(values);
+    public static Vector calculatePID(SequenceI refseq, Vector sequences,
+        int window, int start, int end) {
+        Vector result = new Vector();
 
-	// If start < window/2 then set value to zero.
+        boolean init = true;
 
-	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;
+        Vector prev = null;
 
-	    int winstart = i-window/2;
-	    int winend   = i+window/2;
+        for (int i = start; i <= end; i++) {
+            Vector values = new Vector();
 
-            if (window%2 != 0) {
-              winend++;
-            }
+            result.addElement(values);
 
-	    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++) {
+            // 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;
 
-                    Sequence s = (Sequence)sequences.elementAt(j);
+                int winstart = i - (window / 2);
+                int winend = i + (window / 2);
 
-                    if (s.getSequence().length() > k) {
+                if ((window % 2) != 0) {
+                    winend++;
+                }
 
-                      String res = s.getSequence().substring(k,k+1); // no gapchar test needed
+                for (int j = 0; j < sequences.size(); j++) {
+                    values.addElement(new Integer(0));
+                }
 
-                      if (res.equals(refchar)) {
-                        int val = ((Integer)values.elementAt(j)).intValue();
-                        val++;
-                        values.setElementAt(new Integer(val),j);
-                      }
+                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;
+                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);
+                if ((window % 2) != 0) {
+                    winend++;
                 }
 
-		// 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));
+                // 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);
+                }
 
-	    }
-	    prev = values;
-	}
-    }
+                for (int j = 0; j < sequences.size(); j++) {
+                    // First copy the pid value from i-1
+                    int val = ((Integer) prev.elementAt(j)).intValue();
 
-    return result;
-    }
+                    Sequence s = (Sequence) sequences.elementAt(j);
 
-    public static Hashtable findBlocks(Vector seqs, int start, int end,Vector exc) {
+                    String pre_char = s.getSequence().substring(winstart - 1,
+                            winstart);
 
-	// start and end are in real (not relative coords);
+                    String pos_char = "-";
 
-	// The coords in the hashtable that is returned are in relative coords
-	// i.e. start from 0
+                    if (s.getSequence().length() > winend) {
+                        pos_char = s.getSequence().substring(winend, winend +
+                                1);
+                    }
 
-	Hashtable blocks = new Hashtable();
+                    // 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--;
+                    }
 
-	boolean prev = false;
-	int     bstart = -1;
+                    if ((jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false) &&
+                            pos_char.equals(pos_refchar)) {
+                        val++;
+                    }
 
-	for (int i = start; i <= end ; i++) {
-	    SequenceI seq = (SequenceI)seqs.elementAt(0);
+                    values.addElement(new Integer(val));
+                }
 
-	    char      c   = seq.getCharAt(i);
+                prev = values;
+            }
+        }
 
-	    boolean found = true;
+        return result;
+    }
 
-	    int j = 1;
+    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();
 
-	    while (j < seqs.size() && found == true) {
+        boolean prev = false;
+        int bstart = -1;
 
-		SequenceI jseq  = (SequenceI)seqs.elementAt(j);
+        for (int i = start; i <= end; i++) {
+            SequenceI seq = (SequenceI) seqs.elementAt(0);
 
-		if (!exc.contains(jseq)) {
+            char c = seq.getCharAt(i);
 
-		    char cc = jseq.getCharAt(i);
+            boolean found = true;
 
-		    if ( cc != c) {
-			found = false;
-		    }
-		}
-		j++;
-	    }
+            int j = 1;
 
+            while ((j < seqs.size()) && (found == true)) {
+                SequenceI jseq = (SequenceI) seqs.elementAt(j);
 
-	    if (prev == false && found == true) {
-		bstart = i;
-	    } else if (prev == true && found == false && bstart != -1) {
+                if (!exc.contains(jseq)) {
+                    char cc = jseq.getCharAt(i);
 
-		int blockstart = bstart-start;
-		int blocklen   = i-bstart;
+                    if (cc != c) {
+                        found = false;
+                    }
+                }
 
-		//System.out.println("Start len " + blockstart + " " + blocklen);
+                j++;
+            }
 
-		for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
-		    blocks.put(new Integer(jj),new Integer(blocklen));
-		}
+            if ((prev == false) && (found == true)) {
+                bstart = i;
+            } else if ((prev == true) && (found == false) && (bstart != -1)) {
+                int blockstart = bstart - start;
+                int blocklen = i - bstart;
 
-		bstart = -1;
-	    }
-	    prev = found;
-	}
+                //System.out.println("Start len " + blockstart + " " + blocklen);
+                for (int jj = blockstart; jj < (blockstart + blocklen); jj++) {
+                    blocks.put(new Integer(jj), new Integer(blocklen));
+                }
 
-	if (bstart != -1) {
+                bstart = -1;
+            }
 
-	    int blockstart = bstart-start;
-	    int blocklen   = end-bstart;
+            prev = found;
+        }
 
-	  //  System.out.println("Start len " + blockstart + " " + blocklen);
+        if (bstart != -1) {
+            int blockstart = bstart - start;
+            int blocklen = end - bstart;
 
-	    for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
-		blocks.put(new Integer(blockstart),new Integer(blocklen));
-	    }
+            //  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;
+        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));
 
-    public static Hashtable findKmerCount(SequenceI seq, int start, int end,int window, int step,Vector kmers) {
-
-       int tmpstart = start;
-       Hashtable vals = new Hashtable();
+            int count = 0;
 
-       while (tmpstart <= end) {
+            //System.out.println("Str " + tmpstr);
+            for (int ii = 0; ii < kmers.size(); ii++) {
+                String kmer = ((SequenceI) kmers.elementAt(ii)).getSequence();
 
-           String tmpstr = seq.getSequence().substring(tmpstart-window/2,tmpstart+window/2);
+                int i = -1;
 
-           int count = 0;
+                while (tmpstr.indexOf(kmer, i) != -1) {
+                    i = tmpstr.indexOf(kmer, i);
 
-           //System.out.println("Str " + tmpstr);
-
-	   for (int ii = 0; ii < kmers.size(); ii++) {
-	       String kmer = ((SequenceI)kmers.elementAt(ii)).getSequence();
+                    i++;
+                    count++;
+                }
 
-	       int i = -1;
+                ii++;
+            }
 
-	       while (tmpstr.indexOf(kmer,i) != -1) {
-               i = tmpstr.indexOf(kmer,i);
+            vals.put(new Integer(tmpstart), new Integer(count));
+            tmpstart += step;
+        }
 
-               i++;
-               count++;
-	       }
-	       ii++;
-	   }
-           vals.put(new Integer(tmpstart),new Integer(count));
-           tmpstart += step;
-       }
-       return vals;
+        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
+    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();
 
-	Hashtable blocks = new Hashtable();
+        boolean prev = false;
+        int bstart = -1;
 
-	boolean prev = false;
-	int     bstart = -1;
+        for (int i = start; i <= end; i++) {
+            SequenceI seq = (SequenceI) seqs.elementAt(0);
 
-	for (int i = start; i <= end ; i++) {
-	    SequenceI seq = (SequenceI)seqs.elementAt(0);
+            char c = seq.getCharAt(i);
 
-	    char      c   = seq.getCharAt(i);
+            boolean found = true;
 
-	    boolean found = true;
+            int j = 1;
 
-	    int j = 1;
+            while ((j < seqs.size()) && (found == true)) {
+                SequenceI jseq = (SequenceI) seqs.elementAt(j);
 
-	    while (j < seqs.size() && found == true) {
+                if (!exc.contains(jseq)) {
+                    char cc = jseq.getCharAt(i);
 
-		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) {
+                    if (cc != c) {
+                        found = false;
+                    }
+                }
 
-		int blockstart = bstart-start;
-		int blocklen   = i-bstart;
+                j++;
+            }
 
-		//		System.out.println("Start len " + blockstart + " " + blocklen);
+            if ((prev == false) && (found == true)) {
+                bstart = i;
+            } else if ((prev == true) && (found == false) && (bstart != -1)) {
+                int blockstart = bstart - start;
+                int blocklen = i - bstart;
 
-		//for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
-		    blocks.put(new Integer(blockstart),new Integer(blocklen));
-	//	}
+                //		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;
-	}
+                //	}
+                bstart = -1;
+            }
 
-	if (bstart != -1) {
+            prev = found;
+        }
 
-	    int blockstart = bstart-start;
-	    int blocklen   = end-bstart;
+        if (bstart != -1) {
+            int blockstart = bstart - start;
+            int blocklen = end - bstart;
 
-	  //  System.out.println("Start len " + blockstart + " " + blocklen);
+            //  System.out.println("Start len " + blockstart + " " + blocklen);
+            //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
+            blocks.put(new Integer(blockstart), new Integer(blocklen));
 
-	    //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
-		blocks.put(new Integer(blockstart),new Integer(blocklen));
-	   // }
+            // }
+        }
 
-	}
-	return blocks;
+        return blocks;
     }
-
 }
-
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index e77a0d3..47c17a3 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -16,528 +16,566 @@
 * 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.schemes.*;
 import jalview.datamodel.SequenceI;
-import jalview.util.*;
+
 import jalview.io.*;
 
-import java.util.*;
-import java.io.*;
+import jalview.schemes.*;
+
+import jalview.util.*;
+
 import java.awt.*;
 
+import java.io.*;
+
+import java.util.*;
+
+
 public class AlignSeq {
+    public static java.util.Hashtable dnaHash = new java.util.Hashtable();
+
+    static {
+        dnaHash.put("C", new Integer(0));
+        dnaHash.put("T", new Integer(1));
+        dnaHash.put("A", new Integer(2));
+        dnaHash.put("G", new Integer(3));
+        dnaHash.put("-", new Integer(4));
+    }
+
+    static String[] dna = { "C", "T", "A", "G", "-" };
+    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", "-"
+    };
+    int[][] score;
+    int[][] E;
+    int[][] F;
+    int[][] traceback;
+    int[] seq1;
+    int[] seq2;
+    SequenceI s1;
+    SequenceI s2;
+    String s1str;
+    String s2str;
+    int maxi;
+    int maxj;
+    int[] aseq1;
+    int[] aseq2;
+    String astr1 = "";
+    String astr2 = "";
+    public int seq1start;
+    public int seq1end;
+    public int seq2start;
+    public int seq2end;
+    int count;
+    public int maxscore;
+    float pid;
+    int prev = 0;
+    int gapOpen = 120;
+    int gapExtend = 20;
+    int[][] lookup = ResidueProperties.getBLOSUM62();
+    String[] intToStr = pep;
+    int defInt = 23;
+    String output = "";
+    String type;
+    Runtime rt;
+
+    public AlignSeq() {
+    }
+
+    public AlignSeq(SequenceI s1, SequenceI s2, String type) {
+        rt = Runtime.getRuntime();
+        SeqInit(s1, s2, type);
+    }
+
+    public int getMaxScore() {
+        return maxscore;
+    }
 
-  int[][] score;
-  int[][] E;
-  int[][] F;
-  int[][] traceback;
-
-  int[] seq1;
-  int[] seq2;
-
-  SequenceI s1;
-  SequenceI s2;
-
-  String s1str;
-  String s2str;
-
-  int maxi;
-  int maxj;
-
-  int[] aseq1;
-  int[] aseq2;
-
-  String astr1 = "";
-  String astr2 = "";
-
-  public int seq1start;
-  public int seq1end;
-  public int seq2start;
-  public int seq2end;
-
-  int count;
-
-  public int maxscore;
-  float pid;
-  int prev = 0;
-
-  public static java.util.Hashtable dnaHash = new java.util.Hashtable();
-
-  static  {
-    dnaHash.put("C", new Integer(0));
-    dnaHash.put("T", new Integer(1));
-    dnaHash.put("A", new Integer(2));
-    dnaHash.put("G", new Integer(3));
-    dnaHash.put("-", new Integer(4));
-  }
-
-  static String dna[] = {"C","T","A","G","-"};
-  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","-"};
-
-  int gapOpen = 120;
-  int gapExtend = 20;
-
-  int lookup[][] = ResidueProperties.getBLOSUM62();
-  String intToStr[] = pep;
-  int defInt = 23;
-
-  String output = "";
-
-  String type;
-  Runtime rt;
-  public AlignSeq() {}
-
-  public AlignSeq(SequenceI s1, SequenceI s2,String type) {
-    rt  = Runtime.getRuntime();
-    SeqInit(s1,s2,type);
-  }
-
-  public int getMaxScore() {
-    return maxscore;
-  }
-
-  public int getSeq2Start() {
-    return seq2start;
-  }
-
-  public int getSeq2End() {
-    return seq2end;
-  }
-
-  public int getSeq1Start() {
-    return seq1start;
-  }
-
-  public int getSeq1End() {
-    return seq1end;
-  }
-
-  public String getOutput() {
-    return output;
-  }
-
-  public String getAStr1() {
-    return astr1;
-  }
-  public String getAStr2() {
-    return astr2;
-  }
-  public int [] getASeq1() {
-    return aseq1;
-  }
-  public int [] getASeq2() {
-    return aseq2;
-  }
-  public SequenceI getS1() {
-    return s1;
-  }
-  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);
-
-    this.s1 = s1;
-    this.s2 = s2;
-
-    this.type = type;
-
-    if (type.equals("pep")) {
-      lookup = ResidueProperties.getBLOSUM62();
-      intToStr = pep;
-      defInt = 23;
-    } else if (type.equals("dna")) {
-      lookup = ResidueProperties.getDNA();
-      intToStr = dna;
-      defInt = 4;
-    } else {
-      output = output + ("Wrong type = dna or pep only");
-      System.exit(0);
+    public int getSeq2Start() {
+        return seq2start;
     }
 
+    public int getSeq2End() {
+        return seq2end;
+    }
 
-    //System.out.println("lookuip " + rt.freeMemory() + " "+  rt.totalMemory());
-    seq1 = new int[s1str.length()];
-    //System.out.println("seq1 " + rt.freeMemory() +" "  + rt.totalMemory());
-    seq2 = new int[s2str.length()];
-    //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
-    score = new int[s1str.length()][s2str.length()];
-    //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
-    E = new int[s1str.length()][s2str.length()];
-    //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
-    F = new int[s1str.length()][s2str.length()];
-    traceback = new int[s1str.length()][s2str.length()];
-    //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
-    seq1 = stringToInt(s1str,type);
-    //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
-    seq2 = stringToInt(s2str,type);
-    //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());
-
-    //   long tstart = System.currentTimeMillis();
-    //    calcScoreMatrix();
-    //long tend = System.currentTimeMillis();
-
-    //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms");
-
-
-    //   printScoreMatrix(score);
-    //System.out.println();
-
-    //printScoreMatrix(traceback);
-    //System.out.println();
-
-    //  printScoreMatrix(E);
-    //System.out.println();
-
-    ///printScoreMatrix(F);
-    //System.out.println();
-    // tstart = System.currentTimeMillis();
-    //traceAlignment();
-    //tend = System.currentTimeMillis();
-    //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");
-  }
-
-  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 ) {
-        max = score[i][seq2.length - 1];
-        maxi = i;
-        maxj = seq2.length-1;
-      }
+    public int getSeq1Start() {
+        return seq1start;
     }
-    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;
-      }
+
+    public int getSeq1End() {
+        return seq1end;
     }
 
-    //  System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
-
-    int i = maxi;
-    int j = maxj;
-    int trace;
-    maxscore = score[i][j] / 10;
-
-    seq1end = maxi+1;
-    seq2end = maxj+1;
-
-    aseq1 = new int[seq1.length + seq2.length];
-    aseq2 = new int[seq1.length + seq2.length];
-
-    count = seq1.length + seq2.length - 1;
-
-    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) {
-        aseq2[count] = seq2[j];
-        astr2 = intToStr[seq2[j]] + astr2;
-      }
-      trace = findTrace(i,j);
-      if (trace == 0) {
-        i--;
-        j--;
-
-      } else  if (trace == 1) {
-        j--;
-        aseq1[count] = defInt;
-        astr1 = "-" + astr1.substring(1);
-      } else  if (trace == -1) {
-        i--;
-        aseq2[count] = defInt;
-        astr2 = "-" + astr2.substring(1);
-      }
-      count--;
+    public String getOutput() {
+        return output;
     }
 
-    seq1start = i+1;
-    seq2start = j+1;
+    public String getAStr1() {
+        return astr1;
+    }
 
-    if (aseq1[count] != defInt) {
-      aseq1[count] = seq1[i];
-      astr1 = intToStr[seq1[i]] + astr1;
+    public String getAStr2() {
+        return astr2;
     }
 
-    if (aseq2[count] != defInt) {
-      aseq2[count] = seq2[j];
-      astr2 = intToStr[seq2[j]] + astr2;
+    public int[] getASeq1() {
+        return aseq1;
     }
-  }
 
-  public void printAlignment() {
-    // Find the biggest id length for formatting purposes
-    int maxid = s1.getName().length();
+    public int[] getASeq2() {
+        return aseq2;
+    }
 
-    if (s2.getName().length() > maxid) {
-      maxid = s2.getName().length();
+    public SequenceI getS1() {
+        return s1;
     }
 
-    int len = 72 - maxid - 1;
-    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");
-    output = output + ("Sequence ");
-    output = output + (new Format("%" + maxid + "s").form(s1.getName()));
-    output = output + (" :  " + seq1start + " - " + seq1end + " (Sequence length = " + s1str.length() + ")\n");
-    output = output + ("Sequence ");
-    output = output + (new Format("%" + maxid + "s").form(s2.getName()));
-    output = output + (" :  " + seq2start + " - " + seq2end + " (Sequence length = " + s2str.length() + ")\n\n");
-
-    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) {
-          output = output + (new Format("%s").form(intToStr[aseq1[count + i + j*len]]));
+    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);
+
+        this.s1 = s1;
+        this.s2 = s2;
+
+        this.type = type;
+
+        if (type.equals("pep")) {
+            lookup = ResidueProperties.getBLOSUM62();
+            intToStr = pep;
+            defInt = 23;
+        } else if (type.equals("dna")) {
+            lookup = ResidueProperties.getDNA();
+            intToStr = dna;
+            defInt = 4;
+        } else {
+            output = output + ("Wrong type = dna or pep only");
+            System.exit(0);
         }
-      }
-
-      output = output + ("\n");
-      output = output + (new Format("%" + (maxid) + "s").form(" ") + " ");
-      // Print out the matching chars
-      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("-")) {
-            pid++;
-            output = output + ("|");
-          } else if (type.equals("pep")) {
-            if (ResidueProperties.getPAM250(intToStr[aseq1[count+i+j*len]],intToStr[aseq2[count+i+j*len]]) > 0) {
-              output  = output + (".");
-            } else {
-              output = output + (" ");
+
+        //System.out.println("lookuip " + rt.freeMemory() + " "+  rt.totalMemory());
+        seq1 = new int[s1str.length()];
+
+        //System.out.println("seq1 " + rt.freeMemory() +" "  + rt.totalMemory());
+        seq2 = new int[s2str.length()];
+
+        //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
+        score = new int[s1str.length()][s2str.length()];
+
+        //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
+        E = new int[s1str.length()][s2str.length()];
+
+        //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
+        F = new int[s1str.length()][s2str.length()];
+        traceback = new int[s1str.length()][s2str.length()];
+
+        //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
+        seq1 = stringToInt(s1str, type);
+
+        //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
+        seq2 = stringToInt(s2str, type);
+
+        //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());
+        //   long tstart = System.currentTimeMillis();
+        //    calcScoreMatrix();
+        //long tend = System.currentTimeMillis();
+        //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms");
+        //   printScoreMatrix(score);
+        //System.out.println();
+        //printScoreMatrix(traceback);
+        //System.out.println();
+        //  printScoreMatrix(E);
+        //System.out.println();
+        ///printScoreMatrix(F);
+        //System.out.println();
+        // tstart = System.currentTimeMillis();
+        //traceAlignment();
+        //tend = System.currentTimeMillis();
+        //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");
+    }
+
+    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) {
+                max = score[i][seq2.length - 1];
+                maxi = i;
+                maxj = seq2.length - 1;
             }
-          } else {
-            output = output + (" ");
-          }
+        }
 
+        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;
+            }
         }
-      }
-      // Now print the second aligned sequence
-      output = output + ("\n");
-      output = output + (new Format("%" + (maxid) + "s").form(s2.getName()) + " " );
-      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]]));
+
+        //  System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
+        int i = maxi;
+        int j = maxj;
+        int trace;
+        maxscore = score[i][j] / 10;
+
+        seq1end = maxi + 1;
+        seq2end = maxj + 1;
+
+        aseq1 = new int[seq1.length + seq2.length];
+        aseq2 = new int[seq1.length + seq2.length];
+
+        count = (seq1.length + seq2.length) - 1;
+
+        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)) {
+                aseq2[count] = seq2[j];
+                astr2 = intToStr[seq2[j]] + astr2;
+            }
+
+            trace = findTrace(i, j);
+
+            if (trace == 0) {
+                i--;
+                j--;
+            } else if (trace == 1) {
+                j--;
+                aseq1[count] = defInt;
+                astr1 = "-" + astr1.substring(1);
+            } else if (trace == -1) {
+                i--;
+                aseq2[count] = defInt;
+                astr2 = "-" + astr2.substring(1);
+            }
+
+            count--;
         }
-      }
-      output = output + ("\n\n");
-    }
-    pid = pid/(float)(aseq1.length-count)*100;
-    output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));
 
-  }
+        seq1start = i + 1;
+        seq2start = j + 1;
 
-  public void printScoreMatrix(int[][] mat) {
-    int n = seq1.length;
-    int m = seq2.length;
+        if (aseq1[count] != defInt) {
+            aseq1[count] = seq1[i];
+            astr1 = intToStr[seq1[i]] + astr1;
+        }
 
-    for (int i = 0; i < n;i++) {
-      // Print the top sequence
-      if (i == 0) {
-        Format.print(System.out,"%8s",s2str.substring(0,1));
-        for (int jj = 1;jj < m; jj++) {
-          Format.print(System.out,"%5s",s2str.substring(jj,jj+1));
+        if (aseq2[count] != defInt) {
+            aseq2[count] = seq2[j];
+            astr2 = intToStr[seq2[j]] + astr2;
         }
-        System.out.println();
-      }
+    }
 
-      for (int j = 0;j < m; j++) {
-        if (j == 0) {
-          Format.print(System.out,"%3s",s1str.substring(i,i+1));
+    public void printAlignment() {
+        // Find the biggest id length for formatting purposes
+        int maxid = s1.getName().length();
+
+        if (s2.getName().length() > maxid) {
+            maxid = s2.getName().length();
         }
-        Format.print(System.out,"%3d ",mat[i][j]/10);
-      }
-      System.out.println();
+
+        int len = 72 - maxid - 1;
+        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");
+        output = output + ("Sequence ");
+        output = output + (new Format("%" + maxid + "s").form(s1.getName()));
+        output = output +
+            (" :  " + seq1start + " - " + seq1end + " (Sequence length = " +
+            s1str.length() + ")\n");
+        output = output + ("Sequence ");
+        output = output + (new Format("%" + maxid + "s").form(s2.getName()));
+        output = output +
+            (" :  " + seq2start + " - " + seq2end + " (Sequence length = " +
+            s2str.length() + ")\n\n");
+
+        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) {
+                    output = output +
+                        (new Format("%s").form(intToStr[aseq1[count + i +
+                            (j * len)]]));
+                }
+            }
+
+            output = output + ("\n");
+            output = output +
+                (new Format("%" + (maxid) + "s").form(" ") + " ");
+
+            // Print out the matching chars
+            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("-")) {
+                        pid++;
+                        output = output + ("|");
+                    } else if (type.equals("pep")) {
+                        if (ResidueProperties.getPAM250(
+                                    intToStr[aseq1[count + i + (j * len)]],
+                                    intToStr[aseq2[count + i + (j * len)]]) > 0) {
+                            output = output + (".");
+                        } else {
+                            output = output + (" ");
+                        }
+                    } else {
+                        output = output + (" ");
+                    }
+                }
+            }
+
+            // Now print the second aligned sequence
+            output = output + ("\n");
+            output = output +
+                (new Format("%" + (maxid) + "s").form(s2.getName()) + " ");
+
+            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)]]));
+                }
+            }
+
+            output = output + ("\n\n");
+        }
+
+        pid = pid / (float) (aseq1.length - count) * 100;
+        output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));
     }
-  }
-
-  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) {
-      max = F[i][j];
-      t = -1;
-    } else if (F[i][j] == max) {
-      if (prev == -1) {
-        max = F[i][j];
-        t = -1;
-      }
+
+    public void printScoreMatrix(int[][] mat) {
+        int n = seq1.length;
+        int m = seq2.length;
+
+        for (int i = 0; i < n; i++) {
+            // Print the top sequence
+            if (i == 0) {
+                Format.print(System.out, "%8s", s2str.substring(0, 1));
+
+                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) {
+                    Format.print(System.out, "%3s", s1str.substring(i, i + 1));
+                }
+
+                Format.print(System.out, "%3d ", mat[i][j] / 10);
+            }
+
+            System.out.println();
+        }
     }
-    if (E[i][j] >= max) {
-      max = E[i][j];
-      t = 1;
-    } else if (E[i][j] == max) {
-      if (prev == 1) {
-        max = E[i][j];
-        t = 1;
-      }
+
+    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) {
+            max = F[i][j];
+            t = -1;
+        } else if (F[i][j] == max) {
+            if (prev == -1) {
+                max = F[i][j];
+                t = -1;
+            }
+        }
+
+        if (E[i][j] >= max) {
+            max = E[i][j];
+            t = 1;
+        } else if (E[i][j] == max) {
+            if (prev == 1) {
+                max = E[i][j];
+                t = 1;
+            }
+        }
+
+        prev = t;
+
+        return t;
     }
-    prev = t;
-    return t;
-  }
 
-  public void calcScoreMatrix() {
+    public void calcScoreMatrix() {
+        int n = seq1.length;
+        int m = seq2.length;
 
+        // top left hand element
+        score[0][0] = lookup[seq1[0]][seq2[0]] * 10;
+        E[0][0] = -gapExtend;
+        F[0][0] = 0;
 
-    int n = seq1.length;
-    int m = seq2.length;
+        // Calculate the top row first
+        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;
 
+            score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen,
+                    -gapExtend);
 
-    // top left hand element
-    score[0][0] =  lookup[seq1[0]][seq2[0]] * 10;
-    E[0][0] = -gapExtend;
-    F[0][0] = 0;
+            traceback[0][j] = 1;
+        }
 
-    // Calculate the top row first
-    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;
+        // Now do the left hand column
+        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);
 
-      score[0][j] = max( lookup[seq1[0]][seq2[j]] * 10 ,-gapOpen,-gapExtend);
+            score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);
+            traceback[i][0] = -1;
+        }
 
-      traceback[0][j] = 1;
+        // Now do all the other rows
+        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] -
+                        gapExtend);
+
+                score[i][j] = max(score[i - 1][j - 1] +
+                        (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]);
+                traceback[i][j] = findTrace(i, j);
+            }
+        }
     }
 
-    // Now do the left hand column
-    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);
+    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);
+        }
 
-      score[i][0] = max( lookup[seq1[i]][seq2[0]] * 10 ,E[i][0],F[i][0]);
-      traceback[i][0] = -1;
+        return out;
     }
 
-    // Now do all the other rows
-    for (int i = 1; i < n; i++) {
-      for (int j = 1; j < m; j++) {
+    public static String extractGaps(String gapChar, String seq) {
+        StringTokenizer str = new StringTokenizer(seq, gapChar);
+        String newString = "";
 
-        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] - gapExtend);
+        while (str.hasMoreTokens()) {
+            newString = newString + str.nextToken();
+        }
 
-        score[i][j] = max(score[i-1][j-1] + lookup[seq1[i]][seq2[j]]*10,
-                          E[i][j],
-                          F[i][j]);
-        traceback[i][j] = findTrace(i,j);
-      }
+        return newString;
     }
 
-  }
-  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) {
-    StringTokenizer str = new StringTokenizer(seq,gapChar);
-    String newString = "";
-
-    while (str.hasMoreTokens()) {
-      newString  = newString + str.nextToken();
-    }
-    return newString;
-  }
+    public int max(int i1, int i2, int i3) {
+        int max = i1;
 
+        if (i2 > i1) {
+            max = i2;
+        }
 
-  public int max(int i1, int i2, int i3) {
-    int max = i1;
-    if (i2 > i1)  {
-      max = i2;
-    }
-    if (i3 > max) {
-      max = i3;
-    }
-    return max;
-  }
+        if (i3 > max) {
+            max = i3;
+        }
 
-  public int max(int i1, int i2) {
-    int max = i1;
-    if (i2 > i1)  {
-      max = i2;
+        return max;
     }
-    return max;
-  }
 
-  public int[] stringToInt(String s,String type) {
-    int[] seq1 = new int[s.length()];
+    public int max(int i1, int i2) {
+        int max = i1;
 
-    for (int i = 0;i < s.length(); i++) {
-      String ss = s.substring(i,i+1).toUpperCase();
-      try {
-        if (type.equals("pep")) {
-          seq1[i] = ((Integer)ResidueProperties.aaHash.get(ss)).intValue();
-        } else if (type.equals("dna")) {
-          seq1[i] = ((Integer)dnaHash.get(ss)).intValue();
-        }
-        if (seq1[i] > 23) {
-          seq1[i] = 23;
+        if (i2 > i1) {
+            max = i2;
         }
-      } catch (Exception e) {
-        if (type.equals("dna")) {
-          seq1[i] = 4;
-        } else {
-          seq1[i] = 23;
+
+        return max;
+    }
+
+    public int[] stringToInt(String s, String type) {
+        int[] seq1 = new int[s.length()];
+
+        for (int i = 0; i < s.length(); i++) {
+            String ss = s.substring(i, i + 1).toUpperCase();
+
+            try {
+                if (type.equals("pep")) {
+                    seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();
+                } else if (type.equals("dna")) {
+                    seq1[i] = ((Integer) dnaHash.get(ss)).intValue();
+                }
+
+                if (seq1[i] > 23) {
+                    seq1[i] = 23;
+                }
+            } catch (Exception e) {
+                if (type.equals("dna")) {
+                    seq1[i] = 4;
+                } else {
+                    seq1[i] = 23;
+                }
+            }
         }
-      }
+
+        return seq1;
     }
-    return seq1;
-  }
 
-  public static void displayMatrix(Graphics g, int[][] mat, int n, int m,int psize) {
+    public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
+        int psize) {
+        int max = -1000;
+        int min = 1000;
 
-    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) {
+                    max = mat[i][j];
+                }
 
-    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) {
-          min = mat[i][j];
+                if (mat[i][j] <= min) {
+                    min = mat[i][j];
+                }
+            }
         }
-      }
-    }
-    System.out.println(max + " " + min);
-    for (int i=0; i < n; i++) {
-      for (int j=0; j < m; j++) {
-        int x = psize*i;
-        int y = psize*j;
-        //	System.out.println(mat[i][j]);
-        float score = (float)(mat[i][j] - min)/(float)(max-min);
-        g.setColor(new Color(score,0,0));
-        g.fillRect(x,y,psize,psize);
-        //	System.out.println(x + " " + y + " " + score);
-      }
 
-    }
-  }
+        System.out.println(max + " " + min);
+
+        for (int i = 0; i < n; i++) {
+            for (int j = 0; j < m; j++) {
+                int x = psize * i;
+                int y = psize * j;
+
+                //	System.out.println(mat[i][j]);
+                float score = (float) (mat[i][j] - min) / (float) (max - min);
+                g.setColor(new Color(score, 0, 0));
+                g.fillRect(x, y, psize, psize);
 
+                //	System.out.println(x + " " + y + " " + score);
+            }
+        }
+    }
 }
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 53eb1dd..7c2a554 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -16,296 +16,327 @@
 * 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.*;
-import jalview.util.*;
+
 import jalview.io.*;
 
+import jalview.util.*;
+
 import java.util.*;
 
+
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
 public class AlignmentSorter {
-
-  private AlignmentSorter() {
-    try
-    {
-      jbInit();
+    /**    */
+    static boolean sortIdAscending = true;
+    static int lastGroupHash = 0;
+    static boolean sortGroupAscending = true;
+    static AlignmentOrder lastOrder = null;
+    static boolean sortOrderAscending = true;
+    static NJTree lastTree = null;
+    static boolean sortTreeAscending = true;
+
+    private AlignmentSorter() {
+        try {
+            jbInit();
+        } catch (Exception ex) {
+            ex.printStackTrace();
+        }
     }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
 
-  public static void sortGroups(AlignmentI align) {
-    Vector groups = align.getGroups();
-    int    nGroup = groups.size();
+    public static void sortGroups(AlignmentI align) {
+        Vector groups = align.getGroups();
+        int nGroup = groups.size();
+
+        float[] arr = new float[nGroup];
+        Object[] s = new Object[nGroup];
 
-    float[]  arr = new float [nGroup];
-    Object[] s   = new Object[nGroup];
+        for (int i = 0; i < nGroup; i++) {
+            arr[i] = ((SequenceGroup) groups.elementAt(i)).getSize();
+            s[i] = groups.elementAt(i);
+        }
 
-    for (int i=0; i < nGroup; i++) {
-      arr[i] = ((SequenceGroup)groups.elementAt(i)).getSize();
-      s[i]   = groups.elementAt(i);
+        QuickSort.sort(arr, s);
+
+        //  align..setGroups(newg);
     }
 
-    QuickSort.sort(arr,s);
+    /**
+     * Sort by Percentage Identity
+     *
+     * @param align AlignmentI
+     * @param s SequenceI
+     */
+    public static void sortByPID(AlignmentI align, SequenceI s) {
+        int nSeq = align.getHeight();
 
-    //  align..setGroups(newg);
-  }
+        float[] scores = new float[nSeq];
+        SequenceI[] seqs = new SequenceI[nSeq];
 
-  /**
-   * Sort by Percentage Identity
-   *
-   * @param align AlignmentI
-   * @param s SequenceI
-   */
-  public static void sortByPID(AlignmentI align, SequenceI s) {
-    int nSeq = align.getHeight();
+        for (int i = 0; i < nSeq; i++) {
+            scores[i] = Comparison.PID(align.getSequenceAt(i), s);
+            seqs[i] = align.getSequenceAt(i);
+        }
 
-    float     scores[] = new float[nSeq];
-    SequenceI seqs[]   = new SequenceI[nSeq];
+        QuickSort.sort(scores, 0, scores.length - 1, seqs);
 
-    for (int i = 0; i < nSeq; i++) {
-      scores[i] = Comparison.PID(align.getSequenceAt(i),s);
-      seqs[i]   = align.getSequenceAt(i);
+        setReverseOrder(align, seqs);
     }
 
-    QuickSort.sort(scores,0,scores.length-1,seqs);
+    private static void setReverseOrder(AlignmentI align, SequenceI[] seqs) {
+        int nSeq = seqs.length;
+
+        int len = 0;
 
-   setReverseOrder(align,seqs);
-  }
+        if ((nSeq % 2) == 0) {
+            len = nSeq / 2;
+        } else {
+            len = (nSeq + 1) / 2;
+        }
 
-  private static void setReverseOrder(AlignmentI align, SequenceI [] seqs) {
-    int nSeq = seqs.length;
+        // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+        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);
+        }
+    }
 
-    int len = 0;
-    if (nSeq%2 == 0) {
-      len = nSeq/2;
-    } else {
-      len = (nSeq+1)/2;
+    private static void setOrder(AlignmentI align, Vector tmp) {
+        setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
     }
 
-// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-    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, SequenceI[] seqs) {
+        // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+        Vector algn = align.getSequences();
+
+        for (int i = 0, p = 0; i < seqs.length; i++)
+            algn.setElementAt(seqs[i], p++);
     }
-  }
 
-  private static void setOrder(AlignmentI align, Vector tmp) {
-    setOrder(align,vectorSubsetToArray(tmp, align.getSequences()));
-  }
+    public static void sortByID(AlignmentI align) {
+        int nSeq = align.getHeight();
 
-  private static void setOrder(AlignmentI align, SequenceI [] seqs) {
-      // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+        String[] ids = new String[nSeq];
+        SequenceI[] seqs = new SequenceI[nSeq];
 
-      Vector algn = align.getSequences();
+        for (int i = 0; i < nSeq; i++) {
+            ids[i] = align.getSequenceAt(i).getName();
+            seqs[i] = align.getSequenceAt(i);
+        }
 
-      for (int i = 0, p = 0; i < seqs.length; i++)
-        algn.setElementAt(seqs[i], p++);
-  }
-  /**    */
-  static boolean sortIdAscending = true;
-  public static void sortByID(AlignmentI align) {
-    int nSeq = align.getHeight();
+        QuickSort.sort(ids, seqs);
 
-    String    ids[]   = new String[nSeq];
-    SequenceI seqs[]  = new SequenceI[nSeq];
+        if (sortIdAscending) {
+            setReverseOrder(align, seqs);
+        } else {
+            setOrder(align, seqs);
+        }
 
-    for (int i = 0; i < nSeq; i++) {
-      ids[i]  = align.getSequenceAt(i).getName();
-      seqs[i] = align.getSequenceAt(i);
+        sortIdAscending = !sortIdAscending;
     }
 
-    QuickSort.sort(ids,seqs);
+    public static void sortByGroup(AlignmentI align) {
+        Vector groups = align.getGroups();
+
+        if (groups.hashCode() != lastGroupHash) {
+            sortGroupAscending = true;
+            lastGroupHash = groups.hashCode();
+        } else {
+            sortGroupAscending = !sortGroupAscending;
+        }
+
+        Vector seqs = new Vector();
+
+        for (int i = 0; i < groups.size(); i++) {
+            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+            for (int j = 0; j < sg.getSize(); j++) {
+                seqs.addElement(sg.getSequenceAt(j));
+            }
+        }
+
+        // Deletions can happen so this check may fail
+
+        /*
+         if (seqs.size() != nSeq) {
+          System.err.println("ERROR: tmp.size() != nseq in sortByGroups");
+          if (seqs.size() < nSeq) {
+            addStrays(align,seqs);
+          }
+        }
+        */
+        if (sortGroupAscending) {
+            setOrder(align, seqs);
+        } else {
+            setReverseOrder(align,
+                vectorSubsetToArray(seqs, align.getSequences()));
+        }
+    }
+
+    private static SequenceI[] vectorToArray(Vector tmp) {
+        SequenceI[] seqs = new SequenceI[tmp.size()];
 
-    if(sortIdAscending)
-      setReverseOrder(align,seqs);
-    else
-      setOrder(align, seqs);
+        for (int i = 0; i < tmp.size(); i++) {
+            seqs[i] = (SequenceI) tmp.elementAt(i);
+        }
+
+        return seqs;
+    }
 
-    sortIdAscending = !sortIdAscending;
-  }
-  static int lastGroupHash = 0;
-  static boolean sortGroupAscending = true;
+    private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask) {
+        Vector seqs = new Vector();
+        int i;
+        int m;
+        int p;
+        boolean[] tmask = new boolean[m = mask.size()];
 
-  public static void sortByGroup(AlignmentI align) {
-    Vector groups = align.getGroups();
-    if (groups.hashCode()!=lastGroupHash) {
-      sortGroupAscending=true;
-      lastGroupHash = groups.hashCode();
-    } else
-      sortGroupAscending = ! sortGroupAscending;
+        for (i = 0; i < m; i++)
+            tmask[i] = true;
 
-    Vector seqs = new Vector();
+        for (i = 0; i < tmp.size(); i++) {
+            Object sq;
 
-    for (int i=0; i < groups.size(); i++) {
-      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+            if (mask.contains(sq = tmp.elementAt(i))) {
+                tmask[mask.indexOf(sq)] = false;
+                seqs.addElement(sq);
+                m--;
+            }
+        }
 
-      for (int j = 0; j < sg.getSize(); j++) {
-        seqs.addElement(sg.getSequenceAt(j));
-      }
+        for (i = 0; i < tmask.length; i++)
+            if (tmask[i]) {
+                seqs.addElement(mask.elementAt(i));
+            }
+
+        return vectorToArray(seqs);
     }
 
-    // Deletions can happen so this check may fail
-    /*
-     if (seqs.size() != nSeq) {
-      System.err.println("ERROR: tmp.size() != nseq in sortByGroups");
-      if (seqs.size() < nSeq) {
-        addStrays(align,seqs);
-      }
+    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 (tmp.size()<align.getHeight())
+        //      addStrays(align, tmp);
+        if (lastOrder == order) {
+            sortOrderAscending = !sortOrderAscending;
+        } else {
+            sortOrderAscending = true;
+        }
+
+        if (sortOrderAscending) {
+            setOrder(align, tmp);
+        } else {
+            setReverseOrder(align,
+                vectorSubsetToArray(tmp, align.getSequences()));
+        }
     }
-*/
-    if(sortGroupAscending)
-      setOrder(align,seqs);
-    else
-      setReverseOrder( align, vectorSubsetToArray(seqs, align.getSequences()));
 
-  }
+    public static Vector getOrderByTree(AlignmentI align, NJTree tree) {
+        int nSeq = align.getHeight();
 
-  private static SequenceI [] vectorToArray(Vector tmp) {
-    SequenceI[] seqs = new SequenceI[tmp.size()];
+        Vector tmp = new Vector();
 
-    for (int i=0; i < tmp.size(); i++) {
-      seqs[i] = (SequenceI)tmp.elementAt(i);
-    }
-    return seqs;
-  }
-
-  private static SequenceI [] vectorSubsetToArray(Vector tmp, Vector mask) {
-    Vector seqs = new Vector();
-    int i,m, p;
-    boolean[] tmask = new boolean[m=mask.size()];
-    for (i=0; i<m; i++)
-      tmask[i] = true;
-    for (i=0; i < tmp.size(); i++) {
-      Object sq;
-      if (mask.contains(sq=tmp.elementAt(i))) {
-        tmask[mask.indexOf(sq)] = false;
-        seqs.addElement(sq);
-        m--;
-      }
-    }
-    for (i=0; i<tmask.length; i++)
-      if (tmask[i])
-        seqs.addElement(mask.elementAt(i));
-    return vectorToArray(seqs);
-  }
-
-  static AlignmentOrder lastOrder = null;
-  static boolean sortOrderAscending = true;
-
-  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 (tmp.size()<align.getHeight())
-//      addStrays(align, tmp);
-    if (lastOrder==order)
-      sortOrderAscending=!sortOrderAscending;
-    else
-      sortOrderAscending=true;
-
-    if (sortOrderAscending)
-      setOrder(align, tmp);
-    else
-      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
-  }
-  static NJTree lastTree = null;
-  static boolean sortTreeAscending = true;
-
-  public 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)
-    {
-      // 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)
-      {
-        addStrays(align, tmp);
-      }
-      if (tmp.size() != nSeq)
-        System.err.println("ERROR: tmp.size()="+tmp.size()+" != nseq="+nSeq+" in getOrderByTree");
+        tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
 
+        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) {
+                addStrays(align, tmp);
+            }
+
+            if (tmp.size() != nSeq) {
+                System.err.println("ERROR: tmp.size()=" + tmp.size() +
+                    " != nseq=" + nSeq + " in getOrderByTree");
+            }
+        }
+
+        return tmp;
     }
-    return tmp;
-  }
-
-  public static void sortByTree(AlignmentI align, NJTree tree) {
-    Vector tmp = getOrderByTree(align, tree);
-    // tmp should properly permute align with tree.
-    if(lastTree!=tree) {
-      sortTreeAscending = true;
-      lastTree = tree;
-    } else {
-      sortTreeAscending = !sortTreeAscending;
+
+    public static void sortByTree(AlignmentI align, NJTree tree) {
+        Vector tmp = getOrderByTree(align, tree);
+
+        // tmp should properly permute align with tree.
+        if (lastTree != tree) {
+            sortTreeAscending = true;
+            lastTree = tree;
+        } else {
+            sortTreeAscending = !sortTreeAscending;
+        }
+
+        if (sortTreeAscending) {
+            setOrder(align, tmp);
+        } else {
+            setReverseOrder(align,
+                vectorSubsetToArray(tmp, align.getSequences()));
+        }
     }
-    if(sortTreeAscending)
-      setOrder(align,tmp);
-    else
-      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
-  }
-
-  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))) {
-        seqs.addElement(align.getSequenceAt(i));
-      }
+
+    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))) {
+                seqs.addElement(align.getSequenceAt(i));
+            }
+        }
+
+        if (nSeq != seqs.size()) {
+            System.err.println(
+                "ERROR: Size still not right even after addStrays");
+        }
     }
-    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) {
+            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())) {
+                        tmp.addElement((SequenceI) node.element());
+                    }
+                }
+            }
+
+            return tmp;
+        } else {
+            _sortByTree(left, tmp, seqset);
+            _sortByTree(right, tmp, seqset);
+        }
+
+        return tmp;
     }
-  }
 
-  public static Vector _sortByTree(SequenceNode node, Vector tmp, Vector seqset) {
-    if (node == null) {return tmp;}
+    // Ordering Objects
+    // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
+    //
 
-    SequenceNode left = (SequenceNode)node.left();
-    SequenceNode right = (SequenceNode)node.right();
+    /**
+     * recover the order of sequences given by the safe numbering scheme introducd
+     * SeqsetUtils.uniquify.
+     */
+    public static void recoverOrder(SequenceI[] alignment) {
+        float[] ids = new float[alignment.length];
 
-    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;
+        for (int i = 0; i < alignment.length; i++)
+            ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
 
-    } else {
-      _sortByTree(left,tmp, seqset);
-      _sortByTree(right,tmp, seqset);
+        jalview.util.QuickSort.sort(ids, alignment);
     }
-    return tmp;
-  }
-  // Ordering Objects
-  // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
-  //
-
-  /**
-   * recover the order of sequences given by the safe numbering scheme introducd
-   * SeqsetUtils.uniquify.
-   */
-  public static void recoverOrder(SequenceI[] alignment) {
-    float[] ids = new float[alignment.length];
-    for (int i=0; i<alignment.length; i++)
-      ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
-    jalview.util.QuickSort.sort(ids, alignment);
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-  }
 
+    private void jbInit() throws Exception {
+    }
 }
diff --git a/src/jalview/analysis/AlignmentUtil.java b/src/jalview/analysis/AlignmentUtil.java
index b992f4a..a2e1c71 100755
--- a/src/jalview/analysis/AlignmentUtil.java
+++ b/src/jalview/analysis/AlignmentUtil.java
@@ -16,202 +16,190 @@
 * 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.*;
-import jalview.util.*;
-import java.util.*;
 
-public class AlignmentUtil {
+import jalview.util.*;
 
-  private AlignmentUtil() {
-  }
+import java.util.*;
 
-  public static int[][] percentIdentity2(AlignmentI align) {
-    return percentIdentity2(align,0,align.getWidth()-1);
-  }
 
-  public static int[][] percentIdentity2(AlignmentI align, int start, int end) {
-    int [][] cons2 = new int[align.getWidth()][24];
-    // Initialize the array
-    for (int j=0;j<24;j++) {
-      for (int i=0; i < align.getWidth();i++) {
-        cons2[i][j] = 0;
-      }
+public class AlignmentUtil {
+    private AlignmentUtil() {
     }
 
-    return cons2;
-  }
-  public static int getPixelHeight(int i, int j,int charHeight) {
-    int h=0;
-    while (i < j) {
-      h += charHeight;
-      i++;
+    public static int[][] percentIdentity2(AlignmentI align) {
+        return percentIdentity2(align, 0, align.getWidth() - 1);
     }
-    return h;
-  }
-
-
-    public static Vector substitution_rates (AlignmentI align, int start, int end) {
-
-	Vector rates = new Vector();
-
-	int len = (end-start+1);
-
-	// Turn seqs into char arrays
-
-	int[][] seqint = new int[align.getHeight()][len];
-
-
-	for (int j = 0; j < align.getHeight(); j++) {
-
-	    SequenceI seq = align.getSequenceAt(j);
-
-	    for (int i = 0 ; i < len; i++) {
-		char c = seq.getCharAt(start + i - 1);
-
-		if (c == 'A') {
-		    seqint[j][i] = 0;
-		} else if (c == 'C') {
-		    seqint[j][i] = 1;
-		} else if (c == 'T') {
-		    seqint[j][i] = 2;
-		} else if (c == 'G') {
-		    seqint[j][i] = 3;
-		} else {
-		    seqint[j][i] = -1;
-		}
-
-	    }
-
-	}
-
-
-	//	print_matrix(seqint,2,len);	for (int j = 0; j < align.getHeight(); j++) {
-
-	    for (int j = 0; j < align.getHeight(); j++) {
-
-		for (int k = 0; k < align.getHeight(); k++) {
-
-		int counts[][] = new int[4][4];
-		int tot  = 0;
-		int tots[] = new int[4];
-		int fulltot = 0;
-		int fulltots[] = new int[4];
-
-		for (int i = 0 ; i < len; i++) {
-
-		    if (k != j) {
 
-			//			System.out.println("Seq " + j + " " + k + " " + i + " " + seqint[j][i] + " " + seqint[k][i]);
-			if (seqint[j][i] >= 0 &&
-			    seqint[k][i] >= 0) {
-			    counts[seqint[k][i]][seqint[j][i]]++;
+    public static int[][] percentIdentity2(AlignmentI align, int start, int end) {
+        int[][] cons2 = new int[align.getWidth()][24];
 
-			    //  print_matrix(counts,4,4);
-			    tots[seqint[j][i]]++;
-			    tot++;
-			}
-			if (seqint[j][i] != -1) {
-			    fulltots[seqint[j][i]]++;
-			    fulltot++;
-			}
-		    }
-		}
+        // Initialize the array
+        for (int j = 0; j < 24; j++) {
+            for (int i = 0; i < align.getWidth(); i++) {
+                cons2[i][j] = 0;
+            }
+        }
 
-		if (k != j) {
-
-		    System.out.println();
-
-		    System.out.println("Sequence " + align.getSequenceAt(j).getName() + " "  + align.getSequenceAt(k).getName());
-
-		    System.out.println();
-		    print_matrix(counts,4,4);
-		    System.out.println();
-
-
-
-		    double[][] out = new double[4][4];// = constant_multiply_matrix(counts,1.0/tot,4,4);
-
-		    for (int i = 0; i < 4; i++) {
-			for (int jj = 0; jj < 4; jj++) {
-			    out[i][jj] = (double)counts[i][jj]/tots[jj];
-			}
-		    }
-
-		    print_matrix(out,4,4);
-		    System.out.println();
-
-
-		    System.out.print("RATES\t");
-		    System.out.print(align.getSequenceAt(j).getName() + "\t"  + align.getSequenceAt(k).getName() + "\t");
-
-		    for (int i = 0; i < 4; i++) {
-			for (int jj = 0; jj < 4; jj++) {
-			    Format.print(System.out,"%4.3f\t",out[i][jj]);
-			}
-		    }
-		    System.out.println();
-
- 		    for (int i = 0; i < 4; i++) {
-			Format.print(System.out,"%4.3f\t",(double)fulltots[i]*1.0/fulltot);
-		    }
-
-		    System.out.println();
-		    System.out.print("\nGC ");
-
-		    Format.print(System.out,"%4.3f\t",(double)(100*fulltots[1]+fulltots[3])/fulltot);
-
-		    System.out.print((fulltots[1]+fulltots[3]) + "\t" + fulltot);
+        return cons2;
+    }
 
+    public static int getPixelHeight(int i, int j, int charHeight) {
+        int h = 0;
 
-		    System.out.println();
+        while (i < j) {
+            h += charHeight;
+            i++;
+        }
 
-		    rates.addElement(out);
-		}
+        return h;
+    }
 
-	    }
-	}
-	return rates;
+    public static Vector substitution_rates(AlignmentI align, int start, int end) {
+        Vector rates = new Vector();
+
+        int len = (end - start + 1);
+
+        // Turn seqs into char arrays
+        int[][] seqint = new int[align.getHeight()][len];
+
+        for (int j = 0; j < align.getHeight(); j++) {
+            SequenceI seq = align.getSequenceAt(j);
+
+            for (int i = 0; i < len; i++) {
+                char c = seq.getCharAt((start + i) - 1);
+
+                if (c == 'A') {
+                    seqint[j][i] = 0;
+                } else if (c == 'C') {
+                    seqint[j][i] = 1;
+                } else if (c == 'T') {
+                    seqint[j][i] = 2;
+                } else if (c == 'G') {
+                    seqint[j][i] = 3;
+                } else {
+                    seqint[j][i] = -1;
+                }
+            }
+        }
+
+        //	print_matrix(seqint,2,len);	for (int j = 0; j < align.getHeight(); j++) {
+        for (int j = 0; j < align.getHeight(); j++) {
+            for (int k = 0; k < align.getHeight(); k++) {
+                int[][] counts = new int[4][4];
+                int tot = 0;
+                int[] tots = new int[4];
+                int fulltot = 0;
+                int[] fulltots = new int[4];
+
+                for (int i = 0; i < len; i++) {
+                    if (k != j) {
+                        //			System.out.println("Seq " + j + " " + k + " " + i + " " + seqint[j][i] + " " + seqint[k][i]);
+                        if ((seqint[j][i] >= 0) && (seqint[k][i] >= 0)) {
+                            counts[seqint[k][i]][seqint[j][i]]++;
+
+                            //  print_matrix(counts,4,4);
+                            tots[seqint[j][i]]++;
+                            tot++;
+                        }
+
+                        if (seqint[j][i] != -1) {
+                            fulltots[seqint[j][i]]++;
+                            fulltot++;
+                        }
+                    }
+                }
+
+                if (k != j) {
+                    System.out.println();
+
+                    System.out.println("Sequence " +
+                        align.getSequenceAt(j).getName() + " " +
+                        align.getSequenceAt(k).getName());
+
+                    System.out.println();
+                    print_matrix(counts, 4, 4);
+                    System.out.println();
+
+                    double[][] out = new double[4][4]; // = constant_multiply_matrix(counts,1.0/tot,4,4);
+
+                    for (int i = 0; i < 4; i++) {
+                        for (int jj = 0; jj < 4; jj++) {
+                            out[i][jj] = (double) counts[i][jj] / tots[jj];
+                        }
+                    }
+
+                    print_matrix(out, 4, 4);
+                    System.out.println();
+
+                    System.out.print("RATES\t");
+                    System.out.print(align.getSequenceAt(j).getName() + "\t" +
+                        align.getSequenceAt(k).getName() + "\t");
+
+                    for (int i = 0; i < 4; i++) {
+                        for (int jj = 0; jj < 4; jj++) {
+                            Format.print(System.out, "%4.3f\t", out[i][jj]);
+                        }
+                    }
+
+                    System.out.println();
+
+                    for (int i = 0; i < 4; i++) {
+                        Format.print(System.out, "%4.3f\t",
+                            ((double) fulltots[i] * 1.0) / fulltot);
+                    }
+
+                    System.out.println();
+                    System.out.print("\nGC ");
+
+                    Format.print(System.out, "%4.3f\t",
+                        (double) ((100 * fulltots[1]) + fulltots[3]) / fulltot);
+
+                    System.out.print((fulltots[1] + fulltots[3]) + "\t" +
+                        fulltot);
+
+                    System.out.println();
+
+                    rates.addElement(out);
+                }
+            }
+        }
+
+        return rates;
     }
 
-    public static double[][]  constant_multiply_matrix(int[][] matrix, double c,int n, int m) {
-	double[][] out = new double[n][m];
+    public static double[][] constant_multiply_matrix(int[][] matrix, double c,
+        int n, int m) {
+        double[][] out = new double[n][m];
 
-	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++) {
+                out[i][j] = matrix[i][j] * c;
+            }
+        }
 
-		out[i][j] = matrix[i][j]*c;
-	    }
-	}
-	return out;
+        return out;
     }
 
-
     public static void print_matrix(int[][] matrix, int n, int m) {
+        for (int i = 0; i < n; i++) {
+            for (int j = 0; j < m; j++) {
+                System.out.print(matrix[i][j] + "\t");
+            }
 
-
-	for (int i = 0; i < n; i++) {
-	    for (int j = 0; j < m; j++) {
-
-		System.out.print(matrix[i][j] + "\t");
-	    }
-	    System.out.println();
-	}
+            System.out.println();
+        }
     }
-    public static void print_matrix(double[][] matrix, int n, int m) {
-
-
-	for (int i = 0; i < n; i++) {
-	    for (int j = 0; j < m; j++) {
 
-		Format.print(System.out,"%4.3f\t",matrix[i][j]);
+    public static void print_matrix(double[][] matrix, int n, int m) {
+        for (int i = 0; i < n; i++) {
+            for (int j = 0; j < m; j++) {
+                Format.print(System.out, "%4.3f\t", matrix[i][j]);
+            }
 
-	    }
-	    System.out.println();
-	}
+            System.out.println();
+        }
     }
-
-
 }
diff --git a/src/jalview/analysis/CompareAlignments.java b/src/jalview/analysis/CompareAlignments.java
index e2dd742..2752e6f 100755
--- a/src/jalview/analysis/CompareAlignments.java
+++ b/src/jalview/analysis/CompareAlignments.java
@@ -16,170 +16,161 @@
 * 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.*;
+
 import jalview.io.*;
 
 import java.util.*;
 
-public class CompareAlignments {
 
+public class CompareAlignments {
     Vector align;
     String refId;
     Vector ids;
 
     public CompareAlignments(Vector align) {
+        this.align = align;
 
-	this.align = align;
-
-	ids = new Vector();
+        ids = new Vector();
 
-	Alignment al0 = (Alignment)align.elementAt(0);
+        Alignment al0 = (Alignment) align.elementAt(0);
 
-	for (int i = 0; i < al0.getHeight(); i++) {
-	    SequenceI seq = al0.getSequenceAt(i);
+        for (int i = 0; i < al0.getHeight(); i++) {
+            SequenceI seq = al0.getSequenceAt(i);
 
-	    ids.addElement(seq.getName());
-
-	    if (i == 0) {
-		setReferenceId(seq.getName());
-	    }
-	}
+            ids.addElement(seq.getName());
 
+            if (i == 0) {
+                setReferenceId(seq.getName());
+            }
+        }
     }
 
     public void compare() {
+        Hashtable positions = new Hashtable();
 
-	Hashtable positions = new Hashtable();
-
-	for (int k = 0; k < ids.size(); k++) {
-
-	    String id = (String)ids.elementAt(k);
-
-	    System.out.println("Ids " + id + " " + refId);
+        for (int k = 0; k < ids.size(); k++) {
+            String id = (String) ids.elementAt(k);
 
-	    if (!id.equals(refId)) {
+            System.out.println("Ids " + id + " " + refId);
 
-		Hashtable fullhash = new Hashtable();
+            if (!id.equals(refId)) {
+                Hashtable fullhash = new Hashtable();
 
-		for (int i = 0; i < align.size(); i++) {
-		    System.out.println("Alignment " + i);
+                for (int i = 0; i < align.size(); i++) {
+                    System.out.println("Alignment " + i);
 
-		    Alignment al = (Alignment)align.elementAt(i);
+                    Alignment al = (Alignment) align.elementAt(i);
 
-		    SequenceI refseq = null;
+                    SequenceI refseq = null;
 
-		    for (int j = 0; j < al.getHeight(); j++) {
-			if (((SequenceI)al.getSequenceAt(j)).getName().equals(refId)) {
-			    refseq = (SequenceI)al.getSequenceAt(j);
-			}
-		    }
+                    for (int j = 0; j < al.getHeight(); j++) {
+                        if (((SequenceI) al.getSequenceAt(j)).getName().equals(refId)) {
+                            refseq = (SequenceI) al.getSequenceAt(j);
+                        }
+                    }
 
-		    if (refseq != null) {
+                    if (refseq != null) {
+                        System.out.println("Refseq " + refseq.getName());
 
-			System.out.println("Refseq " + refseq.getName());
+                        for (int jj = 0; jj < al.getHeight(); jj++) {
+                            SequenceI seq = (SequenceI) al.getSequenceAt(jj);
 
-			for (int jj = 0; jj < al.getHeight(); jj++) {
-			    SequenceI seq = (SequenceI)al.getSequenceAt(jj);
+                            if (seq.getName().equals(id)) {
+                                Hashtable hash = getAlignPositions(seq, refseq);
 
-			    if (seq.getName().equals(id)) {
-				Hashtable hash = getAlignPositions(seq,refseq);
+                                Enumeration keys = hash.keys();
 
-				Enumeration keys = hash.keys();
+                                while (keys.hasMoreElements()) {
+                                    Integer key = (Integer) keys.nextElement();
 
-				while (keys.hasMoreElements()) {
-				    Integer key = (Integer)keys.nextElement();
-				    //				System.out.println(key + " " + hash.get(key));
-				    if (fullhash.get(key) == null) {
-					fullhash.put(key,new Vector());
-				    }
+                                    //				System.out.println(key + " " + hash.get(key));
+                                    if (fullhash.get(key) == null) {
+                                        fullhash.put(key, new Vector());
+                                    }
 
-				    Vector tmp = (Vector)fullhash.get(key);
+                                    Vector tmp = (Vector) fullhash.get(key);
 
-				    tmp.addElement(hash.get(key));
-				}
-			    }
+                                    tmp.addElement(hash.get(key));
+                                }
+                            }
+                        }
+                    }
+                }
 
-			}
-		    }
-		}
+                System.out.println("\nId " + id);
 
-		System.out.println ("\nId " + id);
+                Enumeration keys = fullhash.keys();
 
-		Enumeration keys = fullhash.keys();
+                int totdiff = 0;
 
+                while (keys.hasMoreElements()) {
+                    Integer key = (Integer) keys.nextElement();
 
-		int totdiff = 0;
-		while (keys.hasMoreElements()) {
-		    Integer key = (Integer)keys.nextElement();
+                    Vector tmp = (Vector) fullhash.get(key);
 
-		    Vector tmp = (Vector)fullhash.get(key);
+                    int diff0 = ((Integer) tmp.elementAt(0)).intValue();
+                    ;
 
+                    int diff = 0;
 
+                    for (int l = 1; l < tmp.size(); l++) {
+                        diff += Math.abs(diff0 -
+                            ((Integer) tmp.elementAt(l)).intValue());
+                    }
 
-		    int diff0 = ((Integer)tmp.elementAt(0)).intValue();;
-		    int diff = 0;
+                    if (diff > 0) {
+                        totdiff++;
+                        System.out.print(id + " Ref pos " + key + " : " +
+                            diff0 + " " + diff + " : ");
 
-		    for (int l = 1; l < tmp.size(); l++) {
-			diff += Math.abs(diff0 - ((Integer)tmp.elementAt(l)).intValue());
+                        for (int l = 1; l < tmp.size(); l++) {
+                            System.out.print(diff0 -
+                                ((Integer) tmp.elementAt(l)).intValue() + " ");
+                        }
 
-		    }
+                        System.out.println();
+                    }
+                }
 
-		    if (diff > 0) {
-			totdiff++;
-			System.out.print(id + " Ref pos " + key + " : " + diff0 + " " + diff + " : ");
-
-			for (int l = 1; l < tmp.size(); l++) {
-			    System.out.print(diff0 - ((Integer)tmp.elementAt(l)).intValue() + " ");
-			}
-			System.out.println();
-		    }
-		}
-
-		System.out.println("Total " + id + " " + totdiff);
-
-	    }
-	}
+                System.out.println("Total " + id + " " + totdiff);
+            }
+        }
     }
 
-
     public void setReferenceId(String id) {
-	this.refId = id;
+        this.refId = id;
     }
 
     public Hashtable getAlignPositions(SequenceI seq1, SequenceI seq2) {
+        Hashtable hash = new Hashtable();
 
-	Hashtable hash = new Hashtable();
+        int i = 0;
 
-	int i = 0;
+        int pos1 = 0;
+        int pos2 = 0;
 
-	int pos1 = 0;
-	int pos2 = 0;
+        while (i < seq1.getLength()) {
+            char c1 = seq1.getCharAt(i);
+            char c2 = seq2.getCharAt(i);
 
-	while (i < seq1.getLength()) {
+            if (c1 != '-') {
+                pos1++;
+            }
 
-	    char c1 = seq1.getCharAt(i);
-	    char c2 = seq2.getCharAt(i);
+            if (c2 != '-') {
+                pos2++;
+            }
 
-	    if (c1 != '-') {
-		pos1++;
-	    }
+            if (c1 != '-') {
+                hash.put(new Integer(pos1), new Integer(pos2));
+            }
 
-	    if (c2 != '-') {
-		pos2++;
-	    }
+            i++;
+        }
 
-	    if (c1 != '-') {
-		hash.put(new Integer(pos1),new Integer(pos2));
-	    }
-
-	    i++;
-	}
-	return hash;
+        return hash;
     }
-
-
-
 }
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index d3f1e01..bfb2e00 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -16,400 +16,426 @@
 * 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.*;
 
-import java.util.*;
 import jalview.gui.*;
-import jalview.datamodel.*;
+
+import java.util.*;
 
 
 public class Conservation {
-  Vector sequences;
-  int    start;
-  int    end;
-  Vector seqNums; // vector of int vectors where first is sequence checksum
-  int maxLength=0; //  used by quality calcs
-  boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
-  private void calcSeqNums() {
-    for (int i=0; i<sequences.size(); i++) {
-      calcSeqNum(i);
+    Vector sequences;
+    int start;
+    int end;
+    Vector seqNums; // vector of int vectors where first is sequence checksum
+    int maxLength = 0; //  used by quality calcs
+    boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
+    Vector total = new Vector();
+    public Vector quality;
+    public Double[] qualityRange = new Double[2];
+    String consString = "";
+    Sequence consSequence;
+    Hashtable propHash;
+    int threshold;
+    String name = "";
+    int[][] cons2;
+
+    public Conservation(String name, Hashtable propHash, int threshold,
+        Vector sequences, int start, int end) {
+        this.name = name;
+        this.propHash = propHash;
+        this.threshold = threshold;
+        this.sequences = sequences;
+        this.start = start;
+        this.end = end;
+        seqNums = new Vector(sequences.size());
+        calcSeqNums();
     }
-  }
-  private void calcSeqNum(int i) {
-    String sq=null; // for dumb jbuilder not-inited exception warning
-    int[] sqnum = null;
-    if (i>-1 && i<sequences.size()) {
-      sq = ((SequenceI)sequences.elementAt(i)).getSequence();
-      if (seqNums.size()<=i) {
-        seqNums.addElement(new int[sq.length()+1]);
-      }
-      if (sq.hashCode()!=((int[])seqNums.elementAt(i))[0])
-       {
-         int j, len;
-         seqNumsChanged = true;
-         sq = ((SequenceI) sequences.elementAt(i)).getSequence();
-         len = sq.length();
-         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++)
-         {
-           sqnum[j] = ( (Integer) jalview.schemes.ResidueProperties.aaHash.get(new
-               String(sq.substring(j - 1, j)))).intValue(); // yuk
-         }
-         seqNums.setElementAt(sqnum, i);
-       }
-     } else {
-       // JBPNote INFO level debug
-       System.err.println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
-     }
-   }
-   Vector total = new Vector();
-   public Vector quality;
-   public Double[] qualityRange = new Double[2];
-   String consString = "";
-
-   Sequence consSequence;
-   Hashtable        propHash;
-   int              threshold;
-
-  String name = "";
-
-  public Conservation(String name,Hashtable propHash, int threshold, Vector sequences, int start, int end) {
-    this.name      = name;
-    this.propHash  = propHash;
-    this.threshold = threshold;
-    this.sequences = sequences;
-    this.start     = start;
-    this.end       = end;
-    seqNums = new Vector(sequences.size());
-    calcSeqNums();
-  }
-
-
-  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++) {
-        // JBPNote - have to make sure elements of the sequences vector
-        //  are tested like this everywhere...
-        if (sequences.elementAt(j) instanceof Sequence) {
-          Sequence s = (Sequence)sequences.elementAt(j);
-
-          if (s.getLength() > i) {
-            String res = s.getSequence().substring(i,i+1);
-
-            if (residueHash.containsKey(res)) {
-              int count = ((Integer)residueHash.get(res)).intValue() ;
-              count++;
-              residueHash.put(res,new Integer(count));
-            } else {
-              residueHash.put(res,new Integer(1));
+
+    private void calcSeqNums() {
+        for (int i = 0; i < sequences.size(); i++) {
+            calcSeqNum(i);
+        }
+    }
+
+    private void calcSeqNum(int i) {
+        String sq = null; // for dumb jbuilder not-inited exception warning
+        int[] sqnum = null;
+
+        if ((i > -1) && (i < sequences.size())) {
+            sq = ((SequenceI) sequences.elementAt(i)).getSequence();
+
+            if (seqNums.size() <= i) {
+                seqNums.addElement(new int[sq.length() + 1]);
             }
-          } else {
-            if (residueHash.containsKey("-")) {
-              int count = ((Integer)residueHash.get("-")).intValue() ;
-              count++;
-              residueHash.put("-",new Integer(count));
-            } else {
-              residueHash.put("-",new Integer(1));
+
+            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) {
+                    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++) {
+                    sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(new String(
+                                sq.substring(j - 1, j)))).intValue(); // yuk
+                }
+
+                seqNums.setElementAt(sqnum, i);
             }
-          }
+        } else {
+            // JBPNote INFO level debug
+            System.err.println(
+                "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
         }
-      }
+    }
 
-      //What is the count threshold to count the residues in residueHash()
-      int thresh = threshold*(sequences.size())/100;
+    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++) {
+                // JBPNote - have to make sure elements of the sequences vector
+                //  are tested like this everywhere...
+                if (sequences.elementAt(j) instanceof Sequence) {
+                    Sequence s = (Sequence) sequences.elementAt(j);
+
+                    if (s.getLength() > i) {
+                        String res = s.getSequence().substring(i, i + 1);
+
+                        if (residueHash.containsKey(res)) {
+                            int count = ((Integer) residueHash.get(res)).intValue();
+                            count++;
+                            residueHash.put(res, new Integer(count));
+                        } else {
+                            residueHash.put(res, new Integer(1));
+                        }
+                    } else {
+                        if (residueHash.containsKey("-")) {
+                            int count = ((Integer) residueHash.get("-")).intValue();
+                            count++;
+                            residueHash.put("-", new Integer(count));
+                        } else {
+                            residueHash.put("-", new Integer(1));
+                        }
+                    }
+                }
+            }
 
-      //loop over all the found residues
-      Enumeration e = residueHash.keys();
+            //What is the count threshold to count the residues in residueHash()
+            int thresh = (threshold * (sequences.size())) / 100;
+
+            //loop over all the found residues
+            Enumeration e = residueHash.keys();
+
+            while (e.hasMoreElements()) {
+                String res = (String) e.nextElement();
+
+                if (((Integer) residueHash.get(res)).intValue() > thresh) {
+                    //Now loop over the properties
+                    Enumeration e2 = propHash.keys();
+
+                    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)) {
+                                resultHash.put(type, ht.get(res));
+                            } else {
+                                resultHash.put(type, ht.get("-"));
+                            }
+                        } else if (((Integer) resultHash.get(type)).equals(
+                                    (Integer) ht.get(res)) == false) {
+                            resultHash.put(type, new Integer(-1));
+                        }
+                    }
+                }
+            }
+
+            total.addElement(resultHash);
+        }
+    }
 
-      while (e.hasMoreElements()) {
+    public int countGaps(int j) {
+        int count = 0;
 
-        String res = (String)e.nextElement();
-        if (((Integer)residueHash.get(res)).intValue() > thresh) {
+        for (int i = 0; i < sequences.size(); i++) {
+            if ((j + 1) > ((Sequence) sequences.elementAt(i)).getSequence()
+                               .length()) {
+                count++;
 
-          //Now loop over the properties
-          Enumeration e2 = propHash.keys();
+                continue;
+            }
 
-          while (e2.hasMoreElements()) {
-            String    type = (String)e2.nextElement();
-            Hashtable ht   = (Hashtable)propHash.get(type);
+            char c = ((Sequence) sequences.elementAt(i)).getSequence().charAt(j);
 
-            //Have we ticked this before?
-            if (! resultHash.containsKey(type)) {
-              if (ht.containsKey(res)) {
-                resultHash.put(type,ht.get(res));
-              } else {
-                resultHash.put(type,ht.get("-"));
-              }
-            } else if ( ((Integer)resultHash.get(type)).equals((Integer)ht.get(res)) == false) {
-              resultHash.put(type,new Integer(-1));
+            if (jalview.util.Comparison.isGap((c))) {
+                count++;
             }
-          }
         }
-      }
 
-      total.addElement(resultHash);
+        return count;
     }
-  }
 
-  public int countGaps(int j)
-  {
-    int count = 0;
+    /***
+     * countConsNGaps
+     * returns gap count in int[0], and conserved residue count in int[1]
+     */
+    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()) {
+                count++;
+
+                continue;
+            }
 
-    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++;
+            } else {
+                nres++;
+
+                if (nres == 1) {
+                    f = c;
+                    cons++;
+                } else if (f == c) {
+                    cons++;
+                }
+            }
+        }
 
-      char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);
-      if (jalview.util.Comparison.isGap((c)))
-        count++;
+        r[0] = (nres == cons) ? 1 : 0;
+        r[1] = count;
 
+        return r;
     }
-    return count;
-  }
-  /***
-   * countConsNGaps
-   * returns gap count in int[0], and conserved residue count in int[1]
-   */
-  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())
-      {  count++;
-      continue;}
-
-      char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);
-      if (jalview.util.Comparison.isGap((c)))
-        count++;
-      else {
-        nres++;
-        if (nres==1) {
-          f = c;
-          cons++;
-        } else
-          if (f == c) {
-            cons++;
-          }
-      }
+
+    public void verdict(boolean consflag, float percentageGaps) {
+        String consString = "";
+
+        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) {
+                Hashtable resultHash = (Hashtable) total.elementAt(i - start);
+
+                //Now find the verdict
+                int count = 0;
+                Enumeration e3 = resultHash.keys();
+
+                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) {
+                            count++;
+                        }
+                    } else {
+                        if (result.intValue() != -1) {
+                            count++;
+                        }
+                    }
+                }
+
+                if (count < 10) {
+                    consString = consString + String.valueOf(count); // Conserved props!=Identity
+                } else {
+                    consString = consString + ((gapcons[0] == 1) ? "*" : "+");
+                }
+            } else {
+                consString = consString + "-";
+            }
+        }
+
+        consSequence = new Sequence(name, consString, start, end);
     }
-    r[0] = (nres==cons) ? 1 : 0;
-    r[1] = count;
 
+    public Sequence getConsSequence() {
+        return consSequence;
+    }
 
-    return r;
-  }
+    // From Alignment.java in jalview118
+    public void findQuality() {
+        findQuality(0, maxLength - 1);
+    }
 
-  public  void  verdict(boolean consflag, float percentageGaps) {
-    String consString = "";
+    private void percentIdentity2() {
+        calcSeqNums(); // updates maxLength, too.
 
-    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)
-      {
-        Hashtable resultHash = (Hashtable)total.elementAt(i-start);
-
-        //Now find the verdict
-        int         count = 0;
-        Enumeration e3    = resultHash.keys();
-
-        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)
-              count++;
-          }
-          else
-          {
-            if (result.intValue() != -1)
-              count++;
-          }
-        }
+        if ((cons2 == null) || seqNumsChanged) {
+            cons2 = new int[maxLength][24];
 
-        if (count < 10)
-          consString = consString + String.valueOf(count);// Conserved props!=Identity
-        else
-          consString = consString + ((gapcons[0]==1) ? "*" : "+");
+            // Initialize the array
+            for (int j = 0; j < 24; j++) {
+                for (int i = 0; i < maxLength; i++) {
+                    cons2[i][j] = 0;
+                }
+            }
 
-      }
-      else
-      {
-        consString = consString + "-";
-      }
-    }
+            int[] sqnum;
+            int j = 0;
 
-    consSequence = new Sequence(name,consString,start,end);
-  }
+            while (j < sequences.size()) {
+                sqnum = (int[]) seqNums.elementAt(j);
 
-  public Sequence getConsSequence() {
-    return consSequence;
-  }
+                for (int i = 1; i < sqnum.length; i++) {
+                    cons2[i - 1][sqnum[i]]++;
+                }
 
-  // From Alignment.java in jalview118
+                for (int i = sqnum.length - 1; i < maxLength; i++) {
+                    cons2[i][23]++; // gap count
+                }
 
-  public void findQuality() {
-    findQuality(0,maxLength-1);
-  }
+                j++;
+            }
 
-  int[][] cons2;
+            // unnecessary ?
 
-  private void percentIdentity2() {
-    calcSeqNums(); // updates maxLength, too.
-    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++) {
-          cons2[i][j] = 0;
-        }
-      }
-
-      int sqnum[];
-      int j = 0;
-      while(j < sequences.size()) {
-        sqnum=(int[])seqNums.elementAt(j);
-        for (int i = 1; i < sqnum.length; i++) {
-          cons2[i-1][sqnum[i]]++;
-        }
-        for (int i=sqnum.length-1; i<maxLength; i++) {
-          cons2[i][23]++; // gap count
-        }
-        j++;
-      }
-
-      // unnecessary ?
-      /* for (int i=start; i <= end; i++) {
-           int max = -1000;
-    int maxi = -1;
-    int maxj = -1;
-
-    for (int j=0;j<24;j++) {
-        if (cons2[i][j] > max) {
-        max = cons2[i][j];
-        maxi = i;
-        maxj = j;
-      }
+            /* for (int i=start; i <= end; i++) {
+                 int max = -1000;
+            int maxi = -1;
+            int maxj = -1;
 
-    }
-  } */
+            for (int j=0;j<24;j++) {
+              if (cons2[i][j] > max) {
+              max = cons2[i][j];
+              maxi = i;
+              maxj = j;
+            }
+
+            }
+            } */
+        }
     }
 
-}
+    public void findQuality(int start, int end) {
+        quality = new Vector();
+
+        double max = -10000;
+        String s = "";
+        int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+
+        //Loop over columns // JBPNote Profiling info
+        //    long ts = System.currentTimeMillis();
+        //long te = System.currentTimeMillis();
+        percentIdentity2();
+
+        int size = seqNums.size();
+        int[] lengths = new int[size];
+
+        for (int l = 0; l < size; l++)
+            lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
+
+        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++) {
+                x[ii] = 0;
 
+                try {
+                    for (int i2 = 0; i2 < 24; i2++) {
+                        x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) +
+                        4);
+                    }
+                } catch (Exception e) {
+                    System.err.println("Exception during quality calculation.");
+                    e.printStackTrace();
+                }
 
-public void findQuality(int start, int end) {
-    quality = new Vector();
-    double max = -10000;
-    String s = "";
-    int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
-    //Loop over columns // JBPNote Profiling info
-    //    long ts = System.currentTimeMillis();
-    //long te = System.currentTimeMillis();
-    percentIdentity2();
-
-    int size = seqNums.size();
-    int[] lengths = new int[size];
-
-    for (int l = 0; l < size; l++)
-      lengths[l] = ((int[]) seqNums.elementAt(l)).length-1;
-
-    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++) {
-	x[ii] = 0;
-	try {
-	  for (int i2=0; i2 < 24; i2++) {
-	    x[ii]  += (double)cons2[j][i2] * BLOSUM62[ii][i2]+4;
-	  }
-	} catch (Exception e) {
-	  System.err.println("Exception during quality calculation.");
-          e.printStackTrace();
-	}
-	//System.out.println("X " + ii + " " + x[ii]);
-	x[ii] /= (size);
-	//System.out.println("X " + ii + " " + x[ii]);
-      }
-      // Now calculate D for each position and sum
-      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++) {
-          double sr = 0;
-          try {
-            sr = (double)BLOSUM62[i][seqNum]+4;
-          } catch (Exception e) {
-            System.out.println("Exception in sr: " + e);
-            e.printStackTrace();
-          }
-          //Calculate X with another loop over residues
-
-          //  System.out.println("Xi " + i + " " + x[i] + " " + sr);
-          xx[i] = x[i] - sr;
-
-          tot += xx[i]*xx[i];
+                //System.out.println("X " + ii + " " + x[ii]);
+                x[ii] /= (size);
+
+                //System.out.println("X " + ii + " " + x[ii]);
+            }
+
+            // Now calculate D for each position and sum
+            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++) {
+                    double sr = 0;
+
+                    try {
+                        sr = (double) BLOSUM62[i][seqNum] + 4;
+                    } catch (Exception e) {
+                        System.out.println("Exception in sr: " + e);
+                        e.printStackTrace();
+                    }
+
+                    //Calculate X with another loop over residues
+                    //  System.out.println("Xi " + i + " " + x[i] + " " + sr);
+                    xx[i] = x[i] - sr;
+
+                    tot += (xx[i] * xx[i]);
+                }
+
+                bigtot += Math.sqrt(tot);
+            }
+
+            // This is the quality for one column
+            if (max < bigtot) {
+                max = bigtot;
+            }
+
+            //      bigtot  = bigtot * (size-cons2[j][23])/size;
+            quality.addElement(new Double(bigtot));
+
+            s += "-";
+
+            // Need to normalize by gaps
         }
-        bigtot += Math.sqrt(tot);
-      }
-      // This is the quality for one column
-      if (max < bigtot) {max = bigtot;}
-      //      bigtot  = bigtot * (size-cons2[j][23])/size;
 
-      quality.addElement(new Double(bigtot));
+        double newmax = -10000;
 
-      s += "-";
+        for (int j = start; j <= end; j++) {
+            double tmp = ((Double) quality.elementAt(j)).doubleValue();
+            tmp = ((max - tmp) * (size - cons2[j][23])) / size;
 
-      // Need to normalize by gaps
-    }
-    double newmax=-10000;
-    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)
-       newmax = tmp;
-    }
-    //    System.out.println("Quality " + s);
-    qualityRange[0] = new Double(0);
-    qualityRange[1] = new Double(newmax);
-  }
+            //     System.out.println(tmp+ " " + j);
+            quality.setElementAt(new Double(tmp), j);
 
+            if (tmp > newmax) {
+                newmax = tmp;
+            }
+        }
 
+        //    System.out.println("Quality " + s);
+        qualityRange[0] = new Double(0);
+        qualityRange[1] = new Double(newmax);
+    }
 }
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 75d36c1..6daee9b 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -16,750 +16,772 @@
 * 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.*;
-import jalview.util.*;
-import jalview.schemes.ResidueProperties;
-import java.util.*;
 
 import jalview.io.NewickFile;
 
-public class NJTree {
-
-  Vector cluster;
-  SequenceI[] sequence;
-
-  int done[];
-  int noseqs;
-  int noClus;
-
-  float distance[][];
-
-  int mini;
-  int minj;
-  float ri;
-  float rj;
-
-  Vector groups = new Vector();
-  SequenceNode maxdist;
-  SequenceNode top;
-
-  float maxDistValue;
-  float maxheight;
-
-  int ycount;
-
-  Vector node;
-
-  String type;
-  String pwtype;
-
-  Object found = null;
-  Object leaves = null;
-
-  int start;
-  int end;
-
-  public NJTree(SequenceNode node) {
-    top = node;
-    maxheight = findHeight(top);
-  }
-
-  public String toString()
-  {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
-    return fout.print(false,true); // distances only
-  }
-
-  public NJTree(SequenceI[] seqs, NewickFile treefile) {
-    top = treefile.getTree();
-    maxheight = findHeight(top);
-    SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
-
-    Vector leaves = new Vector();
-    findLeaves(top, leaves);
-
-    int i = 0;
-    int namesleft = seqs.length;
-
-    SequenceNode j;
-    SequenceI nam;
-    String realnam;
-    while (i < leaves.size())
-    {
-      j = (SequenceNode) leaves.elementAt(i++);
-      realnam = j.getName();
-      nam = null;
-      if (namesleft>-1)
-        nam = algnIds.findIdMatch(realnam);
-      if (nam != null) {
-        j.setElement(nam);
-        namesleft--;
-      } else {
-        j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
-        j.setPlaceholder(true);
-
-      }
-    }
-  }
-
-  /**
-   *
-   * used when the alignment associated to a tree has changed.
-   *
-   * @param alignment Vector
-   */
-  public void UpdatePlaceHolders(Vector alignment) {
-    Vector leaves = new Vector();
-    findLeaves(top, leaves);
-    int sz = leaves.size();
-    SequenceIdMatcher seqmatcher=null;
-    int i=0;
-    while (i<sz) {
-      SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
-      if (alignment.contains(leaf.element()))
-        leaf.setPlaceholder(false);
-      else {
-        if (seqmatcher==null) {
-          // Only create this the first time we need it
-          SequenceI[] seqs = new SequenceI[alignment.size()];
-          for (int j=0; j<seqs.length; j++)
-            seqs[j] = (SequenceI) alignment.elementAt(j);
-          seqmatcher = new SequenceIdMatcher(seqs);
-        }
-        SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
-        if (nam!=null) {
-          leaf.setPlaceholder(false);
-          leaf.setElement(nam);
-        } else {
-          leaf.setPlaceholder(true);
-        }
-      }
-    }
-  }
+import jalview.schemes.ResidueProperties;
 
-  public NJTree(SequenceI[] sequence,int start, int end) {
-    this(sequence,"NJ","BL",start,end);
-  }
+import jalview.util.*;
 
-  public NJTree(SequenceI[] sequence,String type,String pwtype,int start, int end ) {
+import java.util.*;
 
-    this.sequence = sequence;
-    this.node     = new Vector();
-    this.type     = type;
-    this.pwtype   = pwtype;
-    this.start    = start;
-    this.end      = end;
 
-    if (!(type.equals("NJ"))) {
-      type = "AV";
+public class NJTree {
+    Vector cluster;
+    SequenceI[] sequence;
+    int[] done;
+    int noseqs;
+    int noClus;
+    float[][] distance;
+    int mini;
+    int minj;
+    float ri;
+    float rj;
+    Vector groups = new Vector();
+    SequenceNode maxdist;
+    SequenceNode top;
+    float maxDistValue;
+    float maxheight;
+    int ycount;
+    Vector node;
+    String type;
+    String pwtype;
+    Object found = null;
+    Object leaves = null;
+    int start;
+    int end;
+
+    public NJTree(SequenceNode node) {
+        top = node;
+        maxheight = findHeight(top);
+    }
+
+    public NJTree(SequenceI[] seqs, NewickFile treefile) {
+        top = treefile.getTree();
+        maxheight = findHeight(top);
+
+        SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
+
+        Vector leaves = new Vector();
+        findLeaves(top, leaves);
+
+        int i = 0;
+        int namesleft = seqs.length;
+
+        SequenceNode j;
+        SequenceI nam;
+        String realnam;
+
+        while (i < leaves.size()) {
+            j = (SequenceNode) leaves.elementAt(i++);
+            realnam = j.getName();
+            nam = null;
+
+            if (namesleft > -1) {
+                nam = algnIds.findIdMatch(realnam);
+            }
+
+            if (nam != null) {
+                j.setElement(nam);
+                namesleft--;
+            } else {
+                j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
+                j.setPlaceholder(true);
+            }
+        }
     }
 
-    if (!(pwtype.equals("PID"))) {
-      type = "BL";
+    public NJTree(SequenceI[] sequence, int start, int end) {
+        this(sequence, "NJ", "BL", start, end);
     }
 
-    int i=0;
+    public NJTree(SequenceI[] sequence, String type, String pwtype, int start,
+        int end) {
+        this.sequence = sequence;
+        this.node = new Vector();
+        this.type = type;
+        this.pwtype = pwtype;
+        this.start = start;
+        this.end = end;
 
-    done = new int[sequence.length];
+        if (!(type.equals("NJ"))) {
+            type = "AV";
+        }
 
+        if (!(pwtype.equals("PID"))) {
+            type = "BL";
+        }
 
-    while (i < sequence.length  && sequence[i] != null) {
-      done[i] = 0;
-      i++;
-    }
+        int i = 0;
 
-    noseqs = i++;
+        done = new int[sequence.length];
 
-    distance = findDistances();
+        while ((i < sequence.length) && (sequence[i] != null)) {
+            done[i] = 0;
+            i++;
+        }
 
-    makeLeaves();
+        noseqs = i++;
 
-    noClus = cluster.size();
+        distance = findDistances();
 
-    cluster();
+        makeLeaves();
 
-  }
+        noClus = cluster.size();
 
+        cluster();
+    }
 
-  public void cluster() {
+    public String toString() {
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
 
-    while (noClus > 2) {
-      if (type.equals("NJ")) {
-        float mind = findMinNJDistance();
-      } else {
-        float mind = findMinDistance();
-      }
+        return fout.print(false, true); // distances only
+    }
 
-      Cluster c = joinClusters(mini,minj);
+    /**
+     *
+     * used when the alignment associated to a tree has changed.
+     *
+     * @param alignment Vector
+     */
+    public void UpdatePlaceHolders(Vector alignment) {
+        Vector leaves = new Vector();
+        findLeaves(top, leaves);
 
+        int sz = leaves.size();
+        SequenceIdMatcher seqmatcher = null;
+        int i = 0;
 
-      done[minj] = 1;
+        while (i < sz) {
+            SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
 
-      cluster.setElementAt(null,minj);
-      cluster.setElementAt(c,mini);
+            if (alignment.contains(leaf.element())) {
+                leaf.setPlaceholder(false);
+            } else {
+                if (seqmatcher == null) {
+                    // Only create this the first time we need it
+                    SequenceI[] seqs = new SequenceI[alignment.size()];
 
-      noClus--;
-    }
+                    for (int j = 0; j < seqs.length; j++)
+                        seqs[j] = (SequenceI) alignment.elementAt(j);
 
-    boolean onefound = false;
+                    seqmatcher = new SequenceIdMatcher(seqs);
+                }
 
-    int one = -1;
-    int two = -1;
+                SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
 
-    for (int i=0; i < noseqs; i++) {
-      if (done[i] != 1) {
-        if (onefound == false) {
-          two = i;
-          onefound = true;
-        } else {
-          one = i;
+                if (nam != null) {
+                    leaf.setPlaceholder(false);
+                    leaf.setElement(nam);
+                } else {
+                    leaf.setPlaceholder(true);
+                }
+            }
         }
-      }
     }
 
-    Cluster c = joinClusters(one,two);
-    top = (SequenceNode)(node.elementAt(one));
+    public void cluster() {
+        while (noClus > 2) {
+            if (type.equals("NJ")) {
+                float mind = findMinNJDistance();
+            } else {
+                float mind = findMinDistance();
+            }
 
-    reCount(top);
-    findHeight(top);
-    findMaxDist(top);
+            Cluster c = joinClusters(mini, minj);
 
-  }
+            done[minj] = 1;
 
-  public Cluster joinClusters(int i, int j) {
+            cluster.setElementAt(null, minj);
+            cluster.setElementAt(c, mini);
 
-    float dist = distance[i][j];
+            noClus--;
+        }
 
-    int noi = ((Cluster)cluster.elementAt(i)).value.length;
-    int noj = ((Cluster)cluster.elementAt(j)).value.length;
+        boolean onefound = false;
 
-    int[] value = new int[noi + noj];
+        int one = -1;
+        int two = -1;
 
-    for (int ii = 0; ii < noi;ii++) {
-      value[ii] =  ((Cluster)cluster.elementAt(i)).value[ii];
-    }
+        for (int i = 0; i < noseqs; i++) {
+            if (done[i] != 1) {
+                if (onefound == false) {
+                    two = i;
+                    onefound = true;
+                } else {
+                    one = i;
+                }
+            }
+        }
+
+        Cluster c = joinClusters(one, two);
+        top = (SequenceNode) (node.elementAt(one));
 
-    for (int ii = noi; ii < noi+ noj;ii++) {
-      value[ii] =  ((Cluster)cluster.elementAt(j)).value[ii-noi];
+        reCount(top);
+        findHeight(top);
+        findMaxDist(top);
     }
 
-    Cluster c = new Cluster(value);
+    public Cluster joinClusters(int i, int j) {
+        float dist = distance[i][j];
 
-    ri = findr(i,j);
-    rj = findr(j,i);
+        int noi = ((Cluster) cluster.elementAt(i)).value.length;
+        int noj = ((Cluster) cluster.elementAt(j)).value.length;
 
-    if (type.equals("NJ")) {
-      findClusterNJDistance(i,j);
-    } else {
-      findClusterDistance(i,j);
-    }
+        int[] value = new int[noi + noj];
+
+        for (int ii = 0; ii < noi; ii++) {
+            value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
+        }
 
-    SequenceNode sn = new SequenceNode();
+        for (int ii = noi; ii < (noi + noj); ii++) {
+            value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
+        }
 
-    sn.setLeft((SequenceNode)(node.elementAt(i)));
-    sn.setRight((SequenceNode)(node.elementAt(j)));
+        Cluster c = new Cluster(value);
 
-    SequenceNode tmpi = (SequenceNode)(node.elementAt(i));
-    SequenceNode tmpj = (SequenceNode)(node.elementAt(j));
+        ri = findr(i, j);
+        rj = findr(j, i);
 
-    if (type.equals("NJ")) {
-      findNewNJDistances(tmpi,tmpj,dist);
-    } else {
-      findNewDistances(tmpi,tmpj,dist);
-    }
+        if (type.equals("NJ")) {
+            findClusterNJDistance(i, j);
+        } else {
+            findClusterDistance(i, j);
+        }
 
-    tmpi.setParent(sn);
-    tmpj.setParent(sn);
+        SequenceNode sn = new SequenceNode();
 
-    node.setElementAt(sn,i);
-    return c;
-  }
+        sn.setLeft((SequenceNode) (node.elementAt(i)));
+        sn.setRight((SequenceNode) (node.elementAt(j)));
 
-  public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj, float dist) {
+        SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
+        SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
 
-    float ih = 0;
-    float jh = 0;
+        if (type.equals("NJ")) {
+            findNewNJDistances(tmpi, tmpj, dist);
+        } else {
+            findNewDistances(tmpi, tmpj, dist);
+        }
 
-    SequenceNode sni = tmpi;
-    SequenceNode snj = tmpj;
+        tmpi.setParent(sn);
+        tmpj.setParent(sn);
 
-    tmpi.dist = (dist + ri - rj)/2;
-    tmpj.dist = (dist - tmpi.dist);
+        node.setElementAt(sn, i);
 
-    if (tmpi.dist < 0) {
-      tmpi.dist = 0;
+        return c;
     }
-    if (tmpj.dist < 0) {
-      tmpj.dist = 0;
-    }
-  }
 
-  public void findNewDistances(SequenceNode tmpi,SequenceNode tmpj,float dist) {
+    public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
+        float dist) {
+        float ih = 0;
+        float jh = 0;
 
-    float ih = 0;
-    float jh = 0;
+        SequenceNode sni = tmpi;
+        SequenceNode snj = tmpj;
 
-    SequenceNode sni = tmpi;
-    SequenceNode snj = tmpj;
+        tmpi.dist = ((dist + ri) - rj) / 2;
+        tmpj.dist = (dist - tmpi.dist);
 
-    while (sni != null) {
-      ih = ih + sni.dist;
-      sni = (SequenceNode)sni.left();
-    }
+        if (tmpi.dist < 0) {
+            tmpi.dist = 0;
+        }
 
-    while (snj != null) {
-      jh = jh + snj.dist;
-      snj = (SequenceNode)snj.left();
+        if (tmpj.dist < 0) {
+            tmpj.dist = 0;
+        }
     }
 
-    tmpi.dist = (dist/2 - ih);
-    tmpj.dist = (dist/2 - jh);
-  }
+    public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+        float dist) {
+        float ih = 0;
+        float jh = 0;
 
+        SequenceNode sni = tmpi;
+        SequenceNode snj = tmpj;
 
+        while (sni != null) {
+            ih = ih + sni.dist;
+            sni = (SequenceNode) sni.left();
+        }
 
-  public void findClusterDistance(int i, int j) {
+        while (snj != null) {
+            jh = jh + snj.dist;
+            snj = (SequenceNode) snj.left();
+        }
 
-    int noi = ((Cluster)cluster.elementAt(i)).value.length;
-    int noj = ((Cluster)cluster.elementAt(j)).value.length;
+        tmpi.dist = ((dist / 2) - ih);
+        tmpj.dist = ((dist / 2) - jh);
+    }
 
-    // New distances from cluster to others
-    float[] newdist = new float[noseqs];
+    public void findClusterDistance(int i, int j) {
+        int noi = ((Cluster) cluster.elementAt(i)).value.length;
+        int noj = ((Cluster) cluster.elementAt(j)).value.length;
 
-    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 {
-        newdist[l] = 0;
-      }
-    }
+        // New distances from cluster to others
+        float[] newdist = new float[noseqs];
+
+        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 {
+                newdist[l] = 0;
+            }
+        }
 
-    for (int ii=0; ii < noseqs;ii++) {
-      distance[i][ii] = newdist[ii];
-      distance[ii][i] = newdist[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) {
+    public void findClusterNJDistance(int i, int j) {
+        int noi = ((Cluster) cluster.elementAt(i)).value.length;
+        int noj = ((Cluster) cluster.elementAt(j)).value.length;
 
-    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];
 
-    // New distances from cluster to others
-    float[] newdist = new float[noseqs];
+        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 {
+                newdist[l] = 0;
+            }
+        }
 
-    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 {
-        newdist[l] = 0;
-      }
+        for (int ii = 0; ii < noseqs; ii++) {
+            distance[i][ii] = newdist[ii];
+            distance[ii][i] = newdist[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) {
+        float tmp = 1;
+
+        for (int k = 0; k < noseqs; k++) {
+            if ((k != i) && (k != j) && (done[k] != 1)) {
+                tmp = tmp + distance[i][k];
+            }
+        }
+
+        if (noClus > 2) {
+            tmp = tmp / (noClus - 2);
+        }
+
+        return tmp;
     }
-  }
 
-  public float findr(int i, int j) {
+    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)) {
+                    float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
+
+                    if (tmp < min) {
+                        mini = i;
+                        minj = j;
 
-    float tmp = 1;
-    for (int k=0; k < noseqs;k++) {
-      if (k!= i && k!= j && done[k] != 1) {
-        tmp = tmp + distance[i][k];
-      }
+                        min = tmp;
+                    }
+                }
+            }
+        }
+
+        return min;
     }
 
-    if (noClus > 2) {
-      tmp = tmp/(noClus - 2);
+    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) {
+                        mini = i;
+                        minj = j;
+
+                        min = distance[i][j];
+                    }
+                }
+            }
+        }
+
+        return min;
+    }
+
+    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) {
+                        distance[i][i] = 0;
+                    } else {
+                        distance[i][j] = 100 -
+                            Comparison.PID(sequence[i], sequence[j], start, end);
+                        distance[j][i] = distance[i][j];
+                    }
+                }
+            }
+        } else if (pwtype.equals("BL")) {
+            int maxscore = 0;
+
+            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 {
+                            score += ResidueProperties.getBLOSUM62(sequence[i].getSequence(
+                                    k, k + 1), sequence[j].getSequence(k, k +
+                                    1));
+                        } catch (Exception ex) {
+                            System.err.println("err creating BLOSUM62 tree");
+                            ex.printStackTrace();
+                        }
+                    }
+
+                    distance[i][j] = (float) score;
+
+                    if (score > maxscore) {
+                        maxscore = score;
+                    }
+                }
+            }
+
+            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")) {
+            float max = -1;
+
+            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]) {
+                        max = distance[i][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];
+                }
+            }
+        }
+
+        return distance;
     }
 
-    return tmp;
-  }
+    public void makeLeaves() {
+        cluster = new Vector();
+
+        for (int i = 0; i < noseqs; i++) {
+            SequenceNode sn = new SequenceNode();
 
-  public float findMinNJDistance() {
+            sn.setElement(sequence[i]);
+            sn.setName(sequence[i].getName());
+            node.addElement(sn);
 
-    float min = 100000;
+            int[] value = new int[1];
+            value[0] = i;
 
-    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) {
+            Cluster c = new Cluster(value);
+            cluster.addElement(c);
+        }
+    }
 
-            mini = i;
-            minj = j;
+    public Vector findLeaves(SequenceNode node, Vector leaves) {
+        if (node == null) {
+            return leaves;
+        }
 
-            min = tmp;
+        if ((node.left() == null) && (node.right() == null)) {
+            leaves.addElement(node);
 
-          }
+            return leaves;
+        } else {
+            findLeaves((SequenceNode) node.left(), leaves);
+            findLeaves((SequenceNode) node.right(), leaves);
         }
-      }
+
+        return leaves;
     }
-    return min;
-  }
 
-  public float findMinDistance() {
+    public Object findLeaf(SequenceNode node, int count) {
+        found = _findLeaf(node, count);
 
-    float min = 100000;
+        return found;
+    }
 
-    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;
+    public Object _findLeaf(SequenceNode node, int count) {
+        if (node == null) {
+            return null;
+        }
 
-            min = distance[i][j];
-          }
+        if (node.ycount == count) {
+            found = node.element();
+
+            return found;
+        } else {
+            _findLeaf((SequenceNode) node.left(), count);
+            _findLeaf((SequenceNode) node.right(), count);
         }
-      }
+
+        return found;
     }
-    return min;
-  }
 
-  public float[][] findDistances() {
+    /**
+     * printNode is mainly for debugging purposes.
+     *
+     * @param node SequenceNode
+     */
+    public void printNode(SequenceNode node) {
+        if (node == null) {
+            return;
+        }
+
+        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 {
+            System.out.println("Dist " + ((SequenceNode) node).dist);
+            printNode((SequenceNode) node.left());
+            printNode((SequenceNode) node.right());
+        }
+    }
 
-    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) {
-            distance[i][i] = 0;
-          } else {
-            distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j], start, end);
-            distance[j][i] = distance[i][j];
-          }
+    public void findMaxDist(SequenceNode node) {
+        if (node == null) {
+            return;
         }
-      }
-    } else if (pwtype.equals("BL")) {
-      int   maxscore = 0;
 
-      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{
-              score +=
-                  ResidueProperties.getBLOSUM62(sequence[i].getSequence(k,
-                  k + 1),
-                                                sequence[j].getSequence(k,
-                  k + 1));
-            }catch(Exception ex){System.err.println("err creating BLOSUM62 tree");ex.printStackTrace();}
-          }
-          distance[i][j] = (float)score;
-          if (score > maxscore) {
-            maxscore = score;
-          }
+        if ((node.left() == null) && (node.right() == null)) {
+            float dist = ((SequenceNode) node).dist;
+
+            if (dist > maxDistValue) {
+                maxdist = (SequenceNode) node;
+                maxDistValue = dist;
+            }
+        } else {
+            findMaxDist((SequenceNode) node.left());
+            findMaxDist((SequenceNode) node.right());
         }
-      }
-      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")) {
-      float max = -1;
-      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]) {
-            max = distance[i][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];
-        }
-      }
-    }
-
-    return distance;
-  }
-
-  public void makeLeaves() {
-    cluster = new Vector();
-
-    for (int i=0; i < noseqs; i++) {
-      SequenceNode sn = new SequenceNode();
-
-      sn.setElement(sequence[i]);
-      sn.setName(sequence[i].getName());
-      node.addElement(sn);
-
-      int[] value = new int[1];
-      value[0] = i;
-
-      Cluster c = new Cluster(value);
-      cluster.addElement(c);
-    }
-  }
-
-  public Vector findLeaves(SequenceNode node, Vector leaves) {
-    if (node == null) {
-      return leaves;
-    }
-
-    if (node.left() == null && node.right() == null) {
-      leaves.addElement(node);
-      return leaves;
-    } else {
-      findLeaves((SequenceNode)node.left(),leaves);
-      findLeaves((SequenceNode)node.right(),leaves);
-    }
-    return leaves;
-  }
-
-  public Object findLeaf(SequenceNode node, int count) {
-    found = _findLeaf(node,count);
-
-    return found;
-  }
-  public Object _findLeaf(SequenceNode node,int count) {
-    if (node == null) {
-      return null;
-    }
-    if (node.ycount == count) {
-      found = node.element();
-      return found;
-    } else {
-      _findLeaf((SequenceNode)node.left(),count);
-      _findLeaf((SequenceNode)node.right(),count);
-    }
-
-    return found;
-  }
-
-  /**
-   * printNode is mainly for debugging purposes.
-   *
-   * @param node SequenceNode
-   */
-  public void printNode(SequenceNode node) {
-    if (node == null) {
-      return;
-    }
-    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 {
-      System.out.println("Dist " + ((SequenceNode)node).dist);
-      printNode((SequenceNode)node.left());
-      printNode((SequenceNode)node.right());
-    }
-  }
-  public void findMaxDist(SequenceNode node) {
-    if (node == null) {
-      return;
-    }
-    if (node.left() == null && node.right() == null) {
-
-      float dist = ((SequenceNode)node).dist;
-      if (dist > maxDistValue) {
-          maxdist      = (SequenceNode)node;
-          maxDistValue = dist;
-      }
-    } else {
-      findMaxDist((SequenceNode)node.left());
-      findMaxDist((SequenceNode)node.right());
     }
-  }
+
     public Vector getGroups() {
         return groups;
     }
+
     public float getMaxHeight() {
         return maxheight;
     }
-  public void  groupNodes(SequenceNode node, float threshold) {
-    if (node == null) {
-      return;
+
+    public void groupNodes(SequenceNode node, float threshold) {
+        if (node == null) {
+            return;
+        }
+
+        if ((node.height / maxheight) > threshold) {
+            groups.addElement(node);
+        } else {
+            groupNodes((SequenceNode) node.left(), threshold);
+            groupNodes((SequenceNode) node.right(), threshold);
+        }
     }
 
-    if (node.height/maxheight > threshold) {
-      groups.addElement(node);
-    } else {
-      groupNodes((SequenceNode)node.left(),threshold);
-      groupNodes((SequenceNode)node.right(),threshold);
+    public float findHeight(SequenceNode node) {
+        if (node == null) {
+            return maxheight;
+        }
+
+        if ((node.left() == null) && (node.right() == null)) {
+            node.height = ((SequenceNode) node.parent()).height + node.dist;
+
+            if (node.height > maxheight) {
+                return node.height;
+            } else {
+                return maxheight;
+            }
+        } else {
+            if (node.parent() != null) {
+                node.height = ((SequenceNode) node.parent()).height +
+                    node.dist;
+            } else {
+                maxheight = 0;
+                node.height = (float) 0.0;
+            }
+
+            maxheight = findHeight((SequenceNode) (node.left()));
+            maxheight = findHeight((SequenceNode) (node.right()));
+        }
+
+        return maxheight;
     }
-  }
 
-  public float findHeight(SequenceNode node) {
+    public SequenceNode reRoot() {
+        if (maxdist != null) {
+            ycount = 0;
+
+            float tmpdist = maxdist.dist;
+
+            // New top
+            SequenceNode sn = new SequenceNode();
+            sn.setParent(null);
+
+            // New right hand of top
+            SequenceNode snr = (SequenceNode) maxdist.parent();
+            changeDirection(snr, maxdist);
+            System.out.println("Printing reversed tree");
+            printN(snr);
+            snr.dist = tmpdist / 2;
+            maxdist.dist = tmpdist / 2;
+
+            snr.setParent(sn);
+            maxdist.setParent(sn);
+
+            sn.setRight(snr);
+            sn.setLeft(maxdist);
 
-    if (node == null) {
-      return maxheight;
+            top = sn;
+
+            ycount = 0;
+            reCount(top);
+            findHeight(top);
+        }
+
+        return top;
     }
 
-    if (node.left() == null && node.right() == null) {
-      node.height = ((SequenceNode)node.parent()).height + node.dist;
+    public static void printN(SequenceNode node) {
+        if (node == null) {
+            return;
+        }
 
-      if (node.height > maxheight) {
-        return node.height;
-      } else {
-        return maxheight;
-      }
-    } else {
-      if (node.parent() != null) {
-        node.height = ((SequenceNode)node.parent()).height + node.dist;
-      } else {
-        maxheight = 0;
-        node.height = (float)0.0;
-      }
-
-      maxheight = findHeight((SequenceNode)(node.left()));
-      maxheight = findHeight((SequenceNode)(node.right()));
-    }
-    return maxheight;
-  }
-  public SequenceNode reRoot() {
-    if (maxdist != null) {
-      ycount = 0;
-      float tmpdist = maxdist.dist;
-
-      // New top
-      SequenceNode sn = new SequenceNode();
-      sn.setParent(null);
-
-      // New right hand of top
-      SequenceNode snr = (SequenceNode)maxdist.parent();
-      changeDirection(snr,maxdist);
-      System.out.println("Printing reversed tree");
-      printN(snr);
-      snr.dist = tmpdist/2;
-      maxdist.dist = tmpdist/2;
-
-      snr.setParent(sn);
-      maxdist.setParent(sn);
-
-      sn.setRight(snr);
-      sn.setLeft(maxdist);
-
-      top = sn;
-
-      ycount = 0;
-      reCount(top);
-      findHeight(top);
-
-    }
-    return top;
-  }
-  public static void printN(SequenceNode node) {
-    if (node == null) {
-      return;
-    }
-
-    if (node.left() != null && node.right() != null) {
-      printN((SequenceNode)node.left());
-      printN((SequenceNode)node.right());
-    } else {
-      System.out.println(" name = " + ((SequenceI)node.element()).getName());
-    }
-    System.out.println(" dist = " + ((SequenceNode)node).dist + " " + ((SequenceNode)node).count + " " + ((SequenceNode)node).height);
-  }
+        if ((node.left() != null) && (node.right() != null)) {
+            printN((SequenceNode) node.left());
+            printN((SequenceNode) node.right());
+        } else {
+            System.out.println(" name = " +
+                ((SequenceI) node.element()).getName());
+        }
+
+        System.out.println(" dist = " + ((SequenceNode) node).dist + " " +
+            ((SequenceNode) node).count + " " + ((SequenceNode) node).height);
+    }
 
     public void reCount(SequenceNode node) {
         ycount = 0;
         _reCount(node);
     }
-  public void _reCount(SequenceNode node) {
-    if (node == null) {
-      return;
-    }
 
-    if (node.left() != null && node.right() != null) {
-      _reCount((SequenceNode)node.left());
-      _reCount((SequenceNode)node.right());
+    public void _reCount(SequenceNode node) {
+        if (node == null) {
+            return;
+        }
 
-      SequenceNode l = (SequenceNode)node.left();
-      SequenceNode r = (SequenceNode)node.right();
+        if ((node.left() != null) && (node.right() != null)) {
+            _reCount((SequenceNode) node.left());
+            _reCount((SequenceNode) node.right());
 
-      ((SequenceNode)node).count  = l.count + r.count;
-      ((SequenceNode)node).ycount = (l.ycount + r.ycount)/2;
+            SequenceNode l = (SequenceNode) node.left();
+            SequenceNode r = (SequenceNode) node.right();
 
-    } else {
-      ((SequenceNode)node).count = 1;
-      ((SequenceNode)node).ycount = ycount++;
+            ((SequenceNode) node).count = l.count + r.count;
+            ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+        } else {
+            ((SequenceNode) node).count = 1;
+            ((SequenceNode) node).ycount = ycount++;
+        }
     }
 
-  }
     public void swapNodes(SequenceNode node) {
         if (node == null) {
             return;
         }
-        SequenceNode tmp = (SequenceNode)node.left();
+
+        SequenceNode tmp = (SequenceNode) node.left();
 
         node.setLeft(node.right());
         node.setRight(tmp);
     }
-  public void changeDirection(SequenceNode node, SequenceNode dir) {
-    if (node == null) {
-      return;
-    }
-    if (node.parent() != top) {
-      changeDirection((SequenceNode)node.parent(), node);
-
-      SequenceNode tmp = (SequenceNode)node.parent();
 
-      if (dir == node.left()) {
-        node.setParent(dir);
-        node.setLeft(tmp);
-      } else if (dir == node.right()) {
-        node.setParent(dir);
-        node.setRight(tmp);
-      }
+    public void changeDirection(SequenceNode node, SequenceNode dir) {
+        if (node == null) {
+            return;
+        }
 
-    } else {
-      if (dir == node.left()) {
-        node.setParent(node.left());
+        if (node.parent() != top) {
+            changeDirection((SequenceNode) node.parent(), node);
 
-        if (top.left() == node) {
-          node.setRight(top.right());
-        } else {
-          node.setRight(top.left());
-        }
-      } else {
-        node.setParent(node.right());
+            SequenceNode tmp = (SequenceNode) node.parent();
 
-        if (top.left() == node) {
-          node.setLeft(top.right());
+            if (dir == node.left()) {
+                node.setParent(dir);
+                node.setLeft(tmp);
+            } else if (dir == node.right()) {
+                node.setParent(dir);
+                node.setRight(tmp);
+            }
         } else {
-          node.setLeft(top.left());
+            if (dir == node.left()) {
+                node.setParent(node.left());
+
+                if (top.left() == node) {
+                    node.setRight(top.right());
+                } else {
+                    node.setRight(top.left());
+                }
+            } else {
+                node.setParent(node.right());
+
+                if (top.left() == node) {
+                    node.setLeft(top.right());
+                } else {
+                    node.setLeft(top.left());
+                }
+            }
         }
-      }
     }
-  }
+
     public void setMaxDist(SequenceNode node) {
         this.maxdist = maxdist;
     }
+
     public SequenceNode getMaxDist() {
         return maxdist;
     }
+
     public SequenceNode getTopNode() {
         return top;
     }
-
 }
 
 
-
 class Cluster {
+    int[] value;
 
-  int[] value;
-
-  public Cluster(int[] value) {
-    this.value = value;
-  }
-
+    public Cluster(int[] value) {
+        this.value = value;
+    }
 }
-
diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 3948695..ecbe4ab 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -16,193 +16,202 @@
 * 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.math.*;
 import jalview.datamodel.*;
+
+import jalview.math.*;
+
 import jalview.util.*;
 
 import java.awt.*;
+
 import java.io.*;
 
-public class PCA implements Runnable {
-  Matrix m;
-  Matrix symm;
-  Matrix m2;
 
-  double[] eigenvalue;
-  Matrix eigenvector;
+public class PCA implements Runnable {
+    Matrix m;
+    Matrix symm;
+    Matrix m2;
+    double[] eigenvalue;
+    Matrix eigenvector;
+
+    public PCA(Matrix m) {
+        this.m = m;
+    }
 
-  public PCA(Matrix m) {
-    this.m = m;
-  }
+    public PCA(SequenceI[] s) {
+        Runtime rt = Runtime.getRuntime();
+
+        BinarySequence[] bs = new BinarySequence[s.length];
+        int ii = 0;
+
+        while ((ii < s.length) && (s[ii] != null)) {
+            bs[ii] = new BinarySequence(s[ii]);
+            bs[ii].encode();
+            ii++;
+        }
+
+        BinarySequence[] bs2 = new BinarySequence[s.length];
+        ii = 0;
+
+        while ((ii < s.length) && (s[ii] != null)) {
+            bs2[ii] = new BinarySequence(s[ii]);
+            bs2[ii].blosumEncode();
+            ii++;
+        }
+
+        //System.out.println("Created binary encoding");
+        //printMemory(rt);
+        int count = 0;
+
+        while ((count < bs.length) && (bs[count] != null)) {
+            count++;
+        }
+
+        double[][] seqmat = new double[count][bs[0].getDBinary().length];
+        double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];
+        int i = 0;
+
+        while (i < count) {
+            seqmat[i] = bs[i].getDBinary();
+            seqmat2[i] = bs2[i].getDBinary();
+            i++;
+        }
+
+        //System.out.println("Created array");
+        //printMemory(rt);
+        //    System.out.println(" --- Original matrix ---- ");
+        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 PCA(SequenceI[] s) {
-    Runtime rt = Runtime.getRuntime();
+    public static void printMemory(Runtime rt) {
+        System.out.println("PCA:Free memory = " + rt.freeMemory());
+    }
 
-    BinarySequence[] bs = new BinarySequence[s.length];
-    int ii = 0;
-    while (ii < s.length && s[ii] != null) {
+    public Matrix getM() {
+        return m;
+    }
 
-      bs[ii] = new BinarySequence(s[ii]);
-      bs[ii].encode();
-      ii++;
+    public double[] getEigenvector(int i) {
+        return eigenvector.getColumn(i);
     }
 
-    BinarySequence[] bs2 = new BinarySequence[s.length];
-    ii = 0;
-    while (ii < s.length && s[ii] != null) {
+    public double getEigenvalue(int i) {
+        return eigenvector.d[i];
+    }
 
-      bs2[ii] = new BinarySequence(s[ii]);
-      bs2[ii].blosumEncode();
-      ii++;
+    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) {
+        float[][] out = new float[m.rows][3];
 
-    //System.out.println("Created binary encoding");
-    //printMemory(rt);
+        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;
+        }
 
-    int count=0;
-    while (count < bs.length && bs[count] != null) {
-      count++;
-    }
-    double[][] seqmat = new double[count][bs[0].getDBinary().length];
-    double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];
-    int i=0;
-    while (i < count) {
-      seqmat[i] = bs[i].getDBinary();
-      seqmat2[i] = bs2[i].getDBinary();
-      i++;
+        return out;
     }
-    //System.out.println("Created array");
-    //printMemory(rt);
-    //    System.out.println(" --- Original matrix ---- ");
-    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());
-  }
-
-  public Matrix getM() {
-    return m;
-  }
-
-  public double[] getEigenvector(int i) {
-    return eigenvector.getColumn(i);
-  }
-
-  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) {
-    float[][] out = new float[m.rows][3];
-
-    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;
-    }
-    return out;
-  }
 
-  public double[] component(int n) {
-    // n = index of eigenvector
-    double[] out = new double[m.rows];
+    public double[] component(int n) {
+        // n = index of eigenvector
+        double[] out = new double[m.rows];
 
-    for (int i=0; i < m.rows; i++) {
-      out[i] = component(i,n);
-    }
-    return out;
-  }
-  public double component(int row, int n) {
-    double out = 0.0;
+        for (int i = 0; i < m.rows; i++) {
+            out[i] = component(i, n);
+        }
 
-    for (int i = 0; i < symm.cols; i++) {
-      out += symm.value[row][i] * eigenvector.value[i][n];
+        return out;
     }
-    return out/eigenvector.d[n];
-  }
 
-  public void checkEigenvector(int n,PrintStream ps) {
-    ps.println(" --- Eigenvector " + n  + " --- ");
+    public double component(int row, int n) {
+        double out = 0.0;
 
-    double[] eigenv = eigenvector.getColumn(n);
+        for (int i = 0; i < symm.cols; i++) {
+            out += (symm.value[row][i] * eigenvector.value[i][n]);
+        }
 
-    for (int i=0; i < eigenv.length;i++) {
-      Format.print(ps,"%15.4f",eigenv[i]);
+        return out / eigenvector.d[n];
     }
 
-    System.out.println();
+    public void checkEigenvector(int n, PrintStream ps) {
+        ps.println(" --- Eigenvector " + n + " --- ");
+
+        double[] eigenv = eigenvector.getColumn(n);
 
-    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]);
-      }
+        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();
     }
-    System.out.println();
-  }
-
-  public void run() {
-    Matrix mt = m.transpose();
-    //    System.out.println(" --- OrigT * Orig ---- ");
-    eigenvector = mt.preMultiply(m2);
-    //  eigenvector.print(System.out);
-    symm = eigenvector.copy();
-
-    //TextArea ta = new TextArea(25,72);
-    //TextAreaPrintStream taps = new TextAreaPrintStream(System.out,ta);
-    //Frame f = new Frame("PCA output");
-    //f.resize(500,500);
-    //f.setLayout(new BorderLayout());
-    //f.add("Center",ta);
-    //f.show();
-    //symm.print(taps);
-    long tstart = System.currentTimeMillis();
-    eigenvector.tred();
-    long tend = System.currentTimeMillis();
-    //taps.println("Time take for tred = " + (tend-tstart) + "ms");
-    //taps.println(" ---Tridiag transform matrix ---");
-
-    //taps.println(" --- D vector ---");
-    //eigenvector.printD(taps);
-    //taps.println();
-    //taps.println(" --- E vector ---");
-    //    eigenvector.printE(taps);
-    //taps.println();
-
-    // Now produce the diagonalization matrix
-    tstart = System.currentTimeMillis();
-    eigenvector.tqli();
-    tend = System.currentTimeMillis();
-    //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
-
-    //System.out.println(" --- New diagonalization matrix ---");
-
-    //System.out.println(" --- Eigenvalues ---");
-    //eigenvector.printD(taps);
-
-    //System.out.println();
-
-    // for (int i=0; i < eigenvector.cols; i++) {
-    // checkEigenvector(i,taps);
-    // taps.println();
-    // }
-
-    //  taps.println();
-    //  taps.println("Transformed sequences = ");
-    // Matrix trans =  m.preMultiply(eigenvector);
-    //  trans.print(System.out);
-  }
 
+    public void run() {
+        Matrix mt = m.transpose();
+
+        //    System.out.println(" --- OrigT * Orig ---- ");
+        eigenvector = mt.preMultiply(m2);
+
+        //  eigenvector.print(System.out);
+        symm = eigenvector.copy();
+
+        //TextArea ta = new TextArea(25,72);
+        //TextAreaPrintStream taps = new TextAreaPrintStream(System.out,ta);
+        //Frame f = new Frame("PCA output");
+        //f.resize(500,500);
+        //f.setLayout(new BorderLayout());
+        //f.add("Center",ta);
+        //f.show();
+        //symm.print(taps);
+        long tstart = System.currentTimeMillis();
+        eigenvector.tred();
+
+        long tend = System.currentTimeMillis();
+
+        //taps.println("Time take for tred = " + (tend-tstart) + "ms");
+        //taps.println(" ---Tridiag transform matrix ---");
+        //taps.println(" --- D vector ---");
+        //eigenvector.printD(taps);
+        //taps.println();
+        //taps.println(" --- E vector ---");
+        //    eigenvector.printE(taps);
+        //taps.println();
+        // Now produce the diagonalization matrix
+        tstart = System.currentTimeMillis();
+        eigenvector.tqli();
+        tend = System.currentTimeMillis();
+
+        //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
+        //System.out.println(" --- New diagonalization matrix ---");
+        //System.out.println(" --- Eigenvalues ---");
+        //eigenvector.printD(taps);
+        //System.out.println();
+        // for (int i=0; i < eigenvector.cols; i++) {
+        // checkEigenvector(i,taps);
+        // taps.println();
+        // }
+        //  taps.println();
+        //  taps.println("Transformed sequences = ");
+        // Matrix trans =  m.preMultiply(eigenvector);
+        //  trans.print(System.out);
+    }
 }
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index faa08e1..8a8ae28 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -15,13 +15,14 @@
 * 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;
-
+*/
+package jalview.analysis;
+
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
+
+
 /**
  * <p>Title: </p>
  *
@@ -33,97 +34,105 @@ import java.util.Hashtable;
  *
  * @author not attributable
  * @version 1.0
- */
-public class SeqsetUtils
-{
+ */
+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;
-    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;
-  }
-
-  /**
-   * 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 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;
-  }
-
-}
+ * 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;
+        } 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;
+    }
+
+    /**
+ * 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 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 1c156cd..f786243 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -15,14 +15,15 @@
 * 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 java.util.Vector;
-import java.util.Hashtable;
-import jalview.datamodel.SequenceI;
-
+*/
+package jalview.analysis;
+
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
+
 /**
  * <p>Title: </p>
  * SequenceIdMatcher
@@ -34,123 +35,105 @@ import jalview.datamodel.SequenceI;
  *
  * @author not attributable
  * @version 1.0
- */
-public class SequenceIdMatcher
-{
-
-  private class SeqIdName
-  {
-    String id;
-
-    SeqIdName(String s)
-    {
-      id = new String(s);
-    }
-
-    public int hashCode()
-    {
-      return (id.substring(0, 4).hashCode());
-    }
-
-    public boolean equals(Object s)
-    {
-      if (s instanceof SeqIdName)
-      {
-        return this.equals( (SeqIdName) s);
-      }
-      else
-      {
-        if (s instanceof String)
-        {
-          return this.equals( (String) s);
-        }
-      }
-      return false;
-    }
-
-    public boolean equals(SeqIdName s)
-    {
-      if (id.startsWith(s.id) || s.id.startsWith(id))
-      {
-        return true;
-      }
-      return false;
-    }
-
-    public boolean equals(String s)
-    {
-      if (id.startsWith(s) || s.startsWith(id))
-      {
-        return true;
-      }
-      return false;
-    }
-  }
-
-  private Hashtable names;
-
-  public SequenceIdMatcher(SequenceI[] seqs)
-  {
-    names = new Hashtable();
-    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());
-    if (names.containsKey(nam))
-    {
-      return (SequenceI) names.get(nam);
-    }
-    return null;
-  }
-
-  SequenceI findIdMatch(String seqnam)
-  {
-    SeqIdName nam = new SeqIdName(seqnam);
-    if (names.containsKey(nam))
-    {
-      return (SequenceI) names.get(nam);
-    }
-    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);
-        }
-        else
-        {
-          namedseqs[i] = null;
-        }
-      }
-      while (i++ < seqs.length);
-    }
-    return namedseqs;
-  }
-
-}
+ */
+public class SequenceIdMatcher {
+    private Hashtable names;
+
+    public SequenceIdMatcher(SequenceI[] seqs) {
+        names = new Hashtable();
+
+        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());
+
+        if (names.containsKey(nam)) {
+            return (SequenceI) names.get(nam);
+        }
+
+        return null;
+    }
+
+    SequenceI findIdMatch(String seqnam) {
+        SeqIdName nam = new SeqIdName(seqnam);
+
+        if (names.containsKey(nam)) {
+            return (SequenceI) names.get(nam);
+        }
+
+        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);
+                } else {
+                    namedseqs[i] = null;
+                }
+            } while (i++ < seqs.length);
+        }
+
+        return namedseqs;
+    }
+
+    private class SeqIdName {
+        String id;
+
+        SeqIdName(String s) {
+            id = new String(s);
+        }
+
+        public int hashCode() {
+            return (id.substring(0, 4).hashCode());
+        }
+
+        public boolean equals(Object s) {
+            if (s instanceof SeqIdName) {
+                return this.equals((SeqIdName) s);
+            } else {
+                if (s instanceof String) {
+                    return this.equals((String) s);
+                }
+            }
+
+            return false;
+        }
+
+        public boolean equals(SeqIdName s) {
+            if (id.startsWith(s.id) || s.id.startsWith(id)) {
+                return true;
+            }
+
+            return false;
+        }
+
+        public boolean equals(String s) {
+            if (id.startsWith(s) || s.startsWith(id)) {
+                return true;
+            }
+
+            return false;
+        }
+    }
+}
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 42643d0..42546f9 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,31 +1,33 @@
 /*
-* 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.appletgui;
 
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
 
-public class APopupMenu extends java.awt.PopupMenu
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class APopupMenu
+    extends java.awt.PopupMenu
 {
   Menu groupMenu = new Menu();
   protected MenuItem clustalColour = new MenuItem();
@@ -43,7 +45,6 @@ public class APopupMenu extends java.awt.PopupMenu
   MenuItem noColourmenuItem = new MenuItem();
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 
-
   AlignmentPanel ap;
   Menu sequenceMenu = new Menu();
   MenuItem sequenceName = new MenuItem();
@@ -68,28 +69,36 @@ public class APopupMenu extends java.awt.PopupMenu
     sequence = seq;
 
     try
-    {     jbInit();   }
-    catch(Exception e)
-    {    e.printStackTrace();    }
-
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
 
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg!=null)
+    if (sg != null)
     {
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
     }
 
-    if( !ap.av.alignment.getGroups().contains(sg))
-        groupMenu.remove(unGroupMenuItem);
-
-    if(seq==null)
-       remove(sequenceMenu);
+    if (!ap.av.alignment.getGroups().contains(sg))
+    {
+      groupMenu.remove(unGroupMenuItem);
+    }
 
+    if (seq == null)
+    {
+      remove(sequenceMenu);
+    }
 
   }
-  private void jbInit() throws Exception
+
+  private void jbInit()
+      throws Exception
   {
     groupMenu.setLabel("Group");
     groupMenu.setLabel("Define");
@@ -105,7 +114,6 @@ public class APopupMenu extends java.awt.PopupMenu
       }
     });
 
-
     nucleotideMenuItem.setLabel("Nucleotide");
     nucleotideMenuItem.addActionListener(new ActionListener()
     {
@@ -283,15 +291,16 @@ public class APopupMenu extends java.awt.PopupMenu
     });
     conservationMenuItem.setLabel("Conservation");
 
-
   }
 
   void refresh()
   {
     SequenceGroup sg = getGroup();
-    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
-    if( superG !=null)
-      superG.setSuperGroupProperties( sg );
+    SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
+    if (superG != null)
+    {
+      superG.setSuperGroupProperties(sg);
+    }
 
     ap.seqPanel.seqCanvas.repaint();
   }
@@ -315,7 +324,6 @@ public class APopupMenu extends java.awt.PopupMenu
     refresh();
   }
 
-
   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
     getGroup().cs = new HydrophobicColourScheme();
@@ -352,8 +360,6 @@ public class APopupMenu extends java.awt.PopupMenu
     refresh();
   }
 
-
-
   protected void abovePIDColour_itemStateChanged(ItemEvent ie)
   {
     SequenceGroup sg = getGroup();
@@ -361,15 +367,19 @@ public class APopupMenu extends java.awt.PopupMenu
     {
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
                                                ap.av.alignment.getWidth()));
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+          getGroup().getName());
       if (sg.cs instanceof ResidueColourScheme)
-        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
+      {
+        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+      }
       else if (sg.cs instanceof ScoreColourScheme)
+      {
         ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+      }
 
       SliderPanel.showPIDSlider();
 
-
     }
     else // remove PIDColouring
     {
@@ -382,10 +392,9 @@ public class APopupMenu extends java.awt.PopupMenu
 
   }
 
-
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    new UserDefinedColours( ap, getGroup());
+    new UserDefinedColours(ap, getGroup());
   }
 
   protected void PIDColour_actionPerformed(ActionEvent e)
@@ -393,7 +402,7 @@ public class APopupMenu extends java.awt.PopupMenu
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+                                             ap.av.alignment.getWidth()));
     refresh();
   }
 
@@ -404,34 +413,32 @@ public class APopupMenu extends java.awt.PopupMenu
     sg.cs = new Blosum62ColourScheme();
 
     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+                                             ap.av.alignment.getWidth()));
 
     refresh();
   }
 
-
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
     getGroup().cs = null;
     refresh();
   }
 
-  protected  void conservationMenuItem_itemStateChanged(ItemEvent ie)
+  protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
   {
     SequenceGroup sg = getGroup();
 
-    if(conservationMenuItem.getState())
+    if (conservationMenuItem.getState())
     {
 
-        Conservation c = new Conservation("Group",
-                                          ResidueProperties.propHash, 3,
-                                          sg.sequences, 0,
-                                          ap.av.alignment.getWidth());
-
-        c.calculate();
-        c.verdict(false, ap.av.ConsPercGaps);
-        ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3,
+                                        sg.sequences, 0,
+                                        ap.av.alignment.getWidth());
 
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
+      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
       sg.cs = ccs;
 
@@ -440,32 +447,31 @@ public class APopupMenu extends java.awt.PopupMenu
     }
     else // remove ConservationColouring
     {
-        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-        sg.cs = ccs.cs;
+      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
+      sg.cs = ccs.cs;
     }
 
-     refresh();
+    refresh();
   }
 
-
   protected void analyze_actionPerformed(ActionEvent e)
   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     Frame frame = new Frame();
-     frame.add(cap);
-     jalview.bin.JalviewLite.addFrame(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.elementAt(i);
-       sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
-       sb.append("\n");
-     }
-
-     sb.append("Something amazing will happen soon");
-     cap.setText( sb.toString() );
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(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.elementAt(i);
+      sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
+      sb.append("\n");
+    }
+
+    sb.append("Something amazing will happen soon");
+    cap.setText(sb.toString());
 
   }
 
@@ -481,13 +487,12 @@ public class APopupMenu extends java.awt.PopupMenu
 
   void unGroupMenuItem_actionPerformed(ActionEvent e)
   {
-     SequenceGroup sg = ap.av.getSelectionGroup();
-     ap.av.alignment.deleteGroup(sg);
-     ap.av.setSelectionGroup(null);
-     ap.repaint();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    ap.repaint();
   }
 
-
   public void showColourText_itemStateChanged(ItemEvent itemEvent)
   {
     getGroup().setColourText(showColourText.getState());
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 7d0c985..2783f26 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.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.appletgui;
 
@@ -28,11 +28,11 @@ import java.awt.*;
 import java.awt.event.*;
 import java.util.*;
 
-
-public class AlignFrame extends GAlignFrame
+public class AlignFrame
+    extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
-  final AlignViewport  viewport;
+  final AlignViewport viewport;
   public static final int NEW_WINDOW_WIDTH = 700;
   public static final int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
@@ -61,14 +61,15 @@ public class AlignFrame extends GAlignFrame
       try
       {
         treeFile = treeFile;
-        jalview.io.NewickFile fin = new jalview.io.NewickFile( applet.getCodeBase()+treeFile, "URL");
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+            getCodeBase() + treeFile, "URL");
         fin.parse();
 
         if (fin.getTree() != null)
         {
           TreePanel tp = null;
           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", applet.getCodeBase()+treeFile);
+                             fin, "FromFile", applet.getCodeBase() + treeFile);
           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
           addTreeMenuItem(tp, treeFile);
         }
@@ -79,25 +80,27 @@ public class AlignFrame extends GAlignFrame
       }
     }
 
-
   }
 
   public void inputText_actionPerformed(ActionEvent e)
   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
-     Frame frame = new Frame();
-     frame.add(cap);
-     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500,500);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
   }
 
-
   protected void outputText_actionPerformed(ActionEvent e)
   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     Frame frame = new Frame();
-     frame.add(cap);
-     jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);
-     cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame,
+                                     "Alignment output - " + e.getActionCommand(),
+                                     600, 500);
+    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+                                              viewport.getAlignment().
+                                              getSequences()));
   }
 
   public void closeMenuItem_actionPerformed(ActionEvent e)
@@ -109,100 +112,109 @@ public class AlignFrame extends GAlignFrame
   Stack redoList = new Stack();
 
   void updateEditMenuBar()
-   {
-     if(historyList.size()>0)
-      {
-        undoMenuItem.setEnabled(true);
-        HistoryItem hi = (HistoryItem)historyList.peek();
-        undoMenuItem.setLabel("Undo "+hi.getDescription());
-      }
-     else
-     {
-       undoMenuItem.setEnabled(false);
-       undoMenuItem.setLabel("Undo");
-     }
+  {
+    if (historyList.size() > 0)
+    {
+      undoMenuItem.setEnabled(true);
+      HistoryItem hi = (HistoryItem) historyList.peek();
+      undoMenuItem.setLabel("Undo " + hi.getDescription());
+    }
+    else
+    {
+      undoMenuItem.setEnabled(false);
+      undoMenuItem.setLabel("Undo");
+    }
 
-     if(redoList.size()>0)
-      {
-        redoMenuItem.setEnabled(true);
-        HistoryItem hi = (HistoryItem)redoList.peek();
-        redoMenuItem.setLabel("Redo "+hi.getDescription());
-      }
-     else
-     {
-       redoMenuItem.setEnabled(false);
-       redoMenuItem.setLabel("Redo");
-     }
-   }
-
-   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();
-   }
+    if (redoList.size() > 0)
+    {
+      redoMenuItem.setEnabled(true);
+      HistoryItem hi = (HistoryItem) redoList.peek();
+      redoMenuItem.setLabel("Redo " + hi.getDescription());
+    }
+    else
+    {
+      redoMenuItem.setEnabled(false);
+      redoMenuItem.setLabel("Redo");
+    }
+  }
+
+  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)
+  // used by undo and redo
+  void restoreHistoryItem(HistoryItem hi)
+  {
+    if (hi.getType() == HistoryItem.SORT)
+    {
+      for (int i = 0; i < hi.getSequences().size(); i++)
       {
-           for(int i=0; i<hi.getSequences().size(); i++)
-             viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
+        viewport.alignment.getSequences().setElementAt(hi.getSequences().
+            elementAt(i), i);
       }
-      else
+    }
+    else
+    {
+      for (int i = 0; i < hi.getSequences().size(); i++)
       {
-        for (int i = 0; i < hi.getSequences().size(); i++)
+        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
+        if (restore.getLength() == 0)
         {
-          SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
-          if(restore.getLength()==0)
-          {
-            // log.System.out.println(hi.getHidden().elementAt(i));
-            restore.setSequence(hi.getHidden().elementAt(i).toString());
-            viewport.alignment.getSequences().insertElementAt(
-               restore,
-               hi.getAlignIndex(i));
-          }
-          else
-            restore.setSequence(hi.getHidden().elementAt(i).toString());
+          // log.System.out.println(hi.getHidden().elementAt(i));
+          restore.setSequence(hi.getHidden().elementAt(i).toString());
+          viewport.alignment.getSequences().insertElementAt(
+              restore,
+              hi.getAlignIndex(i));
         }
-        if(hi.getType()==HistoryItem.PASTE)
+        else
         {
-          for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
-            viewport.alignment.deleteSequence(i);
+          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();
-   }
+    updateEditMenuBar();
 
+    viewport.updateConsensus();
+    viewport.updateConservation();
+    alignPanel.repaint();
+  }
 
   public void moveSelectedSequences(boolean up)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
     if (sg == null)
+    {
       return;
+    }
 
     if (up)
     {
@@ -210,11 +222,15 @@ public class AlignFrame extends GAlignFrame
       {
         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);
@@ -226,11 +242,15 @@ public class AlignFrame extends GAlignFrame
       {
         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);
@@ -240,47 +260,52 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();
   }
 
-
   StringBuffer copiedSequences;
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getSelectionGroup()==null)
-     return;
+    if (viewport.getSelectionGroup() == null)
+    {
+      return;
+    }
 
-   SequenceGroup sg = viewport.getSelectionGroup();
-   copiedSequences = new StringBuffer();
-   Hashtable orderedSeqs = new Hashtable();
-   for(int i=0; i<sg.getSize(); i++)
-   {
+    SequenceGroup sg = viewport.getSelectionGroup();
+    copiedSequences = new StringBuffer();
+    Hashtable orderedSeqs = new Hashtable();
+    for (int i = 0; i < sg.getSize(); i++)
+    {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.alignment.findIndex(seq);
-      orderedSeqs.put(index+"", seq);
-   }
+      orderedSeqs.put(index + "", seq);
+    }
 
-   int index=0;
-   for(int i=0; i<sg.getSize(); i++)
-   {
-     SequenceI seq = null;
-     while( seq == null )
-     {
-       if(orderedSeqs.containsKey(index+""))
-       {
-         seq = (SequenceI) orderedSeqs.get(index + "");
-         index++;
-         break;
-       }
-       else
-         index++;
-     }
+    int index = 0;
+    for (int i = 0; i < sg.getSize(); i++)
+    {
+      SequenceI seq = null;
+      while (seq == null)
+      {
+        if (orderedSeqs.containsKey(index + ""))
+        {
+          seq = (SequenceI) orderedSeqs.get(index + "");
+          index++;
+          break;
+        }
+        else
+        {
+          index++;
+        }
+      }
 
-         copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
-                        +seq.findPosition( sg.getEndRes() )+ "\t"
-                        +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
-       }
+      copiedSequences.append(seq.getName() + "\t" +
+                             seq.findPosition(sg.getStartRes()) + "\t"
+                             + seq.findPosition(sg.getEndRes()) + "\t"
+                             +
+                             sg.getSequenceAt(i).getSequence(sg.getStartRes(),
+          sg.getEndRes() + 1) + "\n");
+    }
 
   }
 
-
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
     paste(true);
@@ -288,15 +313,19 @@ public class AlignFrame extends GAlignFrame
 
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
-    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
+    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+                                   HistoryItem.PASTE));
     paste(false);
   }
 
   void paste(boolean newAlignment)
   {
-    try{
+    try
+    {
       if (copiedSequences == null)
+      {
         return;
+      }
 
       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
       Vector seqs = new Vector();
@@ -305,27 +334,38 @@ public class AlignFrame extends GAlignFrame
         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);
+        Sequence sequence = new Sequence(name, st.nextToken(), start, end);
 
-        if(!newAlignment)
+        if (!newAlignment)
+        {
           viewport.alignment.addSequence(sequence);
+        }
         else
+        {
           seqs.addElement(sequence);
+        }
       }
 
-      if(newAlignment)
+      if (newAlignment)
       {
         SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        for(int i=0; i<seqs.size(); i++)
-         newSeqs[i] = (SequenceI)seqs.elementAt(i);
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          newSeqs[i] = (SequenceI) seqs.elementAt(i);
+        }
 
         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
         String newtitle = new String("Copied sequences");
-        if( getTitle().startsWith("Copied sequences"))
-         newtitle = getTitle();
-       else
-         newtitle = newtitle.concat("- from "+getTitle());
-        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+        if (getTitle().startsWith("Copied sequences"))
+        {
+          newtitle = getTitle();
+        }
+        else
+        {
+          newtitle = newtitle.concat("- from " + getTitle());
+        }
+        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
+                                         NEW_WINDOW_HEIGHT);
       }
       else
       {
@@ -336,11 +376,12 @@ public class AlignFrame extends GAlignFrame
         alignPanel.repaint();
       }
 
-    }catch(Exception ex){}// could be anything being pasted in here
+    }
+    catch (Exception ex)
+    {} // could be anything being pasted in here
 
   }
 
-
   protected void cut_actionPerformed(ActionEvent e)
   {
     copy_actionPerformed(null);
@@ -349,39 +390,48 @@ public class AlignFrame extends GAlignFrame
 
   protected void delete_actionPerformed(ActionEvent e)
   {
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                                   HistoryItem.HIDE));
     if (viewport.getSelectionGroup() == null)
+    {
       return;
+    }
 
-     SequenceGroup sg = viewport.getSelectionGroup();
-     for (int i=0;i < sg.sequences.size(); i++)
-     {
-       SequenceI seq = sg.getSequenceAt(i);
-       int index = viewport.getAlignment().findIndex(seq);
-       seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
+    SequenceGroup sg = viewport.getSelectionGroup();
+    for (int i = 0; i < sg.sequences.size(); i++)
+    {
+      SequenceI seq = sg.getSequenceAt(i);
+      int index = viewport.getAlignment().findIndex(seq);
+      seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
-       if(seq.getSequence().length()<1)
-          viewport.getAlignment().deleteSequence(seq);
+      if (seq.getSequence().length() < 1)
+      {
+        viewport.getAlignment().deleteSequence(seq);
+      }
       else
-          viewport.getAlignment().getSequences().setElementAt(seq, index);
-     }
+      {
+        viewport.getAlignment().getSequences().setElementAt(seq, index);
+      }
+    }
 
-     viewport.setSelectionGroup(null);
-     viewport.alignment.deleteGroup(sg);
-     viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);
-     if(viewport.getAlignment().getHeight()<1)
-     try
-     {
-       this.setVisible(false);
-     }catch(Exception ex){}
-   viewport.updateConservation();
-   viewport.updateConsensus();
-     alignPanel.repaint();
+    viewport.setSelectionGroup(null);
+    viewport.alignment.deleteGroup(sg);
+    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
+    if (viewport.getAlignment().getHeight() < 1)
+    {
+      try
+      {
+        this.setVisible(false);
+      }
+      catch (Exception ex)
+      {}
+    }
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
 
   }
 
-
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
@@ -390,13 +440,13 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();
   }
 
-
-
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = new SequenceGroup();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
+    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+    {
+      sg.addSequence(viewport.getAlignment().getSequenceAt(i));
+    }
     sg.setEndRes(viewport.alignment.getWidth());
     viewport.setSelectionGroup(sg);
     alignPanel.repaint();
@@ -414,8 +464,10 @@ public class AlignFrame extends GAlignFrame
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
+    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+    {
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));
+    }
 
     PaintRefresher.Refresh(null);
   }
@@ -425,21 +477,25 @@ public class AlignFrame extends GAlignFrame
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel.size() > 0)
     {
-      addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
+      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
                                      HistoryItem.HIDE));
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0,min);
+      colSel.compensateForEdit(0, min);
 
-      if(viewport.getSelectionGroup()!=null)
+      if (viewport.getSelectionGroup() != null)
+      {
         viewport.getSelectionGroup().adjustForRemoveLeft(min);
+      }
 
       Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if(!sg.adjustForRemoveLeft(min))
+        if (!sg.adjustForRemoveLeft(min))
+        {
           viewport.alignment.deleteGroup(sg);
+        }
       }
 
       alignPanel.repaint();
@@ -451,23 +507,25 @@ public class AlignFrame extends GAlignFrame
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel.size() > 0)
     {
-      addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
+      addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
                                      HistoryItem.HIDE));
       int max = colSel.getMax();
       viewport.getAlignment().trimRight(max);
-      if(viewport.getSelectionGroup()!=null)
+      if (viewport.getSelectionGroup() != null)
+      {
         viewport.getSelectionGroup().adjustForRemoveRight(max);
+      }
 
       Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if(!sg.adjustForRemoveRight(max))
+        if (!sg.adjustForRemoveRight(max))
+        {
           viewport.alignment.deleteGroup(sg);
+        }
       }
 
-
-
       alignPanel.repaint();
     }
 
@@ -491,59 +549,59 @@ public class AlignFrame extends GAlignFrame
                                    HistoryItem.HIDE));
     SequenceI current;
     int jSize;
-    for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
+    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
     {
       current = viewport.getAlignment().getSequenceAt(i);
       jSize = current.getLength();
-      for (int j=0; j < jSize; j++)
-        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
+      for (int j = 0; j < jSize; j++)
+      {
+        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
           current.deleteCharAt(j);
           j--;
           jSize--;
         }
+      }
     }
     viewport.updateConservation();
     viewport.updateConsensus();
     alignPanel.repaint();
   }
 
-
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     Finder finder = new Finder(alignPanel);
   }
 
-
   public void font_actionPerformed(ActionEvent e)
   {
     Frame frame = new Frame();
-    FontChooser fc = new FontChooser( alignPanel, frame);
+    FontChooser fc = new FontChooser(alignPanel, frame);
     frame.add(fc);
-    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);
+    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
 
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
   {
-    viewport.setShowFullId( fullSeqId.getState() );
+    viewport.setShowFullId(fullSeqId.getState());
     alignPanel.fontChanged();
     alignPanel.repaint();
   }
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-      viewport.setColourText( colourTextMenuItem.getState() );
-      alignPanel.repaint();
+    viewport.setColourText(colourTextMenuItem.getState());
+    alignPanel.repaint();
   }
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setWrapAlignment( wrapMenuItem.getState() );
-    alignPanel.setWrapAlignment( wrapMenuItem.getState() );
-    scaleAbove.setEnabled( wrapMenuItem.getState() );
-    scaleLeft.setEnabled( wrapMenuItem.getState());
-    scaleRight.setEnabled( wrapMenuItem.getState());
+    viewport.setWrapAlignment(wrapMenuItem.getState());
+    alignPanel.setWrapAlignment(wrapMenuItem.getState());
+    scaleAbove.setEnabled(wrapMenuItem.getState());
+    scaleLeft.setEnabled(wrapMenuItem.getState());
+    scaleRight.setEnabled(wrapMenuItem.getState());
     alignPanel.repaint();
   }
 
@@ -565,74 +623,73 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();
   }
 
-
-
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowBoxes( viewBoxesMenuItem.getState() );
+    viewport.setShowBoxes(viewBoxesMenuItem.getState());
     alignPanel.repaint();
   }
 
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowText( viewTextMenuItem.getState() );
+    viewport.setShowText(viewTextMenuItem.getState());
     alignPanel.repaint();
   }
 
-
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.getState());
     alignPanel.repaint();
   }
 
-
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
+    if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
     {
       annotationPanelMenuItem.setState(false);
       return;
     }
-    viewport.setShowAnnotation( annotationPanelMenuItem.getState() );
-    alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );
+    viewport.setShowAnnotation(annotationPanelMenuItem.getState());
+    alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
-   if (alignPanel.overviewPanel != null)
+    if (alignPanel.overviewPanel != null)
+    {
       return;
+    }
 
     Frame frame = new Frame();
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.add(overview);
     // +50 must allow for applet frame window
     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
-                             overview.preferredSize().width, overview.preferredSize().height+50);
+                                     overview.preferredSize().width,
+                                     overview.preferredSize().height + 50);
 
     frame.pack();
     frame.addWindowListener(new WindowAdapter()
-    { public void windowClosing(WindowEvent e)
+    {
+      public void windowClosing(WindowEvent e)
       {
-            alignPanel.setOverviewPanel(null);
+        alignPanel.setOverviewPanel(null);
       };
     });
 
-    alignPanel.setOverviewPanel( overview );
-
+    alignPanel.setOverviewPanel(overview);
 
   }
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    changeColour( null );
+    changeColour(null);
   }
 
-
   public void clustalColour_actionPerformed(ActionEvent e)
   {
     abovePIDThreshold.setState(false);
-    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
+                                          viewport.alignment.getWidth()));
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
@@ -645,33 +702,29 @@ public class AlignFrame extends GAlignFrame
     changeColour(new TaylorColourScheme());
   }
 
-
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    changeColour( new HydrophobicColourScheme() );
+    changeColour(new HydrophobicColourScheme());
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new HelixColourScheme() );
+    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() );
+    changeColour(new BuriedColourScheme());
   }
 
   public void nucleotideColour_actionPerformed(ActionEvent e)
@@ -679,35 +732,38 @@ public class AlignFrame extends GAlignFrame
     changeColour(new NucleotideColourScheme());
   }
 
-
   protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
   }
 
-
-
   void changeColour(ColourSchemeI cs)
   {
     int threshold = 0;
 
-    if ( viewport.getAbovePIDThreshold() )
+    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);
-
-
+    }
 
     if (viewport.getConservationSelected())
     {
@@ -725,7 +781,7 @@ public class AlignFrame extends GAlignFrame
       ccs = new ConservationColourScheme(c, cs);
 
       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus( viewport.vconsensus );
+      ccs.setConsensus(viewport.vconsensus);
       viewport.setGlobalColourScheme(ccs);
 
       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
@@ -733,25 +789,27 @@ public class AlignFrame extends GAlignFrame
     }
     else
     {
-        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-        if (cs != null)
-          cs.setConsensus(viewport.vconsensus);
-        viewport.setGlobalColourScheme(cs);
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      if (cs != null)
+      {
+        cs.setConsensus(viewport.vconsensus);
+      }
+      viewport.setGlobalColourScheme(cs);
     }
 
-
-    if(viewport.getColourAppliesToAllGroups())
+    if (viewport.getColourAppliesToAllGroups())
     {
       Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
         if (cs instanceof ClustalxColourScheme)
         {
           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
         else
+        {
           try
           {
             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
@@ -761,28 +819,34 @@ public class AlignFrame extends GAlignFrame
             ex.printStackTrace();
             sg.cs = cs;
           }
+        }
 
-        if(viewport.getAbovePIDThreshold())
+        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()) );
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
         }
 
-        if( viewport.getConservationSelected() )
+        if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.sequences, 0, viewport.alignment.getWidth()-1);
+                                            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()));
+          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
           sg.cs = ccs;
         }
         else
@@ -794,25 +858,27 @@ public class AlignFrame extends GAlignFrame
       }
     }
 
-    if(alignPanel.getOverviewPanel()!=null)
+    if (alignPanel.getOverviewPanel() != null)
+    {
       alignPanel.getOverviewPanel().updateOverviewImage();
+    }
 
     alignPanel.repaint();
   }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-      if(viewport.getAbovePIDThreshold())
-      {
-        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
-                                   "Background");
-        SliderPanel.showPIDSlider();
-      }
+    if (viewport.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+                                     "Background");
+      SliderPanel.showPIDSlider();
+    }
   }
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if(viewport.getConservationSelected())
+    if (viewport.getConservationSelected())
     {
       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
                                         "Background");
@@ -820,19 +886,22 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
-
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.getState());
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setState(false);
 
-   ColourSchemeI cs = viewport.getGlobalColourScheme();
-   if(cs instanceof ConservationColourScheme )
-     changeColour( ((ConservationColourScheme)cs).cs );
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
+    if (cs instanceof ConservationColourScheme)
+    {
+      changeColour( ( (ConservationColourScheme) cs).cs);
+    }
     else
-      changeColour( cs );
+    {
+      changeColour(cs);
+    }
 
     modifyConservation_actionPerformed(null);
   }
@@ -846,51 +915,54 @@ public class AlignFrame extends GAlignFrame
 
     ColourSchemeI cs = viewport.getGlobalColourScheme();
 
-    if(cs instanceof ConservationColourScheme )
-        changeColour( ((ConservationColourScheme)cs).cs );
+    if (cs instanceof ConservationColourScheme)
+    {
+      changeColour( ( (ConservationColourScheme) cs).cs);
+    }
     else
-        changeColour( cs );
+    {
+      changeColour(cs);
+    }
 
     modifyPID_actionPerformed(null);
   }
 
-
-
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
+    UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    changeColour( new PIDColourScheme() );
+    changeColour(new PIDColourScheme());
   }
 
-
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme() );
+    changeColour(new Blosum62ColourScheme());
   }
 
-
-
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
-    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
+    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
+                                   HistoryItem.SORT));
+    AlignmentSorter.sortByPID(viewport.getAlignment(),
+                              viewport.getAlignment().getSequenceAt(0));
     alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
-    AlignmentSorter.sortByID( viewport.getAlignment() );
+    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+                                   HistoryItem.SORT));
+    AlignmentSorter.sortByID(viewport.getAlignment());
     alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
+    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+                                   HistoryItem.SORT));
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
     alignPanel.repaint();
@@ -901,13 +973,14 @@ public class AlignFrame extends GAlignFrame
     RedundancyPanel sp = new RedundancyPanel(alignPanel);
     Frame frame = new Frame();
     frame.add(sp);
-    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);
+    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
+                                     400, 120);
 
   }
 
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelectionGroup().getSize()>1)
+    if (viewport.getSelectionGroup().getSize() > 1)
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(viewport));
@@ -918,21 +991,25 @@ public class AlignFrame extends GAlignFrame
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
 
-    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
-       || viewport.getAlignment().getHeight()<4)
+    if ( (viewport.getSelectionGroup() != null &&
+          viewport.getSelectionGroup().getSize() < 4 &&
+          viewport.getSelectionGroup().getSize() > 0)
+        || viewport.getAlignment().getHeight() < 4)
     {
       return;
     }
 
-    try{
+    try
+    {
       PCAPanel pcaPanel = new PCAPanel(viewport, null);
       Frame frame = new Frame();
       frame.add(pcaPanel);
-      jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);
-   }catch(java.lang.OutOfMemoryError ex)
-   {
-   }
-
+      jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
+                                       400, 400);
+    }
+    catch (java.lang.OutOfMemoryError ex)
+    {
+    }
 
   }
 
@@ -946,7 +1023,6 @@ public class AlignFrame extends GAlignFrame
     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
   }
 
-
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
@@ -960,7 +1036,7 @@ public class AlignFrame extends GAlignFrame
   void NewTreePanel(String type, String pwType, String title)
   {
     //are the sequences aligned?
-    if(!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned())
     {
       return;
     }
@@ -979,9 +1055,9 @@ public class AlignFrame extends GAlignFrame
                          type, pwType, 0, viewport.alignment.getWidth());
     }
 
-   addTreeMenuItem(tp, title);
+    addTreeMenuItem(tp, title);
 
-   jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
   }
 
   void addTreeMenuItem(final TreePanel treePanel, String title)
@@ -1008,7 +1084,8 @@ public class AlignFrame extends GAlignFrame
     });
   }
 
-  protected void documentation_actionPerformed(ActionEvent e) {
+  protected void documentation_actionPerformed(ActionEvent e)
+  {
 
     jalview.bin.JalviewLite.showURL("http://www.jalview.org");
 
@@ -1016,33 +1093,38 @@ public class AlignFrame extends GAlignFrame
 
   protected void about_actionPerformed(ActionEvent e)
   {
-    class AboutPanel extends Canvas
+    class AboutPanel
+        extends Canvas
     {
       public void paint(Graphics g)
       {
         g.setColor(Color.white);
-        g.fillRect(0,0,getSize().width, getSize().height);
+        g.fillRect(0, 0, getSize().width, getSize().height);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
         FontMetrics fm = g.getFontMetrics();
         int fh = fm.getHeight();
-        int y=5, x=7;
+        int y = 5, x = 7;
         g.setColor(Color.black);
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString("JalView - Release 2.0", 200,y+=fh);
+        g.drawString("JalView - Release 2.0", 200, y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
-        g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);
-        g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);
-        g.drawString("For any issues relating to Jalview, email help@jalview.org", x,y+=fh);
-        g.drawString("If  you use JalView, please cite:",x,y+=fh+8);
-        g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);
-        g.drawString("Bioinformatics,  2004 12;426-7.",x,y+=fh);
+        g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
+                     x, y += fh * 2);
+        g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
+                     x, y += fh);
+        g.drawString(
+            "For any issues relating to Jalview, email help@jalview.org", x,
+            y += fh);
+        g.drawString("If  you use JalView, please cite:", x, y += fh + 8);
+        g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
+                     x, y += fh);
+        g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);
       }
     }
+
     Frame frame = new Frame();
     frame.add(new AboutPanel());
-    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);
-
-
+    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
 
   }
 }
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index bdc2359..51478f2 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,30 +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.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
-import jalview.bin.*;
+
 import jalview.analysis.*;
+import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.util.*;
 
 public class AlignViewport
 {
@@ -35,10 +37,10 @@ public class AlignViewport
   int endSeq;
 
   boolean showFullId = true;
-  boolean showText=true;
-  boolean showColourText=false;
-  boolean showBoxes=true;
-  boolean wrapAlignment=false;
+  boolean showText = true;
+  boolean showColourText = false;
+  boolean showBoxes = true;
+  boolean wrapAlignment = false;
   boolean renderGaps = true;
   boolean showSequenceFeatures = false;
   boolean showAnnotation = true;
@@ -53,13 +55,13 @@ public class AlignViewport
 
   SequenceGroup selectionGroup = new SequenceGroup();
 
-  int             charHeight;
-  int             charWidth;
-  int             chunkWidth;
-  int             chunkHeight;
+  int charHeight;
+  int charWidth;
+  int chunkWidth;
+  int chunkHeight;
 
-  Font            font = new Font("SansSerif",Font.PLAIN,10);
-  AlignmentI      alignment;
+  Font font = new Font("SansSerif", Font.PLAIN, 10);
+  AlignmentI alignment;
 
   ColumnSelection colSel = new ColumnSelection();
 
@@ -69,60 +71,70 @@ public class AlignViewport
   NJTree currentTree = null;
 
   boolean scaleAboveWrapped = true;
-  boolean scaleLeftWrapped  = true;
+  boolean scaleLeftWrapped = true;
   boolean scaleRightWrapped = true;
 
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     setAlignment(al);
     this.startRes = 0;
-    this.endRes = al.getWidth()-1;
+    this.endRes = al.getWidth() - 1;
     this.startSeq = 0;
-    this.endSeq = al.getHeight()-1;
+    this.endSeq = al.getHeight() - 1;
     setFont(font);
 
-
-    if(applet!=null)
+    if (applet != null)
     {
       String param = applet.getParameter("showFullId");
       if (param != null)
+      {
         showFullId = Boolean.valueOf(param).booleanValue();
+      }
 
       param = applet.getParameter("showAnnotation");
       if (param != null)
+      {
         showAnnotation = Boolean.valueOf(param).booleanValue();
+      }
 
       param = applet.getParameter("showConservation");
       if (param != null)
+      {
         showConservation = Boolean.valueOf(param).booleanValue();
+      }
 
       param = applet.getParameter("showQuality");
       if (param != null)
+      {
         showQuality = Boolean.valueOf(param).booleanValue();
+      }
 
       param = applet.getParameter("showConsensus");
       if (param != null)
+      {
         showConsensus = Boolean.valueOf(param).booleanValue();
+      }
     }
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
     updateConservation();
     updateConsensus();
 
-    if(applet!=null && applet.getParameter("defaultColour")!=null)
+    if (applet != null && applet.getParameter("defaultColour") != null)
     {
       globalColourScheme = ColourSchemeProperty.getColour(alignment,
           applet.getParameter("defaultColour"));
-      if(globalColourScheme!=null)
-        globalColourScheme.setConsensus( vconsensus );
-   }
- }
-
+      if (globalColourScheme != null)
+      {
+        globalColourScheme.setConsensus(vconsensus);
+      }
+    }
+  }
 
- public void showSequenceFeatures(boolean b)
- {
-   showSequenceFeatures = b;
- }
+  public void showSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
 
   public Vector vconsensus;
   AlignmentAnnotation consensus;
@@ -136,19 +148,21 @@ public class AlignViewport
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
-        alignment.getWidth()-1);
+        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];
+    Annotation[] annotations = new Annotation[alWidth];
+    Annotation[] qannotations = new Annotation[alWidth];
     String sequence = cons.getConsSequence().getSequence();
-    float minR,minG,minB, maxR,maxG,maxB;
+    float minR, minG, minB, maxR, maxG, maxB;
     minR = 0.3f;
     minG = 0.0f;
     minB = 0f;
-    maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality
+    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();
@@ -158,108 +172,131 @@ public class AlignViewport
     {
       float value = 0;
       try
+      {
+        value = Integer.parseInt(sequence.charAt(i) + "");
+      }
+      catch (Exception ex)
+      {
+        if (sequence.charAt(i) == '*')
         {
-          value = Integer.parseInt(sequence.charAt(i) + "");
+          value = 11;
         }
-      catch (Exception ex)
+        if (sequence.charAt(i) == '+')
         {
-          if (sequence.charAt(i) == '*') value = 11;
-          if (sequence.charAt(i) == '+') value = 10;
+          value = 10;
         }
-      float vprop = value-min;
-      vprop/=max;
+      }
+      float vprop = value - min;
+      vprop /= max;
 
       annotations[i] = new Annotation(sequence.charAt(i) + "",
-                                      "", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+                                      "", ' ', value,
+                                      new Color(minR + maxR * vprop,
+                                                minG + maxG * vprop,
+                                                minB + maxB * vprop));
       // Quality calc
-      value = ((Double) cons.quality.elementAt(i)).floatValue();
+      value = ( (Double) cons.quality.elementAt(i)).floatValue();
       vprop = value - qmin;
-      vprop/=qmax;
+      vprop /= qmax;
       qannotations[i] = new Annotation(" ",
-                                      String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+                                       String.valueOf(value), ' ', value,
+                                       new
+                                       Color(minR + maxR * vprop,
+                                             minG + maxG * vprop,
+                                             minB + maxB * vprop));
     }
 
-    if(conservation==null)
+    if (conservation == null)
     {
       conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than "+ConsPercGaps+"% gaps",
+                                             "Conservation of total alignment less than " +
+                                             ConsPercGaps + "% gaps",
                                              annotations,
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
                                              1);
-      if(showConservation)
-      alignment.addAnnotation(conservation);
+      if (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)
+      if (showQuality)
+      {
         alignment.addAnnotation(quality);
+      }
     }
-    else {
+    else
+    {
       conservation.annotations = annotations;
       quality.annotations = qannotations;
       quality.graphMax = cons.qualityRange[1].floatValue();
     }
 
-
   }
 
   public void updateConsensus()
   {
-    Annotation [] annotations = new Annotation[alignment.getWidth()];
+    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();
+    if (vconsensus == null)
+    {
+      vconsensus = alignment.getAAFrequency();
+    }
     else
     {
-        Vector temp = alignment.getAAFrequency();
-        vconsensus.removeAllElements();
-        Enumeration e = temp.elements();
-        while(e.hasMoreElements())
-        {
-          vconsensus.addElement(e.nextElement());
-        }
+      Vector temp = alignment.getAAFrequency();
+      vconsensus.removeAllElements();
+      Enumeration e = temp.elements();
+      while (e.hasMoreElements())
+      {
+        vconsensus.addElement(e.nextElement());
+      }
     }
     Hashtable hash = null;
-    for (int i = 0; i<alignment.getWidth(); i++)
+    for (int i = 0; i < alignment.getWidth(); i++)
     {
-        hash = (Hashtable) vconsensus.elementAt(i);
-        float value = new Float(hash.get("maxCount").toString()).floatValue();
-        value /= new Float(hash.get("size").toString()).floatValue();
-
-        value *= 100;
-        String maxRes = hash.get("maxResidue")+" ";
-        String mouseOver = hash.get("maxResidue")+" ";
-        if(maxRes.length()>2)
-        {
-          mouseOver = "["+maxRes+"] ";
-          maxRes = "+ ";
-        }
+      hash = (Hashtable) vconsensus.elementAt(i);
+      float value = new Float(hash.get("maxCount").toString()).floatValue();
+      value /= new Float(hash.get("size").toString()).floatValue();
+
+      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);
+      mouseOver += (int) value + "%";
+      annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
 
     }
 
-     if(consensus==null)
-     {
-       consensus = new AlignmentAnnotation("Consensus",
-                                           "PID", annotations, 0f, 100f, 1);
-       if(showConsensus)
-         alignment.addAnnotation(consensus);
-     }
-     else
-       consensus.annotations = annotations;
+    if (consensus == null)
+    {
+      consensus = new AlignmentAnnotation("Consensus",
+                                          "PID", annotations, 0f, 100f, 1);
+      if (showConsensus)
+      {
+        alignment.addAnnotation(consensus);
+      }
+    }
+    else
+    {
+      consensus.annotations = annotations;
+    }
 
   }
 
-
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -270,42 +307,44 @@ public class AlignViewport
     selectionGroup = sg;
   }
 
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
 
- public boolean getConservationSelected()
- {
-   return conservationColourSelected;
- }
-
- public void setConservationSelected(boolean b)
- {
-   conservationColourSelected = b;
- }
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
 
- public boolean getAbovePIDThreshold()
- {
-   return abovePIDThreshold;
- }
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
 
- public void setAbovePIDThreshold(boolean b)
- {
-   abovePIDThreshold = b;
- }
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
 
-  public int getStartRes() {
+  public int getStartRes()
+  {
     return startRes;
   }
 
-  public int getEndRes() {
+  public int getEndRes()
+  {
     return endRes;
   }
 
-  public int getStartSeq() {
+  public int getStartSeq()
+  {
     return startSeq;
   }
 
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
-     globalColourScheme = cs;
+    globalColourScheme = cs;
   }
 
   public ColourSchemeI getGlobalColourScheme()
@@ -313,37 +352,50 @@ public class AlignViewport
     return globalColourScheme;
   }
 
-
-  public void setStartRes(int res) {
+  public void setStartRes(int res)
+  {
     this.startRes = res;
   }
-  public void setStartSeq(int seq) {
+
+  public void setStartSeq(int seq)
+  {
     this.startSeq = seq;
   }
-  public void setEndRes(int res) {
-    if (res > alignment.getWidth()-1) {
+
+  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;
+      res = alignment.getWidth() - 1;
     }
-    if (res < 0) {
+    if (res < 0)
+    {
       res = 0;
     }
     this.endRes = res;
   }
-  public void setEndSeq(int seq) {
-    if (seq > alignment.getHeight()) {
+
+  public void setEndSeq(int seq)
+  {
+    if (seq > alignment.getHeight())
+    {
       seq = alignment.getHeight();
     }
-    if (seq < 0) {
+    if (seq < 0)
+    {
       seq = 0;
     }
     this.endSeq = seq;
   }
-  public int getEndSeq() {
+
+  public int getEndSeq()
+  {
     return endSeq;
   }
 
-  public void setFont(Font f) {
+  public void setFont(Font f)
+  {
     font = f;
     java.awt.Frame temp = new java.awt.Frame();
     temp.addNotify();
@@ -352,52 +404,76 @@ public class AlignViewport
     setCharWidth(fm.charWidth('M'));
   }
 
-  public Font getFont() {
+  public Font getFont()
+  {
     return font;
   }
-  public void setCharWidth(int w) {
+
+  public void setCharWidth(int w)
+  {
     this.charWidth = w;
   }
-  public int getCharWidth() {
+
+  public int getCharWidth()
+  {
     return charWidth;
   }
-  public void setCharHeight(int h) {
+
+  public void setCharHeight(int h)
+  {
     this.charHeight = h;
   }
-  public int getCharHeight() {
+
+  public int getCharHeight()
+  {
     return charHeight;
   }
-  public void setChunkWidth(int w) {
+
+  public void setChunkWidth(int w)
+  {
     this.chunkWidth = w;
   }
-  public int getChunkWidth() {
+
+  public int getChunkWidth()
+  {
     return chunkWidth;
   }
-  public void setChunkHeight(int h) {
+
+  public void setChunkHeight(int h)
+  {
     this.chunkHeight = h;
   }
-  public int getChunkHeight() {
+
+  public int getChunkHeight()
+  {
     return chunkHeight;
   }
-  public AlignmentI getAlignment() {
+
+  public AlignmentI getAlignment()
+  {
     return alignment;
   }
-  public void setAlignment(AlignmentI align) {
+
+  public void setAlignment(AlignmentI align)
+  {
     this.alignment = align;
   }
 
-  public void setWrapAlignment(boolean state) {
+  public void setWrapAlignment(boolean state)
+  {
     wrapAlignment = state;
   }
-  public void setShowText(boolean state) {
+
+  public void setShowText(boolean state)
+  {
     showText = state;
   }
 
-  public void setRenderGaps(boolean state){
+  public void setRenderGaps(boolean state)
+  {
     renderGaps = state;
   }
 
-
   public boolean getColourText()
   {
     return showColourText;
@@ -408,80 +484,114 @@ public class AlignViewport
     showColourText = state;
   }
 
-  public void setShowBoxes(boolean state) {
+  public void setShowBoxes(boolean state)
+  {
     showBoxes = state;
   }
 
-  public boolean getWrapAlignment() {
-      return wrapAlignment;
+  public boolean getWrapAlignment()
+  {
+    return wrapAlignment;
   }
-  public boolean getShowText() {
+
+  public boolean getShowText()
+  {
     return showText;
   }
-  public boolean getShowBoxes() {
+
+  public boolean getShowBoxes()
+  {
     return showBoxes;
   }
 
-  public char getGapCharacter() {
+  public char getGapCharacter()
+  {
     return getAlignment().getGapCharacter();
   }
-  public void setGapCharacter(char gap) {
-    if (getAlignment() != null) {
+
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
+    {
       getAlignment().setGapCharacter(gap);
     }
   }
-  public void setThreshold(int thresh) {
+
+  public void setThreshold(int thresh)
+  {
     threshold = thresh;
   }
-  public int getThreshold() {
+
+  public int getThreshold()
+  {
     return threshold;
   }
-  public void setIncrement(int inc) {
+
+  public void setIncrement(int inc)
+  {
     increment = inc;
   }
-  public int getIncrement() {
+
+  public int getIncrement()
+  {
     return increment;
   }
-  public int getIndex(int y) {
-    int y1     = 0;
+
+  public int getIndex(int y)
+  {
+    int y1 = 0;
     int starty = getStartSeq();
-    int endy   = getEndSeq();
+    int endy = getEndSeq();
 
-    for (int i = starty; i <= endy; i++) {
-      if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {
+    for (int i = starty; i <= endy; i++)
+    {
+      if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null)
+      {
         int y2 = y1 + getCharHeight();
 
-        if (y>=y1 && y <=y2) {
+        if (y >= y1 && y <= y2)
+        {
           return i;
         }
-        y1  = y2;
-      } else {
+        y1 = y2;
+      }
+      else
+      {
         return -1;
       }
     }
     return -1;
   }
 
-  public ColumnSelection getColumnSelection() {
+  public ColumnSelection getColumnSelection()
+  {
     return colSel;
   }
 
-  public void resetSeqLimits(int height) {
-    setEndSeq(height/getCharHeight());
+  public void resetSeqLimits(int height)
+  {
+    setEndSeq(height / getCharHeight());
   }
-  public void setCurrentTree(NJTree tree) {
-      currentTree = tree;
+
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
   }
-  public NJTree getCurrentTree() {
+
+  public NJTree getCurrentTree()
+  {
     return currentTree;
   }
 
-
   public void setColourAppliesToAllGroups(boolean b)
-  {   colourAppliesToAllGroups = b; }
+  {
+    colourAppliesToAllGroups = b;
+  }
 
   public boolean getColourAppliesToAllGroups()
-  {return colourAppliesToAllGroups; }
+  {
+    return colourAppliesToAllGroups;
+  }
 
   public boolean getShowFullId()
   {
@@ -504,22 +614,33 @@ public class AlignViewport
   }
 
   public boolean getScaleAboveWrapped()
-  { return scaleAboveWrapped;}
+  {
+    return scaleAboveWrapped;
+  }
 
   public boolean getScaleLeftWrapped()
-  { return scaleLeftWrapped; }
+  {
+    return scaleLeftWrapped;
+  }
 
   public boolean getScaleRightWrapped()
-  { return scaleRightWrapped; }
+  {
+    return scaleRightWrapped;
+  }
 
   public void setScaleAboveWrapped(boolean b)
-  { scaleAboveWrapped = b; }
+  {
+    scaleAboveWrapped = b;
+  }
 
   public void setScaleLeftWrapped(boolean b)
-  { scaleLeftWrapped = b; }
+  {
+    scaleLeftWrapped = b;
+  }
 
   public void setScaleRightWrapped(boolean b)
-  { scaleRightWrapped = b; }
-
+  {
+    scaleRightWrapped = b;
+  }
 
 }
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 9c77e13..754d698 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,38 +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
-*/
+ * 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.appletgui;
 
-import jalview.jbappletgui.GAlignmentPanel;
-import jalview.schemes.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
 import java.awt.*;
 import java.awt.event.*;
 
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
+import jalview.schemes.*;
+
+public class AlignmentPanel
+    extends GAlignmentPanel implements AdjustmentListener
 {
 
-  AlignViewport     av;
+  AlignViewport av;
   OverviewPanel overviewPanel;
-  SeqPanel   seqPanel;
-  IdPanel    idPanel;
+  SeqPanel seqPanel;
+  IdPanel idPanel;
   IdwidthAdjuster idwidthAdjuster;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
@@ -45,14 +47,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   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);
+    this.av = av;
+    seqPanel = new SeqPanel(av, this);
+    idPanel = new IdPanel(av, this);
+    scalePanel = new ScalePanel(av, this);
     idwidthAdjuster = new IdwidthAdjuster(this);
     annotationPanel = new AnnotationPanel(this);
-    alabels         = new AnnotationLabels(this);
-
+    alabels = new AnnotationLabels(this);
 
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
@@ -67,57 +68,67 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
-   seqPanel.seqCanvas.addKeyListener( new MyKeyAdapter() );
-   idPanel.idCanvas.addKeyListener( new MyKeyAdapter() );
+    seqPanel.seqCanvas.addKeyListener(new MyKeyAdapter());
+    idPanel.idCanvas.addKeyListener(new MyKeyAdapter());
 
-   addComponentListener(new ComponentAdapter()
-     {
-       public void componentResized(ComponentEvent evt)
-       {
-         setScrollValues(av.getStartRes(), av.getStartSeq());
-         repaint();
-       }
-     });
+    addComponentListener(new ComponentAdapter()
+    {
+      public void componentResized(ComponentEvent evt)
+      {
+        setScrollValues(av.getStartRes(), av.getStartSeq());
+        repaint();
+      }
+    });
 
-     Dimension d = calculateIdWidth();
-     idPanel.idCanvas.setSize(d);
+    Dimension d = calculateIdWidth();
+    idPanel.idCanvas.setSize(d);
 
-     hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
-     annotationScroller.setSize(annotationPanel.getSize());
+    hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
+    annotationScroller.setSize(annotationPanel.getSize());
 
-     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
-     annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
-     alabels.setSize(d.width,annotationPanel.getSize().height);
+    idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+    annotationSpaceFillerHolder.setSize(d.width,
+                                        annotationPanel.getSize().height);
+    alabels.setSize(d.width, annotationPanel.getSize().height);
 
   }
 
-  class MyKeyAdapter extends KeyAdapter
+  class MyKeyAdapter
+      extends KeyAdapter
   {
-     public void keyPressed(KeyEvent evt)
-     {
-       // System.out.println(evt.getKeyCode()); log.
-       switch(evt.getKeyCode())
-       {
-         case  27: // escape key
-           av.setSelectionGroup(null);
-           alignFrame.alignPanel.repaint();
-           break;
-         case KeyEvent.VK_X:
-           if(evt.isControlDown())
-           alignFrame.cut_actionPerformed(null);
-           break;
-         case KeyEvent.VK_C:
-         if(evt.isControlDown())
-           alignFrame.copy_actionPerformed(null);
-           break;
-         case KeyEvent.VK_V:
-          if(evt.isControlDown())
-           alignFrame.paste(true);
-           break;
-         case KeyEvent.VK_A:
-         if(evt.isControlDown())
-           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
-           break;
+    public void keyPressed(KeyEvent evt)
+    {
+      // System.out.println(evt.getKeyCode()); log.
+      switch (evt.getKeyCode())
+      {
+        case 27: // escape key
+          av.setSelectionGroup(null);
+          alignFrame.alignPanel.repaint();
+          break;
+        case KeyEvent.VK_X:
+          if (evt.isControlDown())
+          {
+            alignFrame.cut_actionPerformed(null);
+          }
+          break;
+        case KeyEvent.VK_C:
+          if (evt.isControlDown())
+          {
+            alignFrame.copy_actionPerformed(null);
+          }
+          break;
+        case KeyEvent.VK_V:
+          if (evt.isControlDown())
+          {
+            alignFrame.paste(true);
+          }
+          break;
+        case KeyEvent.VK_A:
+          if (evt.isControlDown())
+          {
+            alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
+          }
+          break;
         case KeyEvent.VK_DOWN:
           alignFrame.moveSelectedSequences(false);
           break;
@@ -125,11 +136,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
           alignFrame.moveSelectedSequences(true);
           break;
         case KeyEvent.VK_F:
-         if(evt.isControlDown())
-          alignFrame.findMenuItem_actionPerformed(null);
+          if (evt.isControlDown())
+          {
+            alignFrame.findMenuItem_actionPerformed(null);
+          }
           break;
-       }
-     }
+      }
+    }
   }
 
   public void fontChanged()
@@ -138,8 +151,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     // to prevent drawing old image
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    scalePanel.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
-    idwidthAdjuster.setSize(new Dimension(10, av.charHeight+fm.getDescent()));
+    scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
+    idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
 
     annotationPanel.adjustPanelHeight();
     annotationPanel.repaint();
@@ -153,17 +166,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setIdWidth(int w, int h)
   {
-    idPanel.idCanvas.setSize(w,h);
-    idPanelHolder.setSize(w,idPanelHolder.getSize().height);
-    alabels.setSize(w,alabels.getSize().height);
+    idPanel.idCanvas.setSize(w, h);
+    idPanelHolder.setSize(w, idPanelHolder.getSize().height);
+    alabels.setSize(w, alabels.getSize().height);
     validate();
   }
+
   Dimension calculateIdWidth()
   {
     Frame frame = new Frame();
     frame.addNotify();
     Graphics g = frame.getGraphics();
-    if(g==null)
+    if (g == null)
     {
       Frame f = new Frame();
       f.addNotify();
@@ -173,70 +187,77 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     FontMetrics fm = g.getFontMetrics(av.font);
     AlignmentI al = av.getAlignment();
 
-       int i   = 0;
-       int idWidth = 0;
-       String id;
-       while (i < al.getHeight() && al.getSequenceAt(i) != null)
-       {
-         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++;
-       }
-
-       // Also check annotation label widths
-       i=0;
-       if(al.getAlignmentAnnotation()!=null)
-       {
-         fm = g.getFontMetrics(frame.getFont());
-         while (i < al.getAlignmentAnnotation().length)
-         {
-           String label = al.getAlignmentAnnotation()[i].label;
-           if (fm.stringWidth(label) > idWidth)
-             idWidth = fm.stringWidth(label);
-           i++;
-         }
-       }
-
-       return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
-  }
+    int i = 0;
+    int idWidth = 0;
+    String id;
+    while (i < al.getHeight() && al.getSequenceAt(i) != null)
+    {
+      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++;
+    }
 
- public void highlightSearchResults(int [] results)
- {
-   seqPanel.seqCanvas.highlightSearchResults( results );
+    // Also check annotation label widths
+    i = 0;
+    if (al.getAlignmentAnnotation() != null)
+    {
+      fm = g.getFontMetrics(frame.getFont());
+      while (i < al.getAlignmentAnnotation().length)
+      {
+        String label = al.getAlignmentAnnotation()[i].label;
+        if (fm.stringWidth(label) > idWidth)
+        {
+          idWidth = fm.stringWidth(label);
+        }
+        i++;
+      }
+    }
+
+    return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
+  }
+
+  public void highlightSearchResults(int[] results)
+  {
+    seqPanel.seqCanvas.highlightSearchResults(results);
 
-   // do we need to scroll the panel?
-   if(results!=null)
+    // 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
+      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]))
+              || av.getEndSeq() < results[0]))
+      {
         setScrollValues(start, results[0]);
+      }
     }
 
- }
-
-
- public OverviewPanel getOverviewPanel()
- {
-   return overviewPanel;
- }
+  }
 
- public void setOverviewPanel(OverviewPanel op)
- {
-   overviewPanel = op;
- }
+  public OverviewPanel getOverviewPanel()
+  {
+    return overviewPanel;
+  }
 
+  public void setOverviewPanel(OverviewPanel op)
+  {
+    overviewPanel = op;
+  }
 
   public void setAnnotationVisible(boolean b)
   {
@@ -246,7 +267,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     repaint();
   }
 
-
   public void setWrapAlignment(boolean wrap)
   {
     scalePanelHolder.setVisible(!wrap);
@@ -263,49 +283,52 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   }
 
-
   public void setColourScheme()
   {
     ColourSchemeI cs = av.getGlobalColourScheme();
 
-    if(av.getConservationSelected())
+    if (av.getConservationSelected())
     {
 
-       Alignment al = (Alignment)av.getAlignment();
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
+      Alignment al = (Alignment) av.getAlignment();
+      Conservation c = new Conservation("All",
+                                        ResidueProperties.propHash, 3,
+                                        al.getSequences(), 0,
+                                        al.getWidth());
 
-       c.calculate();
-       c.verdict(false, av.ConsPercGaps);
-       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+      c.calculate();
+      c.verdict(false, av.ConsPercGaps);
+      ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
-       av.setGlobalColourScheme( ccs );
+      av.setGlobalColourScheme(ccs);
 
     }
 
     repaint();
   }
 
-
   int hextent = 0;
   int vextent = 0;
 
   // return value is true if the scroll is valid
   public boolean scrollUp(boolean up)
   {
-    if(up)
+    if (up)
     {
-      if(vscroll.getValue()<1)
+      if (vscroll.getValue() < 1)
+      {
         return false;
-      fastPaint  = false;
+      }
+      fastPaint = false;
       vscroll.setValue(vscroll.getValue() - 1);
     }
     else
     {
-     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
-       return false;
-      fastPaint  = false;
+      if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
+      {
+        return false;
+      }
+      fastPaint = false;
       vscroll.setValue(vscroll.getValue() + 1);
     }
     fastPaint = true;
@@ -318,14 +341,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     if (right)
     {
       if (hscroll.getValue() < 1)
+      {
         return false;
+      }
       fastPaint = false;
       hscroll.setValue(hscroll.getValue() - 1);
     }
     else
     {
       if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+      {
         return false;
+      }
       fastPaint = false;
       hscroll.setValue(hscroll.getValue() + 1);
     }
@@ -333,47 +360,57 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     return true;
   }
 
-
   public void setScrollValues(int x, int y)
   {
 
     av.setStartRes(x);
     av.setStartSeq(y);
-    av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
+    av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);
 
-    hextent = seqPanel.seqCanvas.getSize().width/av.charWidth;
-    vextent = seqPanel.seqCanvas.getSize().height/av.charHeight;
+    hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
+    vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
 
-    if(hextent > av.alignment.getWidth())
+    if (hextent > av.alignment.getWidth())
+    {
       hextent = av.alignment.getWidth();
-    if(vextent > av.alignment.getHeight())
+    }
+    if (vextent > av.alignment.getHeight())
+    {
       vextent = av.alignment.getHeight();
+    }
 
-    if(hextent+x  >  av.getAlignment().getWidth())
-      x =  av.getAlignment().getWidth()- hextent;
+    if (hextent + x > av.getAlignment().getWidth())
+    {
+      x = av.getAlignment().getWidth() - hextent;
+    }
 
-    if(vextent+y > av.getAlignment().getHeight())
+    if (vextent + y > av.getAlignment().getHeight())
+    {
       y = av.getAlignment().getHeight() - vextent;
+    }
 
-    if(y<0)
+    if (y < 0)
+    {
       y = 0;
+    }
 
-    if(x<0)
-      x=0;
-
+    if (x < 0)
+    {
+      x = 0;
+    }
 
     int endSeq = y + vextent;
-    if(endSeq>av.alignment.getHeight())
+    if (endSeq > av.alignment.getHeight())
+    {
       endSeq = av.alignment.getHeight();
+    }
 
-
-    av.setEndSeq( endSeq );
-    hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
-    vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+    av.setEndSeq(endSeq);
+    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
+    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
 
   }
 
-
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     int oldX = av.getStartRes();
@@ -383,7 +420,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);
+      av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
+                   1);
     }
 
     if (evt.getSource() == vscroll)
@@ -391,22 +429,28 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       int offy = vscroll.getValue();
       if (av.getWrapAlignment())
       {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-        av.setStartRes( vscroll.getValue() * rowSize );
-        av.setEndRes( (vscroll.getValue()+1) * rowSize );
+        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
+            seqCanvas.getSize().width);
+        av.setStartRes(vscroll.getValue() * rowSize);
+        av.setEndRes( (vscroll.getValue() + 1) * rowSize);
       }
       else
       {
         av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height / av.getCharHeight());
+        av.setEndSeq(offy +
+                     seqPanel.seqCanvas.getSize().height / av.getCharHeight());
       }
     }
 
-    if(overviewPanel!=null)
+    if (overviewPanel != null)
+    {
       overviewPanel.setBoxPosition();
+    }
 
-    if(av.getWrapAlignment() || !fastPaint)
+    if (av.getWrapAlignment() || !fastPaint)
+    {
       repaint();
+    }
     else
     {
       idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
@@ -415,23 +459,25 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
       scalePanel.repaint();
       if (av.getShowAnnotation())
+      {
         annotationPanel.fastPaint(av.getStartRes() - oldX);
+      }
     }
 
   }
 
   public void update(Graphics g)
   {
-    paint (g);
+    paint(g);
   }
 
-
   public void paint(Graphics g)
   {
     Dimension d = idPanel.idCanvas.getSize();
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
-    annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
-    alabels.setSize(d.width,annotationPanel.getSize().height);
+    annotationSpaceFillerHolder.setSize(d.width,
+                                        annotationPanel.getSize().height);
+    alabels.setSize(d.width, annotationPanel.getSize().height);
 
     alabels.repaint();
     idPanel.idCanvas.repaint();
@@ -439,10 +485,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     scalePanel.repaint();
     annotationPanel.repaint();
 
-
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+      int max = av.alignment.getWidth() /
+          seqPanel.seqCanvas.
+          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);
@@ -452,7 +499,5 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-
-
   }
 }
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 095377d..38013d1 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,40 +1,41 @@
-
 /*
-* 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.appletgui;
 
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
+
 import jalview.datamodel.*;
 
-public class AnnotationLabels extends Panel implements ActionListener
+public class AnnotationLabels
+    extends Panel implements ActionListener
 {
   boolean active = false;
-  AlignmentPanel ap ;
+  AlignmentPanel ap;
   boolean resizing = false;
   int oldY, mouseX;
   static String ADDNEW = "Add new row";
   static String HIDE = "Hide this row";
   static String DELETE = "Delete this row";
-  static String SHOWALL="Show all hidden rows";
-  static String OUTPUT_TEXT="Show Values In Textbox";
+  static String SHOWALL = "Show all hidden rows";
+  static String OUTPUT_TEXT = "Show Values In Textbox";
   int selectedRow = 0;
   int scrollOffset = 0;
 
@@ -43,7 +44,8 @@ public class AnnotationLabels extends Panel implements ActionListener
     this.ap = ap;
     setLayout(null);
     addMouseListener(new MouseAdapter()
-    {public void mousePressed(MouseEvent evt)
+    {
+      public void mousePressed(MouseEvent evt)
       {
         doMousePressed(evt);
       }
@@ -60,30 +62,32 @@ public class AnnotationLabels extends Panel implements ActionListener
   {
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
-   if(evt.getActionCommand().equals(HIDE))
-   {
-     aa[selectedRow].visible = false;
-   }
-   else if(evt.getActionCommand().equals(SHOWALL))
-   {
-       for(int i=0; i<aa.length; i++)
-         aa[i].visible = true;
-   }
-   else if (evt.getActionCommand().equals(OUTPUT_TEXT))
-   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     Frame frame = new Frame();
-     frame.add(cap);
-     jalview.bin.JalviewLite.addFrame(frame,
-                                      ap.alignFrame.getTitle() + " - " +
-                                      aa[selectedRow].label, 500, 100);
-     cap.setText(aa[selectedRow].toString());
-   }
-
-   ap.annotationPanel.adjustPanelHeight();
-   setSize(getSize().width,ap.annotationPanel.getSize().height);
-   ap.validate();
-   ap.repaint();
+    if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
+    }
+    else if (evt.getActionCommand().equals(SHOWALL))
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        aa[i].visible = true;
+      }
+    }
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame,
+                                       ap.alignFrame.getTitle() + " - " +
+                                       aa[selectedRow].label, 500, 100);
+      cap.setText(aa[selectedRow].toString());
+    }
+
+    ap.annotationPanel.adjustPanelHeight();
+    setSize(getSize().width, ap.annotationPanel.getSize().height);
+    ap.validate();
+    ap.repaint();
   }
 
   public void doMousePressed(MouseEvent evt)
@@ -94,7 +98,9 @@ public class AnnotationLabels extends Panel implements ActionListener
     for (int i = 0; i < aa.length; i++)
     {
       if (!aa[i].visible)
+      {
         continue;
+      }
 
       height += aa[i].height;
       if (y < height)
@@ -128,33 +134,43 @@ public class AnnotationLabels extends Panel implements ActionListener
   {
     FontMetrics fm = g.getFontMetrics(g.getFont());
     g.setColor(Color.white);
-    g.fillRect(0,0, getSize().width, getSize().height);
+    g.fillRect(0, 0, getSize().width, getSize().height);
 
     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)
-       continue;
-
-     x = getSize().width - fm.stringWidth(aa[i].label)-3;
-
-     if(aa[i].isGraph)
-       y+=(aa[i].height/3);
-
-     g.drawString(aa[i].label, x, y);
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    int y = g.getFont().getSize();
+    int x = 0;
 
-     if(aa[i].isGraph)
-       y+=(2*aa[i].height/3);
-    else
-       y+=aa[i].height;
-   }
+    if (aa != null)
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
+
+        x = getSize().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;
+        }
+      }
+    }
   }
 
 }
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index afdc6db..cd6396f 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,57 +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.appletgui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
-public class AnnotationPanel extends Panel implements AdjustmentListener
+import jalview.datamodel.*;
+
+public class AnnotationPanel
+    extends Panel implements AdjustmentListener
 {
   AlignViewport av;
   AlignmentPanel ap;
-  int activeRow =-1;
+  int activeRow = -1;
 
   Vector activeRes;
-  static String HELIX ="Helix";
-  static String SHEET ="Sheet";
-  static String LABEL ="Label";
-  static String REMOVE="Remove Annotation";
-  static String COLOUR="Colour";
+  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();
 
-
   Image image;
   Graphics gg;
   FontMetrics fm;
-  int imgWidth=0;
+  int imgWidth = 0;
 
   boolean fastPaint = false;
 
   public static int GRAPH_HEIGHT = 40;
 
-
-
   public AnnotationPanel(AlignmentPanel ap)
   {
     this.ap = ap;
@@ -60,16 +59,19 @@ public class AnnotationPanel extends Panel implements AdjustmentListener
     adjustPanelHeight();
 
     addMouseMotionListener(new MouseMotionAdapter()
-    {public void mouseMoved(MouseEvent evt)
-          { doMouseMoved(evt); }
+    {
+      public void mouseMoved(MouseEvent evt)
+      {
+        doMouseMoved(evt);
+      }
     });
 
-   // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
+    // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    ap.alabels.setScrollOffset( -evt.getValue() );
+    ap.alabels.setScrollOffset( -evt.getValue());
   }
 
   public void adjustPanelHeight()
@@ -77,51 +79,68 @@ public class AnnotationPanel extends Panel implements AdjustmentListener
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
     int height = 0;
-    if(aa!=null)
-    for (int i = 0; i < aa.length; i++)
+    if (aa != null)
     {
-      if(!aa[i].visible)
-        continue;
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
 
-      aa[i].height = 0;
+        aa[i].height = 0;
 
-      if(aa[i].hasText)
-        aa[i].height += av.charHeight;
-      if (aa[i].hasIcons)
-        aa[i].height += 16;
+        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].isGraph)
+        {
+          aa[i].height += GRAPH_HEIGHT;
+        }
 
-      if(aa[i].height==0)
-        aa[i].height = 20;
-      height += aa[i].height;
+        if (aa[i].height == 0)
+        {
+          aa[i].height = 20;
+        }
+        height += aa[i].height;
+      }
+    }
+    else
+    {
+      height = 20;
     }
-  else height=20;
 
-   this.setSize(getSize().width, height);
-   ap.annotationScroller.setSize(getSize().width, height);
+    this.setSize(getSize().width, height);
+    ap.annotationScroller.setSize(getSize().width, height);
 
 //  ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
 
-   repaint();
+    repaint();
 
   }
 
   public void addEditableColumn(int i)
   {
-    if(activeRow==-1)
+    if (activeRow == -1)
     {
-      AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-      for(int j=0; j<aa.length; j++)
-        if(aa[j].editable)
+      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+      for (int j = 0; j < aa.length; j++)
+      {
+        if (aa[j].editable)
         {
           activeRow = j;
           break;
         }
+      }
     }
 
-    if(activeRes==null)
+    if (activeRes == null)
     {
       activeRes = new Vector();
       activeRes.addElement(String.valueOf(i));
@@ -131,38 +150,40 @@ public class AnnotationPanel extends Panel implements AdjustmentListener
     activeRes.addElement(String.valueOf(i));
   }
 
- public void doMouseMoved(MouseEvent evt)
- {
-   AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-   if(aa==null)
-     return;
-
-   int row = -1;
-   int height=0;
-   for(int i=0; i<aa.length; i++)
-   {
-
-     if( aa[i].visible )
-       height += aa[i].height;
+  public void doMouseMoved(MouseEvent evt)
+  {
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    if (aa == null)
+    {
+      return;
+    }
 
-     if(evt.getY()<height)
-     {
-       row = i;
-       break;
-     }
-   }
+    int row = -1;
+    int height = 0;
+    for (int i = 0; i < aa.length; i++)
+    {
 
-   int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-   if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)
-   {
-     StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
-                                          "  " +
-                                          aa[row].annotations[res].description);
-     ap.alignFrame.statusBar.setText(text.toString());
-   }
- }
+      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)
+    {
+      StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
+                                           "  " +
+                                           aa[row].annotations[res].description);
+      ap.alignFrame.statusBar.setText(text.toString());
+    }
+  }
 
   public void update(Graphics g)
   {
@@ -171,258 +192,304 @@ public class AnnotationPanel extends Panel implements AdjustmentListener
 
   public void paint(Graphics g)
   {
-    imgWidth = (av.endRes-av.startRes+1) *av.charWidth;
+    imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
-    if(image==null || imgWidth != image.getWidth(this))
-      {
-        image = createImage(imgWidth, ap.annotationPanel.getSize().height);
-        gg = image.getGraphics();
-        gg.setFont(av.getFont());
-        fm = gg.getFontMetrics();
-        fastPaint = false;
+    if (image == null || imgWidth != image.getWidth(this))
+    {
+      image = createImage(imgWidth, ap.annotationPanel.getSize().height);
+      gg = image.getGraphics();
+      gg.setFont(av.getFont());
+      fm = gg.getFontMetrics();
+      fastPaint = false;
     }
 
-    if(fastPaint)
+    if (fastPaint)
     {
       g.drawImage(image, 0, 0, this);
       fastPaint = false;
       return;
     }
 
-    drawComponent( gg, av.startRes, av.endRes+1);
-    g.drawImage( image, 0, 0, this);
+    drawComponent(gg, av.startRes, av.endRes + 1);
+    g.drawImage(image, 0, 0, this);
 
   }
 
   public void fastPaint(int horizontal)
-{
-  if( horizontal == 0
-     || av.alignment.getAlignmentAnnotation()==null
-     || av.alignment.getAlignmentAnnotation().length<1
-    )
   {
-    repaint();
-    return;
-  }
-
-  gg.copyArea( 0,0, imgWidth, getSize().height, -horizontal*av.charWidth, 0 );
-  int sr=av.startRes, er=av.endRes+1, transX=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;
-  }
+    if (horizontal == 0
+        || av.alignment.getAlignmentAnnotation() == null
+        || av.alignment.getAlignmentAnnotation().length < 1
+        )
+    {
+      repaint();
+      return;
+    }
 
+    gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0);
+    int sr = av.startRes, er = av.endRes + 1, transX = 0;
 
-  gg.translate(transX, 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;
+    }
 
-  drawComponent(gg, sr, er);
+    gg.translate(transX, 0);
 
-  gg.translate( -transX, 0 );
+    drawComponent(gg, sr, er);
 
-  fastPaint = true;
-  repaint();
-}
+    gg.translate( -transX, 0);
 
+    fastPaint = true;
+    repaint();
+  }
 
   public void drawComponent(Graphics g, int startRes, int endRes)
   {
     g.setColor(Color.white);
-    g.fillRect(0,0,(endRes-startRes) *av.charWidth, getSize().height);
-    if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)
+    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
+    if (av.alignment.getAlignmentAnnotation() == null ||
+        av.alignment.getAlignmentAnnotation().length < 1)
     {
       g.setColor(Color.white);
-      g.fillRect(0,0,getSize().width, getSize().height);
+      g.fillRect(0, 0, getSize().width, getSize().height);
       g.setColor(Color.black);
-      g.drawString("Alignment has no annotations",20,15);
+      g.drawString("Alignment has no annotations", 20, 15);
       return;
     }
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    int j, x=0, y=0;
-    char [] lastSS = new char[aa.length];
-    int  [] lastSSX= new int[aa.length] ;
-    int iconOffset = av.charHeight/2;
+    int j, x = 0, 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++)
+    for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
-      if(!row.visible)
+      if (!row.visible)
+      {
         continue;
+      }
 
-      if(row.isGraph)
+      if (row.isGraph)
       {
         // this is so that we draw the characters below the graph
         y += row.height;
-        if(row.hasText)
+        if (row.hasText)
+        {
           y -= av.charHeight;
+        }
+      }
+      if (row.hasText)
+      {
+        iconOffset = av.charHeight / 2;
       }
-      if(row.hasText)
-        iconOffset = av.charHeight/2;
       else
+      {
         iconOffset = 0;
+      }
 
-      for(j=startRes; j<endRes; j++)
+      for (j = startRes; j < endRes; j++)
       {
-        if(row.annotations.length<=j || row.annotations[j]==null)
-        validRes = false;
-       else
-         validRes = true;
-
-       x = (j-startRes)*av.charWidth;
-
-
-       if(activeRow==i)
-       {
+        if (row.annotations.length <= j || row.annotations[j] == null)
+        {
+          validRes = false;
+        }
+        else
+        {
+          validRes = true;
+        }
 
-         g.setColor(Color.red);
+        x = (j - startRes) * av.charWidth;
 
-         if(activeRes!=null)
-           for (int n = 0; n < activeRes.size(); n++)
-           {
-             int v = Integer.parseInt(activeRes.elementAt(n).toString()) ;
-             if (v == j)
-               g.fillRect( (j-startRes) * av.charWidth, y, av.charWidth, row.height);
-           }
-       }
+        if (activeRow == i)
+        {
 
+          g.setColor(Color.red);
 
+          if (activeRes != null)
+          {
+            for (int n = 0; n < activeRes.size(); n++)
+            {
+              int v = Integer.parseInt(activeRes.elementAt(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)
+        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)
           {
             if (row.annotations[0].secondaryStructure == 'H'
                 || row.annotations[0].secondaryStructure == 'E')
+            {
               g.drawString(row.annotations[j].displayCharacter, x,
                            y + iconOffset + 2);
+            }
           }
-         else if( (row.annotations[j].secondaryStructure=='H'
-               || row.annotations[j].secondaryStructure=='E') &&
-               (row.annotations[j-1]==null ||
-                row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))
+          else if ( (row.annotations[j].secondaryStructure == 'H'
+                     || row.annotations[j].secondaryStructure == 'E') &&
+                   (row.annotations[j - 1] == null ||
+                    row.annotations[j].secondaryStructure !=
+                    row.annotations[j - 1].secondaryStructure))
+          {
 
-        g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);
+            g.drawString(row.annotations[j].displayCharacter, x,
+                         y + iconOffset + 2);
+          }
 
-        if(!row.hasIcons)
+          if (!row.hasIcons)
+          {
             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);
-             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 );
-       }
+          }
+        }
+
+        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);
+                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);
+        }
 
       }
 
-      x+=av.charWidth;
+      x += av.charWidth;
 
-      if(row.hasIcons)
-      switch (lastSS[i])
+      if (row.hasIcons)
       {
-        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;
+        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 && row.hasText)
-         y+=av.charHeight;
-       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)
+  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));
+    g.fillRect(0, 0, width, y);
+    g.setColor(new Color(0, 0, 180));
     int x = 0;
-    for(int j=0; j<aa.annotations.length; j++)
+    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 );
+      int height = (int) ( (aa.annotations[j].value / aa.graphMax) *
+                          GRAPH_HEIGHT);
       g.fillRect(x, y - height, av.charWidth, height);
-      x+=av.charWidth;
+      x += av.charWidth;
     }
   }
 }
diff --git a/src/jalview/appletgui/ColumnSelection.java b/src/jalview/appletgui/ColumnSelection.java
index cb83c4a..72bec07 100755
--- a/src/jalview/appletgui/ColumnSelection.java
+++ b/src/jalview/appletgui/ColumnSelection.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.appletgui;
 
@@ -24,70 +24,92 @@ import java.util.*;
 /**
  * NOTE: Columns are zero based.
  */
-public class ColumnSelection{
+public class ColumnSelection
+{
   Vector selected = new Vector();
 
-  public void addElement(int col) {
+  public void addElement(int col)
+  {
     selected.addElement(new Integer(col));
   }
 
-  public void clear() {
+  public void clear()
+  {
     selected.removeAllElements();
   }
 
-  public void removeElement(int col) {
+  public void removeElement(int col)
+  {
     Integer colInt = new Integer(col);
-    if (selected.contains(colInt)) {
+    if (selected.contains(colInt))
+    {
       selected.removeElement(colInt);
-    } else {
-      System.err.println("WARNING: Tried to remove Integer NOT in ColumnSelection");
+    }
+    else
+    {
+      System.err.println(
+          "WARNING: Tried to remove Integer NOT in ColumnSelection");
     }
   }
 
-  public boolean contains(int col) {
+  public boolean contains(int col)
+  {
     return selected.contains(new Integer(col));
   }
 
-  public int columnAt(int i) {
-    return ((Integer)selected.elementAt(i)).intValue();
+  public int columnAt(int i)
+  {
+    return ( (Integer) selected.elementAt(i)).intValue();
   }
 
-  public int size() {
+  public int size()
+  {
     return selected.size();
   }
 
-  public int getMax() {
+  public int getMax()
+  {
     int max = -1;
 
-    for (int i=0;i<selected.size();i++) {
-      if (columnAt(i) > max) {
+    for (int i = 0; i < selected.size(); i++)
+    {
+      if (columnAt(i) > max)
+      {
         max = columnAt(i);
       }
     }
     return max;
   }
 
-  public int getMin() {
+  public int getMin()
+  {
     int min = 1000000000;
 
-    for (int i=0;i<selected.size();i++) {
-      if (columnAt(i) < min) {
+    for (int i = 0; i < selected.size(); i++)
+    {
+      if (columnAt(i) < min)
+      {
         min = columnAt(i);
       }
     }
     return min;
   }
 
-  public Vector asVector() {
+  public Vector asVector()
+  {
     return selected;
   }
 
-  public void compensateForEdit(int start, int change) {
-    for (int i=0; i < size();i++) {
+  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);
+      {
+        selected.setElementAt(new Integer(temp - change), i);
+      }
     }
   }
 }
diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 22cfd67..ed89001 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,43 +1,44 @@
 /*
-* 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.appletgui;
 
-import jalview.jbappletgui.GCutAndPasteTransfer;
-import jalview.datamodel.*;
-import jalview.io.*;
 import java.awt.*;
 import java.awt.event.*;
 
-public class CutAndPasteTransfer extends GCutAndPasteTransfer
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbappletgui.*;
+
+public class CutAndPasteTransfer
+    extends GCutAndPasteTransfer
 {
   public CutAndPasteTransfer(boolean forImport)
   {
     super();
 
-    if(!forImport)
+    if (!forImport)
     {
       buttonPanel.setVisible(false);
     }
   }
 
-
   public String getText()
   {
     return textarea.getText();
@@ -48,7 +49,6 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     textarea.setText(text);
   }
 
-
   protected void ok_actionPerformed(ActionEvent e)
   {
     String text = getText();
@@ -68,14 +68,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     Frame frame = (Frame)this.getParent();
     frame.setVisible(false);
-   }
-
-   protected void cancel_actionPerformed(ActionEvent e) {
-     Frame frame = (Frame)this.getParent();
-     frame.setVisible(false);
-   }
-
-
+  }
 
+  protected void cancel_actionPerformed(ActionEvent e)
+  {
+    Frame frame = (Frame)this.getParent();
+    frame.setVisible(false);
+  }
 
 }
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index f6fe0be..291ce5f 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,34 +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.appletgui;
 
-import jalview.datamodel.*;
-import java.awt.*;
 import java.util.*;
 
+import java.awt.*;
+
+import jalview.datamodel.*;
+
 public class FeatureRenderer
 {
   AlignViewport av;
 
   SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
+  SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
 
@@ -37,36 +39,43 @@ public class FeatureRenderer
     this.av = av;
   }
 
-
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)
+  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() )
+    while (e.hasMoreElements())
     {
-      SequenceFeature sf = (SequenceFeature)e.nextElement();
-      if(sf.getStart()>seq.getEnd())
+      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;
+      int fstart = seq.findIndex(sf.getStart()) - 1;
+      int fend = seq.findIndex(sf.getEnd()) - 1;
 
-      if(   (fstart<=end && fend>=start)  )
+      if ( (fstart <= end && fend >= start))
       {
-        if(fstart<0) // fix for if the feature we have starts before the sequence start,
-          fstart = 0;// but the feature end is still valid!!
+        if (fstart < 0) // fix for if the feature we have starts before the sequence start,
+        {
+          fstart = 0; // but the feature end is still valid!!
+        }
 
-        if(fstart==fend)
+        if (fstart == fend)
         {
           g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
+          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);
+          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
@@ -74,11 +83,13 @@ public class FeatureRenderer
           for (int i = fstart; i <= fend; i++)
           {
             char s = seq.getSequence().charAt(i);
-            if( jalview.util.Comparison.isGap(s) )
+            if (jalview.util.Comparison.isGap(s))
+            {
               continue;
+            }
 
             g.setColor(Color.blue);
-            g.fillRect( (i-start) * width, y1, width, height);
+            g.fillRect( (i - start) * width, y1, width, height);
 
             g.setColor(Color.white);
 
@@ -86,13 +97,13 @@ public class FeatureRenderer
             int charOffset = (width - fm.charWidth(s)) / 2;
             int pady = height / 5;
             g.drawString(String.valueOf(s),
-                         charOffset + x1 + width * (i-start),
+                         charOffset + x1 + width * (i - start),
                          y1 + height - pady);
           }
         }
       }
 
     }
-   }
+  }
 
 }
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index e6fb5e6..a3a6124 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,31 +1,34 @@
 /*
-* 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.appletgui;
 
-import jalview.jbappletgui.GFinder;
-import jalview.datamodel.*;
-import java.awt.event.*;
 import java.util.*;
+
 import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
 
-public class Finder extends GFinder
+public class Finder
+    extends GFinder
 {
   AlignViewport av;
   AlignmentPanel ap;
@@ -41,12 +44,15 @@ public class Finder extends GFinder
     this.ap = ap;
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Find", 340,120);
+    jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
     frame.repaint();
     frame.addWindowListener(new WindowAdapter()
-        {public void windowClosing(WindowEvent evt)
-              { ap.highlightSearchResults( null ); }
-        });
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        ap.highlightSearchResults(null);
+      }
+    });
   }
 
   public void textfield_actionPerformed(ActionEvent e)
@@ -61,197 +67,229 @@ public class Finder extends GFinder
 
   public void findAll_actionPerformed(ActionEvent e)
   {
-    resIndex=0;
-    seqIndex=0;
+    resIndex = 0;
+    seqIndex = 0;
     doSearch(true);
   }
 
   public void cancel_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-      ap.highlightSearchResults( null );
-      ap.idPanel.highlightSearchResults( null );
-     // frame.setClosed(true);
-    }catch(Exception ex){ }
+      ap.highlightSearchResults(null);
+      ap.idPanel.highlightSearchResults(null);
+      // frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {}
   }
 
-
   public void createNewGroup_actionPerformed(ActionEvent e)
   {
-   Color [] newColors = new Color[24];
-   for(int i=0; i<24; i++)
-     newColors[i] = new Color(60,160,115);
-
-   jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
-   String searchString = textfield.getText();
+    Color[] newColors = new Color[24];
+    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();
 
+    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
-    for(int i=0; i<searchResults.size(); i+=3)
+    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;
+      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  );
+      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
+                                           startRes, endRes);
       sg.addSequence(seq);
       av.alignment.addGroup(sg);
-      searchGroup.addGroup( sg );
+      searchGroup.addGroup(sg);
 
     }
 
     ap.av.alignment.addSuperGroup(searchGroup);
-    ap.highlightSearchResults( null );
+    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);
+    com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
     searchResults = new Vector();
-    int [] allResults = null;
+    int[] allResults = null;
 
     Sequence seq;
-    String item=null;
+    String item = null;
     boolean found = false;
 
     ////// is the searchString a residue number?
-    try{
+    try
+    {
       int res = Integer.parseInt(searchString);
       found = true;
 
-      if(av.getSelectionGroup().getSize()>0)
-        seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
+      if (av.getSelectionGroup().getSize() > 0)
+      {
+        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+      }
       else
-        seq = (Sequence)av.getAlignment().getSequenceAt(0);
+      {
+        seq = (Sequence) av.getAlignment().getSequenceAt(0);
+      }
 
-      searchResults.addElement( Integer.toString( av.getAlignment().findIndex(seq) ) );
-      searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
-      searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
+      searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));
+      searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));
+      searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));
 
-    }catch(NumberFormatException ex){}
+    }
+    catch (NumberFormatException ex)
+    {}
     ///////////////////////////////////////////////
 
 
     int end = av.alignment.getHeight();
 
     SequenceGroup selection = av.getSelectionGroup();
-    if(selection!=null)
-     if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
-      selection = null;
-
-    while( !found && seqIndex<end)
+    if (selection != null)
     {
-      seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
+      if (selection.getSize() < 1 ||
+          (selection.getEndRes() - selection.getStartRes() < 2))
+      {
+        selection = null;
+      }
+    }
 
+    while (!found && seqIndex < end)
+    {
+      seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 
-      if(selection!=null && !selection.sequences.contains(seq))
+      if (selection != null && !selection.sequences.contains(seq))
       {
         seqIndex++;
-        resIndex=0;
+        resIndex = 0;
         continue;
       }
 
       item = seq.getSequence().toUpperCase();
 
-      if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
-          item = item.substring(0, selection.getEndRes()+1);
+      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;
+      int insertCount = 0;
       Vector spaces = new Vector();
 
-      for (int j=0; j < item.length(); j++)
+      for (int j = 0; j < item.length(); j++)
       {
 
-        if(!jalview.util.Comparison.isGap(item.charAt(j)))
-         {
-           noGaps.append(item.charAt(j));
-           spaces.addElement(new Integer(insertCount));
-         }
+        if (!jalview.util.Comparison.isGap(item.charAt(j)))
+        {
+          noGaps.append(item.charAt(j));
+          spaces.addElement(new Integer(insertCount));
+        }
         else
-           insertCount++;
+        {
+          insertCount++;
+        }
       }
 
-
-
-      for(int r = resIndex; r<noGaps.length(); r++)
+      for (int r = resIndex; r < noGaps.length(); r++)
       {
 
-       if( regex.searchFrom( noGaps.toString(), r ) )
-       {
-         resIndex = regex.matchedFrom();
-         if(selection!=null && ( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) )<selection.getStartRes())
-           continue;
-
-         searchResults.addElement( 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 (regex.searchFrom(noGaps.toString(), r))
+        {
+          resIndex = regex.matchedFrom();
+          if (selection != null &&
+              (resIndex + Integer.parseInt(spaces.elementAt(resIndex).toString())) <
+              selection.getStartRes())
+          {
+            continue;
+          }
+
+          searchResults.addElement(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)
+      if (!found)
       {
         seqIndex++;
         resIndex = 0;
       }
     }
 
-
     Vector idMatch = new Vector();
-    for(int id = 0; id<av.alignment.getHeight(); id++)
+    for (int id = 0; id < av.alignment.getHeight(); id++)
     {
-      if(   regex.search( av.alignment.getSequenceAt(id).getName() ) )
-        idMatch.addElement( av.alignment.getSequenceAt(id) );
+      if (regex.search(av.alignment.getSequenceAt(id).getName()))
+      {
+        idMatch.addElement(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)
+    if (searchResults.size() > 0)
     {
       allResults = new int[searchResults.size()];
-      for(int i=0; i<searchResults.size(); i++)
+      for (int i = 0; i < searchResults.size(); i++)
+      {
         allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());
+      }
 
       createNewGroup.setEnabled(true);
     }
     else
     {
-      resIndex=0;
-      seqIndex=0;
+      resIndex = 0;
+      seqIndex = 0;
     }
 
     // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-    ap.highlightSearchResults( allResults );
+    ap.highlightSearchResults(allResults);
 
     if (findAll)
     {
-      String message =  (searchResults.size()/3) + " matches found.";
+      String message = (searchResults.size() / 3) + " matches found.";
       System.out.println(message);
     }
 
diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java
index eb29211..02a7471 100755
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
@@ -1,31 +1,30 @@
 /*
-* 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.appletgui;
 
-import jalview.jbappletgui.GFontChooser;
-import jalview.appletgui.*;
 import java.awt.*;
-import java.awt.event.*;
 
+import jalview.jbappletgui.*;
 
-public class FontChooser extends GFontChooser
+public class FontChooser
+    extends GFontChooser
 {
   AlignmentPanel ap;
   Font oldFont;
@@ -40,29 +39,35 @@ public class FontChooser extends GFontChooser
 
     this.ap = ap;
     String fonts[] = Toolkit.getDefaultToolkit().getFontList();
-    for(int i=0; i<fonts.length; i++)
+    for (int i = 0; i < fonts.length; i++)
+    {
       fontName.addItem(fonts[i]);
+    }
 
-    for(int i=1; i<31; i++)
-      fontSize.addItem(i+"");
+    for (int i = 1; i < 31; i++)
+    {
+      fontSize.addItem(i + "");
+    }
 
-   fontStyle.addItem("plain");
-   fontStyle.addItem("bold");
-   fontStyle.addItem("italic");
+    fontStyle.addItem("plain");
+    fontStyle.addItem("bold");
+    fontStyle.addItem("italic");
 
-   oldFont = ap.av.getFont();
-   fontName.select(oldFont.getName());
-   fontSize.select(oldFont.getSize()+"");
-   fontStyle.select(oldFont.getStyle());
+    oldFont = ap.av.getFont();
+    fontName.select(oldFont.getName());
+    fontSize.select(oldFont.getSize() + "");
+    fontStyle.select(oldFont.getStyle());
 
-   init = false;
+    init = false;
   }
 
   protected void ok_actionPerformed()
   {
-      frame.setVisible(false);
-   if(ap.getOverviewPanel()!=null)
-     ap.getOverviewPanel().updateOverviewImage();
+    frame.setVisible(false);
+    if (ap.getOverviewPanel() != null)
+    {
+      ap.getOverviewPanel().updateOverviewImage();
+    }
   }
 
   protected void cancel_actionPerformed()
@@ -70,7 +75,7 @@ public class FontChooser extends GFontChooser
     ap.av.setFont(oldFont);
     ap.repaint();
     fontName.select(oldFont.getName());
-    fontSize.select(oldFont.getSize()+"");
+    fontSize.select(oldFont.getSize() + "");
     fontStyle.select(oldFont.getStyle());
 
     frame.setVisible(false);
@@ -80,28 +85,37 @@ public class FontChooser extends GFontChooser
   {
     Font newFont = new Font(fontName.getSelectedItem().toString(),
                             fontStyle.getSelectedIndex(),
-                            Integer.parseInt(fontSize.getSelectedItem().toString())
-                            );
+                            Integer.parseInt(fontSize.getSelectedItem().
+                                             toString())
+        );
     ap.av.setFont(newFont);
     ap.fontChanged();
   }
 
-
   protected void fontName_actionPerformed()
   {
-    if(init) return;
+    if (init)
+    {
+      return;
+    }
     changeFont();
   }
 
   protected void fontSize_actionPerformed()
   {
-    if(init) return;
+    if (init)
+    {
+      return;
+    }
     changeFont();
   }
 
   protected void fontStyle_actionPerformed()
   {
-    if(init) return;
+    if (init)
+    {
+      return;
+    }
     changeFont();
   }
 
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 5b7aa1e..3c3c52c 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,38 +1,41 @@
 /*
-* 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.appletgui;
 
 import java.awt.*;
-import jalview.datamodel.*;
+
 import jalview.analysis.*;
-public class IdCanvas extends Panel
+import jalview.datamodel.*;
+
+public class IdCanvas
+    extends Panel
 {
   protected AlignViewport av;
 
-  protected boolean showScores  = true;
+  protected boolean showScores = true;
 
-  protected int     maxIdLength = -1;
-  protected String  maxIdStr    = null;
+  protected int maxIdLength = -1;
+  protected String maxIdStr = null;
   Image image;
   Graphics gg;
-  int imgHeight=0;
+  int imgHeight = 0;
   boolean fastPaint = false;
 
   java.util.Vector searchResults;
@@ -40,81 +43,103 @@ public class IdCanvas extends Panel
   public IdCanvas(AlignViewport av)
   {
     setLayout(null);
-    this.av         = av;
+    this.av = av;
     PaintRefresher.Register(this);
   }
 
-  public void drawIdString(Graphics gg,SequenceI s,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
+  public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
+                           int ypos)
+  {
+    int charHeight = av.getCharHeight();
 
-      if(searchResults!=null && searchResults.contains(s))
-      {
-        gg.setColor(Color.black);
-        gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,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,getSize().width,charHeight);
-	  gg.setColor(Color.white);
-      } else {
-	  gg.setColor(s.getColor());
-	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getSize().width,charHeight);
-	  gg.setColor(Color.black);
-      }
+    if (searchResults != null && searchResults.contains(s))
+    {
+      gg.setColor(Color.black);
+      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+                  getSize().width, 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,
+                  getSize().width, charHeight);
+      gg.setColor(Color.white);
+    }
+    else
+    {
+      gg.setColor(s.getColor());
+      gg.fillRect(0, AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,
+                  getSize().width, charHeight);
+      gg.setColor(Color.black);
+    }
 
-      String string = s.getName();
-      if(av.getShowFullId())
-        string = s.getDisplayId();
+    String string = s.getName();
+    if (av.getShowFullId())
+    {
+      string = s.getDisplayId();
+    }
 
-      gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight-   (charHeight/5));
+    gg.drawString(string, 0,
+                  AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +
+                  charHeight - (charHeight / 5));
 
   }
 
   public void fastPaint(int vertical)
   {
-    if(gg==null)
-    {  repaint(); return;}
+    if (gg == null)
+    {
+      repaint();
+      return;
+    }
 
-    gg.copyArea( 0,0, getSize().width, imgHeight, 0, -vertical*av.charHeight );
+    gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);
 
-    int ss=av.startSeq, es=av.endSeq, transY = 0;
+    int ss = av.startSeq, es = av.endSeq, transY = 0;
     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(es > av.endSeq)
-         es = av.endSeq;
-     }
-
-
-
-        gg.translate(0, transY);
+    {
+      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 (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
 
-        drawIds(ss, es);
+    gg.translate(0, transY);
 
-        gg.translate( 0, -transY );
+    drawIds(ss, es);
 
+    gg.translate(0, -transY);
 
-      fastPaint = true;
-      repaint();
+    fastPaint = true;
+    repaint();
   }
 
   public void update(Graphics g)
   {
     paint(g);
   }
+
   public void paint(Graphics g)
   {
-    if(getSize().height<0 || getSize().width<0)
+    if (getSize().height < 0 || getSize().width < 0)
+    {
       return;
+    }
     if (fastPaint)
     {
       fastPaint = false;
@@ -125,51 +150,53 @@ public class IdCanvas extends Panel
     imgHeight = getSize().height;
     imgHeight -= imgHeight % av.charHeight;
 
-    if (imgHeight<1)
+    if (imgHeight < 1)
+    {
       return;
+    }
 
-    if(image==null || imgHeight!=image.getHeight(this))
+    if (image == null || imgHeight != image.getHeight(this))
     {
       image = createImage(getSize().width, imgHeight);
       gg = image.getGraphics();
       gg.setFont(av.getFont());
     }
 
-      //Fill in the background
-      gg.setColor(Color.white);
-      Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+    //Fill in the background
+    gg.setColor(Color.white);
+    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
                            av.getFont().getSize());
-      gg.setFont(italic);
+    gg.setFont(italic);
 
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawIds( av.getStartSeq(), av.endSeq);
+    drawIds(av.getStartSeq(), av.endSeq);
     g.drawImage(image, 0, 0, this);
   }
 
   void drawIds(int starty, int endy)
   {
-    Color currentColor     = Color.white;
+    Color currentColor = Color.white;
     Color currentTextColor = Color.black;
 
     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 <= getSize().height && 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);
-            }
-          }
+      int rowSize = av.getEndRes() - av.getStartRes();
+      // Draw the rest of the panels
 
+      for (int ypos = 2 * av.charHeight, row = av.startRes;
+           ypos <= getSize().height && 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
+    }
+    else
     {
 
       //Now draw the id strings
@@ -177,14 +204,17 @@ public class IdCanvas extends Panel
       {
         // Selected sequence colours
 
-        if(searchResults!=null && searchResults.contains(av.alignment.getSequenceAt(i)))
+        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)))
+        }
+        else if (av.getSelectionGroup() != null
+                 &&
+                 av.getSelectionGroup().sequences.contains(av.alignment.
+            getSequenceAt(i)))
         {
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
@@ -204,8 +234,10 @@ public class IdCanvas extends Panel
 
         gg.setColor(currentTextColor);
         String string = av.alignment.getSequenceAt(i).getName();
-        if(av.getShowFullId())
+        if (av.getShowFullId())
+        {
           string = av.alignment.getSequenceAt(i).getDisplayId();
+        }
         gg.drawString(string, 0,
                       AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +
                       av.charHeight - (av.charHeight / 5));
@@ -213,7 +245,7 @@ public class IdCanvas extends Panel
 
       // add a border
       gg.setColor(Color.white);
-      gg.fillRect(getSize().width-4,0,4,getSize().height);
+      gg.fillRect(getSize().width - 4, 0, 4, getSize().height);
     }
 
   }
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 4998360..39fab0a 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.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.appletgui;
 
@@ -24,21 +24,23 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class IdPanel extends Panel implements MouseListener, MouseMotionListener {
+public class IdPanel
+    extends Panel implements MouseListener, MouseMotionListener
+{
 
-  protected IdCanvas       idCanvas;
-  protected AlignViewport  av;
+  protected IdCanvas idCanvas;
+  protected AlignViewport av;
   protected AlignmentPanel alignPanel;
   ScrollThread scrollThread = null;
 
-  int            offy;
-  int            width;
+  int offy;
+  int width;
   int lastid = -1;
   boolean mouseDragging = false;
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
-    this.av         = av;
+    this.av = av;
     alignPanel = parent;
     idCanvas = new IdCanvas(av);
     setLayout(new BorderLayout());
@@ -47,24 +49,33 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
     idCanvas.addMouseMotionListener(this);
   }
 
-  public void mouseMoved(MouseEvent e) {}
+  public void mouseMoved(MouseEvent e)
+  {}
 
-
-  public void mouseDragged(MouseEvent e) {
+  public void mouseDragged(MouseEvent e)
+  {
     mouseDragging = true;
 
     int y = e.getY();
-    if(av.getWrapAlignment())
-      y-=2*av.charHeight;
+    if (av.getWrapAlignment())
+    {
+      y -= 2 * av.charHeight;
+    }
     int seq = av.getIndex(y);
 
-    if(seq<0)
+    if (seq < 0)
+    {
       return;
+    }
 
     if (seq < lastid)
+    {
       selectSeqs(lastid - 1, seq);
+    }
     else if (seq > lastid)
+    {
       selectSeqs(lastid + 1, seq);
+    }
 
     lastid = seq;
     alignPanel.repaint();
@@ -74,57 +85,77 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
   {
     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.bin.JalviewLite.showURL(
-             "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +
-             "]+-vn+2");
-       }catch(Exception ex){ex.printStackTrace();}
+      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.bin.JalviewLite.showURL(
+            "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +
+            "]+-vn+2");
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
     }
 
   }
+
   public void mouseEntered(MouseEvent e)
   {
-    if(scrollThread!=null)
+    if (scrollThread != null)
+    {
       scrollThread.running = false;
+    }
   }
 
-  public void mouseExited (MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
-    if(av.getWrapAlignment())
+    if (av.getWrapAlignment())
+    {
       return;
+    }
 
-    if(mouseDragging && e.getY()<0 && av.getStartSeq()>0)
+    if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
     {
       scrollThread = new ScrollThread(true);
     }
 
-    if(mouseDragging && e.getY()>=getSize().height && av.alignment.getHeight()>av.getEndSeq())
+    if (mouseDragging && e.getY() >= getSize().height &&
+        av.alignment.getHeight() > av.getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
   }
 
-
-  public void mousePressed(MouseEvent e) {
+  public void mousePressed(MouseEvent e)
+  {
     if (e.getClickCount() == 2)
+    {
       return;
+    }
 
     int y = e.getY();
-    if(av.getWrapAlignment())
-      y-=2*av.charHeight;
+    if (av.getWrapAlignment())
+    {
+      y -= 2 * av.charHeight;
+    }
 
     int seq = av.getIndex(y);
     if (seq == -1)
+    {
       return;
+    }
 
-    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
+        InputEvent.BUTTON3_MASK)
     {
       APopupMenu popup = new APopupMenu(alignPanel, null);
       this.add(popup);
@@ -132,31 +163,40 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
       return;
     }
 
-
-    if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)
+    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);
-      for (int i =0; i< sg.getSize(); i++)
+      selection.setEndRes(av.alignment.getWidth() - 1);
+      for (int i = 0; i < sg.getSize(); i++)
+      {
         selection.addSequence(sg.getSequenceAt(i));
+      }
 
       av.setSelectionGroup(selection);
       return;
     }
 
-    if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))
+    if (av.getSelectionGroup() == null ||
+        (!e.isControlDown() && av.getSelectionGroup() != null))
+    {
       av.setSelectionGroup(new SequenceGroup());
+    }
 
     av.getSelectionGroup().setStartRes(0);
-    av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
+    av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
 
-    if(e.isShiftDown() && lastid!=-1)
+    if (e.isShiftDown() && lastid != -1)
+    {
       selectSeqs(lastid, seq);
+    }
     else
+    {
       selectSeq(seq);
+    }
 
     alignPanel.repaint();
   }
@@ -168,44 +208,52 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
     av.getSelectionGroup().addOrRemove(pickedSeq);
   }
 
-  void selectSeqs(int start, int end) {
+  void selectSeqs(int start, int end)
+  {
 
     lastid = start;
     if (end < start)
-     {
-       int tmp = start;
-       start = end;
-       end   = tmp;
-       lastid = end;
-     }
-
-     for (int i = start; i <= end; i++)
-        av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));
+    {
+      int tmp = start;
+      start = end;
+      end = tmp;
+      lastid = end;
+    }
 
-   }
+    for (int i = start; i <= end; i++)
+    {
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));
+    }
 
+  }
 
   public void mouseReleased(MouseEvent e)
   {
-    if(scrollThread!=null)
+    if (scrollThread != null)
+    {
       scrollThread.running = false;
+    }
 
     mouseDragging = false;
     PaintRefresher.Refresh(this);
   }
 
-  public void highlightSearchResults( java.util.Vector found )
+  public void highlightSearchResults(java.util.Vector found)
   {
-    idCanvas.setHighlighted( found );
+    idCanvas.setHighlighted(found);
 
-    if(found == null)
+    if (found == null)
+    {
       return;
+    }
 
-    int index = av.alignment.findIndex( (SequenceI)found.elementAt(0));
+    int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
 
     // do we need to scroll the panel?
-    if(av.getStartSeq()>index || av.getEndSeq()<index)
-        alignPanel.setScrollValues( av.getStartRes(), index);
+    if (av.getStartSeq() > index || av.getEndSeq() < index)
+    {
+      alignPanel.setScrollValues(av.getStartRes(), index);
+    }
   }
 
   // this class allows scrolling off the bottom of the visible alignment
@@ -230,22 +278,30 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
       running = true;
       while (running)
       {
-        if(alignPanel.scrollUp(up))
+        if (alignPanel.scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
           int seq = av.getStartSeq();
-          if(!up)
+          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
@@ -256,6 +312,6 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
         {}
       }
     }
-}
+  }
 
 }
diff --git a/src/jalview/appletgui/IdwidthAdjuster.java b/src/jalview/appletgui/IdwidthAdjuster.java
index 5e5df30..5b4de85 100755
--- a/src/jalview/appletgui/IdwidthAdjuster.java
+++ b/src/jalview/appletgui/IdwidthAdjuster.java
@@ -1,79 +1,103 @@
 /*
-* 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.appletgui;
 
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
 
-
-public class IdwidthAdjuster extends Panel implements MouseListener, MouseMotionListener
+public class IdwidthAdjuster
+    extends Panel implements MouseListener, MouseMotionListener
 {
   boolean active = false;
-  int oldX=0;
+  int oldX = 0;
   Image image;
-  AlignmentPanel ap ;
+  AlignmentPanel ap;
 
   public IdwidthAdjuster(AlignmentPanel ap)
   {
     setLayout(null);
     this.ap = ap;
     java.net.URL url = getClass().getResource("/images/idwidth.gif");
-       if (url != null)
-         image = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+    if (url != null)
+    {
+      image = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+    }
 
     addMouseListener(this);
     addMouseMotionListener(this);
   }
 
   public void mousePressed(MouseEvent evt)
-  { oldX = evt.getX(); }
+  {
+    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 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.getSize();
     int dif = evt.getX() - oldX;
 
-    if(d.width+dif>20 || dif>0)
+    if (d.width + dif > 20 || dif > 0)
     {
-      ap.setIdWidth(d.width + dif,d.height);
+      ap.setIdWidth(d.width + dif, d.height);
       this.setSize(d.width + dif, getSize().height);
     }
 
     oldX = evt.getX();
   }
 
-  public void mouseMoved(MouseEvent evt)   {}
-  public void mouseClicked(MouseEvent evt) {}
+  public void mouseMoved(MouseEvent evt)
+  {}
+
+  public void mouseClicked(MouseEvent evt)
+  {}
 
   public void paint(Graphics g)
   {
     g.setColor(Color.white);
-    g.fillRect(0,0, getSize().width, getSize().height);
-    if(active)
+    g.fillRect(0, 0, getSize().width, getSize().height);
+    if (active)
     {
-      if(image!=null)
-        g.drawImage(image, getSize().width-20, 2, this);
+      if (image != null)
+      {
+        g.drawImage(image, getSize().width - 20, 2, this);
+      }
     }
   }
 
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 97f8147..d02892b 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,28 +1,29 @@
 /*
-* 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.appletgui;
 
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
 
-public class OverviewPanel extends Panel implements Runnable
+public class OverviewPanel
+    extends Panel implements Runnable
 {
   Image miniMe;
   AlignViewport av;
@@ -31,8 +32,8 @@ public class OverviewPanel extends Panel implements Runnable
   float scaleh = 1f;
 
   public int width, sequencesHeight;
-  int graphHeight=30;
-  int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;
+  int graphHeight = 30;
+  int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
 
   boolean resizing = false;
 
@@ -47,47 +48,58 @@ public class OverviewPanel extends Panel implements Runnable
     nullFrame.addNotify();
 
     // 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())
+    float initialScale = (float) av.alignment.getWidth() /
+        (float) av.alignment.getHeight();
+    if (av.alignment.getWidth() > av.alignment.getHeight())
     {
       // wider
       width = 400;
-      sequencesHeight = (int)(400f/initialScale);
+      sequencesHeight = (int) (400f / initialScale);
     }
     else
     {
       // taller
-      width = (int)(400f*initialScale);
+      width = (int) (400f * initialScale);
       sequencesHeight = 300;
-      if(width<120)
+      if (width < 120)
+      {
         width = 120;
+      }
     }
 
-    setSize (new Dimension(width, sequencesHeight+graphHeight));
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
     addComponentListener(new ComponentAdapter()
-   {
+    {
 
-       public void componentResized(ComponentEvent evt)
-       {
-         if( getSize().width!=width || getSize().height!=sequencesHeight+graphHeight)
-         {
-           updateOverviewImage();
-         }
-       }
-   });
+      public void componentResized(ComponentEvent evt)
+      {
+        if (getSize().width != width ||
+            getSize().height != sequencesHeight + graphHeight)
+        {
+          updateOverviewImage();
+        }
+      }
+    });
 
     addMouseMotionListener(new MouseMotionAdapter()
-           {
-             public void mouseDragged(MouseEvent evt)
-             { doMouseDragged(evt);}
-           });
+    {
+      public void mouseDragged(MouseEvent evt)
+      {
+        doMouseDragged(evt);
+      }
+    });
 
     addMouseListener(new MouseAdapter()
     {
       public void mousePressed(MouseEvent evt)
-      { doMousePressed(evt);}
+      {
+        doMousePressed(evt);
+      }
+
       public void mouseReleased(MouseEvent evt)
-      { doMouseReleased(evt);}
+      {
+        doMouseReleased(evt);
+      }
     });
 
     updateOverviewImage();
@@ -108,9 +120,11 @@ public class OverviewPanel extends Panel implements Runnable
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    if(!resizing)
-    ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),
-                        (int)(boxY/scaleh/av.getCharHeight()) );
+    if (!resizing)
+    {
+      ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
+                         (int) (boxY / scaleh / av.getCharHeight()));
+    }
   }
 
   public void doMouseDragged(MouseEvent evt)
@@ -118,9 +132,11 @@ public class OverviewPanel extends Panel implements Runnable
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    if(!resizing)
-    ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),
-                        (int)(boxY/scaleh/av.getCharHeight()) );
+    if (!resizing)
+    {
+      ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
+                         (int) (boxY / scaleh / av.getCharHeight()));
+    }
     repaint();
     ap.repaint();
   }
@@ -128,21 +144,29 @@ public class OverviewPanel extends Panel implements Runnable
   void checkValid()
   {
     if (boxY < 0)
+    {
       boxY = 0;
+    }
 
     if (boxY > sequencesHeight - boxHeight)
-      boxY = sequencesHeight - boxHeight+1;
+    {
+      boxY = sequencesHeight - boxHeight + 1;
+    }
 
     if (boxX < 0)
+    {
       boxX = 0;
+    }
 
     if (boxX > width - boxWidth)
+    {
       boxX = width - boxWidth;
+    }
   }
 
   public void updateOverviewImage()
   {
-    if(resizing)
+    if (resizing)
     {
       return;
     }
@@ -159,15 +183,15 @@ public class OverviewPanel extends Panel implements Runnable
     int alwidth = av.alignment.getWidth();
     int alheight = av.alignment.getHeight();
 
-    if(getSize().width>0 && getSize().height>0)
+    if (getSize().width > 0 && getSize().height > 0)
     {
       width = getSize().width;
       sequencesHeight = getSize().height - graphHeight;
     }
 
-    setSize (new Dimension(width, sequencesHeight+graphHeight));
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
 
-    int fullsizeWidth  = alwidth * av.getCharWidth();
+    int fullsizeWidth = alwidth * av.getCharWidth();
     int fullsizeHeight = alheight * av.getCharHeight();
 
     scalew = (float) width / (float) fullsizeWidth;
@@ -180,62 +204,72 @@ public class OverviewPanel extends Panel implements Runnable
     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);
-
+                 sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);
 
     boolean oldRenderGaps = av.renderGaps;
-    try{
-    // We'll have to draw the full size alignment in chunks, as an image of the
-    // whole alignment requires too much memory
+    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();
+      int maxSize = 2000 / av.getFont().getSize();
       Image block;
-      int blockx=0, blocky=0, blockw=0, blockh=0, eRes=0, eSeq=0;
+      int blockx = 0, blocky = 0, blockw = 0, blockh = 0, eRes = 0, eSeq = 0;
 
       av.setRenderGaps(false);
-      for(int sRes=0, chunkx=0; sRes<alwidth; sRes+=maxSize, chunkx++)
+      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 = 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+=maxSize;
-            if(eSeq>alheight)
-              eSeq = alheight;
+            eSeq = alheight;
+          }
 
-            blocky = 0;
-            blockx = (int)((float)sRes/(float)alwidth * width);
+          blocky = 0;
+          blockx = (int) ( (float) sRes / (float) alwidth * width);
 
-            block = nullFrame.createImage((eRes-sRes)*av.charWidth, (eSeq-sSeq)*av.charHeight);
-            g = block.getGraphics();
+          block = nullFrame.createImage( (eRes - sRes) * av.charWidth,
+                                        (eSeq - sSeq) * av.charHeight);
+          g = block.getGraphics();
 
-           ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq, 0);
+          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;
+          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);
+          blocky += (int) ( (float) sSeq / (float) alheight * sequencesHeight);
 
-           mg.drawImage(block,  blockx,
-                              blocky ,
-                            blockx + blockw,
-                            blocky + blockh,
+          mg.drawImage(block, blockx,
+                       blocky,
+                       blockx + blockw,
+                       blocky + blockh,
 
-                         0, 0, block.getWidth(null),block.getHeight(null), this);
+                       0, 0, block.getWidth(null), block.getHeight(null), this);
 
           block = null;
-          }
+        }
 
       }
 
-    }catch(OutOfMemoryError error)
-    {     System.err.println("Out of memory when trying to calculate the overview window image!");   }
-
+    }
+    catch (OutOfMemoryError error)
+    {
+      System.err.println(
+          "Out of memory when trying to calculate the overview window image!");
+    }
 
     av.setRenderGaps(oldRenderGaps);
     resizing = false;
@@ -245,38 +279,41 @@ public class OverviewPanel extends Panel implements Runnable
 
   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();
+    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 update(Graphics g)
- {
-   paint(g);
- }
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
 
   public void paint(Graphics g)
   {
-    if(resizing)
+    if (resizing)
     {
       g.setColor(Color.white);
       g.fillRect(0, 0, getSize().width, getSize().height);
       g.setColor(Color.black);
 
       g.setFont(new Font("Verdana", Font.BOLD, 15));
-      g.drawString("Recalculating", 5, sequencesHeight/2);
-      g.drawString("Overview.....", 5, sequencesHeight/2 +20);
+      g.drawString("Recalculating", 5, sequencesHeight / 2);
+      g.drawString("Overview.....", 5, sequencesHeight / 2 + 20);
     }
     else
     {
-      if(miniMe!=null)
-        g.drawImage(miniMe, 0,0,this);
+      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.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
     }
   }
 
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index f652aae..1dd05e0 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,33 +1,35 @@
 /*
-* 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.appletgui;
 
-import jalview.datamodel.*;
-import jalview.analysis.PCA;
-import jalview.jbappletgui.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
 
-public class PCAPanel extends GPCAPanel implements Runnable
+public class PCAPanel
+    extends GPCAPanel implements Runnable
 {
   PCA pca;
   int top;
@@ -39,30 +41,34 @@ public class PCAPanel extends GPCAPanel implements Runnable
     // do stuff
   }
 
-  public PCAPanel(AlignViewport av, SequenceI[] s) {
+  public PCAPanel(AlignViewport av, SequenceI[] s)
+  {
 
     this.av = av;
-    if(av.getSelectionGroup().getSize()>3)
+    if (av.getSelectionGroup().getSize() > 3)
     {
       s = new Sequence[av.getSelectionGroup().getSize()];
-      for(int i=0; i<s.length; i++)
+      for (int i = 0; i < s.length; i++)
+      {
         s[i] = av.getSelectionGroup().getSequenceAt(i);
+      }
     }
 
-
-    if(s==null)
+    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;
+    int ii = 0;
     while (ii < s.length && s[ii] != null)
     {
       ii++;
@@ -70,11 +76,11 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
     double[][] comps = new double[ii][ii];
 
-    for (int i=0; i < ii; i++ )
+    for (int i = 0; i < ii; i++)
     {
       if (pca.getEigenvalue(i) > 1e-4)
       {
-        comps[i]  = pca.component(i);
+        comps[i] = pca.component(i);
       }
     }
 
@@ -84,37 +90,39 @@ public class PCAPanel extends GPCAPanel implements Runnable
     yCombobox.select(1);
     zCombobox.select(2);
 
-    top = pca.getM().rows-1;
+    top = pca.getM().rows - 1;
 
     Vector points = new Vector();
-    float[][] scores = pca.getComponents(top-1,top-2,top-3,100);
+    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
-    for (int i =0; i < pca.getM().rows; i++ )
+    for (int i = 0; i < pca.getM().rows; i++)
     {
-      SequencePoint sp = new SequencePoint(s[i],scores[i]);
+      SequencePoint sp = new SequencePoint(s[i], scores[i]);
       points.addElement(sp);
     }
 
-    rc = new RotatableCanvas(av,points,pca.getM().rows);
+    rc = new RotatableCanvas(av, points, pca.getM().rows);
 
     //rc.printPoints();
 
     add(rc, BorderLayout.CENTER);
   }
 
-
   void doDimensionChange()
   {
-    if(top==0)
+    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];
+    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;
diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 0f2c1f6..670af70 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,50 +1,60 @@
 /*
-* 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.appletgui;
-import java.awt.*;
+
 import java.util.*;
 
+import java.awt.*;
+
 public class PaintRefresher
 {
   static Vector components = new Vector();
 
   public static void Register(Component c)
   {
-    if(!components.contains(c))
+    if (!components.contains(c))
+    {
       components.addElement(c);
+    }
     else
+    {
       components.removeElement(c);
+    }
   }
 
   public static void Refresh(Component c)
   {
     Component temp;
     Enumeration e = components.elements();
-    while( e.hasMoreElements() )
+    while (e.hasMoreElements())
     {
-      temp = (Component)e.nextElement();
+      temp = (Component) e.nextElement();
 
-      if(!temp.isValid())
-        components.removeElement( temp );
-      else if( temp == c )
-           continue;
+      if (!temp.isValid())
+      {
+        components.removeElement(temp);
+      }
+      else if (temp == c)
+      {
+        continue;
+      }
 
       temp.repaint();
     }
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 65f40c3..55cf2cc 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,89 +1,97 @@
 /*
-* 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.appletgui;
 
-import jalview.datamodel.*;
-import jalview.jbappletgui.GPairwiseAlignPanel;
-import jalview.analysis.*;
-import java.awt.event.*;
 import java.util.*;
 
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
 
-public class PairwiseAlignPanel extends GPairwiseAlignPanel
+public class PairwiseAlignPanel
+    extends GPairwiseAlignPanel
 {
-    Vector sequences = new Vector();
-    AlignViewport av;
+  Vector sequences = new Vector();
+  AlignViewport av;
 
-    public PairwiseAlignPanel(AlignViewport av)
+  public PairwiseAlignPanel(AlignViewport av)
+  {
+    super();
+    this.av = av;
+    float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().
+        getHeight()];
+    double totscore = 0;
+    int count = av.getSelectionGroup().getSize();
+
+    int acount = 0;
+    for (int i = 1; i < count; i++)
     {
-      super();
-      this.av = av;
-      float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];
-      double totscore = 0;
-      int count = av.getSelectionGroup().getSize();
-
-      int acount = 0;
-        for (int i = 1; i < count; i++)
-        {
-          for (int j = 0; j < i; j++)
-          {
-            acount++;
-            AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
-                                       av.getSelectionGroup().getSequenceAt(j),"pep");
-
-            as.calcScoreMatrix();
-            as.traceAlignment();
-            as.printAlignment();
-            scores[i][j] = (float)as.getMaxScore()/(float)as.getASeq1().length;
-            totscore = totscore + scores[i][j];
+      for (int j = 0; j < i; j++)
+      {
+        acount++;
+        AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
+                                   av.getSelectionGroup().getSequenceAt(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.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));
+        sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));
 
-            textarea.append(as.getOutput());
-            sequences.addElement( new Sequence( as.getS1().getName(), as.getAStr1()) );
-            sequences.addElement( new Sequence( as.getS2().getName(), as.getAStr2()) );
-
-
-          }
-        }
+      }
+    }
 
-        if (count > 2)
+    if (count > 2)
+    {
+      for (int i = 0; i < count; i++)
+      {
+        for (int j = 0; j < i; j++)
         {
-          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);
+          jalview.util.Format.print(System.out, "%7.3f",
+                                    scores[i][j] / totscore);
         }
       }
-
+    }
+  }
 
   protected void viewInEditorButton_actionPerformed(ActionEvent e)
   {
 
-      Sequence [] seq = new Sequence[sequences.size()];
-
-      for (int i=0;i<sequences.size();i++)
-       seq[i] = (Sequence) sequences.elementAt(i);
+    Sequence[] seq = new Sequence[sequences.size()];
 
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      seq[i] = (Sequence) sequences.elementAt(i);
+    }
 
-      AlignFrame af = new AlignFrame(new Alignment(seq));
-      jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",
-                               AlignFrame.NEW_WINDOW_WIDTH,
-                               AlignFrame.NEW_WINDOW_HEIGHT);
+    AlignFrame af = new AlignFrame(new Alignment(seq));
+    jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",
+                                     AlignFrame.NEW_WINDOW_WIDTH,
+                                     AlignFrame.NEW_WINDOW_HEIGHT);
 
   }
 
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 735a579..42ac7f4 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,36 +1,38 @@
 /*
-* 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.appletgui;
 
-import jalview.jbappletgui.*;
-import jalview.datamodel.*;
-import java.awt.event.*;
 import java.util.*;
 
-public class RedundancyPanel extends GSliderPanel
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
+
+public class RedundancyPanel
+    extends GSliderPanel
 {
   AlignmentPanel ap;
 
   SequenceI[] oldAlignment;
 
-
   public RedundancyPanel(AlignmentPanel ap)
   {
     this.ap = ap;
@@ -41,81 +43,87 @@ public class RedundancyPanel extends GSliderPanel
     {
       public void adjustmentValueChanged(AdjustmentEvent evt)
       {
-        valueField.setText( slider.getValue()+"" );
+        valueField.setText(slider.getValue() + "");
       }
     });
 
     slider.setMinimum(0);
     slider.setMaximum(100);
-    slider.setValue(100 );
+    slider.setValue(100);
 
   }
 
   public void applyButton_actionPerformed(ActionEvent e)
   {
-       float threshold = slider.getValue();
-       Vector del;
+    float threshold = slider.getValue();
+    Vector del;
+
+    oldAlignment = new SequenceI[ap.av.alignment.getHeight()];
+    for (int i = 0; i < ap.av.alignment.getHeight(); i++)
+    {
+      oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),
+                                     ap.av.alignment.getSequenceAt(i).
+                                     getSequence());
+    }
+
+    undoButton.setEnabled(true);
+
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg != null && sg.getSize() > 1)
+    {
 
-       oldAlignment = new SequenceI[ap.av.alignment.getHeight()];
-        for (int i = 0; i < ap.av.alignment.getHeight(); i++)
+      del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
+      for (int i = 0; i < del.size(); i++)
+      {
+        if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
         {
-           oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),
-                                ap.av.alignment.getSequenceAt(i).
-                                getSequence());
+          sg.deleteSequence( (SequenceI) del.elementAt(i));
         }
+      }
 
-        undoButton.setEnabled(true);
-
-        SequenceGroup sg = ap.av.getSelectionGroup();
-       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));
-
-         }
-         else
-         {
-           Vector s = new Vector();
-           int i=0;
-           while(i < ap.av.alignment.getHeight())
-           {
-             s.addElement( ap.av.alignment.getSequenceAt(i) );
-             i++;
-           }
-            del = ap.av.alignment.removeRedundancy(threshold,s);
-           for (int j=0; j < del.size(); j++)
-           {
-               if (sg.sequences.contains((SequenceI)del.elementAt(j)))
-               sg.deleteSequence((SequenceI)del.elementAt(j));
-
-           }
-         }
-
-         ap.repaint();
+    }
+    else
+    {
+      Vector s = new Vector();
+      int i = 0;
+      while (i < ap.av.alignment.getHeight())
+      {
+        s.addElement(ap.av.alignment.getSequenceAt(i));
+        i++;
+      }
+      del = ap.av.alignment.removeRedundancy(threshold, s);
+      for (int j = 0; j < del.size(); j++)
+      {
+        if (sg.sequences.contains( (SequenceI) del.elementAt(j)))
+        {
+          sg.deleteSequence( (SequenceI) del.elementAt(j));
+        }
+
+      }
+    }
+
+    ap.repaint();
 
   }
 
   public void undoButton_actionPerformed(ActionEvent e)
   {
-      undoButton.setEnabled(false);
-      ap.av.setAlignment( new Alignment(oldAlignment) );
-      oldAlignment = null;
-      ap.repaint();
+    undoButton.setEnabled(false);
+    ap.av.setAlignment(new Alignment(oldAlignment));
+    oldAlignment = null;
+    ap.repaint();
   }
 
-
   public void valueField_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
     }
-    catch(Exception ex)
+    catch (Exception ex)
     {
-      valueField.setText( slider.getValue()+"" );
+      valueField.setText(slider.getValue() + "");
     }
   }
 }
diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index a13b1a2..7d32b86 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -1,42 +1,43 @@
 /*
-* 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.appletgui;
 
-import jalview.math.*;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.math.*;
+import jalview.util.*;
 
-public class RotatableCanvas extends Panel implements MouseListener,
-                                                       MouseMotionListener,
-                                                       KeyListener
-                                                       //RubberbandListener,
-                                                       //SequenceSelectionListener
+public class RotatableCanvas
+    extends Panel implements MouseListener,
+    MouseMotionListener,
+    KeyListener
+//RubberbandListener,
+//SequenceSelectionListener
 {
-  RotatableMatrix idmat  = new RotatableMatrix(3,3);
-  RotatableMatrix objmat = new RotatableMatrix(3,3);
-  RotatableMatrix rotmat = new RotatableMatrix(3,3);
+  RotatableMatrix idmat = new RotatableMatrix(3, 3);
+  RotatableMatrix objmat = new RotatableMatrix(3, 3);
+  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
 
   //RubberbandRectangle rubberband;
 
@@ -85,7 +86,8 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
 
   public RotatableCanvas(AlignViewport av,
-                          Vector points, int npoint) {
+                         Vector points, int npoint)
+  {
     this.points = points;
     this.npoint = npoint;
     this.av = av;
@@ -94,24 +96,31 @@ public class RotatableCanvas extends Panel implements MouseListener,
     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++) {
+    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++) {
-      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);
+    for (int i = 0; i < 3; i++)
+    {
+      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);
         }
       }
     }
@@ -128,59 +137,70 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
     addMouseListener(this);
     addKeyListener(this);
-   // if (getParent() != null) {
-   //   getParent().addKeyListener(this);
+    // if (getParent() != null) {
+    //   getParent().addKeyListener(this);
     //}
     addMouseMotionListener(this);
 
     // Add rubberband
- //   rubberband  = new RubberbandRectangle(this);
-  //  rubberband.setActive(true);
- //   rubberband.addListener(this);
+    //   rubberband  = new RubberbandRectangle(this);
+    //  rubberband.setActive(true);
+    //   rubberband.addListener(this);
   }
 
- /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
-    redrawneeded = true;
-    repaint();
-    return true;
-  }
+  /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
+     redrawneeded = true;
+     repaint();
+     return true;
+   }
 
-  public void removeNotify() {
-    controller.removeListener(this);
-    super.removeNotify();
-  }*/
+   public void removeNotify() {
+     controller.removeListener(this);
+     super.removeNotify();
+   }*/
 
-  public void initAxes() {
-    for (int i = 0; i < 3; i++) {
-      for (int j=0; j < 3; j++) {
-        if (i != j) {
+  public void initAxes()
+  {
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
+        {
           axes[i][j] = 0;
-        } else {
+        }
+        else
+        {
           axes[i][j] = 1;
         }
       }
     }
   }
 
-  public void findWidth() {
+  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);
-        if (sp.coord[i] >= max[i]) {
+    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]) {
+        if (sp.coord[i] <= min[i])
+        {
           min[i] = sp.coord[i];
         }
       }
@@ -197,130 +217,156 @@ public class RotatableCanvas extends Panel implements MouseListener,
     maxwidth = width[0];
 
     if (width[1] > width[0])
+    {
       maxwidth = width[1];
+    }
     if (width[2] > width[1])
+    {
       maxwidth = width[2];
+    }
 
     //System.out.println("Maxwidth = " + maxwidth);
   }
 
-  public float findScale() {
+  public float findScale()
+  {
     int dim, width, height;
-    if (getSize().width != 0) {
+    if (getSize().width != 0)
+    {
       width = getSize().width;
       height = getSize().height;
-    } else {
+    }
+    else
+    {
       width = prefsize.width;
       height = prefsize.height;
     }
 
-    if (width < height) {
+    if (width < height)
+    {
       dim = width;
-    } else {
+    }
+    else
+    {
       dim = height;
     }
 
-    return (float)(dim*scalefactor/(2*maxwidth));
+    return (float) (dim * scalefactor / (2 * maxwidth));
   }
 
-  public void findCentre() {
+  public void findCentre()
+  {
     //Find centre coordinate
     findWidth();
 
-    centre[0] = (max[0] + min[0])/2;
-    centre[1] = (max[1] + min[1])/2;
-    centre[2] = (max[2] + min[2])/2;
+    centre[0] = (max[0] + min[0]) / 2;
+    centre[1] = (max[1] + min[1]) / 2;
+    centre[2] = (max[2] + min[2]) / 2;
 
     //    System.out.println("Centre x " + centre[0]);
     //System.out.println("Centre y " + centre[1]);
     //System.out.println("Centre z " + centre[2]);
   }
 
-  public Dimension getPreferredSize() {
-    if (prefsize != null) {
+  public Dimension getPreferredSize()
+  {
+    if (prefsize != null)
+    {
       return prefsize;
-    } else {
-      return new Dimension(400,400);
+    }
+    else
+    {
+      return new Dimension(400, 400);
     }
   }
 
-  public Dimension getMinimumSize() {
+  public Dimension getMinimumSize()
+  {
     return getPreferredSize();
   }
 
-  public void paint(Graphics g) {
+  public void paint(Graphics g)
+  {
     //Only create the image at the beginning -
-    if ((img == null) || (prefsize.width != getSize().width) || (prefsize.height != getSize().height)) {
+    if ( (img == null) || (prefsize.width != getSize().width) ||
+        (prefsize.height != getSize().height))
+    {
       prefsize.width = getSize().width;
       prefsize.height = getSize().height;
 
       scale = findScale();
 
       //      System.out.println("New scale = " + scale);
-      img = createImage(getSize().width,getSize().height);
+      img = createImage(getSize().width, getSize().height);
       ig = img.getGraphics();
 
     }
 
+    drawBackground(ig, Color.black);
+    drawScene(ig);
+    if (drawAxes == true)
+    {
+      drawAxes(ig);
+    }
 
-      drawBackground(ig,Color.black);
-      drawScene(ig);
-      if (drawAxes == true)
-      {
-        drawAxes(ig);
-      }
-
-
-    g.drawImage(img,0,0,this);
+    g.drawImage(img, 0, 0, this);
   }
 
-  public void drawAxes(Graphics g) {
+  public void drawAxes(Graphics g)
+  {
 
     g.setColor(Color.yellow);
-    for (int i=0; i < 3 ; i++) {
-      g.drawLine(getSize().width/2,getSize().height/2,
-                 (int)(axes[i][0]*scale*max[0] + getSize().width/2),
-                 (int)(axes[i][1]*scale*max[1] + getSize().height/2));
+    for (int i = 0; i < 3; i++)
+    {
+      g.drawLine(getSize().width / 2, getSize().height / 2,
+                 (int) (axes[i][0] * scale * max[0] + getSize().width / 2),
+                 (int) (axes[i][1] * scale * max[1] + getSize().height / 2));
     }
   }
 
-  public void drawBackground(Graphics g, Color col) {
+  public void drawBackground(Graphics g, Color col)
+  {
     g.setColor(col);
-    g.fillRect(0,0,prefsize.width,prefsize.height);
+    g.fillRect(0, 0, prefsize.width, prefsize.height);
   }
 
-
-  public void drawScene(Graphics g) {
+  public void drawScene(Graphics g)
+  {
     boolean darker = false;
 
-    int halfwidth = getSize().width/2;
-    int halfheight = getSize().height/2;
+    int halfwidth = getSize().width / 2;
+    int halfheight = getSize().height / 2;
 
-    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;
+    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);
+      {
+        g.setColor(Color.white);
+      }
       else
-          g.setColor(sp.sequence.getColor());
-
+      {
+        g.setColor(sp.sequence.getColor());
+      }
 
       if (av.getSelectionGroup() != null)
       {
-        if (av.getSelectionGroup().sequences.contains(((SequencePoint)points.elementAt(i)).sequence))
+        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.fillRect(x - 3, y - 3, 6, 6);
       g.setColor(Color.red);
     }
 //    //Now the rectangle
@@ -331,52 +377,75 @@ public class RotatableCanvas extends Panel implements MouseListener,
 //    }
   }
 
-  public Dimension minimumsize() {
+  public Dimension minimumsize()
+  {
     return prefsize;
   }
 
-  public Dimension preferredsize() {
+  public Dimension preferredsize()
+  {
     return prefsize;
   }
 
-  public void keyTyped(KeyEvent evt) { }
-  public void keyReleased(KeyEvent evt) { }
+  public void keyTyped(KeyEvent evt)
+  {}
 
-  public void keyPressed(KeyEvent evt) {
+  public void keyReleased(KeyEvent evt)
+  {}
+
+  public void keyPressed(KeyEvent evt)
+  {
     requestFocus();
-    if (evt.getKeyCode() == KeyEvent.VK_UP) {
-      scalefactor = (float)(scalefactor * 1.1);
+    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);
+    }
+    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+    {
+      scalefactor = (float) (scalefactor * 0.9);
       scale = findScale();
-    } else if (evt.getKeyChar() == 's') {
+    }
+    else if (evt.getKeyChar() == 's')
+    {
       System.err.println("DEBUG: Rectangle selection"); // log.debug
-      if (rectx2 != -1 && recty2 != -1) {
-        rectSelect(rectx1,recty1,rectx2,recty2);
+      if (rectx2 != -1 && recty2 != -1)
+      {
+        rectSelect(rectx1, recty1, rectx2, recty2);
 
       }
     }
     repaint();
   }
 
-  public void printPoints() {
-    for (int i=0; i < npoint; i++) {
-      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]);
+  public void printPoints()
+  {
+    for (int i = 0; i < npoint; i++)
+    {
+      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) { }
+  public void mouseClicked(MouseEvent evt)
+  {}
 
-  public void mousePressed(MouseEvent evt) {
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
+
+  public void mouseReleased(MouseEvent evt)
+  {}
+
+  public void mousePressed(MouseEvent evt)
+  {
     int x = evt.getX();
     int y = evt.getY();
 
@@ -395,7 +464,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     rectx2 = -1;
     recty2 = -1;
 
-    SequenceI found = findPoint(x,y);
+    SequenceI found = findPoint(x, y);
 
     if (found != null)
     {
@@ -406,45 +475,50 @@ public class RotatableCanvas extends Panel implements MouseListener,
       }
       else
       {
-          av.setSelectionGroup(new SequenceGroup());
-          av.getSelectionGroup().addOrRemove(found);
-          av.getSelectionGroup().setEndRes(av.alignment.getWidth());
+        av.setSelectionGroup(new SequenceGroup());
+        av.getSelectionGroup().addOrRemove(found);
+        av.getSelectionGroup().setEndRes(av.alignment.getWidth());
 
       }
     }
     repaint();
   }
 
- // private void fireSequenceSelectionEvent(Selection sel) {
- //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
+  // private void fireSequenceSelectionEvent(Selection sel) {
+  //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
   //}
 
   public void mouseMoved(MouseEvent evt)
   {
-  // SequenceI found = findPoint(evt.getX(), evt.getY());
+    // SequenceI found = findPoint(evt.getX(), evt.getY());
   }
 
-  public void mouseDragged(MouseEvent evt) {
+  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) {
+    if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
+    {
 //      rectx2 = evt.getX();
 //      recty2 = evt.getY();
-    } else {
+    }
+    else
+    {
       rotmat.setIdentity();
 
-      rotmat.rotate((float)(my-omy),'x');
-      rotmat.rotate((float)(mx-omx),'y');
+      rotmat.rotate( (float) (my - omy), 'x');
+      rotmat.rotate( (float) (mx - omx), 'y');
 
-      for (int i = 0; i < npoint; i++) {
-        SequencePoint sp = (SequencePoint)points.elementAt(i);
+      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 apply the rotation matrix
-        sp.coord= rotmat.vectorMultiply(sp.coord);
+        sp.coord = rotmat.vectorMultiply(sp.coord);
 
         //Now translate back again
         sp.coord[0] += centre[0];
@@ -452,7 +526,8 @@ public class RotatableCanvas extends Panel implements MouseListener,
         sp.coord[2] += centre[2];
       }
 
-      for (int i=0; i < 3; i++) {
+      for (int i = 0; i < 3; i++)
+      {
         axes[i] = rotmat.vectorMultiply(axes[i]);
       }
       omx = mx;
@@ -463,15 +538,21 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
   }
 
-  public void rectSelect(int x1, int y1, int x2, int y2) {
+  public void rectSelect(int x1, int y1, int x2, int y2)
+  {
     boolean changedSel = false;
-    for (int i=0; i < npoint; i++) {
-      SequencePoint sp = (SequencePoint)points.elementAt(i);
-      int tmp1 = (int)((sp.coord[0] - centre[0])*scale + (float)getSize().width/2.0);
-      int tmp2 = (int)((sp.coord[1] - centre[1])*scale + (float)getSize().height/2.0);
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int tmp1 = (int) ( (sp.coord[0] - centre[0]) * scale +
+                        (float) getSize().width / 2.0);
+      int tmp2 = (int) ( (sp.coord[1] - centre[1]) * scale +
+                        (float) getSize().height / 2.0);
 
-      if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) {
-        if (av != null) {
+      if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
+      {
+        if (av != null)
+        {
           if (!av.getSelectionGroup().sequences.contains(sp.sequence))
           {
             changedSel = true;
@@ -480,54 +561,60 @@ public class RotatableCanvas extends Panel implements MouseListener,
         }
       }
     }
-   // if (changedSel) {
-   //    fireSequenceSelectionEvent(av.getSelection());
-   // }
+    // if (changedSel) {
+    //    fireSequenceSelectionEvent(av.getSelection());
+    // }
   }
-  public SequenceI findPoint(int x, int y) {
 
-    int halfwidth = getSize().width/2;
-    int halfheight = getSize().height/2;
+  public SequenceI findPoint(int x, int y)
+  {
+
+    int halfwidth = getSize().width / 2;
+    int halfheight = getSize().height / 2;
 
     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;
+    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 ) {
+      if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
+      {
         found = i;
       }
     }
-    if (found != -1) {
-      return ((SequencePoint)points.elementAt(found)).sequence;
-    } else {
+    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/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 24460ba..71d360d 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,33 +1,35 @@
 /*
-* 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.appletgui;
 
-import jalview.datamodel.*;
 import java.awt.*;
 import java.awt.event.*;
 
-public class ScalePanel extends Panel
+import jalview.datamodel.*;
+
+public class ScalePanel
+    extends Panel
 {
 
   protected int offy = 4;
-  public    int width;
+  public int width;
 
   protected AlignViewport av;
   AlignmentPanel ap;
@@ -37,7 +39,7 @@ public class ScalePanel extends Panel
   public ScalePanel(AlignViewport av, AlignmentPanel ap)
   {
     setLayout(null);
-    this.av         = av;
+    this.av = av;
     this.ap = ap;
 
     addMouseListener(new MouseAdapter()
@@ -46,6 +48,7 @@ public class ScalePanel extends Panel
       {
         doMousePressed(evt);
       }
+
       public void mouseReleased(MouseEvent evt)
       {
         doMouseReleased(evt);
@@ -62,21 +65,25 @@ public class ScalePanel extends Panel
 
   }
 
-
-  public void doMousePressed(MouseEvent evt) {
+  public void doMousePressed(MouseEvent evt)
+  {
     int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
+    int res = x / av.getCharWidth() + av.getStartRes();
     SequenceGroup sg = null;
 
     if (av.getColumnSelection().contains(res))
+    {
       av.getColumnSelection().removeElement(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));
+      }
 
       sg.setStartRes(res);
       sg.setEndRes(res);
@@ -89,41 +96,53 @@ public class ScalePanel extends Panel
 
   public void doMouseReleased(MouseEvent evt)
   {
-    if(!stretchingGroup)
+    if (!stretchingGroup)
+    {
       return;
+    }
 
     int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
+    int res = x / av.getCharWidth() + av.getStartRes();
 
-   if (! av.getColumnSelection().contains(res))
-     av.getColumnSelection().addElement(res);
+    if (!av.getColumnSelection().contains(res))
+    {
+      av.getColumnSelection().addElement(res);
+    }
 
-   SequenceGroup sg = av.getSelectionGroup();
+    SequenceGroup sg = av.getSelectionGroup();
 
-   if(res>sg.getStartRes())
-     sg.setEndRes(res);
-   else if(res<sg.getStartRes())
-     sg.setStartRes(res);
+    if (res > sg.getStartRes())
+    {
+      sg.setEndRes(res);
+    }
+    else if (res < sg.getStartRes())
+    {
+      sg.setStartRes(res);
+    }
 
-   stretchingGroup = false;
-   ap.repaint();
+    stretchingGroup = false;
+    ap.repaint();
   }
 
   public void doMouseDragged(MouseEvent evt)
   {
     int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
+    int res = x / av.getCharWidth() + av.getStartRes();
 
     SequenceGroup sg = av.getSelectionGroup();
-    if(sg!=null)
+    if (sg != null)
     {
       stretchingGroup = true;
       if (res > sg.getStartRes())
+      {
         sg.setEndRes(res);
+      }
       else if (res < sg.getStartRes())
+      {
         sg.setStartRes(res);
+      }
 
-       ap.annotationPanel.addEditableColumn(res);
+      ap.annotationPanel.addEditableColumn(res);
       ap.repaint();
     }
   }
@@ -135,60 +154,65 @@ public class ScalePanel extends Panel
 
   public void paint(Graphics g)
   {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width, getSize().height);
+    drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,
+              getSize().height);
   }
 
 // scalewidth will normally be screenwidth,
-  public void drawScale(Graphics gg, int startx, int endx, int width, int height)
+  public void drawScale(Graphics gg, int startx, int endx, int width,
+                        int height)
   {
     gg.setFont(av.getFont());
 
     //Fill in the background
     gg.setColor(Color.white);
-    gg.fillRect(0,0,width, height);
+    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++)
+    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, getSize().height);
+      int sel = cs.columnAt(i);
+      if (sel >= startx && sel <= endx)
+      {
+        gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,
+                    getSize().height);
+      }
     }
 
-
     // Draw the scale numbers
     gg.setColor(Color.black);
-    int scalestartx = (startx/10) * 10;
+    int scalestartx = (startx / 10) * 10;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = av.charHeight -fm.getDescent();
+    int y = av.charHeight - fm.getDescent();
 
-    if(scalestartx%10==0)
-      scalestartx+=5;
+    if (scalestartx % 10 == 0)
+    {
+      scalestartx += 5;
+    }
 
-    for (int i=scalestartx;i < endx; i+= 5)
+    for (int i = scalestartx; i < endx; i += 5)
     {
-      if(i%10==0)
+      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,
+                    y + 2,
                     (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),
-                    y+fm.getDescent()*2);
+                    y + fm.getDescent() * 2);
       }
       else
+      {
         gg.drawLine( (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),
-                    y+fm.getDescent(),
+                    y + fm.getDescent(),
                     (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),
-                   y+fm.getDescent()*2);
-
+                    y + fm.getDescent() * 2);
+      }
 
     }
   }
 
-
 }
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 6855468..438d7ad 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,60 +1,61 @@
 /*
-* 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.appletgui;
 
 import java.awt.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
 
-public class SeqCanvas extends Panel
+public class SeqCanvas
+    extends Panel
 {
-    FeatureRenderer fr;
-    SequenceRenderer sr;
-    Image             img;
-    Graphics          gg;
-    int               imgWidth;
-    int               imgHeight;
-
-    AlignViewport     av;
+  FeatureRenderer fr;
+  SequenceRenderer sr;
+  Image img;
+  Graphics gg;
+  int imgWidth;
+  int imgHeight;
 
-    boolean showScores = false;
-    boolean displaySearch = false;
-    int [] searchResults = null;
+  AlignViewport av;
 
-    int chunkHeight;
-    int chunkWidth;
+  boolean showScores = false;
+  boolean displaySearch = false;
+  int[] searchResults = null;
 
-    boolean fastPaint = false;
+  int chunkHeight;
+  int chunkWidth;
 
+  boolean fastPaint = false;
 
-    public SeqCanvas(AlignViewport av)
-    {
-	this.av         = av;
-       fr = new FeatureRenderer(av);
-       sr = new SequenceRenderer(av);
-       PaintRefresher.Register(this);
+  public SeqCanvas(AlignViewport av)
+  {
+    this.av = av;
+    fr = new FeatureRenderer(av);
+    sr = new SequenceRenderer(av);
+    PaintRefresher.Register(this);
 
-    }
+  }
 
-  void drawNorthScale(Graphics g, int startx, int endx,int ypos) {
+  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  {
     int scalestartx = startx - startx % 10 + 10;
 
     g.setColor(Color.black);
@@ -76,8 +77,8 @@ public class SeqCanvas extends Panel
   void drawWestScale(Graphics g, int startx, int endx, int ypos)
   {
     FontMetrics fm = getFontMetrics(av.getFont());
-    ypos+= av.charHeight;
-      // EAST SCALE
+    ypos += av.charHeight;
+    // EAST SCALE
     for (int i = 0; i < av.alignment.getHeight(); i++)
     {
       SequenceI seq = av.alignment.getSequenceAt(i);
@@ -94,46 +95,50 @@ public class SeqCanvas extends Panel
         value = av.alignment.getSequenceAt(i).findPosition(index);
         break;
       }
-      if(value!=-1)
+      if (value != -1)
       {
-        int x = LABEL_WEST - fm.stringWidth(value+"");
-        g.drawString(value + "", x,  ypos +  i*av.charHeight - av.charHeight/5);
+        int x = LABEL_WEST - fm.stringWidth(value + "");
+        g.drawString(value + "", x,
+                     ypos + i * av.charHeight - av.charHeight / 5);
       }
     }
   }
 
   void drawEastScale(Graphics g, int startx, int endx, int ypos)
-{
-    ypos+= av.charHeight;
-    // EAST SCALE
-  for (int i = 0; i < av.alignment.getHeight(); i++)
   {
-    SequenceI seq = av.alignment.getSequenceAt(i);
-    int index = endx;
-    int value = -1;
-    while (index > startx)
+    ypos += av.charHeight;
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-      if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = endx;
+      int value = -1;
+      while (index > startx)
       {
-        index--;
-        continue;
-      }
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index--;
+          continue;
+        }
 
-      value = av.alignment.getSequenceAt(i).findPosition(index);
-      break;
+        value = av.alignment.getSequenceAt(i).findPosition(index);
+        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)
+  public void fastPaint(int horizontal, int vertical)
+  {
+    if (horizontal == 0 && vertical == 0 || gg == null)
+    {
       return;
+    }
 
     gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
                 -vertical * av.charHeight);
@@ -146,46 +151,53 @@ public void fastPaint(int horizontal, int vertical)
       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
+      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(es > av.endSeq)
+      if (es > av.endSeq)
+      {
         es = av.endSeq;
+      }
     }
 
-
     gg.translate(transX, transY);
 
     gg.setColor(Color.white);
-    gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight);
+    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.
- */
+  /**
+   * 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.
+   */
   public void update(Graphics g)
   {
     paint(g);
@@ -201,36 +213,43 @@ public void fastPaint(int horizontal, int vertical)
     }
 
     // this draws the whole of the alignment
-      imgWidth  = this.getSize().width;
-      imgHeight = this.getSize().height;
+    imgWidth = this.getSize().width;
+    imgHeight = this.getSize().height;
 
-      imgWidth -= imgWidth%av.charWidth;
-      imgHeight-= imgHeight%av.charHeight;
+    imgWidth -= imgWidth % av.charWidth;
+    imgHeight -= imgHeight % av.charHeight;
 
-      if(imgWidth<1 || imgHeight<1)
-              return;
+    if (imgWidth < 1 || imgHeight < 1)
+    {
+      return;
+    }
 
-      if(img==null || imgWidth!=img.getWidth(this) || imgHeight!=img.getHeight(this))
-      {
-        img = createImage(imgWidth, imgHeight);
-        gg = img.getGraphics();
-        gg.setFont(av.getFont());
-      }
+    if (img == null || imgWidth != img.getWidth(this) ||
+        imgHeight != img.getHeight(this))
+    {
+      img = createImage(imgWidth, imgHeight);
+      gg = img.getGraphics();
+      gg.setFont(av.getFont());
+    }
 
-      gg.setColor(Color.white);
-      gg.fillRect(0,0,imgWidth,imgHeight);
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
 
-    chunkWidth  =   getWrappedCanvasWidth( getSize().width );
-    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    chunkWidth = getWrappedCanvasWidth(getSize().width);
+    chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
     av.setChunkHeight(chunkHeight);
     av.setChunkWidth(chunkWidth);
 
-
     if (av.getWrapAlignment())
+    {
       drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);
+    }
     else
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);
+    {
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes,
+                av.startSeq, 0);
+    }
 
     g.drawImage(img, 0, 0, this);
 
@@ -244,84 +263,102 @@ public void fastPaint(int horizontal, int vertical)
     LABEL_EAST = 0;
     LABEL_WEST = 0;
 
-    if(av.scaleRightWrapped)
-      LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+    }
 
-    if(av.scaleLeftWrapped)
-      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
+    }
 
-    return  (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
+    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
   }
 
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
+                               int startRes)
   {
-      AlignmentI al = av.getAlignment();
+    AlignmentI al = av.getAlignment();
 
-      FontMetrics fm = getFontMetrics(av.getFont());
+    FontMetrics fm = getFontMetrics(av.getFont());
 
-      int LABEL_EAST = 0;
-      if(av.scaleRightWrapped)
-        LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );
-      int LABEL_WEST = 0;
-      if(av.scaleLeftWrapped)
-        LABEL_WEST = fm.stringWidth(al.getWidth()+"0");
+    int LABEL_EAST = 0;
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+    }
+    int LABEL_WEST = 0;
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
+    }
 
+    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
-      int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
-      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    av.endRes = av.startRes + cWidth;
 
-      av.endRes = av.startRes + cWidth;
+    int endx = startRes + cWidth - 1;
+    int ypos = 2 * av.charHeight;
 
-      int  endx   = startRes+cWidth-1;
-      int  ypos  = 2*av.charHeight;
+    while (ypos <= canvasHeight && startRes < av.alignment.getWidth())
+    {
+      g.setColor(Color.black);
 
-      while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )
+      if (av.scaleLeftWrapped)
       {
-        g.setColor(Color.black);
+        drawWestScale(g, startRes, endx, ypos);
+      }
 
-        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);
+      }
 
-        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);
+      }
 
-        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().y,
-                    cWidth*av.charWidth,
-                    (int)clip.getBounds().height
-                    );
-
-        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();
+      // 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().y,
+                  cWidth * av.charWidth,
+                  (int) clip.getBounds().height
+            );
       }
 
-  }
+      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;
 
-  synchronized public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
+      if (endx > al.getWidth())
+      {
+        endx = al.getWidth();
+      }
+    }
+
+  }
+
+  synchronized public void drawPanel(Graphics g, int x1, int x2, int y1, int y2,
+                                     int startx, int starty, int offset)
+  {
 
     g.setFont(av.getFont());
     sr.renderGaps(av.renderGaps);
@@ -330,23 +367,24 @@ public void fastPaint(int horizontal, int vertical)
 
     /// First draw the sequences
     /////////////////////////////
-    for (int i = y1 ; i < y2 ;i++)
+    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);
-     }
+      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);
+      }
     }
     //
     /////////////////////////////////////
@@ -365,42 +403,47 @@ public void fastPaint(int horizontal, int vertical)
     }
 
     if (group != null)
+    {
       do
       {
         int oldY = -1;
         int i = 0;
         boolean inGroup = false;
-        int top=-1, bottom =-1;
+        int top = -1, 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;
+          ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1;
 
           if (sx < getSize().width
               && ex > 0
               && group.sequences.contains(av.alignment.getSequenceAt(i)))
           {
-            if (bottom == -1 && (i==av.alignment.getHeight()-1 ||
-                !group.sequences.contains(av.alignment.getSequenceAt(i + 1))))
-              bottom = sy + av.charHeight ;
+            if (bottom == -1 && (i == av.alignment.getHeight() - 1 ||
+                                 !group.sequences.contains(av.alignment.
+                getSequenceAt(i + 1))))
+            {
+              bottom = sy + av.charHeight;
+            }
 
             if (!inGroup)
             {
-              if (top == -1 && i==0 ||
+              if (top == -1 && i == 0 ||
                   !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))
+              {
                 top = sy;
-
+              }
 
               oldY = sy;
               inGroup = true;
               if (group == av.getSelectionGroup())
               {
-                    g.setColor(new Color(255,0,0));
+                g.setColor(new Color(255, 0, 0));
               }
               else
               {
-                    g.setColor(group.getOutlineColour());
+                g.setColor(group.getOutlineColour());
               }
             }
           }
@@ -408,13 +451,13 @@ public void fastPaint(int horizontal, int vertical)
           {
             if (inGroup)
             {
-              g.drawLine(sx, oldY, sx, sy );
-              g.drawLine(sx+ex, oldY, sx+ex, sy );
+              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;
+                top = -1;
               }
               if (bottom != -1)
               {
@@ -422,7 +465,6 @@ public void fastPaint(int horizontal, int vertical)
                 bottom = -1;
               }
 
-
               inGroup = false;
             }
           }
@@ -431,37 +473,39 @@ public void fastPaint(int horizontal, int vertical)
         if (inGroup)
         {
 
-          if(top!=-1)
+          if (top != -1)
           {
             g.drawLine(sx, top, sx + ex, top);
-            top =-1;
+            top = -1;
           }
-          if(bottom!=-1)
-           {
-             g.drawLine(sx, bottom-1, sx + ex, bottom-1);
-             bottom = -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 );
+          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());
-
+    }
 
     /// Highlight search Results once all sequences have been drawn
     //////////////////////////////////////////////////////////
-    if(displaySearch)
+    if (displaySearch)
     {
-      for(int r=0; r<searchResults.length; r+=3)
+      for (int r = 0; r < searchResults.length; r += 3)
       {
         int searchSeq = searchResults[r];
 
@@ -469,21 +513,26 @@ public void fastPaint(int horizontal, int vertical)
         {
           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;
-          if(searchStart<x1)
+          if (searchStart < x1)
+          {
             searchStart = x1;
-          if(searchEnd > x2)
+          }
+          if (searchEnd > x2)
+          {
             searchEnd = x2;
+          }
 
           ssr.drawHighlightedText(seq,
                                   searchStart,
                                   searchEnd,
                                   (searchStart - startx) * av.charWidth,
                                   offset +
-                                  AlignmentUtil.getPixelHeight(starty, searchSeq,
+                                  AlignmentUtil.getPixelHeight(starty,
+              searchSeq,
               av.charHeight),
                                   av.charWidth,
                                   av.charHeight);
@@ -493,20 +542,21 @@ public void fastPaint(int horizontal, int vertical)
 
   }
 
-
-
-  public void highlightSearchResults(int [] results)
+  public void highlightSearchResults(int[] results)
   {
     // results are in the order sequence, startRes, endRes
-    if(results==null)
+    if (results == null)
+    {
       displaySearch = false;
+    }
     else
+    {
       displaySearch = true;
+    }
 
     searchResults = results;
 
     repaint();
   }
 
-
 }
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 163b967..1720edc 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,41 +1,43 @@
 /*
-* 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.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
+
 import jalview.datamodel.*;
-import java.util.*;
 import jalview.schemes.*;
 
-
-public class SeqPanel extends Panel
+public class SeqPanel
+    extends Panel
 {
 
-  public    SeqCanvas         seqCanvas;
-  public    AlignmentPanel    ap;
+  public SeqCanvas seqCanvas;
+  public AlignmentPanel ap;
 
   protected int lastres;
   protected int startseq;
-  int startEdit=-1;
-  int endEdit=-1;
+  int startEdit = -1;
+  int endEdit = -1;
 
   protected AlignViewport av;
 
@@ -48,74 +50,101 @@ public class SeqPanel extends Panel
   boolean editingSeqs = false;
   boolean groupEditing = false;
 
+  public SeqPanel(AlignViewport avp, AlignmentPanel p)
+  {
+    this.av = avp;
 
-
-  public SeqPanel(AlignViewport avp, AlignmentPanel p) {
-    this.av         = avp;
-
-    seqCanvas  = new SeqCanvas(avp);
+    seqCanvas = new SeqCanvas(avp);
     setLayout(new BorderLayout());
     add(seqCanvas);
 
     ap = p;
 
-    seqCanvas.addMouseMotionListener( new MouseMotionAdapter()
+    seqCanvas.addMouseMotionListener(new MouseMotionAdapter()
     {
       public void mouseMoved(MouseEvent evt)
       {
-       if(av.getWrapAlignment())
-         return;
-        doMouseMoved(evt);    }
+        if (av.getWrapAlignment())
+        {
+          return;
+        }
+        doMouseMoved(evt);
+      }
 
       public void mouseDragged(MouseEvent evt)
       {
-        if(av.getWrapAlignment())
-         return;
-        if( editingSeqs )
+        if (av.getWrapAlignment())
+        {
+          return;
+        }
+        if (editingSeqs)
+        {
           doMouseDragged(evt);
+        }
         else
+        {
           doMouseDraggedDefineMode(evt);
+        }
       }
     });
 
-    seqCanvas.addMouseListener( new MouseAdapter()
+    seqCanvas.addMouseListener(new MouseAdapter()
     {
       public void mouseReleased(MouseEvent evt)
       {
-        if(av.getWrapAlignment())
-         return;
-        if(editingSeqs)
+        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 (av.getWrapAlignment())
         {
-          if(evt.isAltDown() || evt.isControlDown())
+          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);
+        {
+          return;
+        }
+        doMouseExitedDefineMode(evt);
 
       }
+
       public void mouseEntered(MouseEvent evt)
       {
         if (av.getWrapAlignment() || editingSeqs)
+        {
           return;
+        }
         doMouseEnteredDefineMode(evt);
       }
 
@@ -123,31 +152,34 @@ public class SeqPanel extends Panel
     seqCanvas.repaint();
   }
 
+  public void doMouseReleased(MouseEvent evt)
+  {
 
-  public void doMouseReleased(MouseEvent evt) {
-
-    if(seqEditOccurred>-1)
+    if (seqEditOccurred > -1)
+    {
       editOccurred(seqEditOccurred);
+    }
 
     startseq = -1;
-    lastres  = -1;
+    lastres = -1;
     seqEditOccurred = -1;
-    editingSeqs  = false;
+    editingSeqs = false;
     groupEditing = false;
     ap.repaint();
   }
 
-  public void doMousePressed(MouseEvent evt) {
-    ap.alignFrame.addHistoryItem( new HistoryItem(
-        "Edit Sequence",av.alignment, HistoryItem.EDIT));
+  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();
 
-    res = x/av.getCharWidth() + av.getStartRes();
-    seq = y/av.getCharHeight() + av.getStartSeq();
+    res = x / av.getCharWidth() + av.getStartRes();
+    seq = y / av.getCharHeight() + av.getStartSeq();
 
     if (seq < av.getAlignment().getHeight() &&
         res < av.getAlignment().getSequenceAt(seq).getLength())
@@ -170,217 +202,248 @@ public class SeqPanel extends Panel
 
   public void doMouseMoved(MouseEvent evt)
   {
-    int res=0, seq=0;
+    int res = 0, seq = 0;
     int x = evt.getX();
     int y = evt.getY();
-    if(av.wrapAlignment)
+    if (av.wrapAlignment)
     {
-      y -= 2*av.charHeight;
-      int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
+      y -= 2 * av.charHeight;
+      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
-
-      res =   (int)((y/chunkHeight)*(getSize().width/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();
+      res = (int) ( (y / chunkHeight) * (getSize().width / av.charWidth)) +
+          x / av.getCharWidth() + av.getStartRes();
 
       y %= chunkHeight;
-      seq =     y / av.getCharHeight() + av.getStartSeq();
+      seq = y / av.getCharHeight() + av.getStartSeq();
 
     }
     else
     {
-      res = x / av.getCharWidth()  + av.getStartRes();
+      res = x / av.getCharWidth() + av.getStartRes();
       seq = y / av.getCharHeight() + av.getStartSeq();
     }
 
-
-    if(seq>=av.getAlignment().getHeight())
+    if (seq >= av.getAlignment().getHeight())
+    {
       return;
+    }
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    if(res>sequence.getLength())
+    if (res > sequence.getLength())
+    {
       return;
+    }
 
-    Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
+    Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
     String aa = "";
-    if(obj!=null)
-         aa = obj.toString();
+    if (obj != null)
+    {
+      aa = obj.toString();
+    }
 
-    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
-    if(aa!="")
-      text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                                         sequence.getName());
+    if (aa != "")
+    {
+      text.append("  Residue: " + aa + " (" +
+                  av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+    }
 
     ap.alignFrame.statusBar.setText(text.toString());
 
     // use aa to see if the mouse pointer is on a
-    if(  av.showSequenceFeatures)
+    if (av.showSequenceFeatures)
     {
       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(sbuffer.length()>0)
+          if (sbuffer.length() > 0)
+          {
             sbuffer.append("; ");
+          }
           sbuffer.append(sf.getType() + " " + sf.getDescription());
-          if(sf.getStatus().length()>0)
-            sbuffer.append(" ("+sf.getStatus()+")");
+          if (sf.getStatus().length() > 0)
+          {
+            sbuffer.append(" (" + sf.getStatus() + ")");
+          }
         }
 
       }
     }
 
-
   }
 
-  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;
-
-      boolean dragRight = true;
-      if (res < av.getAlignment().getWidth() && res < lastres)
-        dragRight = false;
-
-
-      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;
-               }
-             }
-           }
-
-         }
-     }
-
-     endEdit = res;
-     lastres = res;
-      seqCanvas.repaint();
+  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;
+    }
+
+    boolean dragRight = true;
+    if (res < av.getAlignment().getWidth() && res < lastres)
+    {
+      dragRight = false;
+    }
+
+    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;
+            }
+          }
+        }
+
+      }
+    }
+
+    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);
+  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;
+    seqEditOccurred = seq;
   }
 
   public void deleteChar(int j, int seq)
   {
 
     av.alignment.getSequenceAt(seq).deleteCharAt(j);
-    seqEditOccurred=seq;
+    seqEditOccurred = seq;
     av.alignment.getWidth();
     repaint();
   }
 
-
   void editOccurred(int i)
   {
-    if(endEdit==startEdit)
+    if (endEdit == startEdit)
     {
       ap.alignFrame.historyList.pop();
       ap.alignFrame.updateEditMenuBar();
@@ -391,34 +454,33 @@ public class SeqPanel extends Panel
 
     // Y O Y CLUSTALX
     ColourSchemeI cs = av.getGlobalColourScheme();
-    if(cs instanceof ConservationColourScheme)
+    if (cs instanceof ConservationColourScheme)
     {
-      ConservationColourScheme ccs =  (ConservationColourScheme) cs;
-      if(ccs.cs instanceof ClustalxColourScheme)
-     {
+      ConservationColourScheme ccs = (ConservationColourScheme) cs;
+      if (ccs.cs instanceof ClustalxColourScheme)
+      {
         jalview.analysis.Conservation c = new jalview.analysis.Conservation
             ("All",
-            ResidueProperties.propHash, 3,
-            av.alignment.getSequences(), 0,
-            av.alignment.getWidth() - 1);
+             ResidueProperties.propHash, 3,
+             av.alignment.getSequences(), 0,
+             av.alignment.getWidth() - 1);
         c.calculate();
         c.verdict(false, av.ConsPercGaps);
 
-        ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;
-        cxs.resetClustalX(av.alignment.getSequences(),  av.alignment.getWidth());
+        ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
+        cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());
         ccs = new ConservationColourScheme(c, cxs);
         av.setGlobalColourScheme(ccs);
-     }
+      }
     }
 
-    if(cs instanceof ClustalxColourScheme)
+    if (cs instanceof ClustalxColourScheme)
     {
-      ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
-                                    av.alignment.getWidth());
+      ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
+                                                 av.alignment.getWidth());
       av.setGlobalColourScheme(cs);
     }
 
-
   }
 
 //////////////////////////////////////////
@@ -427,78 +489,99 @@ public class SeqPanel extends Panel
   int oldSeq = -1;
   public void doMousePressedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int seq = evt.getY() / av.getCharHeight() + av.getStartSeq();
     oldSeq = seq;
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
-    if(sequence==null || res>sequence.getLength())
+    if (sequence == null || res > sequence.getLength())
+    {
       return;
+    }
 
     stretchGroup = av.getSelectionGroup();
 
-    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;
-
-       SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
-
-       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;
-           }
-     }
-
-    if(stretchGroup==null)
+    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;
+
+      SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+
+      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;
+          }
+        }
+      }
+    }
+
+    if (stretchGroup == null)
     {
       // define a new group here
       SequenceGroup sg = new SequenceGroup();
       sg.setStartRes(res);
       sg.setEndRes(res);
-      sg.addSequence( sequence );
-      av.setSelectionGroup( sg );
+      sg.addSequence(sequence);
+      av.setSelectionGroup(sg);
       stretchGroup = sg;
 
-      if(av.getConservationSelected())
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
-      if(av.getAbovePIDThreshold())
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
+      if (av.getConservationSelected())
+      {
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+                                          "Background");
+      }
+      if (av.getAbovePIDThreshold())
+      {
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                                       "Background");
+      }
 
     }
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )
+    else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
+             InputEvent.BUTTON3_MASK)
     {
       APopupMenu popup = new APopupMenu(ap, null);
       this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
     }
 
-
-    if(stretchGroup!=null && stretchGroup.getEndRes()==res)
+    if (stretchGroup != null && stretchGroup.getEndRes() == res)
+    {
       // Edit end res position of selected group
       changeEndRes = true;
+    }
 
-   else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
+    else if (stretchGroup != null && stretchGroup.getStartRes() == res)
+    {
       // Edit end res position of selected group
       changeStartRes = true;
+    }
 
   }
 
@@ -512,85 +595,106 @@ public class SeqPanel extends Panel
   {
     mouseDragging = false;
 
-    if(stretchGroup==null)
+    if (stretchGroup == null)
+    {
       return;
+    }
 
-    if(stretchGroup.cs instanceof ClustalxColourScheme)
+    if (stretchGroup.cs instanceof ClustalxColourScheme)
     {
-      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
+      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,
+                                                 av.alignment.getWidth());
       seqCanvas.repaint();
     }
 
-    else if(stretchGroup.cs instanceof ConservationColourScheme)
+    else if (stretchGroup.cs instanceof ConservationColourScheme)
     {
-       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
-       stretchGroup.cs = ccs;
-       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
+      ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
+      stretchGroup.cs = ccs;
+      SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                                        stretchGroup.getName());
 
-       seqCanvas.repaint();
+      seqCanvas.repaint();
     }
     else
     {
-      if(stretchGroup.cs !=null)
+      if (stretchGroup.cs != null)
       {
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                                       stretchGroup.getName());
       }
 
     }
 
-
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
     ap.repaint();
   }
 
-
   boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int y = evt.getY() / av.getCharHeight() + av.getStartSeq();
 
-    if(stretchGroup==null)
+    if (stretchGroup == null)
+    {
       return;
+    }
 
-    if(res>av.alignment.getWidth())
-      res = av.alignment.getWidth()-1;
-
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
 
-    if(stretchGroup.getEndRes()==res)
+    if (stretchGroup.getEndRes() == res)
+    {
       // Edit end res position of selected group
       changeEndRes = true;
+    }
 
-    else if(stretchGroup.getStartRes()==res)
+    else if (stretchGroup.getStartRes() == res)
+    {
       // Edit start res position of selected group
       changeStartRes = true;
+    }
 
-
-    if(res<av.getStartRes())
+    if (res < av.getStartRes())
+    {
       res = av.getStartRes();
-    else if(res>av.getEndRes())
+    }
+    else if (res > av.getEndRes())
+    {
       res = av.getEndRes();
+    }
 
-    if(changeEndRes)
+    if (changeEndRes)
     {
-      if(res>stretchGroup.getStartRes()-1)
-        stretchGroup.setEndRes( res );
+      if (res > stretchGroup.getStartRes() - 1)
+      {
+        stretchGroup.setEndRes(res);
+      }
     }
-    else if(changeStartRes)
+    else if (changeStartRes)
     {
-      if(res<stretchGroup.getEndRes()+1)
-        stretchGroup.setStartRes( res );
+      if (res < stretchGroup.getEndRes() + 1)
+      {
+        stretchGroup.setStartRes(res);
+      }
     }
 
     int dragDirection = 0;
     if (y > oldSeq)
+    {
       dragDirection = 1;
+    }
     else if (y < oldSeq)
+    {
       dragDirection = -1;
+    }
 
-    while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
+    while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
@@ -606,15 +710,19 @@ public class SeqPanel extends Panel
       }
       else
       {
-       if(seq!=null)
-        stretchGroup.addSequence(seq);
+        if (seq != null)
+        {
+          stretchGroup.addSequence(seq);
+        }
         stretchGroup.addSequence(nextSeq);
       }
     }
     oldSeq = y;
     mouseDragging = true;
-    if(scrollThread!=null)
+    if (scrollThread != null)
+    {
       scrollThread.setEvent(evt);
+    }
 
     seqCanvas.repaint();
   }
@@ -622,20 +730,28 @@ public class SeqPanel extends Panel
   public void doMouseEnteredDefineMode(MouseEvent e)
   {
     if (scrollThread != null)
+    {
       scrollThread.running = false;
+    }
   }
 
   public void doMouseExitedDefineMode(MouseEvent e)
   {
     if (av.getWrapAlignment())
+    {
       return;
+    }
 
-    if(mouseDragging)
+    if (mouseDragging)
+    {
       scrollThread = new ScrollThread();
+    }
 
   }
+
   // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread extends Thread
+  class ScrollThread
+      extends Thread
   {
     MouseEvent evt;
     boolean running = false;
@@ -659,21 +775,29 @@ public class SeqPanel extends Panel
       running = true;
       while (running)
       {
-        if(evt!=null)
+        if (evt != null)
         {
 
           if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+          {
             running = ap.scrollUp(true);
+          }
 
           if (mouseDragging && evt.getY() >= getSize().height &&
               av.alignment.getHeight() > av.getEndSeq())
+          {
             running = ap.scrollUp(false);
+          }
 
           if (mouseDragging && evt.getX() < 0)
+          {
             running = ap.scrollRight(true);
+          }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
+          {
             running = ap.scrollRight(false);
+          }
         }
 
         try
@@ -684,12 +808,6 @@ public class SeqPanel extends Panel
         {}
       }
     }
-}
-
-
+  }
 
 }
-
-
-
-
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 321edef..9a722f2 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,27 +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.appletgui;
 
+import java.awt.*;
+
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.awt.*;
 
 public class SequenceRenderer
 {
@@ -29,7 +30,7 @@ public class SequenceRenderer
   FontMetrics fm;
   boolean renderGaps = true;
   SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
+  SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
 
@@ -38,7 +39,6 @@ public class SequenceRenderer
     this.av = av;
   }
 
-
   public void renderGaps(boolean b)
   {
     renderGaps = b;
@@ -52,13 +52,19 @@ public class SequenceRenderer
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
-   if (cs != null)
-       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
-   else
-       resBoxColour = Color.white;
+    if (cs != null)
+    {
+      resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+    }
+    else
+    {
+      resBoxColour = Color.white;
+    }
   }
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)
+  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
+                           int start, int end, int x1, int y1, int width,
+                           int height)
   {
     allGroups = sg;
 
@@ -67,12 +73,14 @@ public class SequenceRenderer
     drawBoxes(seq, start, end, x1, y1, (int) width, height);
 
     fm = g.getFontMetrics();
-    drawText(seq,start,end,x1,y1,(int)width,height);
+    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;
+  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;
@@ -81,23 +89,33 @@ public class SequenceRenderer
     Color tempColour = null;
     while (i <= end && i < length)
     {
-      if(inCurrentSequenceGroup(i))
+      if (inCurrentSequenceGroup(i))
       {
-        if( currentSequenceGroup.getDisplayBoxes())
-             getBoxColour(currentSequenceGroup.cs, seq, i);
+        if (currentSequenceGroup.getDisplayBoxes())
+        {
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+        }
         else
-             resBoxColour = Color.white;
+        {
+          resBoxColour = Color.white;
+        }
+      }
+      else if (av.getShowBoxes())
+      {
+        getBoxColour(av.getGlobalColourScheme(), seq, i);
       }
-      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);
+        if (tempColour != null)
+        {
+          graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,
+                            height);
+        }
         graphics.setColor(resBoxColour);
 
         curStart = i;
@@ -106,104 +124,126 @@ public class SequenceRenderer
 
       }
       else
+      {
         curWidth += width;
+      }
 
       i++;
     }
 
-
-     graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+    graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);
   }
 
-  public void drawText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
+  public void drawText(SequenceI seq, int start, int end, int x1, int y1,
+                       int width, int height)
   {
-    int pady = height/5;
-    int charOffset=0;
+    int pady = height / 5;
+    int charOffset = 0;
     char s;
     // Need to find the sequence position here.
 
-    String sequence  = seq.getSequence();
+    String sequence = seq.getSequence();
     for (int i = start; i <= end; i++)
     {
-        graphics.setColor(Color.black);
-        if(i<sequence.length())
-          s = sequence.charAt(i);
-        else
-          s = ' ';
+      graphics.setColor(Color.black);
+      if (i < sequence.length())
+      {
+        s = sequence.charAt(i);
+      }
+      else
+      {
+        s = ' ';
+      }
 
-        if(!renderGaps && jalview.util.Comparison.isGap(s))
-          continue;
+      if (!renderGaps && jalview.util.Comparison.isGap(s))
+      {
+        continue;
+      }
 
+      if (inCurrentSequenceGroup(i))
+      {
+        if (!currentSequenceGroup.getDisplayText())
+        {
+          continue;
+        }
 
-        if (inCurrentSequenceGroup(i))
+        if (currentSequenceGroup.getColourText())
         {
-          if(!currentSequenceGroup.getDisplayText())
-            continue;
-
-            if (currentSequenceGroup.getColourText())
-            {
-              getBoxColour(currentSequenceGroup.cs, seq, i);
-              graphics.setColor(resBoxColour.darker());
-            }
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+          graphics.setColor(resBoxColour.darker());
         }
-        else
+      }
+      else
+      {
+        if (!av.getShowText())
         {
-          if(!av.getShowText())
-            continue;
-
-          if(av.getColourText())
-           {
-             getBoxColour(av.getGlobalColourScheme(), seq, i);
-             if(av.getShowBoxes())
-              graphics.setColor(resBoxColour.darker());
-            else
-              graphics.setColor(resBoxColour);
-           }
+          continue;
         }
 
-          charOffset =  (width - fm.charWidth(s))/2;
-          graphics.drawString(String.valueOf(s),
-                              charOffset + x1 + width * (i - start),
-                              y1 + height - pady);
+        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);
+    }
 
   }
 
   boolean inCurrentSequenceGroup(int res)
   {
-    if(allGroups ==null)
+    if (allGroups == null)
+    {
       return false;
+    }
 
-    for(int i=0; i<allGroups.length; i++)
-      if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)
+    for (int i = 0; i < allGroups.length; i++)
+    {
+      if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
       {
-         currentSequenceGroup = allGroups[i];
-         return true;
+        currentSequenceGroup = allGroups[i];
+        return true;
       }
+    }
 
     return false;
   }
 
-  public void drawHighlightedText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
+  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+                                  int y1, int width, int height)
   {
-    int pady = height/5;
-    int charOffset=0;
+    int pady = height / 5;
+    int charOffset = 0;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1,y1,width*(end-start+1),height);
+    graphics.fillRect(x1, y1, width * (end - start + 1), height);
     graphics.setColor(Color.white);
 
-    char s='~';
+    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);
+      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);
+      charOffset = (width - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s),
+                          charOffset + x1 + width * (i - start),
+                          y1 + height - pady);
     }
   }
 
-
 }
diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 6c89fb7..caabbf9 100755
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -1,32 +1,35 @@
 /*
-* 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.appletgui;
 
-import jalview.jbappletgui.*;
-import jalview.schemes.*;
-import jalview.datamodel.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
-public class SliderPanel extends GSliderPanel
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
+import jalview.schemes.*;
+
+public class SliderPanel
+    extends GSliderPanel
 {
   AlignmentPanel ap;
   boolean forConservation = true;
@@ -35,12 +38,13 @@ public class SliderPanel extends GSliderPanel
   static Frame conservationSlider;
   static Frame PIDSlider;
 
-  public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs, String source)
+  public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs,
+                                          String source)
   {
     SliderPanel sp = null;
-    ConservationColourScheme ccs = (ConservationColourScheme)cs;
+    ConservationColourScheme ccs = (ConservationColourScheme) cs;
 
-    if(conservationSlider == null)
+    if (conservationSlider == null)
     {
       sp = new SliderPanel(ap, ccs.inc, true, cs);
       conservationSlider = new Frame();
@@ -48,30 +52,38 @@ public class SliderPanel extends GSliderPanel
     }
     else
     {
-        sp = (SliderPanel)conservationSlider.getComponent(0);
-        sp.cs = cs;
+      sp = (SliderPanel) conservationSlider.getComponent(0);
+      sp.cs = cs;
     }
 
-    conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");
-    if(ap.av.alignment.getGroups()!=null)
-      sp.setAllGroupsCheckEnabled( true );
+    conservationSlider.setTitle("Conservation Colour Increment  (" + source +
+                                ")");
+    if (ap.av.alignment.getGroups() != null)
+    {
+      sp.setAllGroupsCheckEnabled(true);
+    }
     else
-      sp.setAllGroupsCheckEnabled( false);
+    {
+      sp.setAllGroupsCheckEnabled(false);
+    }
 
     return sp.getValue();
   }
 
   public static void showConservationSlider()
   {
-    try{
+    try
+    {
       PIDSlider.setVisible(false);
       PIDSlider = null;
-    }catch(Exception ex){}
-
+    }
+    catch (Exception ex)
+    {}
 
-    if(!conservationSlider.isVisible())
+    if (!conservationSlider.isVisible())
     {
-      jalview.bin.JalviewLite.addFrame(conservationSlider, conservationSlider.getTitle(), 420, 100);
+      jalview.bin.JalviewLite.addFrame(conservationSlider,
+                                       conservationSlider.getTitle(), 420, 100);
       conservationSlider.addWindowListener(new WindowAdapter()
       {
         public void windowClosing(WindowEvent e)
@@ -84,41 +96,50 @@ public class SliderPanel extends GSliderPanel
 
   }
 
-  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
-   {
-     SliderPanel pid = null;
-     if(PIDSlider == null)
-     {
-       pid = new SliderPanel(ap, 50, false, cs);
-       PIDSlider = new Frame();
-       PIDSlider.add(pid);
-     }
-     else
-     {
-         pid = (SliderPanel)PIDSlider.getComponent(0);
-         pid.cs = cs;
-     }
-     PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
-
-     if (ap.av.alignment.getGroups() != null)
-       pid.setAllGroupsCheckEnabled(true);
-     else
-       pid.setAllGroupsCheckEnabled(false);
-
-     return pid.getValue();
-
-   }
-
-   public static void showPIDSlider()
-   {
-     try{
-       conservationSlider.setVisible(false);
-       conservationSlider = null;
-     }catch(Exception ex){}
-
-     if(!PIDSlider.isVisible())
-    {
-      jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420, 100);
+  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
+                                       String source)
+  {
+    SliderPanel pid = null;
+    if (PIDSlider == null)
+    {
+      pid = new SliderPanel(ap, 50, false, cs);
+      PIDSlider = new Frame();
+      PIDSlider.add(pid);
+    }
+    else
+    {
+      pid = (SliderPanel) PIDSlider.getComponent(0);
+      pid.cs = cs;
+    }
+    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+
+    if (ap.av.alignment.getGroups() != null)
+    {
+      pid.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      pid.setAllGroupsCheckEnabled(false);
+    }
+
+    return pid.getValue();
+
+  }
+
+  public static void showPIDSlider()
+  {
+    try
+    {
+      conservationSlider.setVisible(false);
+      conservationSlider = null;
+    }
+    catch (Exception ex)
+    {}
+
+    if (!PIDSlider.isVisible())
+    {
+      jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420,
+                                       100);
       PIDSlider.addWindowListener(new WindowAdapter()
       {
         public void windowClosing(WindowEvent e)
@@ -128,76 +149,82 @@ public class SliderPanel extends GSliderPanel
       });
     }
 
-   }
-
+  }
 
-  public SliderPanel(AlignmentPanel ap, int value, boolean forConserve, 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)
+    if (forConservation)
     {
       label.setText("Modify conservation visibility");
       slider.setMinimum(0);
-      slider.setMaximum(50+slider.getVisibleAmount());
+      slider.setMaximum(50 + slider.getVisibleAmount());
       slider.setUnitIncrement(1);
     }
     else
     {
       label.setText("Colour residues above % occurence");
       slider.setMinimum(0);
-      slider.setMaximum(100+slider.getVisibleAmount());
+      slider.setMaximum(100 + slider.getVisibleAmount());
       slider.setBlockIncrement(1);
     }
 
-
-    slider.addAdjustmentListener( new AdjustmentListener()
+    slider.addAdjustmentListener(new AdjustmentListener()
     {
       public void adjustmentValueChanged(AdjustmentEvent evt)
       {
-        valueField.setText( slider.getValue()+"" );
-        valueChanged( slider.getValue() );
+        valueField.setText(slider.getValue() + "");
+        valueChanged(slider.getValue());
       }
     });
 
     slider.setValue(value);
-    valueField.setText(value+"");
+    valueField.setText(value + "");
   }
 
   public void valueChanged(int i)
   {
-    if(cs == null)
+    if (cs == null)
+    {
       return;
+    }
 
     ColourSchemeI toChange = null;
     Vector allGroups = null;
     int groupIndex = 0;
 
-    if(allGroupsCheck.getState())
+    if (allGroupsCheck.getState())
     {
       allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size()-1;
+      groupIndex = allGroups.size() - 1;
     }
     else
+    {
       toChange = cs;
+    }
 
-
-    while( groupIndex > -1 )
+    while (groupIndex > -1)
     {
-      if(allGroups!=null)
-        toChange = ((SequenceGroup)allGroups.elementAt(groupIndex)).cs;
+      if (allGroups != null)
+      {
+        toChange = ( (SequenceGroup) allGroups.elementAt(groupIndex)).cs;
+      }
 
       if (forConservation)
       {
         if (toChange instanceof ConservationColourScheme)
+        {
           ( (ConservationColourScheme) toChange).inc = i;
+        }
       }
       else
       {
-          ( (ResidueColourScheme) toChange).setThreshold(i);
+        ( (ResidueColourScheme) toChange).setThreshold(i);
       }
 
       groupIndex--;
@@ -212,16 +239,16 @@ public class SliderPanel extends GSliderPanel
     allGroupsCheck.setEnabled(b);
   }
 
-
   public void valueField_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
     }
-    catch(Exception ex)
+    catch (Exception ex)
     {
-      valueField.setText( slider.getValue()+"" );
+      valueField.setText(slider.getValue() + "");
     }
   }
 
@@ -229,10 +256,10 @@ public class SliderPanel extends GSliderPanel
   {
     slider.setValue(value);
   }
+
   public int getValue()
   {
     return Integer.parseInt(valueField.getText());
   }
 
-
 }
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index be37813..434ad60 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,42 +1,43 @@
 /*
-* 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.appletgui;
 
+import java.util.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.util.*;
-import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.*;
 
-public class TreeCanvas extends Panel implements MouseListener
+public class TreeCanvas
+    extends Panel implements MouseListener
 {
   NJTree tree;
   ScrollPane scrollPane;
   AlignViewport av;
-  public static final String PLACEHOLDER=" * ";
+  public static final String PLACEHOLDER = " * ";
   Font font;
-  int  fontSize = 12;
+  int fontSize = 12;
 
   boolean fitToWindow = true;
   boolean showDistances = false;
@@ -49,19 +50,20 @@ public class TreeCanvas extends Panel implements MouseListener
   float threshold;
 
   String longestName;
-  int labelLength=-1;
+  int labelLength = -1;
 
   //RubberbandRectangle rubberband;
 
-  Vector    listeners;
+  Vector listeners;
 
   Hashtable nameHash = new Hashtable();
   Hashtable nodeHash = new Hashtable();
 
-  public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller, String label)
+  public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller,
+                    String label)
   {
     this.av = av;
-    this.tree     = tree;
+    this.tree = tree;
     scrollPane = scroller;
     addMouseListener(this);
     tree.findHeight(tree.getTopNode());
@@ -70,10 +72,11 @@ public class TreeCanvas extends Panel implements MouseListener
 
     PaintRefresher.Register(this);
   }
+
   public void TreeSelectionChanged(Sequence sequence)
- {
+  {
     SequenceGroup selected = av.getSelectionGroup();
-    if(selected == null)
+    if (selected == null)
     {
       selected = new SequenceGroup();
       av.setSelectionGroup(selected);
@@ -82,373 +85,450 @@ public class TreeCanvas extends Panel implements MouseListener
     selected.setEndRes(av.alignment.getWidth());
     selected.addOrRemove(sequence);
 
-
     PaintRefresher.Refresh(this);
     repaint();
- }
-
-
+  }
 
-  public void setTree(NJTree tree) {
+  public void setTree(NJTree tree)
+  {
     this.tree = tree;
     tree.findHeight(tree.getTopNode());
   }
 
-    public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
-    if (node == null) {
+  public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,
+                       int width, int offx, int offy)
+  {
+    if (node == null)
+    {
       return;
     }
 
-    if (node.left() == null && node.right() == null) {
+    if (node.left() == null && node.right() == null)
+    {
       // Drawing leaf node
 
       float height = node.height;
-      float dist   = node.dist;
+      float dist = node.dist;
 
-      int xstart = (int)((height-dist)*scale) + offx;
-      int xend =   (int)(height*scale)        + offx;
+      int xstart = (int) ( (height - dist) * scale) + offx;
+      int xend = (int) (height * scale) + offx;
 
-      int ypos = (int)(node.ycount * chunk) + offy;
+      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());
+        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);
-
+      {
+        g.setColor(Color.black);
+      }
 
       // Draw horizontal line
-      g.drawLine(xstart,ypos,xend,ypos);
+      g.drawLine(xstart, ypos, xend, ypos);
 
       String nodeLabel = "";
-      if (showDistances && node.dist > 0) {
+      if (showDistances && node.dist > 0)
+      {
         nodeLabel = new Format("%5.2f").form(node.dist);
       }
-      if (showBootstrap) {
-        if (showDistances) {
+      if (showBootstrap)
+      {
+        if (showDistances)
+        {
           nodeLabel = nodeLabel + " : ";
         }
         nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
       }
-      if (! nodeLabel.equals("")) {
-      g.drawString(nodeLabel,xstart,ypos - 10);
+      if (!nodeLabel.equals(""))
+      {
+        g.drawString(nodeLabel, xstart, ypos - 10);
       }
 
-      String name    = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER+node.getName()) : node.getName();
+      String name = (markPlaceholders && node.isPlaceholder()) ?
+          (PLACEHOLDER + node.getName()) : node.getName();
       FontMetrics fm = g.getFontMetrics(font);
-      int charWidth  = fm.stringWidth(name) + 3;
+      int charWidth = fm.stringWidth(name) + 3;
       int charHeight = fm.getHeight();
 
-      Rectangle rect = new Rectangle(xend+20,ypos-charHeight,
-                                     charWidth,charHeight);
+      Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,
+                                     charWidth, charHeight);
 
-      nameHash.put((SequenceI)node.element(),rect);
+      nameHash.put( (SequenceI) node.element(), rect);
 
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
-      if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {
+      if (selected != null &&
+          selected.sequences.contains( (SequenceI) node.element()))
+      {
         g.setColor(Color.gray);
 
-        g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);
+        g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight);
         g.setColor(Color.white);
       }
-      g.drawString(name,xend+10,ypos);
+      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);
+    }
+    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;
+      float dist = node.dist;
 
-      int xstart = (int)((height-dist)*scale) + offx;
-      int xend   = (int)(height       *scale) + offx;
-      int ypos   = (int)(node.ycount  *chunk) + offy;
+      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());
+      g.setColor( ( (SequenceNode) node).color.darker());
 
       // Draw horizontal line
-      g.drawLine(xstart,ypos,xend,ypos);
-      g.fillRect(xend-2, ypos-2, 4,4);
+      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;
+      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);
+      Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
+      nodeHash.put(node, pos);
 
-      g.drawLine((int)(height*scale) + offx, ystart,
-                 (int)(height*scale) + offx, yend);
+      g.drawLine( (int) (height * scale) + offx, ystart,
+                 (int) (height * scale) + offx, yend);
 
-      if (showDistances && node.dist > 0) {
-        g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
+      if (showDistances && node.dist > 0)
+      {
+        g.drawString(new Format("%5.2f").form(node.dist), xstart, ypos - 5);
       }
 
     }
   }
-  public Object findElement(int x, int y) {
-       Enumeration keys = nameHash.keys();
 
-    while (keys.hasMoreElements()) {
-            Object ob = keys.nextElement();
-            Rectangle rect = (Rectangle)nameHash.get(ob);
+  public Object findElement(int x, int y)
+  {
+    Enumeration keys = nameHash.keys();
 
-            if (x >= rect.x && x <= (rect.x + rect.width) &&
-              y >= rect.y && y <= (rect.y + rect.height)) {
-              return ob;
-            }
-  }
-  keys = nodeHash.keys();
+    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;
+      }
+    }
+    keys = nodeHash.keys();
 
-    while (keys.hasMoreElements()) {
-            Object ob = keys.nextElement();
-            Rectangle rect = (Rectangle)nodeHash.get(ob);
+    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;
-            }
+      if (x >= rect.x && x <= (rect.x + rect.width) &&
+          y >= rect.y && y <= (rect.y + rect.height))
+      {
+        return ob;
+      }
     }
-      return null;
+    return null;
 
   }
 
-  public void pickNodes(Rectangle pickBox) {
-    int width  = getSize().width;
+  public void pickNodes(Rectangle pickBox)
+  {
+    int width = getSize().width;
     int height = getSize().height;
 
     SequenceNode top = tree.getTopNode();
 
-    float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()
-;
-    if (top.count == 0) {
-      top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
+    float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight()
+        ;
+    if (top.count == 0)
+    {
+      top.count = ( (SequenceNode) top.left()).count +
+          ( (SequenceNode) top.right()).count;
     }
-    float chunk = (float)(height-offy*2)/top.count;
+    float chunk = (float) (height - offy * 2) / top.count;
 
-    pickNode(pickBox,top,chunk,wscale,width,offx,offy);
+    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) {
+  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+                       float scale, int width, int offx, int offy)
+  {
+    if (node == null)
+    {
       return;
     }
 
-    if (node.left() == null && node.right() == null) {
+    if (node.left() == null && node.right() == null)
+    {
       float height = node.height;
-      float dist   = node.dist;
+      float dist = node.dist;
 
-      int xstart = (int)((height-dist)*scale) + offx;
-      int xend   = (int)(height*scale) + offx;
+      int xstart = (int) ( (height - dist) * scale) + offx;
+      int xend = (int) (height * scale) + offx;
 
-      int ypos = (int)(node.ycount * chunk) + offy;
+      int ypos = (int) (node.ycount * chunk) + offy;
 
-      if (pickBox.contains(new Point(xend,ypos))) {
-        if (node.element() instanceof SequenceI) {
-          SequenceI seq = (SequenceI)node.element();
+      if (pickBox.contains(new Point(xend, ypos)))
+      {
+        if (node.element() instanceof SequenceI)
+        {
+          SequenceI seq = (SequenceI) node.element();
           SequenceGroup sg = av.getSelectionGroup();
-          if(sg!=null)
+          if (sg != null)
+          {
             sg.addOrRemove(seq);
+          }
         }
       }
-    } else {
-      pickNode(pickBox,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
-      pickNode(pickBox,(SequenceNode)node.right(),chunk,scale,width,offx,offy);
+    }
+    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)
+    {
       return;
+    }
 
     if (node.left() == null && node.right() == null)
     {
       node.color = c;
 
       if (node.element() instanceof SequenceI)
-          ((SequenceI)node.element()).setColor(c);
-    } else
+      {
+        ( (SequenceI) node.element()).setColor(c);
+      }
+    }
+    else
     {
       node.color = c;
-      setColor((SequenceNode)node.left(),c);
-      setColor((SequenceNode)node.right(),c);
+      setColor( (SequenceNode) node.left(), c);
+      setColor( (SequenceNode) node.right(), c);
     }
   }
 
-
   public void paint(Graphics g)
   {
 
-    font = new Font("Verdana",Font.PLAIN,fontSize);
+    font = new Font("Verdana", Font.PLAIN, fontSize);
     g.setFont(font);
 
     FontMetrics fm = g.getFontMetrics(font);
 
-    if(nameHash.size()==0)
+    if (nameHash.size() == 0)
+    {
       repaint();
+    }
 
-
-    if( fitToWindow || (!fitToWindow && scrollPane.getSize().height > fm.getHeight() * nameHash.size()+offy ) )
-     {
-         draw(g,scrollPane.getSize().width,scrollPane.getSize().height);
-     }
+    if (fitToWindow ||
+        (!fitToWindow &&
+         scrollPane.getSize().height > fm.getHeight() * nameHash.size() + offy))
+    {
+      draw(g, scrollPane.getSize().width, scrollPane.getSize().height);
+    }
     else
-     {
-         setSize(new Dimension(scrollPane.getSize().width, fm.getHeight() * nameHash.size()));
-         draw( g,scrollPane.getSize().width, fm.getHeight() * nameHash.size());
-     }
+    {
+      setSize(new Dimension(scrollPane.getSize().width,
+                            fm.getHeight() * nameHash.size()));
+      draw(g, scrollPane.getSize().width, fm.getHeight() * nameHash.size());
+    }
 
     scrollPane.validate();
   }
-    public int getFontSize() {
-        return fontSize;
-    }
-    public void setFontSize(int fontSize) {
-        this.fontSize = fontSize;
-        repaint();
-    }
-  public void draw(Graphics g, int width, int height) {
 
-      g.setColor(Color.white);
-      g.fillRect(0,0,width,height);
+  public int getFontSize()
+  {
+    return fontSize;
+  }
 
+  public void setFontSize(int fontSize)
+  {
+    this.fontSize = fontSize;
+    repaint();
+  }
 
-      labelLength = g.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar
+  public void draw(Graphics g, int width, int height)
+  {
 
-      float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();
+    g.setColor(Color.white);
+    g.fillRect(0, 0, width, height);
 
-      SequenceNode top = tree.getTopNode();
+    labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
 
-      if (top.count == 0) {
-          top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
-      }
-      float chunk = (float)(height-offy*2)/top.count ;
+    float wscale = (float) (width - labelLength - offx * 2) / tree.getMaxHeight();
 
-      drawNode(g,tree.getTopNode(),chunk,wscale,width,offx,offy);
+    SequenceNode top = tree.getTopNode();
 
-      if (threshold != 0)
-      {
-        if(av.getCurrentTree() == tree)
-          g.setColor(Color.red);
-        else
-          g.setColor(Color.gray);
+    if (top.count == 0)
+    {
+      top.count = ( (SequenceNode) top.left()).count +
+          ( (SequenceNode) top.right()).count;
+    }
+    float chunk = (float) (height - offy * 2) / top.count;
 
-          int x = (int)(    threshold * (float)(getSize().width-labelLength - 2*offx) +offx   ) ;
+    drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);
 
-          g.drawLine(x,0,x,getSize().height);
+    if (threshold != 0)
+    {
+      if (av.getCurrentTree() == tree)
+      {
+        g.setColor(Color.red);
+      }
+      else
+      {
+        g.setColor(Color.gray);
       }
 
-  }
-
-  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) {
+      int x = (int) (threshold *
+                     (float) (getSize().width - labelLength - 2 * offx) + offx);
 
-      av.setCurrentTree(tree);
+      g.drawLine(x, 0, x, getSize().height);
+    }
 
-      int x = e.getX();
-      int y = e.getY();
+  }
 
-      Object ob = findElement(x,y);
+  public void mouseReleased(MouseEvent e)
+  {}
 
-      if (ob instanceof SequenceI)
-      {
-          TreeSelectionChanged((Sequence)ob);
-          repaint();
-          return;
+  public void mouseEntered(MouseEvent e)
+  {}
 
-      } else if (ob instanceof SequenceNode) {
-          SequenceNode tmpnode = (SequenceNode)ob;
-          tree.swapNodes(tmpnode);
-          tree.reCount(tree.getTopNode());
-          tree.findHeight(tree.getTopNode());
-      } else {
-          // Find threshold
+  public void mouseExited(MouseEvent e)
+  {}
 
-          if (tree.getMaxHeight() != 0) {
-              threshold = (float)(x - offx)/(float)(getSize().width-labelLength - 2*offx);
+  public void mouseClicked(MouseEvent e)
+  {
+  }
 
-              tree.getGroups().removeAllElements();
-              tree.groupNodes(tree.getTopNode(),threshold);
-              setColor(tree.getTopNode(),Color.black);
+  public void mousePressed(MouseEvent e)
+  {
 
-              av.setSelectionGroup(null);
-              av.alignment.deleteAllGroups();
+    av.setCurrentTree(tree);
 
-              for (int i=0; i < tree.getGroups().size(); i++)
-              {
+    int x = e.getX();
+    int y = e.getY();
 
-                  Color col = new Color((int)(Math.random()*255),
-                                        (int)(Math.random()*255),
-                                        (int)(Math.random()*255));
-                  setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());
+    Object ob = findElement(x, y);
 
-                  Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
-                  SequenceGroup sg = null;
-                  for (int j = 0; j < l.size(); j++)
-                  {
-                    SequenceNode sn = (SequenceNode) l.elementAt(j);
-                    if(sg==null)
-                       sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());
+    if (ob instanceof SequenceI)
+    {
+      TreeSelectionChanged( (Sequence) ob);
+      repaint();
+      return;
 
-                    sg.addSequence( (Sequence) sn.element());
-                  }
+    }
+    else if (ob instanceof SequenceNode)
+    {
+      SequenceNode tmpnode = (SequenceNode) ob;
+      tree.swapNodes(tmpnode);
+      tree.reCount(tree.getTopNode());
+      tree.findHeight(tree.getTopNode());
+    }
+    else
+    {
+      // Find threshold
 
-                  if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
-                  {
-                    ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();
-                    Conservation c = new Conservation("Group",
-                                                      ResidueProperties.propHash, 3,
-                                                      sg.sequences, sg.getStartRes(),
-                                                      sg.getEndRes());
+      if (tree.getMaxHeight() != 0)
+      {
+        threshold = (float) (x - offx) /
+            (float) (getSize().width - 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());
+          SequenceGroup sg = null;
+          for (int j = 0; j < l.size(); j++)
+          {
+            SequenceNode sn = (SequenceNode) l.elementAt(j);
+            if (sg == null)
+            {
+              sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true, false,
+                                     0, av.alignment.getWidth());
+            }
 
-                    c.calculate();
-                    c.verdict(false, av.ConsPercGaps);
-                    ccs = new ConservationColourScheme(c, ccs.cs);
+            sg.addSequence( (Sequence) sn.element());
+          }
 
-                    sg.cs = ccs;
+          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);
+          av.alignment.addGroup(sg);
 
-              }
-          }
+        }
       }
+    }
 
-      PaintRefresher.Refresh(this);
-      repaint();
+    PaintRefresher.Refresh(this);
+    repaint();
 
   }
 
-    public void setShowDistances(boolean state) {
-        this.showDistances = state;
-        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();
-    }
+  public void setShowBootstrap(boolean state)
+  {
+    this.showBootstrap = state;
+    repaint();
+  }
 
-}
+  public void setMarkPlaceholders(boolean state)
+  {
+    this.markPlaceholders = state;
+    repaint();
+  }
 
+}
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index c33975b..58da074 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,34 +1,35 @@
 /*
-* 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.appletgui;
 
-import jalview.datamodel.*;
-import jalview.io.NewickFile;
-import jalview.analysis.*;
-import jalview.jbappletgui.GTreePanel;
-import java.awt.event.*;
 import java.util.*;
-import jalview.io.NewickFile;
 
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbappletgui.*;
 
-public class TreePanel extends GTreePanel
+public class TreePanel
+    extends GTreePanel
 {
   SequenceI[] seq;
   String type;
@@ -44,7 +45,8 @@ public class TreePanel extends GTreePanel
     return tree;
   }
 
-  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
+  public TreePanel(AlignViewport av, Vector seqVector, String type,
+                   String pwtype, int s, int e)
   {
     super();
 
@@ -55,12 +57,14 @@ public class TreePanel extends GTreePanel
     end = e;
 
     String longestName = "";
-    seq = new Sequence [seqVector.size()];
-    for (int i=0;i < seqVector.size();i++)
+    seq = new Sequence[seqVector.size()];
+    for (int i = 0; i < seqVector.size(); i++)
     {
       seq[i] = (Sequence) seqVector.elementAt(i);
-      if(seq[i].getName().length()>longestName.length())
+      if (seq[i].getName().length() > longestName.length())
+      {
         longestName = seq[i].getName();
+      }
     }
 
     tree = new NJTree(seq, type, pwtype, start, end);
@@ -72,49 +76,61 @@ public class TreePanel extends GTreePanel
     scrollPane.add(treeCanvas);
 
   }
+
   public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
                    String type, String pwtype)
-    {
-      super();
-      // These are probably only  arbitrary strings reflecting source of tree
-      this.type = type;
-      this.pwtype = pwtype;
+  {
+    super();
+    // These are probably only  arbitrary strings reflecting source of tree
+    this.type = type;
+    this.pwtype = pwtype;
 
-      start = 0;
-      end = seqVector.size();
+    start = 0;
+    end = seqVector.size();
+
+    String longestName = "";
+    seq = new Sequence[seqVector.size()];
+    for (int i = 0; i < seqVector.size(); i++)
+    {
+      seq[i] = (Sequence) seqVector.elementAt(i);
+    }
+    // This constructor matches sequence names to treenodes and sets up the tree layouts.
+    tree = new NJTree(seq, newtree);
+    // Now have to calculate longest name based on the leaves
+    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
 
-      String longestName = "";
-      seq = new Sequence [seqVector.size()];
-      for (int i=0;i < seqVector.size();i++)
+    for (int i = 0; i < leaves.size(); i++)
+    {
+      if (longestName.length() <
+          ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().
+          length())
       {
-        seq[i] = (Sequence) seqVector.elementAt(i);
+        longestName = TreeCanvas.PLACEHOLDER +
+            ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).
+            getName();
       }
-      // This constructor matches sequence names to treenodes and sets up the tree layouts.
-      tree = new NJTree(seq, newtree);
-      // Now have to calculate longest name based on the leaves
-      Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
-
-      for (int i=0;i < leaves.size();i++)
-        if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
-          longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).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());
-      distanceMenu.setState(newtree.HasDistances());
-      bootstrapMenu.setState(newtree.HasBootstrap());
-      if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
-        placeholdersMenu.setState(treeCanvas.markPlaceholders);
-      scrollPane.add(treeCanvas);
+    }
+
+    tree.reCount(tree.getTopNode());
+    tree.findHeight(tree.getTopNode());
 
+    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+    treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+    treeCanvas.setShowDistances(newtree.HasDistances());
+    distanceMenu.setState(newtree.HasDistances());
+    bootstrapMenu.setState(newtree.HasBootstrap());
+    if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
+    {
+      placeholdersMenu.setState(treeCanvas.markPlaceholders);
     }
+    scrollPane.add(treeCanvas);
 
-public String getText(String format) {
-  return null;
-}
+  }
+
+  public String getText(String format)
+  {
+    return null;
+  }
 
   protected void fitToWindow_actionPerformed(ActionEvent e)
   {
@@ -130,33 +146,31 @@ public String getText(String format) {
     cap.setText(output);
     java.awt.Frame frame = new java.awt.Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,100);
+    jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
   }
 
-
-
   protected void fontSize_actionPerformed(ActionEvent e)
   {
- /*   if( treeCanvas==null )
-     return;
-
-   String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
-
-   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);
-   if(selection!=null)
-   {
-     fontSize.setText("Font Size - " + selection);
-
-     int i = Integer.parseInt(selection.toString());
-     treeCanvas.setFontSize(i);
-   }
-    scrollPane.setViewportView(treeCanvas);
-*/
+    /*   if( treeCanvas==null )
+        return;
+
+      String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
+
+      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);
+      if(selection!=null)
+      {
+        fontSize.setText("Font Size - " + selection);
+
+        int i = Integer.parseInt(selection.toString());
+        treeCanvas.setFontSize(i);
+      }
+       scrollPane.setViewportView(treeCanvas);
+     */
   }
 
   protected void distanceMenu_actionPerformed(ActionEvent e)
@@ -171,7 +185,7 @@ public String getText(String format) {
 
   protected void placeholdersMenu_actionPerformed(ActionEvent e)
   {
-      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+    treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
   }
 
 }
diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 0c7e685..80d91ef 100755
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -1,35 +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.appletgui;
 
-import jalview.jbappletgui.GUserDefinedColours;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.io.*;
 import java.io.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.jbappletgui.*;
+import jalview.schemes.*;
 
-public class UserDefinedColours extends GUserDefinedColours
+public class UserDefinedColours
+    extends GUserDefinedColours
 {
 
   AlignmentPanel ap;
@@ -52,98 +53,120 @@ public class UserDefinedColours extends GUserDefinedColours
     super();
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420,345 );
-
-    if(sg!=null)
-        frame.setTitle( frame.getTitle()+ " ("+sg.getName()+")");
+    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);
 
+    if (sg != null)
+    {
+      frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");
+    }
 
     this.ap = ap;
     seqGroup = sg;
 
+    if (seqGroup != null)
+    {
+      oldColourScheme = seqGroup.cs;
+    }
+    else
+    {
+      oldColourScheme = ap.av.getGlobalColourScheme();
+    }
 
-      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]);
+    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", "'.','-',' '");
 
   }
 
-  protected void rText_actionPerformed(ActionEvent e) {
-    try{
+  protected void rText_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       int i = Integer.parseInt(rText.getText());
       rScroller.setValue(i);
-    }catch(NumberFormatException ex){}
+    }
+    catch (NumberFormatException ex)
+    {}
   }
 
-  protected void gText_actionPerformed(ActionEvent e) {
-    try{
+  protected void gText_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       int i = Integer.parseInt(gText.getText());
       gScroller.setValue(i);
-    }catch(NumberFormatException ex){}
+    }
+    catch (NumberFormatException ex)
+    {}
 
   }
 
-  protected void bText_actionPerformed(ActionEvent e) {
-    try{
+  protected void bText_actionPerformed(ActionEvent e)
+  {
+    try
+    {
       int i = Integer.parseInt(bText.getText());
       bScroller.setValue(i);
-    }catch(NumberFormatException ex){}
+    }
+    catch (NumberFormatException ex)
+    {}
 
   }
 
-
-  protected void rScroller_adjustmentValueChanged(AdjustmentEvent e) {
+  protected void rScroller_adjustmentValueChanged(AdjustmentEvent e)
+  {
     R = rScroller.getValue();
-    rText.setText(R+"");
+    rText.setText(R + "");
     colourChanged();
   }
 
-  protected void gScroller_adjustmentValueChanged(AdjustmentEvent e) {
+  protected void gScroller_adjustmentValueChanged(AdjustmentEvent e)
+  {
     G = gScroller.getValue();
-    gText.setText(G+"");
+    gText.setText(G + "");
     colourChanged();
   }
 
-  protected void bScroller_adjustmentValueChanged(AdjustmentEvent e) {
+  protected void bScroller_adjustmentValueChanged(AdjustmentEvent e)
+  {
     B = bScroller.getValue();
-    bText.setText(B+"");
+    bText.setText(B + "");
     colourChanged();
   }
 
- public void colourChanged()
- {
-   Color col = new Color(R,G,B);
-   target.setBackground( col );
+  public void colourChanged()
+  {
+    Color col = new Color(R, G, B);
+    target.setBackground(col);
 
-   if(selectedButton!=null)
-     selectedButton.setBackground( col );
- }
+    if (selectedButton != null)
+    {
+      selectedButton.setBackground(col);
+    }
+  }
 
   public void colourButtonPressed(MouseEvent e)
   {
-     selectedButton = (Button)e.getSource();
-     Color col = selectedButton.getBackground();
-     R = col.getRed();
-     G = col.getGreen();
-     B = col.getBlue();
-     rScroller.setValue(R);
-     gScroller.setValue(G);
-     bScroller.setValue(B);
-     rText.setText(R+"");
-     gText.setText(G+"");
-     bText.setText(B+"");
-
-     colourChanged();
+    selectedButton = (Button) e.getSource();
+    Color col = selectedButton.getBackground();
+    R = col.getRed();
+    G = col.getGreen();
+    B = col.getBlue();
+    rScroller.setValue(R);
+    gScroller.setValue(G);
+    bScroller.setValue(B);
+    rText.setText(R + "");
+    gText.setText(G + "");
+    bText.setText(B + "");
+
+    colourChanged();
   }
 
   void makeButton(String label, String aa)
@@ -151,15 +174,17 @@ public class UserDefinedColours extends GUserDefinedColours
     final Button button = new Button();
     Color col = Color.white;
 
-
-    try{
+    try
+    {
       col = oldColourScheme.findColour(aa, -1);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {}
 
-    button.setBackground(  col );
-    oldColours.addElement( col );
-    button.setLabel( label );
-    button.setForeground( col.darker().darker().darker() );
+    button.setBackground(col);
+    oldColours.addElement(col);
+    button.setLabel(label);
+    button.setForeground(col.darker().darker().darker());
     button.setFont(new java.awt.Font("Verdana", 1, 10));
     button.addMouseListener(new java.awt.event.MouseAdapter()
     {
@@ -172,42 +197,44 @@ public class UserDefinedColours extends GUserDefinedColours
     buttonPanel.add(button, null);
   }
 
-
   protected void okButton_actionPerformed(ActionEvent e)
   {
     applyButton_actionPerformed(null);
-   frame.setVisible(false);
+    frame.setVisible(false);
   }
 
   protected void applyButton_actionPerformed(ActionEvent e)
   {
 
-    Color [] newColours = new Color[24];
-    for(int i=0; i<24; i++)
+    Color[] newColours = new Color[24];
+    for (int i = 0; i < 24; i++)
     {
-          Button button = (Button)buttonPanel.getComponent(i);
-          newColours[i] = button.getBackground();
+      Button button = (Button) buttonPanel.getComponent(i);
+      newColours[i] = button.getBackground();
     }
 
-    UserColourScheme ucs = new UserColourScheme( newColours );
+    UserColourScheme ucs = new UserColourScheme(newColours);
     ucs.setThreshold(0);
 
-    if(seqGroup!=null)
+    if (seqGroup != null)
+    {
       seqGroup.cs = ucs;
+    }
     else
+    {
       ap.av.setGlobalColourScheme(ucs);
+    }
 
     ap.repaint();
   }
 
-
   public static UserColourScheme loadDefaultColours(String file)
   {
     UserColourScheme ucs = null;
     try
     {
       BufferedReader in = new BufferedReader(new FileReader(file));
-      Color [] newColours = new Color[24];
+      Color[] newColours = new Color[24];
       for (int i = 0; i < 24; i++)
       {
         newColours[i] = new Color(Integer.parseInt(in.readLine()));
@@ -223,28 +250,30 @@ public class UserDefinedColours extends GUserDefinedColours
     return ucs;
   }
 
-
   protected void cancelButton_actionPerformed(ActionEvent e)
   {
 
-    Color [] newColours = new Color[24];
-    for(int i=0; i<24; i++)
+    Color[] newColours = new Color[24];
+    for (int i = 0; i < 24; i++)
     {
-          newColours[i] = (Color)oldColours.elementAt(i);
-          buttonPanel.getComponent(i).setBackground(newColours[i]);
+      newColours[i] = (Color) oldColours.elementAt(i);
+      buttonPanel.getComponent(i).setBackground(newColours[i]);
     }
 
-    UserColourScheme ucs = new UserColourScheme( newColours );
+    UserColourScheme ucs = new UserColourScheme(newColours);
 
     if (seqGroup != null)
+    {
       seqGroup.cs = ucs;
+    }
     else
+    {
       ap.av.setGlobalColourScheme(ucs);
+    }
 
     ap.repaint();
 
     frame.setVisible(false);
   }
 
-
 }
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index d939a7e..9857f44 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -16,95 +16,88 @@
 * 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.util.*;
+
 import java.io.*;
 
+import java.util.*;
 import java.util.jar.*;
-public class Cache
-{
-  public static String  VERSION = "Release 2.0";
-  public static String  BUILD_DATE = "";
-
-  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)
-  // jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.
-  public static void loadProperties()
-  {
-    // get last build time.
-    long date = 0;
-    try{
-          String localFile = Cache.class.getProtectionDomain().getCodeSource().getLocation().toString();
-          localFile = localFile.concat("!/");
-          String tmpString = "jar:";
-          String localJarFileString = tmpString.concat(localFile);
-          java.net.URL localJarFileURL = new java.net.URL(localJarFileString);
-          java.net.JarURLConnection localJarFile = (java.net.JarURLConnection)localJarFileURL.openConnection();
-          date = localJarFile.getLastModified();
-    }catch(Exception ex){ex.printStackTrace();}
-    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
-
-
-     java.io.File f = new java.io.File(System.getProperty("user.dir") + "/jalview/bin/Cache.class" );
-     date = f.lastModified();
-    }
-
-    if(date!=0)
-      BUILD_DATE = new Date( date ).toString();
 
-    applicationProperties = new Properties();
 
-    try
-    {
-      FileInputStream in = new FileInputStream(System.getProperty("user.home") +
-                                               "/.jalview_properties");
-      applicationProperties = new Properties();
-      applicationProperties.load(in);
-      in.close();
+public class Cache {
+    public static String VERSION = "Release 2.0";
+    public static String BUILD_DATE = "";
+    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)
+    // jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do.
+    public static void loadProperties() {
+        // get last build time.
+        long date = 0;
+
+        try {
+            String localFile = Cache.class.getProtectionDomain().getCodeSource()
+                                          .getLocation().toString();
+            localFile = localFile.concat("!/");
+
+            String tmpString = "jar:";
+            String localJarFileString = tmpString.concat(localFile);
+            java.net.URL localJarFileURL = new java.net.URL(localJarFileString);
+            java.net.JarURLConnection localJarFile = (java.net.JarURLConnection) localJarFileURL.openConnection();
+            date = localJarFile.getLastModified();
+        } catch (Exception ex) {
+            ex.printStackTrace();
+        }
+
+        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
+            java.io.File f = new java.io.File(System.getProperty("user.dir") +
+                    "/jalview/bin/Cache.class");
+            date = f.lastModified();
+        }
+
+        if (date != 0) {
+            BUILD_DATE = new Date(date).toString();
+        }
+
+        applicationProperties = new Properties();
+
+        try {
+            FileInputStream in = new FileInputStream(System.getProperty(
+                        "user.home") + "/.jalview_properties");
+            applicationProperties = new Properties();
+            applicationProperties.load(in);
+            in.close();
+        } catch (Exception ex) {
+        }
     }
-    catch (Exception ex)
-    { }
-  }
-
-  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");
-
-      applicationProperties.setProperty(key, obj);
-
-      applicationProperties.store(out, "---JalviewX Properties File---");
-      out.close();
-    }
-    catch (Exception ex)
-    {}
-
-    return obj;
-
-  }
 
+    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");
 
+            applicationProperties.setProperty(key, obj);
 
+            applicationProperties.store(out, "---JalviewX Properties File---");
+            out.close();
+        } catch (Exception ex) {
+        }
 
+        return obj;
+    }
 }
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2524abd..07958b4 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -16,141 +16,139 @@
 * 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 javax.swing.*;
-import java.awt.event.*;
+
 import jalview.io.*;
 
 import org.apache.log4j.*;
 
-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);
+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() {
-    Logger l = Logger.getLogger("org.apache.axis");
-    if (Cache.getProperty("logs.Axis.Level")==null) {
-      Cache.setProperty("logs.Axis.Level", Level.INFO.toString());
+
+    public void destroy() {
+        if (applet != null) {
+            applet.stop();
+        } else {
+            System.exit(0);
+        }
+
+        frame.setVisible(false);
     }
 
-    l.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));
-    ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),"System.err");
-    ap.setName("Axis");
-    l.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();
+    private static void initLogger() {
+        Logger l = Logger.getLogger("org.apache.axis");
+
+        if (Cache.getProperty("logs.Axis.Level") == null) {
+            Cache.setProperty("logs.Axis.Level", Level.INFO.toString());
+        }
+
+        l.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));
+
+        ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+                "System.err");
+        ap.setName("Axis");
+        l.addAppender(ap);
     }
-    try{
-       UIManager.setLookAndFeel(
-   //   "javax.swing.plaf.metal.MetalLookAndFeel"
-    //  "javax.swing.plaf.multi.MultiLookAndFeel"
-         UIManager.getSystemLookAndFeelClassName()
-     //    UIManager.getCrossPlatformLookAndFeelClassName()
-       // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
-       //   "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
-       //  "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
-     );
-     }
-     catch (Exception ex)
-     {}
-
-     Desktop frame = new Desktop();
-     frame.setResizable(true);
-     frame.setVisible(true);
-
-
-
-     if(args!=null && args.length>0)
-     {
-         String file=null;
-         if(args[0].equals("-open"))
-           file = args[1];
-         else
-           file = args[0];
-
-         String protocol = "File";
-         if(file.indexOf("http:")>-1)
-           protocol = "URL";
-
-         String format = jalview.io.IdentifyFile.Identify(file, protocol);
-
-         frame.LoadFile(file, protocol, format);
-     }
-
-     if(jalview.gui.Preferences.showStartupFile &&
-         jalview.gui.Preferences.startupFile!=null)
-     {
-       String file = jalview.gui.Preferences.startupFile;
-       String 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);
-       }
-     }
-
-
-
-   }
 
+    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 {
+            UIManager.setLookAndFeel(
+            //   "javax.swing.plaf.metal.MetalLookAndFeel"
+            //  "javax.swing.plaf.multi.MultiLookAndFeel"
+            UIManager.getSystemLookAndFeelClassName());
+        } catch (Exception ex) {
+        }
+
+        Desktop frame = new Desktop();
+        frame.setResizable(true);
+        frame.setVisible(true);
+
+        if ((args != null) && (args.length > 0)) {
+            String file = null;
+
+            if (args[0].equals("-open")) {
+                file = args[1];
+            } else {
+                file = args[0];
+            }
+
+            String protocol = "File";
+
+            if (file.indexOf("http:") > -1) {
+                protocol = "URL";
+            }
+
+            String format = jalview.io.IdentifyFile.Identify(file, protocol);
+
+            frame.LoadFile(file, protocol, format);
+        }
+
+        if (jalview.gui.Preferences.showStartupFile &&
+                (jalview.gui.Preferences.startupFile != null)) {
+            String file = jalview.gui.Preferences.startupFile;
+            String 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);
+            }
+        }
+    }
 }
-
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index bd5abb0..35ebecc 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -16,126 +16,118 @@
 * 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.appletgui.AlignFrame;
+
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
 import java.applet.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.appletgui.AlignFrame;
 
-public class JalviewLite extends Applet
-{
-  static int lastFrameX = 200;
-  static int lastFrameY = 200;
-  static Applet applet;
-  boolean fileFound = true;
-  String file = "No file";
-  Button launcher = new Button("Start Jalview");
-
-  public void init()
-  {
-    applet = this;
-    this.setBackground(Color.white);
-
-    file = getParameter("file");
-    if (file != null)
-    {
-      add(launcher);
-      file = applet.getCodeBase() + file;
-      launcher.addActionListener(new java.awt.event.ActionListener()
-     {
-       public void actionPerformed(ActionEvent e)
-       {
-         String format = jalview.io.IdentifyFile.Identify( file, "URL");
-         LoadFile(file, "URL", format);
-       }
-     });
+
+public class JalviewLite extends Applet {
+    static int lastFrameX = 200;
+    static int lastFrameY = 200;
+    static Applet applet;
+    boolean fileFound = true;
+    String file = "No file";
+    Button launcher = new Button("Start Jalview");
+
+    public void init() {
+        applet = this;
+        this.setBackground(Color.white);
+
+        file = getParameter("file");
+
+        if (file != null) {
+            add(launcher);
+            file = applet.getCodeBase() + file;
+            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 {
+            file = "NO FILE";
+            fileFound = false;
+        }
+    }
+
+    public static void showURL(String url) {
+        try {
+            applet.getAppletContext().showDocument(new java.net.URL(url),
+                "HELP_WINDOW");
+        } catch (Exception ex) {
+        }
     }
-     else
-     {
-       file = "NO FILE";
-       fileFound = false;
-     }
-   }
-
-
-   public static void showURL(String url)
-   {
-     try{
-       applet.getAppletContext().showDocument(new java.net.URL(url), "HELP_WINDOW");
-     }catch(Exception ex){}
-   }
-
-   public void LoadFile(String file, String protocol,  String format)
-   {
-     LoadingThread loader = new LoadingThread(file, protocol, format, this);
-     loader.start();
-   }
-
-   public static void addFrame(final Frame frame, String title, int width, 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.dispose();
-      }
-    });
-    frame.setVisible(true);
-   }
-
-
-   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);
-       g.setColor(Color.red);
-       g.drawString("Jalview can't open file", 5, 15);
-       g.drawString("\""+ file+"\"", 5, 30);
-     }
-   }
-
-   class LoadingThread extends Thread
-   {
-     String file, protocol, format;
-     JalviewLite jlapplet;
-
-     public LoadingThread(String file, String protocol,  String format, JalviewLite applet)
-     {
-       this.file = file;
-       this.protocol = protocol;
-       this.format = format;
-       this.jlapplet = applet;
-     }
-     public void run()
-     {
-       SequenceI [] sequences = null;
-       sequences = FormatAdapter.readFile(file, protocol, format);
-
-       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
-       {
-         fileFound = false;
-         remove(launcher);
-         repaint();
-       }
-     }
-   }
-}
 
+    public void LoadFile(String file, String protocol, String format) {
+        LoadingThread loader = new LoadingThread(file, protocol, format, this);
+        loader.start();
+    }
 
+    public static void addFrame(final Frame frame, String title, int width,
+        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.dispose();
+                }
+            });
+        frame.setVisible(true);
+    }
+
+    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);
+            g.setColor(Color.red);
+            g.drawString("Jalview can't open file", 5, 15);
+            g.drawString("\"" + file + "\"", 5, 30);
+        }
+    }
+
+    class LoadingThread extends Thread {
+        String file;
+        String protocol;
+        String format;
+        JalviewLite jlapplet;
+
+        public LoadingThread(String file, String protocol, String format,
+            JalviewLite applet) {
+            this.file = file;
+            this.protocol = protocol;
+            this.format = format;
+            this.jlapplet = applet;
+        }
+
+        public void run() {
+            SequenceI[] sequences = null;
+            sequences = FormatAdapter.readFile(file, protocol, format);
+
+            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 {
+                fileFound = false;
+                remove(launcher);
+                repaint();
+            }
+        }
+    }
+}
diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 644cd03..093ae6f 100755
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,33 +22,32 @@
 * 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.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 -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -62,30 +60,19 @@ public class Alignment implements java.io.Serializable {
      */
     private jalview.binding.SequenceSet _sequenceSet;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- 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'.
-     */
-    public jalview.binding.Annotation getAnnotation()
-    {
+    public jalview.binding.Annotation getAnnotation() {
         return this._annotation;
-    } //-- jalview.binding.Annotation getAnnotation()
+    }
+     //-- jalview.binding.Annotation getAnnotation()
 
     /**
      * Returns the value of field 'sequenceSet'.
@@ -93,10 +80,10 @@ public class Alignment implements java.io.Serializable {
      * @return SequenceSet
      * @return the value of field 'sequenceSet'.
      */
-    public jalview.binding.SequenceSet getSequenceSet()
-    {
+    public jalview.binding.SequenceSet getSequenceSet() {
         return this._sequenceSet;
-    } //-- jalview.binding.SequenceSet getSequenceSet()
+    }
+     //-- jalview.binding.SequenceSet getSequenceSet()
 
     /**
      * Method isValid
@@ -105,16 +92,16 @@ public class Alignment implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -124,11 +111,11 @@ public class Alignment implements java.io.Serializable {
      * @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
@@ -138,31 +125,31 @@ public class Alignment implements java.io.Serializable {
      * @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)
-    {
+    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)
-    {
+    public void setSequenceSet(jalview.binding.SequenceSet sequenceSet) {
         this._sequenceSet = sequenceSet;
-    } //-- void setSequenceSet(jalview.binding.SequenceSet)
+    }
+     //-- void setSequenceSet(jalview.binding.SequenceSet)
 
     /**
      * Method unmarshal
@@ -173,20 +160,20 @@ public class Alignment implements java.io.Serializable {
      * @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.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 4af694f..6879c96 100755
--- a/src/jalview/binding/Annotation.java
+++ b/src/jalview/binding/Annotation.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,24 +22,26 @@
 * 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.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 Annotation.
@@ -48,10 +49,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class Annotation implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -79,33 +78,22 @@ public class Annotation implements java.io.Serializable {
      */
     private java.lang.String _description;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public Annotation() {
         super();
         _annotationElementList = new Vector();
-    } //-- jalview.binding.Annotation()
-
+    }
+     //-- jalview.binding.Annotation()
+ //-----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addAnnotationElement
-     *
-     *
-     *
-     * @param vAnnotationElement
-     */
-    public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    public void addAnnotationElement(
+        jalview.binding.AnnotationElement vAnnotationElement)
+        throws java.lang.IndexOutOfBoundsException {
         _annotationElementList.addElement(vAnnotationElement);
-    } //-- void addAnnotationElement(jalview.binding.AnnotationElement)
+    }
+     //-- void addAnnotationElement(jalview.binding.AnnotationElement)
 
     /**
      * Method addAnnotationElement
@@ -115,20 +103,21 @@ public class Annotation implements java.io.Serializable {
      * @param index
      * @param vAnnotationElement
      */
-    public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    public void addAnnotationElement(int index,
+        jalview.binding.AnnotationElement vAnnotationElement)
+        throws java.lang.IndexOutOfBoundsException {
         _annotationElementList.insertElementAt(vAnnotationElement, index);
-    } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)
+    }
+     //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)
 
     /**
      * Method deleteGraph
      *
      */
-    public void deleteGraph()
-    {
-        this._has_graph= false;
-    } //-- void deleteGraph()
+    public void deleteGraph() {
+        this._has_graph = false;
+    }
+     //-- void deleteGraph()
 
     /**
      * Method enumerateAnnotationElement
@@ -137,10 +126,10 @@ public class Annotation implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateAnnotationElement()
-    {
+    public java.util.Enumeration enumerateAnnotationElement() {
         return _annotationElementList.elements();
-    } //-- java.util.Enumeration enumerateAnnotationElement()
+    }
+     //-- java.util.Enumeration enumerateAnnotationElement()
 
     /**
      * Method getAnnotationElement
@@ -151,15 +140,15 @@ public class Annotation implements java.io.Serializable {
      * @return AnnotationElement
      */
     public jalview.binding.AnnotationElement getAnnotationElement(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- jalview.binding.AnnotationElement getAnnotationElement(int)
 
     /**
      * Method getAnnotationElement
@@ -168,15 +157,17 @@ public class Annotation implements java.io.Serializable {
      *
      * @return AnnotationElement
      */
-    public jalview.binding.AnnotationElement[] getAnnotationElement()
-    {
+    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()
+    }
+     //-- jalview.binding.AnnotationElement[] getAnnotationElement()
 
     /**
      * Method getAnnotationElementCount
@@ -185,10 +176,10 @@ public class Annotation implements java.io.Serializable {
      *
      * @return int
      */
-    public int getAnnotationElementCount()
-    {
+    public int getAnnotationElementCount() {
         return _annotationElementList.size();
-    } //-- int getAnnotationElementCount()
+    }
+     //-- int getAnnotationElementCount()
 
     /**
      * Returns the value of field 'description'.
@@ -196,10 +187,10 @@ public class Annotation implements java.io.Serializable {
      * @return String
      * @return the value of field 'description'.
      */
-    public java.lang.String getDescription()
-    {
+    public java.lang.String getDescription() {
         return this._description;
-    } //-- java.lang.String getDescription()
+    }
+     //-- java.lang.String getDescription()
 
     /**
      * Returns the value of field 'graph'.
@@ -207,10 +198,10 @@ public class Annotation implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'graph'.
      */
-    public boolean getGraph()
-    {
+    public boolean getGraph() {
         return this._graph;
-    } //-- boolean getGraph()
+    }
+     //-- boolean getGraph()
 
     /**
      * Returns the value of field 'label'.
@@ -218,10 +209,10 @@ public class Annotation implements java.io.Serializable {
      * @return String
      * @return the value of field 'label'.
      */
-    public java.lang.String getLabel()
-    {
+    public java.lang.String getLabel() {
         return this._label;
-    } //-- java.lang.String getLabel()
+    }
+     //-- java.lang.String getLabel()
 
     /**
      * Method hasGraph
@@ -230,10 +221,10 @@ public class Annotation implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasGraph()
-    {
+    public boolean hasGraph() {
         return this._has_graph;
-    } //-- boolean hasGraph()
+    }
+     //-- boolean hasGraph()
 
     /**
      * Method isValid
@@ -242,16 +233,16 @@ public class Annotation implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -261,11 +252,11 @@ public class Annotation implements java.io.Serializable {
      * @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
@@ -275,20 +266,20 @@ public class Annotation implements java.io.Serializable {
      * @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 removeAllAnnotationElement
      *
      */
-    public void removeAllAnnotationElement()
-    {
+    public void removeAllAnnotationElement() {
         _annotationElementList.removeAllElements();
-    } //-- void removeAllAnnotationElement()
+    }
+     //-- void removeAllAnnotationElement()
 
     /**
      * Method removeAnnotationElement
@@ -298,12 +289,13 @@ public class Annotation implements java.io.Serializable {
      * @param index
      * @return AnnotationElement
      */
-    public jalview.binding.AnnotationElement removeAnnotationElement(int index)
-    {
+    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)
+    }
+     //-- jalview.binding.AnnotationElement removeAnnotationElement(int)
 
     /**
      * Method setAnnotationElement
@@ -313,15 +305,17 @@ public class Annotation implements java.io.Serializable {
      * @param index
      * @param vAnnotationElement
      */
-    public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    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)
+    }
+     //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)
 
     /**
      * Method setAnnotationElement
@@ -330,45 +324,47 @@ public class Annotation implements java.io.Serializable {
      *
      * @param annotationElementArray
      */
-    public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray)
-    {
+    public void setAnnotationElement(
+        jalview.binding.AnnotationElement[] annotationElementArray) {
         //-- copy array
         _annotationElementList.removeAllElements();
+
         for (int i = 0; i < annotationElementArray.length; i++) {
             _annotationElementList.addElement(annotationElementArray[i]);
         }
-    } //-- void setAnnotationElement(jalview.binding.AnnotationElement)
+    }
+     //-- 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)
-    {
+    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 'graph'.
      *
      * @param graph the value of field 'graph'.
      */
-    public void setGraph(boolean graph)
-    {
+    public void setGraph(boolean graph) {
         this._graph = graph;
         this._has_graph = true;
-    } //-- void setGraph(boolean)
+    }
+     //-- void setGraph(boolean)
 
     /**
      * Sets the value of field 'label'.
      *
      * @param label the value of field 'label'.
      */
-    public void setLabel(java.lang.String label)
-    {
+    public void setLabel(java.lang.String label) {
         this._label = label;
-    } //-- void setLabel(java.lang.String)
+    }
+     //-- void setLabel(java.lang.String)
 
     /**
      * Method unmarshal
@@ -379,20 +375,20 @@ public class Annotation implements java.io.Serializable {
      * @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)
+        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
-    {
+    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/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java
index 211810d..3c6eba4 100755
--- a/src/jalview/binding/AnnotationElement.java
+++ b/src/jalview/binding/AnnotationElement.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,33 +22,32 @@
 * 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.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 -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -87,37 +85,28 @@ public class AnnotationElement implements java.io.Serializable {
      */
     private boolean _has_value;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public AnnotationElement() {
         super();
-    } //-- jalview.binding.AnnotationElement()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+    }
+     //-- jalview.binding.AnnotationElement()
+ //-----------/
 
-    /**
-     * Method deletePosition
-     *
-     */
-    public void deletePosition()
-    {
-        this._has_position= false;
-    } //-- void deletePosition()
+    public void deletePosition() {
+        this._has_position = false;
+    }
+     //-- void deletePosition()
 
     /**
      * Method deleteValue
      *
      */
-    public void deleteValue()
-    {
-        this._has_value= false;
-    } //-- void deleteValue()
+    public void deleteValue() {
+        this._has_value = false;
+    }
+     //-- void deleteValue()
 
     /**
      * Returns the value of field 'description'.
@@ -125,10 +114,10 @@ public class AnnotationElement implements java.io.Serializable {
      * @return String
      * @return the value of field 'description'.
      */
-    public java.lang.String getDescription()
-    {
+    public java.lang.String getDescription() {
         return this._description;
-    } //-- java.lang.String getDescription()
+    }
+     //-- java.lang.String getDescription()
 
     /**
      * Returns the value of field 'displayCharacter'.
@@ -136,10 +125,10 @@ public class AnnotationElement implements java.io.Serializable {
      * @return String
      * @return the value of field 'displayCharacter'.
      */
-    public java.lang.String getDisplayCharacter()
-    {
+    public java.lang.String getDisplayCharacter() {
         return this._displayCharacter;
-    } //-- java.lang.String getDisplayCharacter()
+    }
+     //-- java.lang.String getDisplayCharacter()
 
     /**
      * Returns the value of field 'position'.
@@ -147,10 +136,10 @@ public class AnnotationElement implements java.io.Serializable {
      * @return int
      * @return the value of field 'position'.
      */
-    public int getPosition()
-    {
+    public int getPosition() {
         return this._position;
-    } //-- int getPosition()
+    }
+     //-- int getPosition()
 
     /**
      * Returns the value of field 'secondaryStructure'.
@@ -158,10 +147,10 @@ public class AnnotationElement implements java.io.Serializable {
      * @return String
      * @return the value of field 'secondaryStructure'.
      */
-    public java.lang.String getSecondaryStructure()
-    {
+    public java.lang.String getSecondaryStructure() {
         return this._secondaryStructure;
-    } //-- java.lang.String getSecondaryStructure()
+    }
+     //-- java.lang.String getSecondaryStructure()
 
     /**
      * Returns the value of field 'value'.
@@ -169,10 +158,10 @@ public class AnnotationElement implements java.io.Serializable {
      * @return float
      * @return the value of field 'value'.
      */
-    public float getValue()
-    {
+    public float getValue() {
         return this._value;
-    } //-- float getValue()
+    }
+     //-- float getValue()
 
     /**
      * Method hasPosition
@@ -181,10 +170,10 @@ public class AnnotationElement implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasPosition()
-    {
+    public boolean hasPosition() {
         return this._has_position;
-    } //-- boolean hasPosition()
+    }
+     //-- boolean hasPosition()
 
     /**
      * Method hasValue
@@ -193,10 +182,10 @@ public class AnnotationElement implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasValue()
-    {
+    public boolean hasValue() {
         return this._has_value;
-    } //-- boolean hasValue()
+    }
+     //-- boolean hasValue()
 
     /**
      * Method isValid
@@ -205,16 +194,16 @@ public class AnnotationElement implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -224,11 +213,11 @@ public class AnnotationElement implements java.io.Serializable {
      * @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
@@ -238,42 +227,42 @@ public class AnnotationElement implements java.io.Serializable {
      * @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)
-    {
+    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)
-    {
+    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)
-    {
+    public void setPosition(int position) {
         this._position = position;
         this._has_position = true;
-    } //-- void setPosition(int)
+    }
+     //-- void setPosition(int)
 
     /**
      * Sets the value of field 'secondaryStructure'.
@@ -281,21 +270,21 @@ public class AnnotationElement implements java.io.Serializable {
      * @param secondaryStructure the value of field
      * 'secondaryStructure'.
      */
-    public void setSecondaryStructure(java.lang.String 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)
-    {
+    public void setValue(float value) {
         this._value = value;
         this._has_value = true;
-    } //-- void setValue(float)
+    }
+     //-- void setValue(float)
 
     /**
      * Method unmarshal
@@ -306,20 +295,20 @@ public class AnnotationElement implements java.io.Serializable {
      * @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.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 2a3423d..7cd04b3 100755
--- a/src/jalview/binding/Colour.java
+++ b/src/jalview/binding/Colour.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,33 +22,32 @@
 * 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.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 -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -62,30 +60,19 @@ public class Colour implements java.io.Serializable {
      */
     private java.lang.String _RGB;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public Colour() {
         super();
-    } //-- jalview.binding.Colour()
-
+    }
+     //-- jalview.binding.Colour()
+ //-----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'name'.
-     *
-     * @return String
-     * @return the value of field 'name'.
-     */
-    public java.lang.String getName()
-    {
+    public java.lang.String getName() {
         return this._name;
-    } //-- java.lang.String getName()
+    }
+     //-- java.lang.String getName()
 
     /**
      * Returns the value of field 'RGB'.
@@ -93,10 +80,10 @@ public class Colour implements java.io.Serializable {
      * @return String
      * @return the value of field 'RGB'.
      */
-    public java.lang.String getRGB()
-    {
+    public java.lang.String getRGB() {
         return this._RGB;
-    } //-- java.lang.String getRGB()
+    }
+     //-- java.lang.String getRGB()
 
     /**
      * Method isValid
@@ -105,16 +92,16 @@ public class Colour implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -124,11 +111,11 @@ public class Colour implements java.io.Serializable {
      * @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
@@ -138,31 +125,31 @@ public class Colour implements java.io.Serializable {
      * @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)
-    {
+    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)
-    {
+    public void setRGB(java.lang.String RGB) {
         this._RGB = RGB;
-    } //-- void setRGB(java.lang.String)
+    }
+     //-- void setRGB(java.lang.String)
 
     /**
      * Method unmarshal
@@ -173,20 +160,20 @@ public class Colour implements java.io.Serializable {
      * @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.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 eef4a28..3b5c0b8 100755
--- a/src/jalview/binding/JGroup.java
+++ b/src/jalview/binding/JGroup.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,24 +22,26 @@
 * 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.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.
@@ -48,10 +49,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class JGroup implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -149,33 +148,20 @@ public class JGroup implements java.io.Serializable {
      */
     private java.util.Vector _seqList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public JGroup() {
         super();
         _seqList = new Vector();
-    } //-- jalview.binding.JGroup()
-
+    }
+     //-- jalview.binding.JGroup()
+ //-----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addSeq
-     *
-     *
-     *
-     * @param vSeq
-     */
-    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
@@ -186,82 +172,82 @@ public class JGroup implements java.io.Serializable {
      * @param vSeq
      */
     public void addSeq(int index, int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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()
+    public void deleteColourText() {
+        this._has_colourText = false;
+    }
+     //-- void deleteColourText()
 
     /**
      * Method deleteConsThreshold
      *
      */
-    public void deleteConsThreshold()
-    {
-        this._has_consThreshold= false;
-    } //-- void deleteConsThreshold()
+    public void deleteConsThreshold() {
+        this._has_consThreshold = false;
+    }
+     //-- void deleteConsThreshold()
 
     /**
      * Method deleteDisplayBoxes
      *
      */
-    public void deleteDisplayBoxes()
-    {
-        this._has_displayBoxes= false;
-    } //-- void deleteDisplayBoxes()
+    public void deleteDisplayBoxes() {
+        this._has_displayBoxes = false;
+    }
+     //-- void deleteDisplayBoxes()
 
     /**
      * Method deleteDisplayText
      *
      */
-    public void deleteDisplayText()
-    {
-        this._has_displayText= false;
-    } //-- void deleteDisplayText()
+    public void deleteDisplayText() {
+        this._has_displayText = false;
+    }
+     //-- void deleteDisplayText()
 
     /**
      * Method deleteEnd
      *
      */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd()
+    public void deleteEnd() {
+        this._has_end = false;
+    }
+     //-- void deleteEnd()
 
     /**
      * Method deleteOutlineColour
      *
      */
-    public void deleteOutlineColour()
-    {
-        this._has_outlineColour= false;
-    } //-- void deleteOutlineColour()
+    public void deleteOutlineColour() {
+        this._has_outlineColour = false;
+    }
+     //-- void deleteOutlineColour()
 
     /**
      * Method deletePidThreshold
      *
      */
-    public void deletePidThreshold()
-    {
-        this._has_pidThreshold= false;
-    } //-- void deletePidThreshold()
+    public void deletePidThreshold() {
+        this._has_pidThreshold = false;
+    }
+     //-- void deletePidThreshold()
 
     /**
      * Method deleteStart
      *
      */
-    public void deleteStart()
-    {
-        this._has_start= false;
-    } //-- void deleteStart()
+    public void deleteStart() {
+        this._has_start = false;
+    }
+     //-- void deleteStart()
 
     /**
      * Method enumerateSeq
@@ -270,10 +256,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateSeq()
-    {
+    public java.util.Enumeration enumerateSeq() {
         return _seqList.elements();
-    } //-- java.util.Enumeration enumerateSeq()
+    }
+     //-- java.util.Enumeration enumerateSeq()
 
     /**
      * Returns the value of field 'colour'.
@@ -281,10 +267,10 @@ public class JGroup implements java.io.Serializable {
      * @return String
      * @return the value of field 'colour'.
      */
-    public java.lang.String getColour()
-    {
+    public java.lang.String getColour() {
         return this._colour;
-    } //-- java.lang.String getColour()
+    }
+     //-- java.lang.String getColour()
 
     /**
      * Returns the value of field 'colourText'.
@@ -292,10 +278,10 @@ public class JGroup implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'colourText'.
      */
-    public boolean getColourText()
-    {
+    public boolean getColourText() {
         return this._colourText;
-    } //-- boolean getColourText()
+    }
+     //-- boolean getColourText()
 
     /**
      * Returns the value of field 'consThreshold'.
@@ -303,10 +289,10 @@ public class JGroup implements java.io.Serializable {
      * @return int
      * @return the value of field 'consThreshold'.
      */
-    public int getConsThreshold()
-    {
+    public int getConsThreshold() {
         return this._consThreshold;
-    } //-- int getConsThreshold()
+    }
+     //-- int getConsThreshold()
 
     /**
      * Returns the value of field 'displayBoxes'.
@@ -314,10 +300,10 @@ public class JGroup implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'displayBoxes'.
      */
-    public boolean getDisplayBoxes()
-    {
+    public boolean getDisplayBoxes() {
         return this._displayBoxes;
-    } //-- boolean getDisplayBoxes()
+    }
+     //-- boolean getDisplayBoxes()
 
     /**
      * Returns the value of field 'displayText'.
@@ -325,10 +311,10 @@ public class JGroup implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'displayText'.
      */
-    public boolean getDisplayText()
-    {
+    public boolean getDisplayText() {
         return this._displayText;
-    } //-- boolean getDisplayText()
+    }
+     //-- boolean getDisplayText()
 
     /**
      * Returns the value of field 'end'.
@@ -336,10 +322,10 @@ public class JGroup implements java.io.Serializable {
      * @return int
      * @return the value of field 'end'.
      */
-    public int getEnd()
-    {
+    public int getEnd() {
         return this._end;
-    } //-- int getEnd()
+    }
+     //-- int getEnd()
 
     /**
      * Returns the value of field 'name'.
@@ -347,10 +333,10 @@ public class JGroup implements java.io.Serializable {
      * @return String
      * @return the value of field 'name'.
      */
-    public java.lang.String getName()
-    {
+    public java.lang.String getName() {
         return this._name;
-    } //-- java.lang.String getName()
+    }
+     //-- java.lang.String getName()
 
     /**
      * Returns the value of field 'outlineColour'.
@@ -358,10 +344,10 @@ public class JGroup implements java.io.Serializable {
      * @return int
      * @return the value of field 'outlineColour'.
      */
-    public int getOutlineColour()
-    {
+    public int getOutlineColour() {
         return this._outlineColour;
-    } //-- int getOutlineColour()
+    }
+     //-- int getOutlineColour()
 
     /**
      * Returns the value of field 'pidThreshold'.
@@ -369,10 +355,10 @@ public class JGroup implements java.io.Serializable {
      * @return int
      * @return the value of field 'pidThreshold'.
      */
-    public int getPidThreshold()
-    {
+    public int getPidThreshold() {
         return this._pidThreshold;
-    } //-- int getPidThreshold()
+    }
+     //-- int getPidThreshold()
 
     /**
      * Method getSeq
@@ -382,16 +368,15 @@ public class JGroup implements java.io.Serializable {
      * @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())) {
             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
@@ -400,15 +385,17 @@ public class JGroup implements java.io.Serializable {
      *
      * @return int
      */
-    public int[] getSeq()
-    {
+    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();
+            mArray[index] = ((java.lang.Integer) _seqList.elementAt(index)).intValue();
         }
+
         return mArray;
-    } //-- int[] getSeq()
+    }
+     //-- int[] getSeq()
 
     /**
      * Method getSeqCount
@@ -417,10 +404,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return int
      */
-    public int getSeqCount()
-    {
+    public int getSeqCount() {
         return _seqList.size();
-    } //-- int getSeqCount()
+    }
+     //-- int getSeqCount()
 
     /**
      * Returns the value of field 'start'.
@@ -428,10 +415,10 @@ public class JGroup implements java.io.Serializable {
      * @return int
      * @return the value of field 'start'.
      */
-    public int getStart()
-    {
+    public int getStart() {
         return this._start;
-    } //-- int getStart()
+    }
+     //-- int getStart()
 
     /**
      * Method hasColourText
@@ -440,10 +427,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasColourText()
-    {
+    public boolean hasColourText() {
         return this._has_colourText;
-    } //-- boolean hasColourText()
+    }
+     //-- boolean hasColourText()
 
     /**
      * Method hasConsThreshold
@@ -452,10 +439,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasConsThreshold()
-    {
+    public boolean hasConsThreshold() {
         return this._has_consThreshold;
-    } //-- boolean hasConsThreshold()
+    }
+     //-- boolean hasConsThreshold()
 
     /**
      * Method hasDisplayBoxes
@@ -464,10 +451,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasDisplayBoxes()
-    {
+    public boolean hasDisplayBoxes() {
         return this._has_displayBoxes;
-    } //-- boolean hasDisplayBoxes()
+    }
+     //-- boolean hasDisplayBoxes()
 
     /**
      * Method hasDisplayText
@@ -476,10 +463,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasDisplayText()
-    {
+    public boolean hasDisplayText() {
         return this._has_displayText;
-    } //-- boolean hasDisplayText()
+    }
+     //-- boolean hasDisplayText()
 
     /**
      * Method hasEnd
@@ -488,10 +475,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasEnd()
-    {
+    public boolean hasEnd() {
         return this._has_end;
-    } //-- boolean hasEnd()
+    }
+     //-- boolean hasEnd()
 
     /**
      * Method hasOutlineColour
@@ -500,10 +487,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasOutlineColour()
-    {
+    public boolean hasOutlineColour() {
         return this._has_outlineColour;
-    } //-- boolean hasOutlineColour()
+    }
+     //-- boolean hasOutlineColour()
 
     /**
      * Method hasPidThreshold
@@ -512,10 +499,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasPidThreshold()
-    {
+    public boolean hasPidThreshold() {
         return this._has_pidThreshold;
-    } //-- boolean hasPidThreshold()
+    }
+     //-- boolean hasPidThreshold()
 
     /**
      * Method hasStart
@@ -524,10 +511,10 @@ public class JGroup implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasStart()
-    {
+    public boolean hasStart() {
         return this._has_start;
-    } //-- boolean hasStart()
+    }
+     //-- boolean hasStart()
 
     /**
      * Method isValid
@@ -536,16 +523,16 @@ public class JGroup implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -555,11 +542,11 @@ public class JGroup implements java.io.Serializable {
      * @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
@@ -569,20 +556,20 @@ public class JGroup implements java.io.Serializable {
      * @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()
-    {
+    public void removeAllSeq() {
         _seqList.removeAllElements();
-    } //-- void removeAllSeq()
+    }
+     //-- void removeAllSeq()
 
     /**
      * Method removeSeq
@@ -592,109 +579,110 @@ public class JGroup implements java.io.Serializable {
      * @param index
      * @return int
      */
-    public int removeSeq(int index)
-    {
+    public int removeSeq(int index) {
         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)
-    {
+    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)
-    {
+    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)
-    {
+    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)
-    {
+    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)
-    {
+    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)
-    {
+    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)
-    {
+    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)
-    {
+    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)
-    {
+    public void setPidThreshold(int pidThreshold) {
         this._pidThreshold = pidThreshold;
         this._has_pidThreshold = true;
-    } //-- void setPidThreshold(int)
+    }
+     //-- void setPidThreshold(int)
 
     /**
      * Method setSeq
@@ -705,14 +693,15 @@ public class JGroup implements java.io.Serializable {
      * @param vSeq
      */
     public void setSeq(int index, int vSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         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
@@ -721,25 +710,26 @@ public class JGroup implements java.io.Serializable {
      *
      * @param seqArray
      */
-    public void setSeq(int[] seqArray)
-    {
+    public void setSeq(int[] seqArray) {
         //-- copy array
         _seqList.removeAllElements();
+
         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)
-    {
+    public void setStart(int start) {
         this._start = start;
         this._has_start = true;
-    } //-- void setStart(int)
+    }
+     //-- void setStart(int)
 
     /**
      * Method unmarshal
@@ -750,20 +740,20 @@ public class JGroup implements java.io.Serializable {
      * @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.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 9e02e60..cabf5c8 100755
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,33 +22,32 @@
 * 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.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 -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -92,55 +90,46 @@ public class JSeq implements java.io.Serializable {
      */
     private boolean _has_id;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public JSeq() {
         super();
-    } //-- jalview.binding.JSeq()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+    }
+     //-- jalview.binding.JSeq()
+ //-----------/
 
-    /**
-     * Method deleteColour
-     *
-     */
-    public void deleteColour()
-    {
-        this._has_colour= false;
-    } //-- void deleteColour()
+    public void deleteColour() {
+        this._has_colour = false;
+    }
+     //-- void deleteColour()
 
     /**
      * Method deleteEnd
      *
      */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd()
+    public void deleteEnd() {
+        this._has_end = false;
+    }
+     //-- void deleteEnd()
 
     /**
      * Method deleteId
      *
      */
-    public void deleteId()
-    {
-        this._has_id= false;
-    } //-- void deleteId()
+    public void deleteId() {
+        this._has_id = false;
+    }
+     //-- void deleteId()
 
     /**
      * Method deleteStart
      *
      */
-    public void deleteStart()
-    {
-        this._has_start= false;
-    } //-- void deleteStart()
+    public void deleteStart() {
+        this._has_start = false;
+    }
+     //-- void deleteStart()
 
     /**
      * Returns the value of field 'colour'.
@@ -148,10 +137,10 @@ public class JSeq implements java.io.Serializable {
      * @return int
      * @return the value of field 'colour'.
      */
-    public int getColour()
-    {
+    public int getColour() {
         return this._colour;
-    } //-- int getColour()
+    }
+     //-- int getColour()
 
     /**
      * Returns the value of field 'end'.
@@ -159,10 +148,10 @@ public class JSeq implements java.io.Serializable {
      * @return int
      * @return the value of field 'end'.
      */
-    public int getEnd()
-    {
+    public int getEnd() {
         return this._end;
-    } //-- int getEnd()
+    }
+     //-- int getEnd()
 
     /**
      * Returns the value of field 'id'.
@@ -170,10 +159,10 @@ public class JSeq implements java.io.Serializable {
      * @return int
      * @return the value of field 'id'.
      */
-    public int getId()
-    {
+    public int getId() {
         return this._id;
-    } //-- int getId()
+    }
+     //-- int getId()
 
     /**
      * Returns the value of field 'start'.
@@ -181,10 +170,10 @@ public class JSeq implements java.io.Serializable {
      * @return int
      * @return the value of field 'start'.
      */
-    public int getStart()
-    {
+    public int getStart() {
         return this._start;
-    } //-- int getStart()
+    }
+     //-- int getStart()
 
     /**
      * Method hasColour
@@ -193,10 +182,10 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasColour()
-    {
+    public boolean hasColour() {
         return this._has_colour;
-    } //-- boolean hasColour()
+    }
+     //-- boolean hasColour()
 
     /**
      * Method hasEnd
@@ -205,10 +194,10 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasEnd()
-    {
+    public boolean hasEnd() {
         return this._has_end;
-    } //-- boolean hasEnd()
+    }
+     //-- boolean hasEnd()
 
     /**
      * Method hasId
@@ -217,10 +206,10 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasId()
-    {
+    public boolean hasId() {
         return this._has_id;
-    } //-- boolean hasId()
+    }
+     //-- boolean hasId()
 
     /**
      * Method hasStart
@@ -229,10 +218,10 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasStart()
-    {
+    public boolean hasStart() {
         return this._has_start;
-    } //-- boolean hasStart()
+    }
+     //-- boolean hasStart()
 
     /**
      * Method isValid
@@ -241,16 +230,16 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -260,11 +249,11 @@ public class JSeq implements java.io.Serializable {
      * @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
@@ -274,55 +263,55 @@ public class JSeq implements java.io.Serializable {
      * @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)
-    {
+    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)
-    {
+    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)
-    {
+    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)
-    {
+    public void setStart(int start) {
         this._start = start;
         this._has_start = true;
-    } //-- void setStart(int)
+    }
+     //-- void setStart(int)
 
     /**
      * Method unmarshal
@@ -333,20 +322,20 @@ public class JSeq implements java.io.Serializable {
      * @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.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 d30e97d..85bfe26 100755
--- a/src/jalview/binding/JalviewModel.java
+++ b/src/jalview/binding/JalviewModel.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,23 +22,25 @@
 * 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.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.
@@ -47,10 +48,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class JalviewModel implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -68,30 +67,19 @@ public class JalviewModel implements java.io.Serializable {
      */
     private jalview.binding.JalviewModelSequence _jalviewModelSequence;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- 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'.
-     */
-    public java.util.Date getCreationDate()
-    {
+    public java.util.Date getCreationDate() {
         return this._creationDate;
-    } //-- java.util.Date getCreationDate()
+    }
+     //-- java.util.Date getCreationDate()
 
     /**
      * Returns the value of field 'jalviewModelSequence'.
@@ -99,10 +87,10 @@ public class JalviewModel implements java.io.Serializable {
      * @return JalviewModelSequence
      * @return the value of field 'jalviewModelSequence'.
      */
-    public jalview.binding.JalviewModelSequence getJalviewModelSequence()
-    {
+    public jalview.binding.JalviewModelSequence getJalviewModelSequence() {
         return this._jalviewModelSequence;
-    } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence()
+    }
+     //-- jalview.binding.JalviewModelSequence getJalviewModelSequence()
 
     /**
      * Returns the value of field 'vamsasModel'.
@@ -110,10 +98,10 @@ public class JalviewModel implements java.io.Serializable {
      * @return VamsasModel
      * @return the value of field 'vamsasModel'.
      */
-    public jalview.binding.VamsasModel getVamsasModel()
-    {
+    public jalview.binding.VamsasModel getVamsasModel() {
         return this._vamsasModel;
-    } //-- jalview.binding.VamsasModel getVamsasModel()
+    }
+     //-- jalview.binding.VamsasModel getVamsasModel()
 
     /**
      * Method isValid
@@ -122,16 +110,16 @@ public class JalviewModel implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -141,11 +129,11 @@ public class JalviewModel implements java.io.Serializable {
      * @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
@@ -155,21 +143,21 @@ public class JalviewModel implements java.io.Serializable {
      * @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)
-    {
+    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'.
@@ -177,20 +165,21 @@ public class JalviewModel implements java.io.Serializable {
      * @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)
-    {
+    public void setVamsasModel(jalview.binding.VamsasModel vamsasModel) {
         this._vamsasModel = vamsasModel;
-    } //-- void setVamsasModel(jalview.binding.VamsasModel)
+    }
+     //-- void setVamsasModel(jalview.binding.VamsasModel)
 
     /**
      * Method unmarshal
@@ -201,20 +190,20 @@ public class JalviewModel implements java.io.Serializable {
      * @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.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 d22dcd4..2abee13 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,24 +22,26 @@
 * 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.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 JalviewModelSequence.
@@ -48,10 +49,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class JalviewModelSequence implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -74,36 +73,24 @@ public class JalviewModelSequence implements java.io.Serializable {
      */
     private java.util.Vector _userColoursList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public JalviewModelSequence() {
         super();
         _JSeqList = new Vector();
         _JGroupList = new Vector();
         _viewportList = new Vector();
         _userColoursList = new Vector();
-    } //-- jalview.binding.JalviewModelSequence()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+    }
+     //-- jalview.binding.JalviewModelSequence()
+ //-----------/
 
-    /**
-     * Method addJGroup
-     *
-     *
-     *
-     * @param vJGroup
-     */
     public void addJGroup(jalview.binding.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _JGroupList.addElement(vJGroup);
-    } //-- void addJGroup(jalview.binding.JGroup)
+    }
+     //-- void addJGroup(jalview.binding.JGroup)
 
     /**
      * Method addJGroup
@@ -114,10 +101,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param vJGroup
      */
     public void addJGroup(int index, jalview.binding.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _JGroupList.insertElementAt(vJGroup, index);
-    } //-- void addJGroup(int, jalview.binding.JGroup)
+    }
+     //-- void addJGroup(int, jalview.binding.JGroup)
 
     /**
      * Method addJSeq
@@ -127,10 +114,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param vJSeq
      */
     public void addJSeq(jalview.binding.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _JSeqList.addElement(vJSeq);
-    } //-- void addJSeq(jalview.binding.JSeq)
+    }
+     //-- void addJSeq(jalview.binding.JSeq)
 
     /**
      * Method addJSeq
@@ -141,10 +128,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param vJSeq
      */
     public void addJSeq(int index, jalview.binding.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _JSeqList.insertElementAt(vJSeq, index);
-    } //-- void addJSeq(int, jalview.binding.JSeq)
+    }
+     //-- void addJSeq(int, jalview.binding.JSeq)
 
     /**
      * Method addUserColours
@@ -154,10 +141,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param vUserColours
      */
     public void addUserColours(jalview.binding.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _userColoursList.addElement(vUserColours);
-    } //-- void addUserColours(jalview.binding.UserColours)
+    }
+     //-- void addUserColours(jalview.binding.UserColours)
 
     /**
      * Method addUserColours
@@ -167,11 +154,12 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param index
      * @param vUserColours
      */
-    public void addUserColours(int index, jalview.binding.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    public void addUserColours(int index,
+        jalview.binding.UserColours vUserColours)
+        throws java.lang.IndexOutOfBoundsException {
         _userColoursList.insertElementAt(vUserColours, index);
-    } //-- void addUserColours(int, jalview.binding.UserColours)
+    }
+     //-- void addUserColours(int, jalview.binding.UserColours)
 
     /**
      * Method addViewport
@@ -181,10 +169,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param vViewport
      */
     public void addViewport(jalview.binding.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _viewportList.addElement(vViewport);
-    } //-- void addViewport(jalview.binding.Viewport)
+    }
+     //-- void addViewport(jalview.binding.Viewport)
 
     /**
      * Method addViewport
@@ -195,10 +183,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param vViewport
      */
     public void addViewport(int index, jalview.binding.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _viewportList.insertElementAt(vViewport, index);
-    } //-- void addViewport(int, jalview.binding.Viewport)
+    }
+     //-- void addViewport(int, jalview.binding.Viewport)
 
     /**
      * Method enumerateJGroup
@@ -207,10 +195,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateJGroup()
-    {
+    public java.util.Enumeration enumerateJGroup() {
         return _JGroupList.elements();
-    } //-- java.util.Enumeration enumerateJGroup()
+    }
+     //-- java.util.Enumeration enumerateJGroup()
 
     /**
      * Method enumerateJSeq
@@ -219,10 +207,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateJSeq()
-    {
+    public java.util.Enumeration enumerateJSeq() {
         return _JSeqList.elements();
-    } //-- java.util.Enumeration enumerateJSeq()
+    }
+     //-- java.util.Enumeration enumerateJSeq()
 
     /**
      * Method enumerateUserColours
@@ -231,10 +219,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateUserColours()
-    {
+    public java.util.Enumeration enumerateUserColours() {
         return _userColoursList.elements();
-    } //-- java.util.Enumeration enumerateUserColours()
+    }
+     //-- java.util.Enumeration enumerateUserColours()
 
     /**
      * Method enumerateViewport
@@ -243,10 +231,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateViewport()
-    {
+    public java.util.Enumeration enumerateViewport() {
         return _viewportList.elements();
-    } //-- java.util.Enumeration enumerateViewport()
+    }
+     //-- java.util.Enumeration enumerateViewport()
 
     /**
      * Method getJGroup
@@ -257,15 +245,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @return JGroup
      */
     public jalview.binding.JGroup getJGroup(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- jalview.binding.JGroup getJGroup(int)
 
     /**
      * Method getJGroup
@@ -274,15 +262,17 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return JGroup
      */
-    public jalview.binding.JGroup[] getJGroup()
-    {
+    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()
+    }
+     //-- jalview.binding.JGroup[] getJGroup()
 
     /**
      * Method getJGroupCount
@@ -291,10 +281,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return int
      */
-    public int getJGroupCount()
-    {
+    public int getJGroupCount() {
         return _JGroupList.size();
-    } //-- int getJGroupCount()
+    }
+     //-- int getJGroupCount()
 
     /**
      * Method getJSeq
@@ -305,15 +295,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @return JSeq
      */
     public jalview.binding.JSeq getJSeq(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- jalview.binding.JSeq getJSeq(int)
 
     /**
      * Method getJSeq
@@ -322,15 +312,17 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return JSeq
      */
-    public jalview.binding.JSeq[] getJSeq()
-    {
+    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()
+    }
+     //-- jalview.binding.JSeq[] getJSeq()
 
     /**
      * Method getJSeqCount
@@ -339,10 +331,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return int
      */
-    public int getJSeqCount()
-    {
+    public int getJSeqCount() {
         return _JSeqList.size();
-    } //-- int getJSeqCount()
+    }
+     //-- int getJSeqCount()
 
     /**
      * Method getUserColours
@@ -353,15 +345,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @return UserColours
      */
     public jalview.binding.UserColours getUserColours(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- jalview.binding.UserColours getUserColours(int)
 
     /**
      * Method getUserColours
@@ -370,15 +362,17 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return UserColours
      */
-    public jalview.binding.UserColours[] getUserColours()
-    {
+    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()
+    }
+     //-- jalview.binding.UserColours[] getUserColours()
 
     /**
      * Method getUserColoursCount
@@ -387,10 +381,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return int
      */
-    public int getUserColoursCount()
-    {
+    public int getUserColoursCount() {
         return _userColoursList.size();
-    } //-- int getUserColoursCount()
+    }
+     //-- int getUserColoursCount()
 
     /**
      * Method getViewport
@@ -401,15 +395,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @return Viewport
      */
     public jalview.binding.Viewport getViewport(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- jalview.binding.Viewport getViewport(int)
 
     /**
      * Method getViewport
@@ -418,15 +412,17 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return Viewport
      */
-    public jalview.binding.Viewport[] getViewport()
-    {
+    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()
+    }
+     //-- jalview.binding.Viewport[] getViewport()
 
     /**
      * Method getViewportCount
@@ -435,10 +431,10 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return int
      */
-    public int getViewportCount()
-    {
+    public int getViewportCount() {
         return _viewportList.size();
-    } //-- int getViewportCount()
+    }
+     //-- int getViewportCount()
 
     /**
      * Method isValid
@@ -447,16 +443,16 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -466,11 +462,11 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @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
@@ -480,47 +476,47 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @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 removeAllJGroup
      *
      */
-    public void removeAllJGroup()
-    {
+    public void removeAllJGroup() {
         _JGroupList.removeAllElements();
-    } //-- void removeAllJGroup()
+    }
+     //-- void removeAllJGroup()
 
     /**
      * Method removeAllJSeq
      *
      */
-    public void removeAllJSeq()
-    {
+    public void removeAllJSeq() {
         _JSeqList.removeAllElements();
-    } //-- void removeAllJSeq()
+    }
+     //-- void removeAllJSeq()
 
     /**
      * Method removeAllUserColours
      *
      */
-    public void removeAllUserColours()
-    {
+    public void removeAllUserColours() {
         _userColoursList.removeAllElements();
-    } //-- void removeAllUserColours()
+    }
+     //-- void removeAllUserColours()
 
     /**
      * Method removeAllViewport
      *
      */
-    public void removeAllViewport()
-    {
+    public void removeAllViewport() {
         _viewportList.removeAllElements();
-    } //-- void removeAllViewport()
+    }
+     //-- void removeAllViewport()
 
     /**
      * Method removeJGroup
@@ -530,12 +526,13 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param index
      * @return JGroup
      */
-    public jalview.binding.JGroup removeJGroup(int index)
-    {
+    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)
+    }
+     //-- jalview.binding.JGroup removeJGroup(int)
 
     /**
      * Method removeJSeq
@@ -545,12 +542,13 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param index
      * @return JSeq
      */
-    public jalview.binding.JSeq removeJSeq(int index)
-    {
+    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)
+    }
+     //-- jalview.binding.JSeq removeJSeq(int)
 
     /**
      * Method removeUserColours
@@ -560,12 +558,13 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param index
      * @return UserColours
      */
-    public jalview.binding.UserColours removeUserColours(int index)
-    {
+    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)
+    }
+     //-- jalview.binding.UserColours removeUserColours(int)
 
     /**
      * Method removeViewport
@@ -575,12 +574,13 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param index
      * @return Viewport
      */
-    public jalview.binding.Viewport removeViewport(int index)
-    {
+    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)
+    }
+     //-- jalview.binding.Viewport removeViewport(int)
 
     /**
      * Method setJGroup
@@ -591,14 +591,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param vJGroup
      */
     public void setJGroup(int index, jalview.binding.JGroup vJGroup)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- void setJGroup(int, jalview.binding.JGroup)
 
     /**
      * Method setJGroup
@@ -607,14 +608,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @param JGroupArray
      */
-    public void setJGroup(jalview.binding.JGroup[] 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)
+    }
+     //-- void setJGroup(jalview.binding.JGroup)
 
     /**
      * Method setJSeq
@@ -625,14 +627,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param vJSeq
      */
     public void setJSeq(int index, jalview.binding.JSeq vJSeq)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- void setJSeq(int, jalview.binding.JSeq)
 
     /**
      * Method setJSeq
@@ -641,14 +644,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @param JSeqArray
      */
-    public void setJSeq(jalview.binding.JSeq[] 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)
+    }
+     //-- void setJSeq(jalview.binding.JSeq)
 
     /**
      * Method setUserColours
@@ -658,15 +662,17 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param index
      * @param vUserColours
      */
-    public void setUserColours(int index, jalview.binding.UserColours vUserColours)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    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)
+    }
+     //-- void setUserColours(int, jalview.binding.UserColours)
 
     /**
      * Method setUserColours
@@ -675,14 +681,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @param userColoursArray
      */
-    public void setUserColours(jalview.binding.UserColours[] 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)
+    }
+     //-- void setUserColours(jalview.binding.UserColours)
 
     /**
      * Method setViewport
@@ -693,14 +700,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @param vViewport
      */
     public void setViewport(int index, jalview.binding.Viewport vViewport)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- void setViewport(int, jalview.binding.Viewport)
 
     /**
      * Method setViewport
@@ -709,14 +717,15 @@ public class JalviewModelSequence implements java.io.Serializable {
      *
      * @param viewportArray
      */
-    public void setViewport(jalview.binding.Viewport[] 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)
+    }
+     //-- void setViewport(jalview.binding.Viewport)
 
     /**
      * Method unmarshal
@@ -727,20 +736,20 @@ public class JalviewModelSequence implements java.io.Serializable {
      * @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)
+        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
-    {
+    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/JalviewModelSequence2.java b/src/jalview/binding/JalviewModelSequence2.java
index 0cf1942..add536e 100755
--- a/src/jalview/binding/JalviewModelSequence2.java
+++ b/src/jalview/binding/JalviewModelSequence2.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,24 +22,26 @@
 * 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.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.
@@ -48,10 +49,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class JalviewModelSequence2 implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -59,33 +58,22 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      */
     private java.util.Vector _items;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public JalviewModelSequence2() {
         super();
         _items = new Vector();
-    } //-- jalview.binding.JalviewModelSequence2()
-
+    }
+     //-- jalview.binding.JalviewModelSequence2()
+ //-----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addJalviewModelSequence2Item
-     *
-     *
-     *
-     * @param vJalviewModelSequence2Item
-     */
-    public void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    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
@@ -95,11 +83,12 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      * @param index
      * @param vJalviewModelSequence2Item
      */
-    public void addJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    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
@@ -108,10 +97,10 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateJalviewModelSequence2Item()
-    {
+    public java.util.Enumeration enumerateJalviewModelSequence2Item() {
         return _items.elements();
-    } //-- java.util.Enumeration enumerateJalviewModelSequence2Item()
+    }
+     //-- java.util.Enumeration enumerateJalviewModelSequence2Item()
 
     /**
      * Method getJalviewModelSequence2Item
@@ -121,16 +110,16 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      * @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())) {
             throw new IndexOutOfBoundsException();
         }
 
         return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);
-    } //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int)
+    }
+     //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int)
 
     /**
      * Method getJalviewModelSequence2Item
@@ -139,15 +128,17 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      *
      * @return JalviewModelSequence2Item
      */
-    public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()
-    {
+    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++) {
             mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()
+    }
+     //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()
 
     /**
      * Method getJalviewModelSequence2ItemCount
@@ -156,10 +147,10 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      *
      * @return int
      */
-    public int getJalviewModelSequence2ItemCount()
-    {
+    public int getJalviewModelSequence2ItemCount() {
         return _items.size();
-    } //-- int getJalviewModelSequence2ItemCount()
+    }
+     //-- int getJalviewModelSequence2ItemCount()
 
     /**
      * Method isValid
@@ -168,16 +159,16 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -187,11 +178,11 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      * @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
@@ -201,20 +192,20 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      * @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()
-    {
+    public void removeAllJalviewModelSequence2Item() {
         _items.removeAllElements();
-    } //-- void removeAllJalviewModelSequence2Item()
+    }
+     //-- void removeAllJalviewModelSequence2Item()
 
     /**
      * Method removeJalviewModelSequence2Item
@@ -224,12 +215,14 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      * @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
@@ -239,15 +232,17 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      * @param index
      * @param vJalviewModelSequence2Item
      */
-    public void setJalviewModelSequence2Item(int index, jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    public void setJalviewModelSequence2Item(int index,
+        jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         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
@@ -256,14 +251,16 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      *
      * @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++) {
             _items.addElement(jalviewModelSequence2ItemArray[i]);
         }
-    } //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)
+    }
+     //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item)
 
     /**
      * Method unmarshal
@@ -274,20 +271,20 @@ public class JalviewModelSequence2 implements java.io.Serializable {
      * @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.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 dcd3ebc..7998794 100755
--- a/src/jalview/binding/JalviewModelSequence2Item.java
+++ b/src/jalview/binding/JalviewModelSequence2Item.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,18 +22,19 @@
 * 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.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
 
+//---------------------------------/
+//- 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;
+
 
 /**
  * Class JalviewModelSequence2Item.
@@ -42,10 +42,8 @@ import org.exolab.castor.xml.Unmarshaller;
  * @version $Revision$ $Date$
  */
 public class JalviewModelSequence2Item implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -53,33 +51,22 @@ public class JalviewModelSequence2Item implements java.io.Serializable {
      */
     private java.util.Vector _userColourSchemeList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public JalviewModelSequence2Item() {
         super();
         _userColourSchemeList = new Vector();
-    } //-- jalview.binding.JalviewModelSequence2Item()
-
+    }
+     //-- jalview.binding.JalviewModelSequence2Item()
+ //-----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addUserColourScheme
-     *
-     *
-     *
-     * @param vUserColourScheme
-     */
-    public void addUserColourScheme(jalview.binding.UserColourScheme vUserColourScheme)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    public void addUserColourScheme(
+        jalview.binding.UserColourScheme vUserColourScheme)
+        throws java.lang.IndexOutOfBoundsException {
         _userColourSchemeList.addElement(vUserColourScheme);
-    } //-- void addUserColourScheme(jalview.binding.UserColourScheme)
+    }
+     //-- void addUserColourScheme(jalview.binding.UserColourScheme)
 
     /**
      * Method addUserColourScheme
@@ -89,11 +76,12 @@ public class JalviewModelSequence2Item implements java.io.Serializable {
      * @param index
      * @param vUserColourScheme
      */
-    public void addUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    public void addUserColourScheme(int index,
+        jalview.binding.UserColourScheme vUserColourScheme)
+        throws java.lang.IndexOutOfBoundsException {
         _userColourSchemeList.insertElementAt(vUserColourScheme, index);
-    } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme)
+    }
+     //-- void addUserColourScheme(int, jalview.binding.UserColourScheme)
 
     /**
      * Method enumerateUserColourScheme
@@ -102,10 +90,10 @@ public class JalviewModelSequence2Item implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateUserColourScheme()
-    {
+    public java.util.Enumeration enumerateUserColourScheme() {
         return _userColourSchemeList.elements();
-    } //-- java.util.Enumeration enumerateUserColourScheme()
+    }
+     //-- java.util.Enumeration enumerateUserColourScheme()
 
     /**
      * Method getUserColourScheme
@@ -116,15 +104,15 @@ public class JalviewModelSequence2Item implements java.io.Serializable {
      * @return UserColourScheme
      */
     public jalview.binding.UserColourScheme getUserColourScheme(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- jalview.binding.UserColourScheme getUserColourScheme(int)
 
     /**
      * Method getUserColourScheme
@@ -133,15 +121,17 @@ public class JalviewModelSequence2Item implements java.io.Serializable {
      *
      * @return UserColourScheme
      */
-    public jalview.binding.UserColourScheme[] getUserColourScheme()
-    {
+    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()
+    }
+     //-- jalview.binding.UserColourScheme[] getUserColourScheme()
 
     /**
      * Method getUserColourSchemeCount
@@ -150,19 +140,19 @@ public class JalviewModelSequence2Item implements java.io.Serializable {
      *
      * @return int
      */
-    public int getUserColourSchemeCount()
-    {
+    public int getUserColourSchemeCount() {
         return _userColourSchemeList.size();
-    } //-- int getUserColourSchemeCount()
+    }
+     //-- int getUserColourSchemeCount()
 
     /**
      * Method removeAllUserColourScheme
      *
      */
-    public void removeAllUserColourScheme()
-    {
+    public void removeAllUserColourScheme() {
         _userColourSchemeList.removeAllElements();
-    } //-- void removeAllUserColourScheme()
+    }
+     //-- void removeAllUserColourScheme()
 
     /**
      * Method removeUserColourScheme
@@ -172,12 +162,13 @@ public class JalviewModelSequence2Item implements java.io.Serializable {
      * @param index
      * @return UserColourScheme
      */
-    public jalview.binding.UserColourScheme removeUserColourScheme(int index)
-    {
+    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)
+    }
+     //-- jalview.binding.UserColourScheme removeUserColourScheme(int)
 
     /**
      * Method setUserColourScheme
@@ -187,15 +178,17 @@ public class JalviewModelSequence2Item implements java.io.Serializable {
      * @param index
      * @param vUserColourScheme
      */
-    public void setUserColourScheme(int index, jalview.binding.UserColourScheme vUserColourScheme)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    public void setUserColourScheme(int index,
+        jalview.binding.UserColourScheme vUserColourScheme)
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         if ((index < 0) || (index > _userColourSchemeList.size())) {
             throw new IndexOutOfBoundsException();
         }
+
         _userColourSchemeList.setElementAt(vUserColourScheme, index);
-    } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme)
+    }
+     //-- void setUserColourScheme(int, jalview.binding.UserColourScheme)
 
     /**
      * Method setUserColourScheme
@@ -204,13 +197,14 @@ public class JalviewModelSequence2Item implements java.io.Serializable {
      *
      * @param userColourSchemeArray
      */
-    public void setUserColourScheme(jalview.binding.UserColourScheme[] userColourSchemeArray)
-    {
+    public void setUserColourScheme(
+        jalview.binding.UserColourScheme[] userColourSchemeArray) {
         //-- copy array
         _userColourSchemeList.removeAllElements();
+
         for (int i = 0; i < userColourSchemeArray.length; i++) {
             _userColourSchemeList.addElement(userColourSchemeArray[i]);
         }
-    } //-- void setUserColourScheme(jalview.binding.UserColourScheme)
-
+    }
+     //-- void setUserColourScheme(jalview.binding.UserColourScheme)
 }
diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java
index 354dc2f..bbb1b97 100755
--- a/src/jalview/binding/JalviewUserColours.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,24 +22,26 @@
 * 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.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.
@@ -48,10 +49,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class JalviewUserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -59,33 +58,21 @@ public class JalviewUserColours implements java.io.Serializable {
      */
     private java.util.Vector _colourList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public JalviewUserColours() {
         super();
         _colourList = new Vector();
-    } //-- jalview.binding.JalviewUserColours()
-
+    }
+     //-- jalview.binding.JalviewUserColours()
+ //-----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addColour
-     *
-     *
-     *
-     * @param vColour
-     */
     public void addColour(jalview.binding.Colour vColour)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _colourList.addElement(vColour);
-    } //-- void addColour(jalview.binding.Colour)
+    }
+     //-- void addColour(jalview.binding.Colour)
 
     /**
      * Method addColour
@@ -96,10 +83,10 @@ public class JalviewUserColours implements java.io.Serializable {
      * @param vColour
      */
     public void addColour(int index, jalview.binding.Colour vColour)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _colourList.insertElementAt(vColour, index);
-    } //-- void addColour(int, jalview.binding.Colour)
+    }
+     //-- void addColour(int, jalview.binding.Colour)
 
     /**
      * Method enumerateColour
@@ -108,10 +95,10 @@ public class JalviewUserColours implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateColour()
-    {
+    public java.util.Enumeration enumerateColour() {
         return _colourList.elements();
-    } //-- java.util.Enumeration enumerateColour()
+    }
+     //-- java.util.Enumeration enumerateColour()
 
     /**
      * Method getColour
@@ -122,15 +109,15 @@ public class JalviewUserColours implements java.io.Serializable {
      * @return Colour
      */
     public jalview.binding.Colour getColour(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         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
@@ -139,15 +126,17 @@ public class JalviewUserColours implements java.io.Serializable {
      *
      * @return Colour
      */
-    public jalview.binding.Colour[] getColour()
-    {
+    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++) {
             mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.Colour[] getColour()
+    }
+     //-- jalview.binding.Colour[] getColour()
 
     /**
      * Method getColourCount
@@ -156,10 +145,10 @@ public class JalviewUserColours implements java.io.Serializable {
      *
      * @return int
      */
-    public int getColourCount()
-    {
+    public int getColourCount() {
         return _colourList.size();
-    } //-- int getColourCount()
+    }
+     //-- int getColourCount()
 
     /**
      * Method isValid
@@ -168,16 +157,16 @@ public class JalviewUserColours implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -187,11 +176,11 @@ public class JalviewUserColours implements java.io.Serializable {
      * @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
@@ -201,20 +190,20 @@ public class JalviewUserColours implements java.io.Serializable {
      * @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()
-    {
+    public void removeAllColour() {
         _colourList.removeAllElements();
-    } //-- void removeAllColour()
+    }
+     //-- void removeAllColour()
 
     /**
      * Method removeColour
@@ -224,12 +213,13 @@ public class JalviewUserColours implements java.io.Serializable {
      * @param index
      * @return Colour
      */
-    public jalview.binding.Colour removeColour(int index)
-    {
+    public jalview.binding.Colour removeColour(int index) {
         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
@@ -240,14 +230,15 @@ public class JalviewUserColours implements java.io.Serializable {
      * @param vColour
      */
     public void setColour(int index, jalview.binding.Colour vColour)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         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
@@ -256,14 +247,15 @@ public class JalviewUserColours implements java.io.Serializable {
      *
      * @param colourArray
      */
-    public void setColour(jalview.binding.Colour[] colourArray)
-    {
+    public void setColour(jalview.binding.Colour[] colourArray) {
         //-- copy array
         _colourList.removeAllElements();
+
         for (int i = 0; i < colourArray.length; i++) {
             _colourList.addElement(colourArray[i]);
         }
-    } //-- void setColour(jalview.binding.Colour)
+    }
+     //-- void setColour(jalview.binding.Colour)
 
     /**
      * Method unmarshal
@@ -274,20 +266,20 @@ public class JalviewUserColours implements java.io.Serializable {
      * @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.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 b7abdc5..ae96562 100755
--- a/src/jalview/binding/JalviewUserColoursItem.java
+++ b/src/jalview/binding/JalviewUserColoursItem.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,27 +22,25 @@
 * 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.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 -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -51,39 +48,27 @@ public class JalviewUserColoursItem implements java.io.Serializable {
      */
     private jalview.binding.Colour _colour;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public JalviewUserColoursItem() {
         super();
-    } //-- jalview.binding.JalviewUserColoursItem()
-
+    }
+     //-- jalview.binding.JalviewUserColoursItem()
+ //-----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'colour'.
-     *
-     * @return Colour
-     * @return the value of field 'colour'.
-     */
-    public jalview.binding.Colour getColour()
-    {
+    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)
-    {
+    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 9e68130..ff0cb63 100755
--- a/src/jalview/binding/Residue.java
+++ b/src/jalview/binding/Residue.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,33 +22,32 @@
 * 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.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 Residue.
  *
  * @version $Revision$ $Date$
  */
 public class Residue implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -67,28 +65,19 @@ public class Residue implements java.io.Serializable {
      */
     private boolean _has_RGB;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public Residue() {
         super();
-    } //-- jalview.binding.Residue()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+    }
+     //-- jalview.binding.Residue()
+ //-----------/
 
-    /**
-     * Method deleteRGB
-     *
-     */
-    public void deleteRGB()
-    {
-        this._has_RGB= false;
-    } //-- void deleteRGB()
+    public void deleteRGB() {
+        this._has_RGB = false;
+    }
+     //-- void deleteRGB()
 
     /**
      * Returns the value of field 'name'.
@@ -96,10 +85,10 @@ public class Residue implements java.io.Serializable {
      * @return String
      * @return the value of field 'name'.
      */
-    public java.lang.String getName()
-    {
+    public java.lang.String getName() {
         return this._name;
-    } //-- java.lang.String getName()
+    }
+     //-- java.lang.String getName()
 
     /**
      * Returns the value of field 'RGB'.
@@ -107,10 +96,10 @@ public class Residue implements java.io.Serializable {
      * @return int
      * @return the value of field 'RGB'.
      */
-    public int getRGB()
-    {
+    public int getRGB() {
         return this._RGB;
-    } //-- int getRGB()
+    }
+     //-- int getRGB()
 
     /**
      * Method hasRGB
@@ -119,10 +108,10 @@ public class Residue implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasRGB()
-    {
+    public boolean hasRGB() {
         return this._has_RGB;
-    } //-- boolean hasRGB()
+    }
+     //-- boolean hasRGB()
 
     /**
      * Method isValid
@@ -131,16 +120,16 @@ public class Residue implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -150,11 +139,11 @@ public class Residue implements java.io.Serializable {
      * @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
@@ -164,32 +153,32 @@ public class Residue implements java.io.Serializable {
      * @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)
-    {
+    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(int RGB)
-    {
+    public void setRGB(int RGB) {
         this._RGB = RGB;
         this._has_RGB = true;
-    } //-- void setRGB(int)
+    }
+     //-- void setRGB(int)
 
     /**
      * Method unmarshal
@@ -200,20 +189,20 @@ public class Residue implements java.io.Serializable {
      * @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)
+        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
-    {
+    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/Sequence.java b/src/jalview/binding/Sequence.java
index 290354e..628e209 100755
--- a/src/jalview/binding/Sequence.java
+++ b/src/jalview/binding/Sequence.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,63 +22,49 @@
 * 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.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 Sequence.
  *
  * @version $Revision$ $Date$
  */
-public class Sequence extends SequenceType
-implements java.io.Serializable
-{
-
-
-      //----------------/
-     //- Constructors -/
+public class Sequence extends SequenceType implements java.io.Serializable {
+    //----------------/
+    //- Constructors -/
     //----------------/
-
     public Sequence() {
         super();
-    } //-- jalview.binding.Sequence()
+    }
+     //-- jalview.binding.Sequence()
+ //-----------/
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid
-     *
-     *
-     *
-     * @return boolean
-     */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -89,11 +74,11 @@ implements java.io.Serializable
      * @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
@@ -103,11 +88,11 @@ implements java.io.Serializable
      * @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
@@ -118,20 +103,20 @@ implements java.io.Serializable
      * @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)
+        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
-    {
+    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/SequenceSet.java b/src/jalview/binding/SequenceSet.java
index 7ef5fe7..4300c39 100755
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,24 +22,26 @@
 * 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.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.
@@ -48,10 +49,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class SequenceSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -79,34 +78,22 @@ public class SequenceSet implements java.io.Serializable {
      */
     private java.util.Vector _annotationList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public SequenceSet() {
         super();
         _sequenceList = new Vector();
         _annotationList = new Vector();
-    } //-- jalview.binding.SequenceSet()
+    }
+     //-- jalview.binding.SequenceSet()
+ //-----------/
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addAnnotation
-     *
-     *
-     *
-     * @param vAnnotation
-     */
     public void addAnnotation(jalview.binding.Annotation vAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _annotationList.addElement(vAnnotation);
-    } //-- void addAnnotation(jalview.binding.Annotation)
+    }
+     //-- void addAnnotation(jalview.binding.Annotation)
 
     /**
      * Method addAnnotation
@@ -117,10 +104,10 @@ public class SequenceSet implements java.io.Serializable {
      * @param vAnnotation
      */
     public void addAnnotation(int index, jalview.binding.Annotation vAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _annotationList.insertElementAt(vAnnotation, index);
-    } //-- void addAnnotation(int, jalview.binding.Annotation)
+    }
+     //-- void addAnnotation(int, jalview.binding.Annotation)
 
     /**
      * Method addSequence
@@ -130,10 +117,10 @@ public class SequenceSet implements java.io.Serializable {
      * @param vSequence
      */
     public void addSequence(jalview.binding.Sequence vSequence)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _sequenceList.addElement(vSequence);
-    } //-- void addSequence(jalview.binding.Sequence)
+    }
+     //-- void addSequence(jalview.binding.Sequence)
 
     /**
      * Method addSequence
@@ -144,19 +131,19 @@ public class SequenceSet implements java.io.Serializable {
      * @param vSequence
      */
     public void addSequence(int index, jalview.binding.Sequence vSequence)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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()
+    public void deleteAligned() {
+        this._has_aligned = false;
+    }
+     //-- void deleteAligned()
 
     /**
      * Method enumerateAnnotation
@@ -165,10 +152,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateAnnotation()
-    {
+    public java.util.Enumeration enumerateAnnotation() {
         return _annotationList.elements();
-    } //-- java.util.Enumeration enumerateAnnotation()
+    }
+     //-- java.util.Enumeration enumerateAnnotation()
 
     /**
      * Method enumerateSequence
@@ -177,10 +164,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateSequence()
-    {
+    public java.util.Enumeration enumerateSequence() {
         return _sequenceList.elements();
-    } //-- java.util.Enumeration enumerateSequence()
+    }
+     //-- java.util.Enumeration enumerateSequence()
 
     /**
      * Returns the value of field 'aligned'.
@@ -188,10 +175,10 @@ public class SequenceSet implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'aligned'.
      */
-    public boolean getAligned()
-    {
+    public boolean getAligned() {
         return this._aligned;
-    } //-- boolean getAligned()
+    }
+     //-- boolean getAligned()
 
     /**
      * Method getAnnotation
@@ -202,15 +189,15 @@ public class SequenceSet implements java.io.Serializable {
      * @return Annotation
      */
     public jalview.binding.Annotation getAnnotation(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         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
@@ -219,15 +206,17 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return Annotation
      */
-    public jalview.binding.Annotation[] getAnnotation()
-    {
+    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++) {
             mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.Annotation[] getAnnotation()
+    }
+     //-- jalview.binding.Annotation[] getAnnotation()
 
     /**
      * Method getAnnotationCount
@@ -236,10 +225,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return int
      */
-    public int getAnnotationCount()
-    {
+    public int getAnnotationCount() {
         return _annotationList.size();
-    } //-- int getAnnotationCount()
+    }
+     //-- int getAnnotationCount()
 
     /**
      * Returns the value of field 'gapChar'.
@@ -247,10 +236,10 @@ public class SequenceSet implements java.io.Serializable {
      * @return String
      * @return the value of field 'gapChar'.
      */
-    public java.lang.String getGapChar()
-    {
+    public java.lang.String getGapChar() {
         return this._gapChar;
-    } //-- java.lang.String getGapChar()
+    }
+     //-- java.lang.String getGapChar()
 
     /**
      * Method getSequence
@@ -261,15 +250,15 @@ public class SequenceSet implements java.io.Serializable {
      * @return Sequence
      */
     public jalview.binding.Sequence getSequence(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         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
@@ -278,15 +267,17 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return Sequence
      */
-    public jalview.binding.Sequence[] getSequence()
-    {
+    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++) {
             mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.Sequence[] getSequence()
+    }
+     //-- jalview.binding.Sequence[] getSequence()
 
     /**
      * Method getSequenceCount
@@ -295,10 +286,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return int
      */
-    public int getSequenceCount()
-    {
+    public int getSequenceCount() {
         return _sequenceList.size();
-    } //-- int getSequenceCount()
+    }
+     //-- int getSequenceCount()
 
     /**
      * Method hasAligned
@@ -307,10 +298,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasAligned()
-    {
+    public boolean hasAligned() {
         return this._has_aligned;
-    } //-- boolean hasAligned()
+    }
+     //-- boolean hasAligned()
 
     /**
      * Method isValid
@@ -319,16 +310,16 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -338,11 +329,11 @@ public class SequenceSet implements java.io.Serializable {
      * @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
@@ -352,29 +343,29 @@ public class SequenceSet implements java.io.Serializable {
      * @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()
-    {
+    public void removeAllAnnotation() {
         _annotationList.removeAllElements();
-    } //-- void removeAllAnnotation()
+    }
+     //-- void removeAllAnnotation()
 
     /**
      * Method removeAllSequence
      *
      */
-    public void removeAllSequence()
-    {
+    public void removeAllSequence() {
         _sequenceList.removeAllElements();
-    } //-- void removeAllSequence()
+    }
+     //-- void removeAllSequence()
 
     /**
      * Method removeAnnotation
@@ -384,12 +375,13 @@ public class SequenceSet implements java.io.Serializable {
      * @param index
      * @return Annotation
      */
-    public jalview.binding.Annotation removeAnnotation(int index)
-    {
+    public jalview.binding.Annotation removeAnnotation(int index) {
         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
@@ -399,23 +391,24 @@ public class SequenceSet implements java.io.Serializable {
      * @param index
      * @return Sequence
      */
-    public jalview.binding.Sequence removeSequence(int index)
-    {
+    public jalview.binding.Sequence removeSequence(int index) {
         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)
-    {
+    public void setAligned(boolean aligned) {
         this._aligned = aligned;
         this._has_aligned = true;
-    } //-- void setAligned(boolean)
+    }
+     //-- void setAligned(boolean)
 
     /**
      * Method setAnnotation
@@ -426,14 +419,15 @@ public class SequenceSet implements java.io.Serializable {
      * @param vAnnotation
      */
     public void setAnnotation(int index, jalview.binding.Annotation vAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         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
@@ -442,24 +436,25 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @param annotationArray
      */
-    public void setAnnotation(jalview.binding.Annotation[] annotationArray)
-    {
+    public void setAnnotation(jalview.binding.Annotation[] annotationArray) {
         //-- copy array
         _annotationList.removeAllElements();
+
         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)
-    {
+    public void setGapChar(java.lang.String gapChar) {
         this._gapChar = gapChar;
-    } //-- void setGapChar(java.lang.String)
+    }
+     //-- void setGapChar(java.lang.String)
 
     /**
      * Method setSequence
@@ -470,14 +465,15 @@ public class SequenceSet implements java.io.Serializable {
      * @param vSequence
      */
     public void setSequence(int index, jalview.binding.Sequence vSequence)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         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
@@ -486,14 +482,15 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @param sequenceArray
      */
-    public void setSequence(jalview.binding.Sequence[] sequenceArray)
-    {
+    public void setSequence(jalview.binding.Sequence[] sequenceArray) {
         //-- copy array
         _sequenceList.removeAllElements();
+
         for (int i = 0; i < sequenceArray.length; i++) {
             _sequenceList.addElement(sequenceArray[i]);
         }
-    } //-- void setSequence(jalview.binding.Sequence)
+    }
+     //-- void setSequence(jalview.binding.Sequence)
 
     /**
      * Method unmarshal
@@ -504,20 +501,20 @@ public class SequenceSet implements java.io.Serializable {
      * @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.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 bf560bb..6060e77 100755
--- a/src/jalview/binding/SequenceType.java
+++ b/src/jalview/binding/SequenceType.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,33 +22,32 @@
 * 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.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 SequenceType.
  *
  * @version $Revision$ $Date$
  */
 public class SequenceType implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -67,30 +65,19 @@ public class SequenceType implements java.io.Serializable {
      */
     private java.lang.String _name;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public SequenceType() {
         super();
-    } //-- jalview.binding.SequenceType()
-
+    }
+     //-- jalview.binding.SequenceType()
+ //-----------/
 
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'id'.
-     *
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
+    public java.lang.String getId() {
         return this._id;
-    } //-- java.lang.String getId()
+    }
+     //-- java.lang.String getId()
 
     /**
      * Returns the value of field 'name'.
@@ -98,10 +85,10 @@ public class SequenceType implements java.io.Serializable {
      * @return String
      * @return the value of field 'name'.
      */
-    public java.lang.String getName()
-    {
+    public java.lang.String getName() {
         return this._name;
-    } //-- java.lang.String getName()
+    }
+     //-- java.lang.String getName()
 
     /**
      * Returns the value of field 'sequence'.
@@ -109,10 +96,10 @@ public class SequenceType implements java.io.Serializable {
      * @return String
      * @return the value of field 'sequence'.
      */
-    public java.lang.String getSequence()
-    {
+    public java.lang.String getSequence() {
         return this._sequence;
-    } //-- java.lang.String getSequence()
+    }
+     //-- java.lang.String getSequence()
 
     /**
      * Method isValid
@@ -121,16 +108,16 @@ public class SequenceType implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -140,11 +127,11 @@ public class SequenceType implements java.io.Serializable {
      * @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
@@ -154,41 +141,41 @@ public class SequenceType implements java.io.Serializable {
      * @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 'id'.
      *
      * @param id the value of field 'id'.
      */
-    public void setId(java.lang.String id)
-    {
+    public void setId(java.lang.String id) {
         this._id = id;
-    } //-- void setId(java.lang.String)
+    }
+     //-- 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)
-    {
+    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 'sequence'.
      *
      * @param sequence the value of field 'sequence'.
      */
-    public void setSequence(java.lang.String sequence)
-    {
+    public void setSequence(java.lang.String sequence) {
         this._sequence = sequence;
-    } //-- void setSequence(java.lang.String)
+    }
+     //-- void setSequence(java.lang.String)
 
     /**
      * Method unmarshal
@@ -199,20 +186,20 @@ public class SequenceType implements java.io.Serializable {
      * @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)
+        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
-    {
+    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 fba081c..3ecb7bc 100755
--- a/src/jalview/binding/UserColour.java
+++ b/src/jalview/binding/UserColour.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,33 +22,32 @@
 * 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.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 UserColour.
  *
  * @version $Revision$ $Date$
  */
 public class UserColour implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -67,28 +65,19 @@ public class UserColour implements java.io.Serializable {
      */
     private jalview.binding.UserColourScheme _userColourScheme;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public UserColour() {
         super();
-    } //-- jalview.binding.UserColour()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+    }
+     //-- jalview.binding.UserColour()
+ //-----------/
 
-    /**
-     * Method deleteId
-     *
-     */
-    public void deleteId()
-    {
-        this._has_id= false;
-    } //-- void deleteId()
+    public void deleteId() {
+        this._has_id = false;
+    }
+     //-- void deleteId()
 
     /**
      * Returns the value of field 'id'.
@@ -96,10 +85,10 @@ public class UserColour implements java.io.Serializable {
      * @return int
      * @return the value of field 'id'.
      */
-    public int getId()
-    {
+    public int getId() {
         return this._id;
-    } //-- int getId()
+    }
+     //-- int getId()
 
     /**
      * Returns the value of field 'userColourScheme'.
@@ -107,10 +96,10 @@ public class UserColour implements java.io.Serializable {
      * @return UserColourScheme
      * @return the value of field 'userColourScheme'.
      */
-    public jalview.binding.UserColourScheme getUserColourScheme()
-    {
+    public jalview.binding.UserColourScheme getUserColourScheme() {
         return this._userColourScheme;
-    } //-- jalview.binding.UserColourScheme getUserColourScheme()
+    }
+     //-- jalview.binding.UserColourScheme getUserColourScheme()
 
     /**
      * Method hasId
@@ -119,10 +108,10 @@ public class UserColour implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasId()
-    {
+    public boolean hasId() {
         return this._has_id;
-    } //-- boolean hasId()
+    }
+     //-- boolean hasId()
 
     /**
      * Method isValid
@@ -131,16 +120,16 @@ public class UserColour implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -150,11 +139,11 @@ public class UserColour implements java.io.Serializable {
      * @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
@@ -164,32 +153,33 @@ public class UserColour implements java.io.Serializable {
      * @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 'id'.
      *
      * @param id the value of field 'id'.
      */
-    public void setId(int id)
-    {
+    public void setId(int id) {
         this._id = id;
         this._has_id = true;
-    } //-- void setId(int)
+    }
+     //-- void setId(int)
 
     /**
      * Sets the value of field 'userColourScheme'.
      *
      * @param userColourScheme the value of field 'userColourScheme'
      */
-    public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)
-    {
+    public void setUserColourScheme(
+        jalview.binding.UserColourScheme userColourScheme) {
         this._userColourScheme = userColourScheme;
-    } //-- void setUserColourScheme(jalview.binding.UserColourScheme)
+    }
+     //-- void setUserColourScheme(jalview.binding.UserColourScheme)
 
     /**
      * Method unmarshal
@@ -200,20 +190,20 @@ public class UserColour implements java.io.Serializable {
      * @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)
+        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
-    {
+    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/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java
index f8c2fdb..e66e468 100755
--- a/src/jalview/binding/UserColourScheme.java
+++ b/src/jalview/binding/UserColourScheme.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,63 +22,50 @@
 * 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.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 UserColourScheme.
  *
  * @version $Revision$ $Date$
  */
 public class UserColourScheme extends JalviewUserColours
-implements java.io.Serializable
-{
-
-
-      //----------------/
-     //- Constructors -/
+    implements java.io.Serializable {
+    //----------------/
+    //- Constructors -/
     //----------------/
-
     public UserColourScheme() {
         super();
-    } //-- jalview.binding.UserColourScheme()
+    }
+     //-- jalview.binding.UserColourScheme()
+ //-----------/
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid
-     *
-     *
-     *
-     * @return boolean
-     */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -89,11 +75,11 @@ implements java.io.Serializable
      * @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
@@ -103,11 +89,11 @@ implements java.io.Serializable
      * @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
@@ -118,20 +104,20 @@ implements java.io.Serializable
      * @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)
+        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
-    {
+    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/UserColours.java b/src/jalview/binding/UserColours.java
index 2c4e91b..2dbffc1 100755
--- a/src/jalview/binding/UserColours.java
+++ b/src/jalview/binding/UserColours.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,33 +22,32 @@
 * 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.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 UserColours.
  *
  * @version $Revision$ $Date$
  */
 public class UserColours implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -62,30 +60,19 @@ public class UserColours implements java.io.Serializable {
      */
     private jalview.binding.UserColourScheme _userColourScheme;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public UserColours() {
         super();
-    } //-- jalview.binding.UserColours()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+    }
+     //-- jalview.binding.UserColours()
+ //-----------/
 
-    /**
-     * Returns the value of field 'id'.
-     *
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
+    public java.lang.String getId() {
         return this._id;
-    } //-- java.lang.String getId()
+    }
+     //-- java.lang.String getId()
 
     /**
      * Returns the value of field 'userColourScheme'.
@@ -93,10 +80,10 @@ public class UserColours implements java.io.Serializable {
      * @return UserColourScheme
      * @return the value of field 'userColourScheme'.
      */
-    public jalview.binding.UserColourScheme getUserColourScheme()
-    {
+    public jalview.binding.UserColourScheme getUserColourScheme() {
         return this._userColourScheme;
-    } //-- jalview.binding.UserColourScheme getUserColourScheme()
+    }
+     //-- jalview.binding.UserColourScheme getUserColourScheme()
 
     /**
      * Method isValid
@@ -105,16 +92,16 @@ public class UserColours implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -124,11 +111,11 @@ public class UserColours implements java.io.Serializable {
      * @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
@@ -138,31 +125,32 @@ public class UserColours implements java.io.Serializable {
      * @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 'id'.
      *
      * @param id the value of field 'id'.
      */
-    public void setId(java.lang.String id)
-    {
+    public void setId(java.lang.String id) {
         this._id = id;
-    } //-- void setId(java.lang.String)
+    }
+     //-- 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)
-    {
+    public void setUserColourScheme(
+        jalview.binding.UserColourScheme userColourScheme) {
         this._userColourScheme = userColourScheme;
-    } //-- void setUserColourScheme(jalview.binding.UserColourScheme)
+    }
+     //-- void setUserColourScheme(jalview.binding.UserColourScheme)
 
     /**
      * Method unmarshal
@@ -173,20 +161,20 @@ public class UserColours implements java.io.Serializable {
      * @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)
+        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
-    {
+    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/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index 2190b2f..5bc9b12 100755
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,24 +22,26 @@
 * 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.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 VAMSAS.
@@ -48,10 +49,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class VAMSAS implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -69,35 +68,23 @@ public class VAMSAS implements java.io.Serializable {
      */
     private java.util.Vector _sequenceSetList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public VAMSAS() {
         super();
         _alignmentList = new Vector();
         _treeList = new Vector();
         _sequenceSetList = new Vector();
-    } //-- jalview.binding.VAMSAS()
+    }
+     //-- jalview.binding.VAMSAS()
+ //-----------/
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addAlignment
-     *
-     *
-     *
-     * @param vAlignment
-     */
     public void addAlignment(jalview.binding.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _alignmentList.addElement(vAlignment);
-    } //-- void addAlignment(jalview.binding.Alignment)
+    }
+     //-- void addAlignment(jalview.binding.Alignment)
 
     /**
      * Method addAlignment
@@ -108,10 +95,10 @@ public class VAMSAS implements java.io.Serializable {
      * @param vAlignment
      */
     public void addAlignment(int index, jalview.binding.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _alignmentList.insertElementAt(vAlignment, index);
-    } //-- void addAlignment(int, jalview.binding.Alignment)
+    }
+     //-- void addAlignment(int, jalview.binding.Alignment)
 
     /**
      * Method addSequenceSet
@@ -121,10 +108,10 @@ public class VAMSAS implements java.io.Serializable {
      * @param vSequenceSet
      */
     public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _sequenceSetList.addElement(vSequenceSet);
-    } //-- void addSequenceSet(jalview.binding.SequenceSet)
+    }
+     //-- void addSequenceSet(jalview.binding.SequenceSet)
 
     /**
      * Method addSequenceSet
@@ -134,11 +121,12 @@ public class VAMSAS implements java.io.Serializable {
      * @param index
      * @param vSequenceSet
      */
-    public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    public void addSequenceSet(int index,
+        jalview.binding.SequenceSet vSequenceSet)
+        throws java.lang.IndexOutOfBoundsException {
         _sequenceSetList.insertElementAt(vSequenceSet, index);
-    } //-- void addSequenceSet(int, jalview.binding.SequenceSet)
+    }
+     //-- void addSequenceSet(int, jalview.binding.SequenceSet)
 
     /**
      * Method addTree
@@ -148,10 +136,10 @@ public class VAMSAS implements java.io.Serializable {
      * @param vTree
      */
     public void addTree(java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _treeList.addElement(vTree);
-    } //-- void addTree(java.lang.String)
+    }
+     //-- void addTree(java.lang.String)
 
     /**
      * Method addTree
@@ -162,10 +150,10 @@ public class VAMSAS implements java.io.Serializable {
      * @param vTree
      */
     public void addTree(int index, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _treeList.insertElementAt(vTree, index);
-    } //-- void addTree(int, java.lang.String)
+    }
+     //-- void addTree(int, java.lang.String)
 
     /**
      * Method enumerateAlignment
@@ -174,10 +162,10 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateAlignment()
-    {
+    public java.util.Enumeration enumerateAlignment() {
         return _alignmentList.elements();
-    } //-- java.util.Enumeration enumerateAlignment()
+    }
+     //-- java.util.Enumeration enumerateAlignment()
 
     /**
      * Method enumerateSequenceSet
@@ -186,10 +174,10 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateSequenceSet()
-    {
+    public java.util.Enumeration enumerateSequenceSet() {
         return _sequenceSetList.elements();
-    } //-- java.util.Enumeration enumerateSequenceSet()
+    }
+     //-- java.util.Enumeration enumerateSequenceSet()
 
     /**
      * Method enumerateTree
@@ -198,10 +186,10 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateTree()
-    {
+    public java.util.Enumeration enumerateTree() {
         return _treeList.elements();
-    } //-- java.util.Enumeration enumerateTree()
+    }
+     //-- java.util.Enumeration enumerateTree()
 
     /**
      * Method getAlignment
@@ -212,15 +200,15 @@ public class VAMSAS implements java.io.Serializable {
      * @return Alignment
      */
     public jalview.binding.Alignment getAlignment(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- jalview.binding.Alignment getAlignment(int)
 
     /**
      * Method getAlignment
@@ -229,15 +217,17 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return Alignment
      */
-    public jalview.binding.Alignment[] getAlignment()
-    {
+    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()
+    }
+     //-- jalview.binding.Alignment[] getAlignment()
 
     /**
      * Method getAlignmentCount
@@ -246,10 +236,10 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return int
      */
-    public int getAlignmentCount()
-    {
+    public int getAlignmentCount() {
         return _alignmentList.size();
-    } //-- int getAlignmentCount()
+    }
+     //-- int getAlignmentCount()
 
     /**
      * Method getSequenceSet
@@ -260,15 +250,15 @@ public class VAMSAS implements java.io.Serializable {
      * @return SequenceSet
      */
     public jalview.binding.SequenceSet getSequenceSet(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- jalview.binding.SequenceSet getSequenceSet(int)
 
     /**
      * Method getSequenceSet
@@ -277,15 +267,17 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return SequenceSet
      */
-    public jalview.binding.SequenceSet[] getSequenceSet()
-    {
+    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()
+    }
+     //-- jalview.binding.SequenceSet[] getSequenceSet()
 
     /**
      * Method getSequenceSetCount
@@ -294,10 +286,10 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return int
      */
-    public int getSequenceSetCount()
-    {
+    public int getSequenceSetCount() {
         return _sequenceSetList.size();
-    } //-- int getSequenceSetCount()
+    }
+     //-- int getSequenceSetCount()
 
     /**
      * Method getTree
@@ -308,15 +300,15 @@ public class VAMSAS implements java.io.Serializable {
      * @return String
      */
     public java.lang.String getTree(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+        return (String) _treeList.elementAt(index);
+    }
+     //-- java.lang.String getTree(int)
 
     /**
      * Method getTree
@@ -325,15 +317,17 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return String
      */
-    public java.lang.String[] getTree()
-    {
+    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);
+            mArray[index] = (String) _treeList.elementAt(index);
         }
+
         return mArray;
-    } //-- java.lang.String[] getTree()
+    }
+     //-- java.lang.String[] getTree()
 
     /**
      * Method getTreeCount
@@ -342,10 +336,10 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return int
      */
-    public int getTreeCount()
-    {
+    public int getTreeCount() {
         return _treeList.size();
-    } //-- int getTreeCount()
+    }
+     //-- int getTreeCount()
 
     /**
      * Method isValid
@@ -354,16 +348,16 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -373,11 +367,11 @@ public class VAMSAS implements java.io.Serializable {
      * @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
@@ -387,11 +381,11 @@ public class VAMSAS implements java.io.Serializable {
      * @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 removeAlignment
@@ -401,39 +395,40 @@ public class VAMSAS implements java.io.Serializable {
      * @param index
      * @return Alignment
      */
-    public jalview.binding.Alignment removeAlignment(int index)
-    {
+    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)
+    }
+     //-- jalview.binding.Alignment removeAlignment(int)
 
     /**
      * Method removeAllAlignment
      *
      */
-    public void removeAllAlignment()
-    {
+    public void removeAllAlignment() {
         _alignmentList.removeAllElements();
-    } //-- void removeAllAlignment()
+    }
+     //-- void removeAllAlignment()
 
     /**
      * Method removeAllSequenceSet
      *
      */
-    public void removeAllSequenceSet()
-    {
+    public void removeAllSequenceSet() {
         _sequenceSetList.removeAllElements();
-    } //-- void removeAllSequenceSet()
+    }
+     //-- void removeAllSequenceSet()
 
     /**
      * Method removeAllTree
      *
      */
-    public void removeAllTree()
-    {
+    public void removeAllTree() {
         _treeList.removeAllElements();
-    } //-- void removeAllTree()
+    }
+     //-- void removeAllTree()
 
     /**
      * Method removeSequenceSet
@@ -443,12 +438,13 @@ public class VAMSAS implements java.io.Serializable {
      * @param index
      * @return SequenceSet
      */
-    public jalview.binding.SequenceSet removeSequenceSet(int index)
-    {
+    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)
+    }
+     //-- jalview.binding.SequenceSet removeSequenceSet(int)
 
     /**
      * Method removeTree
@@ -458,12 +454,13 @@ public class VAMSAS implements java.io.Serializable {
      * @param index
      * @return String
      */
-    public java.lang.String removeTree(int index)
-    {
+    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)
+
+        return (String) obj;
+    }
+     //-- java.lang.String removeTree(int)
 
     /**
      * Method setAlignment
@@ -474,14 +471,15 @@ public class VAMSAS implements java.io.Serializable {
      * @param vAlignment
      */
     public void setAlignment(int index, jalview.binding.Alignment vAlignment)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- void setAlignment(int, jalview.binding.Alignment)
 
     /**
      * Method setAlignment
@@ -490,14 +488,15 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @param alignmentArray
      */
-    public void setAlignment(jalview.binding.Alignment[] 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)
+    }
+     //-- void setAlignment(jalview.binding.Alignment)
 
     /**
      * Method setSequenceSet
@@ -507,15 +506,17 @@ public class VAMSAS implements java.io.Serializable {
      * @param index
      * @param vSequenceSet
      */
-    public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
-        throws java.lang.IndexOutOfBoundsException
-    {
+    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)
+    }
+     //-- void setSequenceSet(int, jalview.binding.SequenceSet)
 
     /**
      * Method setSequenceSet
@@ -524,14 +525,15 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @param sequenceSetArray
      */
-    public void setSequenceSet(jalview.binding.SequenceSet[] 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)
+    }
+     //-- void setSequenceSet(jalview.binding.SequenceSet)
 
     /**
      * Method setTree
@@ -542,14 +544,15 @@ public class VAMSAS implements java.io.Serializable {
      * @param vTree
      */
     public void setTree(int index, java.lang.String vTree)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        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)
+    }
+     //-- void setTree(int, java.lang.String)
 
     /**
      * Method setTree
@@ -558,14 +561,15 @@ public class VAMSAS implements java.io.Serializable {
      *
      * @param treeArray
      */
-    public void setTree(java.lang.String[] 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)
+    }
+     //-- void setTree(java.lang.String)
 
     /**
      * Method unmarshal
@@ -576,20 +580,20 @@ public class VAMSAS implements java.io.Serializable {
      * @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)
+        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
-    {
+    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/VamsasModel.java b/src/jalview/binding/VamsasModel.java
index 4133b84..f802039 100755
--- a/src/jalview/binding/VamsasModel.java
+++ b/src/jalview/binding/VamsasModel.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,63 +22,49 @@
 * 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.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
-{
-
-
-      //----------------/
-     //- Constructors -/
+public class VamsasModel extends VAMSAS implements java.io.Serializable {
+    //----------------/
+    //- Constructors -/
     //----------------/
-
     public VamsasModel() {
         super();
-    } //-- jalview.binding.VamsasModel()
+    }
+     //-- jalview.binding.VamsasModel()
+ //-----------/
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method isValid
-     *
-     *
-     *
-     * @return boolean
-     */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -89,11 +74,11 @@ implements java.io.Serializable
      * @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
@@ -103,11 +88,11 @@ implements java.io.Serializable
      * @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
@@ -118,20 +103,20 @@ implements java.io.Serializable
      * @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.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        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)
 
     /**
      * 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 99dbd1b..8bdee5d 100755
--- a/src/jalview/binding/Viewport.java
+++ b/src/jalview/binding/Viewport.java
@@ -16,30 +16,29 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 /*
  * 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;
 
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
 
-package jalview.binding;
+import org.xml.sax.ContentHandler;
 
-  //---------------------------------/
- //- 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;
+
 
 /**
  * Class Viewport.
@@ -47,10 +46,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class Viewport implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -298,226 +295,217 @@ public class Viewport implements java.io.Serializable {
      */
     private boolean _has_fontStyle;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public Viewport() {
         super();
-    } //-- jalview.binding.Viewport()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+    }
+     //-- jalview.binding.Viewport()
+ //-----------/
 
-    /**
-     * Method deleteConsThreshold
-     *
-     */
-    public void deleteConsThreshold()
-    {
-        this._has_consThreshold= false;
-    } //-- void deleteConsThreshold()
+    public void deleteConsThreshold() {
+        this._has_consThreshold = false;
+    }
+     //-- void deleteConsThreshold()
 
     /**
      * Method deleteConservationSelected
      *
      */
-    public void deleteConservationSelected()
-    {
-        this._has_conservationSelected= false;
-    } //-- void deleteConservationSelected()
+    public void deleteConservationSelected() {
+        this._has_conservationSelected = false;
+    }
+     //-- void deleteConservationSelected()
 
     /**
      * Method deleteFontSize
      *
      */
-    public void deleteFontSize()
-    {
-        this._has_fontSize= false;
-    } //-- void deleteFontSize()
+    public void deleteFontSize() {
+        this._has_fontSize = false;
+    }
+     //-- void deleteFontSize()
 
     /**
      * Method deleteFontStyle
      *
      */
-    public void deleteFontStyle()
-    {
-        this._has_fontStyle= false;
-    } //-- void deleteFontStyle()
+    public void deleteFontStyle() {
+        this._has_fontStyle = false;
+    }
+     //-- void deleteFontStyle()
 
     /**
      * Method deleteHeight
      *
      */
-    public void deleteHeight()
-    {
-        this._has_height= false;
-    } //-- void deleteHeight()
+    public void deleteHeight() {
+        this._has_height = false;
+    }
+     //-- void deleteHeight()
 
     /**
      * Method deletePidSelected
      *
      */
-    public void deletePidSelected()
-    {
-        this._has_pidSelected= false;
-    } //-- void deletePidSelected()
+    public void deletePidSelected() {
+        this._has_pidSelected = false;
+    }
+     //-- void deletePidSelected()
 
     /**
      * Method deletePidThreshold
      *
      */
-    public void deletePidThreshold()
-    {
-        this._has_pidThreshold= false;
-    } //-- void deletePidThreshold()
+    public void deletePidThreshold() {
+        this._has_pidThreshold = false;
+    }
+     //-- void deletePidThreshold()
 
     /**
      * Method deleteRenderGaps
      *
      */
-    public void deleteRenderGaps()
-    {
-        this._has_renderGaps= false;
-    } //-- void deleteRenderGaps()
+    public void deleteRenderGaps() {
+        this._has_renderGaps = false;
+    }
+     //-- void deleteRenderGaps()
 
     /**
      * Method deleteShowAnnotation
      *
      */
-    public void deleteShowAnnotation()
-    {
-        this._has_showAnnotation= false;
-    } //-- void deleteShowAnnotation()
+    public void deleteShowAnnotation() {
+        this._has_showAnnotation = false;
+    }
+     //-- void deleteShowAnnotation()
 
     /**
      * Method deleteShowBoxes
      *
      */
-    public void deleteShowBoxes()
-    {
-        this._has_showBoxes= false;
-    } //-- void deleteShowBoxes()
+    public void deleteShowBoxes() {
+        this._has_showBoxes = false;
+    }
+     //-- void deleteShowBoxes()
 
     /**
      * Method deleteShowColourText
      *
      */
-    public void deleteShowColourText()
-    {
-        this._has_showColourText= false;
-    } //-- void deleteShowColourText()
+    public void deleteShowColourText() {
+        this._has_showColourText = false;
+    }
+     //-- void deleteShowColourText()
 
     /**
      * Method deleteShowConservation
      *
      */
-    public void deleteShowConservation()
-    {
-        this._has_showConservation= false;
-    } //-- void deleteShowConservation()
+    public void deleteShowConservation() {
+        this._has_showConservation = false;
+    }
+     //-- void deleteShowConservation()
 
     /**
      * Method deleteShowFullId
      *
      */
-    public void deleteShowFullId()
-    {
-        this._has_showFullId= false;
-    } //-- void deleteShowFullId()
+    public void deleteShowFullId() {
+        this._has_showFullId = false;
+    }
+     //-- void deleteShowFullId()
 
     /**
      * Method deleteShowIdentity
      *
      */
-    public void deleteShowIdentity()
-    {
-        this._has_showIdentity= false;
-    } //-- void deleteShowIdentity()
+    public void deleteShowIdentity() {
+        this._has_showIdentity = false;
+    }
+     //-- void deleteShowIdentity()
 
     /**
      * Method deleteShowQuality
      *
      */
-    public void deleteShowQuality()
-    {
-        this._has_showQuality= false;
-    } //-- void deleteShowQuality()
+    public void deleteShowQuality() {
+        this._has_showQuality = false;
+    }
+     //-- void deleteShowQuality()
 
     /**
      * Method deleteShowSequenceFeatures
      *
      */
-    public void deleteShowSequenceFeatures()
-    {
-        this._has_showSequenceFeatures= false;
-    } //-- void deleteShowSequenceFeatures()
+    public void deleteShowSequenceFeatures() {
+        this._has_showSequenceFeatures = false;
+    }
+     //-- void deleteShowSequenceFeatures()
 
     /**
      * Method deleteShowText
      *
      */
-    public void deleteShowText()
-    {
-        this._has_showText= false;
-    } //-- void deleteShowText()
+    public void deleteShowText() {
+        this._has_showText = false;
+    }
+     //-- void deleteShowText()
 
     /**
      * Method deleteStartRes
      *
      */
-    public void deleteStartRes()
-    {
-        this._has_startRes= false;
-    } //-- void deleteStartRes()
+    public void deleteStartRes() {
+        this._has_startRes = false;
+    }
+     //-- void deleteStartRes()
 
     /**
      * Method deleteStartSeq
      *
      */
-    public void deleteStartSeq()
-    {
-        this._has_startSeq= false;
-    } //-- void deleteStartSeq()
+    public void deleteStartSeq() {
+        this._has_startSeq = false;
+    }
+     //-- void deleteStartSeq()
 
     /**
      * Method deleteWidth
      *
      */
-    public void deleteWidth()
-    {
-        this._has_width= false;
-    } //-- void deleteWidth()
+    public void deleteWidth() {
+        this._has_width = false;
+    }
+     //-- void deleteWidth()
 
     /**
      * Method deleteWrapAlignment
      *
      */
-    public void deleteWrapAlignment()
-    {
-        this._has_wrapAlignment= false;
-    } //-- void deleteWrapAlignment()
+    public void deleteWrapAlignment() {
+        this._has_wrapAlignment = false;
+    }
+     //-- void deleteWrapAlignment()
 
     /**
      * Method deleteXpos
      *
      */
-    public void deleteXpos()
-    {
-        this._has_xpos= false;
-    } //-- void deleteXpos()
+    public void deleteXpos() {
+        this._has_xpos = false;
+    }
+     //-- void deleteXpos()
 
     /**
      * Method deleteYpos
      *
      */
-    public void deleteYpos()
-    {
-        this._has_ypos= false;
-    } //-- void deleteYpos()
+    public void deleteYpos() {
+        this._has_ypos = false;
+    }
+     //-- void deleteYpos()
 
     /**
      * Returns the value of field 'bgColour'.
@@ -525,10 +513,10 @@ public class Viewport implements java.io.Serializable {
      * @return String
      * @return the value of field 'bgColour'.
      */
-    public java.lang.String getBgColour()
-    {
+    public java.lang.String getBgColour() {
         return this._bgColour;
-    } //-- java.lang.String getBgColour()
+    }
+     //-- java.lang.String getBgColour()
 
     /**
      * Returns the value of field 'consThreshold'.
@@ -536,10 +524,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'consThreshold'.
      */
-    public int getConsThreshold()
-    {
+    public int getConsThreshold() {
         return this._consThreshold;
-    } //-- int getConsThreshold()
+    }
+     //-- int getConsThreshold()
 
     /**
      * Returns the value of field 'conservationSelected'.
@@ -547,10 +535,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'conservationSelected'.
      */
-    public boolean getConservationSelected()
-    {
+    public boolean getConservationSelected() {
         return this._conservationSelected;
-    } //-- boolean getConservationSelected()
+    }
+     //-- boolean getConservationSelected()
 
     /**
      * Returns the value of field 'fontName'.
@@ -558,10 +546,10 @@ public class Viewport implements java.io.Serializable {
      * @return String
      * @return the value of field 'fontName'.
      */
-    public java.lang.String getFontName()
-    {
+    public java.lang.String getFontName() {
         return this._fontName;
-    } //-- java.lang.String getFontName()
+    }
+     //-- java.lang.String getFontName()
 
     /**
      * Returns the value of field 'fontSize'.
@@ -569,10 +557,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'fontSize'.
      */
-    public int getFontSize()
-    {
+    public int getFontSize() {
         return this._fontSize;
-    } //-- int getFontSize()
+    }
+     //-- int getFontSize()
 
     /**
      * Returns the value of field 'fontStyle'.
@@ -580,10 +568,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'fontStyle'.
      */
-    public int getFontStyle()
-    {
+    public int getFontStyle() {
         return this._fontStyle;
-    } //-- int getFontStyle()
+    }
+     //-- int getFontStyle()
 
     /**
      * Returns the value of field 'height'.
@@ -591,10 +579,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'height'.
      */
-    public int getHeight()
-    {
+    public int getHeight() {
         return this._height;
-    } //-- int getHeight()
+    }
+     //-- int getHeight()
 
     /**
      * Returns the value of field 'pidSelected'.
@@ -602,10 +590,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'pidSelected'.
      */
-    public boolean getPidSelected()
-    {
+    public boolean getPidSelected() {
         return this._pidSelected;
-    } //-- boolean getPidSelected()
+    }
+     //-- boolean getPidSelected()
 
     /**
      * Returns the value of field 'pidThreshold'.
@@ -613,10 +601,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'pidThreshold'.
      */
-    public int getPidThreshold()
-    {
+    public int getPidThreshold() {
         return this._pidThreshold;
-    } //-- int getPidThreshold()
+    }
+     //-- int getPidThreshold()
 
     /**
      * Returns the value of field 'renderGaps'.
@@ -624,10 +612,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'renderGaps'.
      */
-    public boolean getRenderGaps()
-    {
+    public boolean getRenderGaps() {
         return this._renderGaps;
-    } //-- boolean getRenderGaps()
+    }
+     //-- boolean getRenderGaps()
 
     /**
      * Returns the value of field 'showAnnotation'.
@@ -635,10 +623,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'showAnnotation'.
      */
-    public boolean getShowAnnotation()
-    {
+    public boolean getShowAnnotation() {
         return this._showAnnotation;
-    } //-- boolean getShowAnnotation()
+    }
+     //-- boolean getShowAnnotation()
 
     /**
      * Returns the value of field 'showBoxes'.
@@ -646,10 +634,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'showBoxes'.
      */
-    public boolean getShowBoxes()
-    {
+    public boolean getShowBoxes() {
         return this._showBoxes;
-    } //-- boolean getShowBoxes()
+    }
+     //-- boolean getShowBoxes()
 
     /**
      * Returns the value of field 'showColourText'.
@@ -657,10 +645,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'showColourText'.
      */
-    public boolean getShowColourText()
-    {
+    public boolean getShowColourText() {
         return this._showColourText;
-    } //-- boolean getShowColourText()
+    }
+     //-- boolean getShowColourText()
 
     /**
      * Returns the value of field 'showConservation'.
@@ -668,10 +656,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'showConservation'.
      */
-    public boolean getShowConservation()
-    {
+    public boolean getShowConservation() {
         return this._showConservation;
-    } //-- boolean getShowConservation()
+    }
+     //-- boolean getShowConservation()
 
     /**
      * Returns the value of field 'showFullId'.
@@ -679,10 +667,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'showFullId'.
      */
-    public boolean getShowFullId()
-    {
+    public boolean getShowFullId() {
         return this._showFullId;
-    } //-- boolean getShowFullId()
+    }
+     //-- boolean getShowFullId()
 
     /**
      * Returns the value of field 'showIdentity'.
@@ -690,10 +678,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'showIdentity'.
      */
-    public boolean getShowIdentity()
-    {
+    public boolean getShowIdentity() {
         return this._showIdentity;
-    } //-- boolean getShowIdentity()
+    }
+     //-- boolean getShowIdentity()
 
     /**
      * Returns the value of field 'showQuality'.
@@ -701,10 +689,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'showQuality'.
      */
-    public boolean getShowQuality()
-    {
+    public boolean getShowQuality() {
         return this._showQuality;
-    } //-- boolean getShowQuality()
+    }
+     //-- boolean getShowQuality()
 
     /**
      * Returns the value of field 'showSequenceFeatures'.
@@ -712,10 +700,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'showSequenceFeatures'.
      */
-    public boolean getShowSequenceFeatures()
-    {
+    public boolean getShowSequenceFeatures() {
         return this._showSequenceFeatures;
-    } //-- boolean getShowSequenceFeatures()
+    }
+     //-- boolean getShowSequenceFeatures()
 
     /**
      * Returns the value of field 'showText'.
@@ -723,10 +711,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'showText'.
      */
-    public boolean getShowText()
-    {
+    public boolean getShowText() {
         return this._showText;
-    } //-- boolean getShowText()
+    }
+     //-- boolean getShowText()
 
     /**
      * Returns the value of field 'startRes'.
@@ -734,10 +722,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'startRes'.
      */
-    public int getStartRes()
-    {
+    public int getStartRes() {
         return this._startRes;
-    } //-- int getStartRes()
+    }
+     //-- int getStartRes()
 
     /**
      * Returns the value of field 'startSeq'.
@@ -745,10 +733,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'startSeq'.
      */
-    public int getStartSeq()
-    {
+    public int getStartSeq() {
         return this._startSeq;
-    } //-- int getStartSeq()
+    }
+     //-- int getStartSeq()
 
     /**
      * Returns the value of field 'title'.
@@ -756,10 +744,10 @@ public class Viewport implements java.io.Serializable {
      * @return String
      * @return the value of field 'title'.
      */
-    public java.lang.String getTitle()
-    {
+    public java.lang.String getTitle() {
         return this._title;
-    } //-- java.lang.String getTitle()
+    }
+     //-- java.lang.String getTitle()
 
     /**
      * Returns the value of field 'width'.
@@ -767,10 +755,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'width'.
      */
-    public int getWidth()
-    {
+    public int getWidth() {
         return this._width;
-    } //-- int getWidth()
+    }
+     //-- int getWidth()
 
     /**
      * Returns the value of field 'wrapAlignment'.
@@ -778,10 +766,10 @@ public class Viewport implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'wrapAlignment'.
      */
-    public boolean getWrapAlignment()
-    {
+    public boolean getWrapAlignment() {
         return this._wrapAlignment;
-    } //-- boolean getWrapAlignment()
+    }
+     //-- boolean getWrapAlignment()
 
     /**
      * Returns the value of field 'xpos'.
@@ -789,10 +777,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'xpos'.
      */
-    public int getXpos()
-    {
+    public int getXpos() {
         return this._xpos;
-    } //-- int getXpos()
+    }
+     //-- int getXpos()
 
     /**
      * Returns the value of field 'ypos'.
@@ -800,10 +788,10 @@ public class Viewport implements java.io.Serializable {
      * @return int
      * @return the value of field 'ypos'.
      */
-    public int getYpos()
-    {
+    public int getYpos() {
         return this._ypos;
-    } //-- int getYpos()
+    }
+     //-- int getYpos()
 
     /**
      * Method hasConsThreshold
@@ -812,10 +800,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasConsThreshold()
-    {
+    public boolean hasConsThreshold() {
         return this._has_consThreshold;
-    } //-- boolean hasConsThreshold()
+    }
+     //-- boolean hasConsThreshold()
 
     /**
      * Method hasConservationSelected
@@ -824,10 +812,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasConservationSelected()
-    {
+    public boolean hasConservationSelected() {
         return this._has_conservationSelected;
-    } //-- boolean hasConservationSelected()
+    }
+     //-- boolean hasConservationSelected()
 
     /**
      * Method hasFontSize
@@ -836,10 +824,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasFontSize()
-    {
+    public boolean hasFontSize() {
         return this._has_fontSize;
-    } //-- boolean hasFontSize()
+    }
+     //-- boolean hasFontSize()
 
     /**
      * Method hasFontStyle
@@ -848,10 +836,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasFontStyle()
-    {
+    public boolean hasFontStyle() {
         return this._has_fontStyle;
-    } //-- boolean hasFontStyle()
+    }
+     //-- boolean hasFontStyle()
 
     /**
      * Method hasHeight
@@ -860,10 +848,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasHeight()
-    {
+    public boolean hasHeight() {
         return this._has_height;
-    } //-- boolean hasHeight()
+    }
+     //-- boolean hasHeight()
 
     /**
      * Method hasPidSelected
@@ -872,10 +860,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasPidSelected()
-    {
+    public boolean hasPidSelected() {
         return this._has_pidSelected;
-    } //-- boolean hasPidSelected()
+    }
+     //-- boolean hasPidSelected()
 
     /**
      * Method hasPidThreshold
@@ -884,10 +872,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasPidThreshold()
-    {
+    public boolean hasPidThreshold() {
         return this._has_pidThreshold;
-    } //-- boolean hasPidThreshold()
+    }
+     //-- boolean hasPidThreshold()
 
     /**
      * Method hasRenderGaps
@@ -896,10 +884,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasRenderGaps()
-    {
+    public boolean hasRenderGaps() {
         return this._has_renderGaps;
-    } //-- boolean hasRenderGaps()
+    }
+     //-- boolean hasRenderGaps()
 
     /**
      * Method hasShowAnnotation
@@ -908,10 +896,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasShowAnnotation()
-    {
+    public boolean hasShowAnnotation() {
         return this._has_showAnnotation;
-    } //-- boolean hasShowAnnotation()
+    }
+     //-- boolean hasShowAnnotation()
 
     /**
      * Method hasShowBoxes
@@ -920,10 +908,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasShowBoxes()
-    {
+    public boolean hasShowBoxes() {
         return this._has_showBoxes;
-    } //-- boolean hasShowBoxes()
+    }
+     //-- boolean hasShowBoxes()
 
     /**
      * Method hasShowColourText
@@ -932,10 +920,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasShowColourText()
-    {
+    public boolean hasShowColourText() {
         return this._has_showColourText;
-    } //-- boolean hasShowColourText()
+    }
+     //-- boolean hasShowColourText()
 
     /**
      * Method hasShowConservation
@@ -944,10 +932,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasShowConservation()
-    {
+    public boolean hasShowConservation() {
         return this._has_showConservation;
-    } //-- boolean hasShowConservation()
+    }
+     //-- boolean hasShowConservation()
 
     /**
      * Method hasShowFullId
@@ -956,10 +944,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasShowFullId()
-    {
+    public boolean hasShowFullId() {
         return this._has_showFullId;
-    } //-- boolean hasShowFullId()
+    }
+     //-- boolean hasShowFullId()
 
     /**
      * Method hasShowIdentity
@@ -968,10 +956,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasShowIdentity()
-    {
+    public boolean hasShowIdentity() {
         return this._has_showIdentity;
-    } //-- boolean hasShowIdentity()
+    }
+     //-- boolean hasShowIdentity()
 
     /**
      * Method hasShowQuality
@@ -980,10 +968,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasShowQuality()
-    {
+    public boolean hasShowQuality() {
         return this._has_showQuality;
-    } //-- boolean hasShowQuality()
+    }
+     //-- boolean hasShowQuality()
 
     /**
      * Method hasShowSequenceFeatures
@@ -992,10 +980,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasShowSequenceFeatures()
-    {
+    public boolean hasShowSequenceFeatures() {
         return this._has_showSequenceFeatures;
-    } //-- boolean hasShowSequenceFeatures()
+    }
+     //-- boolean hasShowSequenceFeatures()
 
     /**
      * Method hasShowText
@@ -1004,10 +992,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasShowText()
-    {
+    public boolean hasShowText() {
         return this._has_showText;
-    } //-- boolean hasShowText()
+    }
+     //-- boolean hasShowText()
 
     /**
      * Method hasStartRes
@@ -1016,10 +1004,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasStartRes()
-    {
+    public boolean hasStartRes() {
         return this._has_startRes;
-    } //-- boolean hasStartRes()
+    }
+     //-- boolean hasStartRes()
 
     /**
      * Method hasStartSeq
@@ -1028,10 +1016,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasStartSeq()
-    {
+    public boolean hasStartSeq() {
         return this._has_startSeq;
-    } //-- boolean hasStartSeq()
+    }
+     //-- boolean hasStartSeq()
 
     /**
      * Method hasWidth
@@ -1040,10 +1028,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasWidth()
-    {
+    public boolean hasWidth() {
         return this._has_width;
-    } //-- boolean hasWidth()
+    }
+     //-- boolean hasWidth()
 
     /**
      * Method hasWrapAlignment
@@ -1052,10 +1040,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasWrapAlignment()
-    {
+    public boolean hasWrapAlignment() {
         return this._has_wrapAlignment;
-    } //-- boolean hasWrapAlignment()
+    }
+     //-- boolean hasWrapAlignment()
 
     /**
      * Method hasXpos
@@ -1064,10 +1052,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasXpos()
-    {
+    public boolean hasXpos() {
         return this._has_xpos;
-    } //-- boolean hasXpos()
+    }
+     //-- boolean hasXpos()
 
     /**
      * Method hasYpos
@@ -1076,10 +1064,10 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasYpos()
-    {
+    public boolean hasYpos() {
         return this._has_ypos;
-    } //-- boolean hasYpos()
+    }
+     //-- boolean hasYpos()
 
     /**
      * Method isValid
@@ -1088,16 +1076,16 @@ public class Viewport implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         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
@@ -1107,11 +1095,11 @@ public class Viewport implements java.io.Serializable {
      * @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
@@ -1121,32 +1109,32 @@ public class Viewport implements java.io.Serializable {
      * @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 'bgColour'.
      *
      * @param bgColour the value of field 'bgColour'.
      */
-    public void setBgColour(java.lang.String bgColour)
-    {
+    public void setBgColour(java.lang.String bgColour) {
         this._bgColour = bgColour;
-    } //-- void setBgColour(java.lang.String)
+    }
+     //-- void setBgColour(java.lang.String)
 
     /**
      * Sets the value of field 'consThreshold'.
      *
      * @param consThreshold the value of field 'consThreshold'.
      */
-    public void setConsThreshold(int consThreshold)
-    {
+    public void setConsThreshold(int consThreshold) {
         this._consThreshold = consThreshold;
         this._has_consThreshold = true;
-    } //-- void setConsThreshold(int)
+    }
+     //-- void setConsThreshold(int)
 
     /**
      * Sets the value of field 'conservationSelected'.
@@ -1154,164 +1142,164 @@ public class Viewport implements java.io.Serializable {
      * @param conservationSelected the value of field
      * 'conservationSelected'.
      */
-    public void setConservationSelected(boolean conservationSelected)
-    {
+    public void setConservationSelected(boolean conservationSelected) {
         this._conservationSelected = conservationSelected;
         this._has_conservationSelected = true;
-    } //-- void setConservationSelected(boolean)
+    }
+     //-- void setConservationSelected(boolean)
 
     /**
      * Sets the value of field 'fontName'.
      *
      * @param fontName the value of field 'fontName'.
      */
-    public void setFontName(java.lang.String fontName)
-    {
+    public void setFontName(java.lang.String fontName) {
         this._fontName = fontName;
-    } //-- void setFontName(java.lang.String)
+    }
+     //-- void setFontName(java.lang.String)
 
     /**
      * Sets the value of field 'fontSize'.
      *
      * @param fontSize the value of field 'fontSize'.
      */
-    public void setFontSize(int fontSize)
-    {
+    public void setFontSize(int fontSize) {
         this._fontSize = fontSize;
         this._has_fontSize = true;
-    } //-- void setFontSize(int)
+    }
+     //-- void setFontSize(int)
 
     /**
      * Sets the value of field 'fontStyle'.
      *
      * @param fontStyle the value of field 'fontStyle'.
      */
-    public void setFontStyle(int fontStyle)
-    {
+    public void setFontStyle(int fontStyle) {
         this._fontStyle = fontStyle;
         this._has_fontStyle = true;
-    } //-- void setFontStyle(int)
+    }
+     //-- void setFontStyle(int)
 
     /**
      * Sets the value of field 'height'.
      *
      * @param height the value of field 'height'.
      */
-    public void setHeight(int height)
-    {
+    public void setHeight(int height) {
         this._height = height;
         this._has_height = true;
-    } //-- void setHeight(int)
+    }
+     //-- void setHeight(int)
 
     /**
      * Sets the value of field 'pidSelected'.
      *
      * @param pidSelected the value of field 'pidSelected'.
      */
-    public void setPidSelected(boolean pidSelected)
-    {
+    public void setPidSelected(boolean pidSelected) {
         this._pidSelected = pidSelected;
         this._has_pidSelected = true;
-    } //-- void setPidSelected(boolean)
+    }
+     //-- void setPidSelected(boolean)
 
     /**
      * Sets the value of field 'pidThreshold'.
      *
      * @param pidThreshold the value of field 'pidThreshold'.
      */
-    public void setPidThreshold(int pidThreshold)
-    {
+    public void setPidThreshold(int pidThreshold) {
         this._pidThreshold = pidThreshold;
         this._has_pidThreshold = true;
-    } //-- void setPidThreshold(int)
+    }
+     //-- void setPidThreshold(int)
 
     /**
      * Sets the value of field 'renderGaps'.
      *
      * @param renderGaps the value of field 'renderGaps'.
      */
-    public void setRenderGaps(boolean renderGaps)
-    {
+    public void setRenderGaps(boolean renderGaps) {
         this._renderGaps = renderGaps;
         this._has_renderGaps = true;
-    } //-- void setRenderGaps(boolean)
+    }
+     //-- void setRenderGaps(boolean)
 
     /**
      * Sets the value of field 'showAnnotation'.
      *
      * @param showAnnotation the value of field 'showAnnotation'.
      */
-    public void setShowAnnotation(boolean showAnnotation)
-    {
+    public void setShowAnnotation(boolean showAnnotation) {
         this._showAnnotation = showAnnotation;
         this._has_showAnnotation = true;
-    } //-- void setShowAnnotation(boolean)
+    }
+     //-- void setShowAnnotation(boolean)
 
     /**
      * Sets the value of field 'showBoxes'.
      *
      * @param showBoxes the value of field 'showBoxes'.
      */
-    public void setShowBoxes(boolean showBoxes)
-    {
+    public void setShowBoxes(boolean showBoxes) {
         this._showBoxes = showBoxes;
         this._has_showBoxes = true;
-    } //-- void setShowBoxes(boolean)
+    }
+     //-- void setShowBoxes(boolean)
 
     /**
      * Sets the value of field 'showColourText'.
      *
      * @param showColourText the value of field 'showColourText'.
      */
-    public void setShowColourText(boolean showColourText)
-    {
+    public void setShowColourText(boolean showColourText) {
         this._showColourText = showColourText;
         this._has_showColourText = true;
-    } //-- void setShowColourText(boolean)
+    }
+     //-- void setShowColourText(boolean)
 
     /**
      * Sets the value of field 'showConservation'.
      *
      * @param showConservation the value of field 'showConservation'
      */
-    public void setShowConservation(boolean showConservation)
-    {
+    public void setShowConservation(boolean showConservation) {
         this._showConservation = showConservation;
         this._has_showConservation = true;
-    } //-- void setShowConservation(boolean)
+    }
+     //-- void setShowConservation(boolean)
 
     /**
      * Sets the value of field 'showFullId'.
      *
      * @param showFullId the value of field 'showFullId'.
      */
-    public void setShowFullId(boolean showFullId)
-    {
+    public void setShowFullId(boolean showFullId) {
         this._showFullId = showFullId;
         this._has_showFullId = true;
-    } //-- void setShowFullId(boolean)
+    }
+     //-- void setShowFullId(boolean)
 
     /**
      * Sets the value of field 'showIdentity'.
      *
      * @param showIdentity the value of field 'showIdentity'.
      */
-    public void setShowIdentity(boolean showIdentity)
-    {
+    public void setShowIdentity(boolean showIdentity) {
         this._showIdentity = showIdentity;
         this._has_showIdentity = true;
-    } //-- void setShowIdentity(boolean)
+    }
+     //-- void setShowIdentity(boolean)
 
     /**
      * Sets the value of field 'showQuality'.
      *
      * @param showQuality the value of field 'showQuality'.
      */
-    public void setShowQuality(boolean showQuality)
-    {
+    public void setShowQuality(boolean showQuality) {
         this._showQuality = showQuality;
         this._has_showQuality = true;
-    } //-- void setShowQuality(boolean)
+    }
+     //-- void setShowQuality(boolean)
 
     /**
      * Sets the value of field 'showSequenceFeatures'.
@@ -1319,98 +1307,98 @@ public class Viewport implements java.io.Serializable {
      * @param showSequenceFeatures the value of field
      * 'showSequenceFeatures'.
      */
-    public void setShowSequenceFeatures(boolean showSequenceFeatures)
-    {
+    public void setShowSequenceFeatures(boolean showSequenceFeatures) {
         this._showSequenceFeatures = showSequenceFeatures;
         this._has_showSequenceFeatures = true;
-    } //-- void setShowSequenceFeatures(boolean)
+    }
+     //-- void setShowSequenceFeatures(boolean)
 
     /**
      * Sets the value of field 'showText'.
      *
      * @param showText the value of field 'showText'.
      */
-    public void setShowText(boolean showText)
-    {
+    public void setShowText(boolean showText) {
         this._showText = showText;
         this._has_showText = true;
-    } //-- void setShowText(boolean)
+    }
+     //-- void setShowText(boolean)
 
     /**
      * Sets the value of field 'startRes'.
      *
      * @param startRes the value of field 'startRes'.
      */
-    public void setStartRes(int startRes)
-    {
+    public void setStartRes(int startRes) {
         this._startRes = startRes;
         this._has_startRes = true;
-    } //-- void setStartRes(int)
+    }
+     //-- void setStartRes(int)
 
     /**
      * Sets the value of field 'startSeq'.
      *
      * @param startSeq the value of field 'startSeq'.
      */
-    public void setStartSeq(int startSeq)
-    {
+    public void setStartSeq(int startSeq) {
         this._startSeq = startSeq;
         this._has_startSeq = true;
-    } //-- void setStartSeq(int)
+    }
+     //-- void setStartSeq(int)
 
     /**
      * Sets the value of field 'title'.
      *
      * @param title the value of field 'title'.
      */
-    public void setTitle(java.lang.String 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)
-    {
+    public void setWidth(int width) {
         this._width = width;
         this._has_width = true;
-    } //-- void setWidth(int)
+    }
+     //-- void setWidth(int)
 
     /**
      * Sets the value of field 'wrapAlignment'.
      *
      * @param wrapAlignment the value of field 'wrapAlignment'.
      */
-    public void setWrapAlignment(boolean wrapAlignment)
-    {
+    public void setWrapAlignment(boolean wrapAlignment) {
         this._wrapAlignment = wrapAlignment;
         this._has_wrapAlignment = true;
-    } //-- void setWrapAlignment(boolean)
+    }
+     //-- void setWrapAlignment(boolean)
 
     /**
      * Sets the value of field 'xpos'.
      *
      * @param xpos the value of field 'xpos'.
      */
-    public void setXpos(int 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)
-    {
+    public void setYpos(int ypos) {
         this._ypos = ypos;
         this._has_ypos = true;
-    } //-- void setYpos(int)
+    }
+     //-- void setYpos(int)
 
     /**
      * Method unmarshal
@@ -1421,20 +1409,20 @@ public class Viewport implements java.io.Serializable {
      * @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)
+        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
-    {
+    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/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 804414a..b3cf890 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -16,568 +16,562 @@
 * 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.*;
+
 import jalview.util.*;
+
 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 = '-';
+    public AlignmentAnnotation[] annotations;
+    public boolean featuresAdded = false;
+
+    /** Make an alignment from an array of Sequences.
+    *
+    * @param sequences
+    */
+    public Alignment(SequenceI[] seqs) {
+        sequences = new Vector();
 
-  protected Vector      sequences;
-  protected Vector      groups = new Vector();
-  protected Vector   superGroup = new Vector();
-  protected char        gapCharacter = '-';
-  public AlignmentAnnotation [] annotations;
+        for (int i = 0; i < seqs.length; i++)
+            sequences.addElement(seqs[i]);
 
-  public boolean featuresAdded = false;
+        getWidth();
+    }
 
-  /** Make an alignment from an array of Sequences.
-  *
-  * @param sequences
-  */
-  public Alignment(SequenceI[] seqs) {
-    sequences = new Vector();
+    public Vector getSequences() {
+        return sequences;
+    }
 
-    for (int i=0; i < seqs.length; i++)
-      sequences.addElement(seqs[i]);
+    public SequenceI getSequenceAt(int i) {
+        if (i < sequences.size()) {
+            return (SequenceI) sequences.elementAt(i);
+        }
 
-    getWidth();
-  }
+        return null;
+    }
 
-  public Vector      getSequences() {
-    return sequences;
-  }
+    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
+     *
+     * @param snew
+     */
+    public void addSequence(SequenceI snew) {
+        sequences.addElement(snew);
+    }
 
-  public SequenceI getSequenceAt(int i) {
-    if (i < sequences.size()) {
-      return (SequenceI)sequences.elementAt(i);
+    public void addSequence(SequenceI[] seq) {
+        for (int i = 0; i < seq.length; i++) {
+            addSequence(seq[i]);
+        }
     }
 
-    return null;
-  }
+    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
+      *
+     * @param snew
+     */
+    public void setSequenceAt(int i, SequenceI snew) {
+        SequenceI oldseq = getSequenceAt(i);
+        deleteSequence(oldseq);
 
-  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   *
-   * @param snew
-   */
-  public void addSequence(SequenceI snew) {
-    sequences.addElement(snew);
-  }
+        sequences.setElementAt(snew, i);
+    }
 
-  public void addSequence(SequenceI[] seq) {
-    for (int i=0; i < seq.length; i++) {
-      addSequence(seq[i]);
+    public Vector getGroups() {
+        return groups;
     }
-  }
 
-  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-    *
-   * @param snew
-   */
-  public void setSequenceAt(int i,SequenceI snew) {
-    SequenceI oldseq = getSequenceAt(i);
-    deleteSequence(oldseq);
+    /** Sorts the sequences by sequence group size - largest to smallest.
+     * Uses QuickSort.
+     */
+    public void sortGroups() {
+        float[] arr = new float[groups.size()];
+        Object[] s = new Object[groups.size()];
 
-    sequences.setElementAt(snew,i);
-  }
+        for (int i = 0; i < groups.size(); i++) {
+            arr[i] = ((SequenceGroup) groups.elementAt(i)).sequences.size();
+            s[i] = groups.elementAt(i);
+        }
 
-  public Vector getGroups() {
-    return groups;
-  }
-
-  /** Sorts the sequences by sequence group size - largest to smallest.
-   * Uses QuickSort.
-   */
-  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);
 
-    QuickSort.sort(arr,s);
+        Vector newg = new Vector(groups.size());
 
-    Vector newg = new Vector(groups.size());
+        for (int i = groups.size() - 1; i >= 0; i--) {
+            newg.addElement(s[i]);
+        }
 
-    for (int i=groups.size()-1; i >= 0; i--) {
-      newg.addElement(s[i]);
+        groups = newg;
     }
 
-    groups = newg;
-  }
+    /** Takes out columns consisting entirely of gaps (-,.," ")
+     */
+    public void removeGaps() {
+        SequenceI current;
+        int iSize = getWidth();
+
+        for (int i = 0; i < iSize; i++) {
+            boolean delete = true;
+
+            for (int j = 0; j < getHeight(); j++) {
+                current = getSequenceAt(j);
+
+                if (current.getLength() > i) {
+                    /* MC Should move this to a method somewhere */
+                    if (!jalview.util.Comparison.isGap(current.getCharAt(i))) {
+                        delete = false;
+                    }
+                }
+            }
+
+            if (delete) {
+                deleteColumns(i, i);
+                iSize--;
+                i--;
+            }
+        }
+    }
 
-  /** Takes out columns consisting entirely of gaps (-,.," ")
-   */
-  public void removeGaps()
-  {
+    /** 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);
+    }
 
-    SequenceI current;
-    int iSize = getWidth();
-    for (int i=0; i < iSize; i++)
-    {
-      boolean delete = true;
-      for (int j=0; j < getHeight(); j++)
-      {
-        current = getSequenceAt(j);
-        if (current.getLength() > i)
-        {
-	    /* MC Should move this to a method somewhere */
-          if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
-            delete = false;
+    /** 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) {
+        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++) {
+                getSequenceAt(j).deleteCharAt(start);
+            }
         }
-      }
+    }
 
-      if ( delete )
-      {
-        deleteColumns(i,i);
-        iSize--;
-        i--;
-      }
+    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));
+        }
 
-  /** 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) {
-    deleteColumns(0,getHeight()-1,start,end);
-  }
+        return seqs;
+    }
 
-  public void deleteColumns(int seq1, int seq2, int start, int end) {
+    public void trimLeft(int i) {
+        for (int j = 0; j < getHeight(); j++) {
+            SequenceI s = getSequenceAt(j);
+            int newstart = s.findPosition(i);
 
-    for (int i=0; i <= (end-start); i++) {
-      for (int j=seq1; j <= seq2; j++) {
-        getSequenceAt(j).deleteCharAt(start);
-      }
+            s.setStart(newstart);
+            s.setSequence(s.getSequence().substring(i));
+        }
     }
-  }
 
-  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 void trimRight(int i) {
+        for (int j = 0; j < getHeight(); j++) {
+            SequenceI s = getSequenceAt(j);
+            int newend = s.findPosition(i);
 
+            s.setEnd(newend);
+            s.setSequence(s.getSequence().substring(0, i + 1));
+        }
     }
-  }
 
-  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));
+    public void deleteSequence(SequenceI s) {
+        for (int i = 0; i < getHeight(); i++)
+            if (getSequenceAt(i) == s) {
+                deleteSequence(i);
+            }
     }
-    return seqs;
-  }
 
-  public void trimLeft(int i) {
-    for (int j = 0;j< getHeight();j++) {
+    public void deleteSequence(int i) {
+        sequences.removeElementAt(i);
+    }
 
-      SequenceI s        = getSequenceAt(j);
-      int       newstart = s.findPosition(i);
+    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++) {
+                // Only do the comparison if either have not been deleted
+                if (!del.contains((SequenceI) sel.elementAt(i)) ||
+                        !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) {
+                        // Delete the shortest one
+                        if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel
+                                                                                         .elementAt(
+                                    i)).getSequence().length()) {
+                            del.addElement(sel.elementAt(i));
+                        } else {
+                            del.addElement(sel.elementAt(i));
+                        }
+                    }
+                }
+            }
+        }
 
-      s.setStart(newstart);
-      s.setSequence(s.getSequence().substring(i));
+        // Now delete the sequences
+        for (int i = 0; i < del.size(); i++)
+            deleteSequence((SequenceI) del.elementAt(i));
 
+        return del;
     }
-  }
 
-  public void  trimRight(int i) {
-    for (int j = 0;j< getHeight();j++) {
-      SequenceI s      = getSequenceAt(j);
-      int       newend = s.findPosition(i);
+    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;
+        }
 
-      s.setEnd(newend);
-      s.setSequence(s.getSequence().substring(0,i+1));
+        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 deleteSequence(SequenceI s)
-  {
-    for (int i=0; i < getHeight(); i++)
-      if (getSequenceAt(i) == s)
-        deleteSequence(i);
-  }
+    public void sortByID() {
+        String[] ids = new String[getHeight()];
+        SequenceI[] seqs = new SequenceI[getHeight()];
 
-  public void  deleteSequence(int i)
-  {
-    sequences.removeElementAt(i);
-  }
+        for (int i = 0; i < getHeight(); i++) {
+            ids[i] = getSequenceAt(i).getName();
+            seqs[i] = getSequenceAt(i);
+        }
 
+        QuickSort.sort(ids, seqs);
 
-  public Vector removeRedundancy(float threshold, Vector sel) {
-    Vector del = new Vector();
+        int len = 0;
 
-    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)))
-        {
-          // use PID instead of Comparison (which is really not pleasant)
-          float pid = Comparison.PID( (SequenceI) sel.elementAt(j),
-                                         (SequenceI) sel.elementAt(i));
+        if ((getHeight() % 2) == 0) {
+            len = getHeight() / 2;
+        } else {
+            len = (getHeight() + 1) / 2;
+            System.out.println("DEBUG:Sort len is odd = " + len); // log.
+        }
 
-          if (pid >= threshold)
-          {
-            // Delete the shortest one
-            if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >
-                ( (SequenceI) sel.elementAt(i)).getSequence().length())
-              del.addElement(sel.elementAt(i));
-            else
-              del.addElement(sel.elementAt(i));
-          }
+        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);
         }
-      }
     }
 
-    // Now delete the sequences
-    for (int i=0; i < del.size(); i++)
-      deleteSequence((SequenceI)del.elementAt(i));
-
-    return del;
-  }
+    /**    */
+    public SequenceGroup findGroup(int i) {
+        return findGroup(getSequenceAt(i));
+    }
 
-  public void sortByPID(SequenceI s) {
+    /**    */
+    public SequenceGroup findGroup(SequenceI s) {
+        for (int i = 0; i < this.groups.size(); i++) {
+            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-    float     scores[] = new float[getHeight()];
-    SequenceI seqs[]   = new SequenceI[getHeight()];
+            if (sg.sequences.contains(s)) {
+                return sg;
+            }
+        }
 
-    for (int i = 0; i < getHeight(); i++) {
-      scores[i] = Comparison.compare(getSequenceAt(i),s);
-      seqs[i]   = getSequenceAt(i);
+        return null;
     }
 
-    QuickSort.sort(scores,0,scores.length-1,seqs);
+    public SequenceGroup[] findAllGroups(SequenceI s) {
+        Vector temp = new Vector();
+
+        for (int i = 0; i < this.groups.size(); i++) {
+            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+            if (sg.sequences.contains(s)) {
+                temp.addElement(sg);
+            }
+        }
+
+        SequenceGroup[] ret = new SequenceGroup[temp.size()];
 
-    int len = 0;
+        for (int i = 0; i < temp.size(); i++)
+            ret[i] = (SequenceGroup) temp.elementAt(i);
 
-    if (getHeight()%2 == 0) {
-      len = getHeight()/2;
-    } else {
-      len = (getHeight()+1)/2;
+        return ret;
     }
 
-    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 addToGroup(SequenceGroup g, SequenceI s) {
+        if (!(g.sequences.contains(s))) {
+            g.sequences.addElement(s);
+        }
     }
-  }
 
-  public void sortByID() {
-    String    ids[]   = new String[getHeight()];
-    SequenceI seqs[]  = new SequenceI[getHeight()];
+    /**    */
+    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);
+                }
+            }
+        }
+    }
 
-    for (int i = 0; i < getHeight(); i++) {
-      ids[i]  = getSequenceAt(i).getName();
-      seqs[i] = getSequenceAt(i);
+    public void addSuperGroup(SuperGroup sg) {
+        superGroup.addElement(sg);
     }
 
-    QuickSort.sort(ids,seqs);
+    public void removeSuperGroup(SuperGroup sg) {
+        superGroup.removeElement(sg);
+    }
 
-    int len = 0;
+    public SuperGroup getSuperGroup(SequenceGroup sg) {
+        for (int i = 0; i < this.superGroup.size(); i++) {
+            SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
 
-    if (getHeight()%2 == 0) {
-      len = getHeight()/2;
-    } else {
-      len = (getHeight()+1)/2;
-      System.out.println("DEBUG:Sort len is odd = " + len); // log.
+            if (temp.sequenceGroups.contains(sg)) {
+                return temp;
+            }
+        }
+
+        return null;
     }
-    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);
+
+    /**    */
+    public void addGroup(SequenceGroup sg) {
+        if (!groups.contains(sg)) {
+            groups.addElement(sg);
+        }
     }
-  }
 
-  /**    */
-  public SequenceGroup findGroup(int i) {
-    return findGroup(getSequenceAt(i));
-  }
+    public void deleteAllGroups() {
+        groups.removeAllElements();
+        superGroup.removeAllElements();
+
+        int i = 0;
 
-  /**    */
-  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))
-        return sg;
+        while (i < sequences.size()) {
+            SequenceI s = getSequenceAt(i);
+            s.setColor(java.awt.Color.white);
+            i++;
+        }
+    }
 
+    /**    */
+    public void deleteGroup(SequenceGroup g) {
+        if (groups.contains(g)) {
+            groups.removeElement(g);
+        }
     }
-    return null;
-  }
 
-  public SequenceGroup [] findAllGroups(SequenceI s)
-  {
+    /**    */
+    public SequenceI findName(String name) {
+        int i = 0;
 
-    Vector temp = new Vector();
+        while (i < sequences.size()) {
+            SequenceI s = getSequenceAt(i);
 
-    for (int i = 0; i < this.groups.size();i++)
-    {
-      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+            if (s.getName().equals(name)) {
+                return s;
+            }
 
-      if (sg.sequences.contains(s))
-       temp.addElement(sg);
+            i++;
+        }
+
+        return null;
     }
 
-    SequenceGroup [] ret = new SequenceGroup[temp.size()];
-    for(int i=0; i<temp.size(); i++)
-      ret[i] = (SequenceGroup)temp.elementAt(i);
+    /**    */
+    public SequenceI findbyDisplayId(String name) {
+        int i = 0;
+
+        while (i < sequences.size()) {
+            SequenceI s = getSequenceAt(i);
 
-    return ret;
+            if (s.getDisplayId().equals(name)) {
+                return s;
+            }
 
-  }
-  /**    */
-  public void addToGroup(SequenceGroup g, SequenceI s) {
-    if (!(g.sequences.contains(s))) {
-      g.sequences.addElement(s);
+            i++;
+        }
+
+        return null;
     }
-  }
-  /**    */
-  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);
+
+    /**    */
+    public int findIndex(SequenceI s) {
+        int i = 0;
+
+        while (i < sequences.size()) {
+            if (s == getSequenceAt(i)) {
+                return i;
+            }
+
+            i++;
         }
-      }
+
+        return -1;
+    }
+
+    public int getHeight() {
+        return sequences.size();
     }
-  }
 
-  public void addSuperGroup(SuperGroup sg)
-  {
-    superGroup.addElement(sg);
-  }
+    public int getWidth() {
+        int maxLength = -1;
 
-  public void removeSuperGroup(SuperGroup sg)
-  {
-    superGroup.removeElement(sg);
-  }
+        for (int i = 0; i < sequences.size(); i++) {
+            if (getSequenceAt(i).getLength() > maxLength) {
+                maxLength = getSequenceAt(i).getLength();
+            }
+        }
 
-  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))
-        return temp;
+        return maxLength;
     }
-    return null;
-  }
 
-  /**    */
-  public void addGroup(SequenceGroup sg) {
-    if(!groups.contains(sg))
-      groups.addElement(sg);
-  }
+    public int getMaxIdLength() {
+        int max = 0;
+        int i = 0;
 
-  public void deleteAllGroups()
-  {
-    groups.removeAllElements();
-    superGroup.removeAllElements();
-   int i=0;
-    while (i < sequences.size()) {
-     SequenceI s = getSequenceAt(i);
-     s.setColor(java.awt.Color.white);
-     i++;
-   }
-
-
-  }
-
-  /**    */
-  public void deleteGroup(SequenceGroup g) {
-    if (groups.contains(g)) {
-      groups.removeElement(g);
-    }
-  }
-
-  /**    */
-  public SequenceI findName(String name) {
-    int i = 0;
-    while (i < sequences.size()) {
-      SequenceI s = getSequenceAt(i);
-      if (s.getName().equals(name))
-        return s;
-
-      i++;
-    }
-    return null;
-  }
-
-  /**    */
-  public SequenceI findbyDisplayId(String name) {
-    int i = 0;
-    while (i < sequences.size()) {
-      SequenceI s = getSequenceAt(i);
-      if (s.getDisplayId().equals(name))
-        return s;
-
-      i++;
-    }
-    return null;
-  }
-
-  /**    */
-  public int findIndex(SequenceI s)
-  {
-    int i=0;
-    while (i < sequences.size())
-    {
-      if (s == getSequenceAt(i))
-        return i;
-
-      i++;
-    }
-    return -1;
-  }
-
-  public int getHeight() {
-    return sequences.size();
-  }
-
-
-  public int getWidth()
-  {
-    int maxLength = -1;
-    for (int i = 0; i < sequences.size(); i++)
-    {
-      if (getSequenceAt(i).getLength() > maxLength)
-        maxLength = getSequenceAt(i).getLength();
-    }
-
-    return maxLength;
-  }
-
-
-  public int getMaxIdLength() {
-    int max = 0;
-    int i   = 0;
-
-    while (i < sequences.size()) {
-      SequenceI seq = getSequenceAt(i);
-      String    tmp = seq.getName() + "/" + seq.getStart() + "-" + seq.getEnd();
-
-      if (tmp.length() > max) {
-        max = tmp.length();
-      }
-
-      i++;
-    }
-    return max;
-  }
-
-  public void setGapCharacter(char gc)
-  {
-    gapCharacter = gc;
-    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);
-     }
-  }
+        while (i < sequences.size()) {
+            SequenceI seq = getSequenceAt(i);
+            String tmp = seq.getName() + "/" + seq.getStart() + "-" +
+                seq.getEnd();
 
-  public char getGapCharacter() {
-    return gapCharacter;
-  }
+            if (tmp.length() > max) {
+                max = tmp.length();
+            }
 
-  public Vector getAAFrequency()
-  {
-    return AAFrequency.calculate(sequences, 0, getWidth());
-  }
+            i++;
+        }
 
-  public boolean isAligned()
-  {
-    int width = getWidth();
-    for (int i = 0; i < sequences.size(); i++)
-      if (getSequenceAt(i).getLength() != width)
-        return false;
-
-    return true;
-  }
+        return max;
+    }
 
-   public void deleteAnnotation(AlignmentAnnotation aa)
-   {
-     int aSize = 1;
-     if(annotations!=null)
-       aSize = annotations.length;
+    public void setGapCharacter(char gc) {
+        gapCharacter = gc;
 
-     AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize-1];
+        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);
+        }
+    }
 
-     int tIndex = 0;
-     for (int i = 0; i < aSize; i++)
-      {
-        if(annotations[i]==aa)
-          continue;
+    public char getGapCharacter() {
+        return gapCharacter;
+    }
 
+    public Vector getAAFrequency() {
+        return AAFrequency.calculate(sequences, 0, getWidth());
+    }
 
-        temp[tIndex] = annotations[i];
-        tIndex++;
-      }
+    public boolean isAligned() {
+        int width = getWidth();
 
-     annotations = temp;
+        for (int i = 0; i < sequences.size(); i++)
+            if (getSequenceAt(i).getLength() != width) {
+                return false;
+            }
 
-   }
+        return true;
+    }
 
-  public void addAnnotation(AlignmentAnnotation aa)
-  {
-    int aSize = 1;
-    if(annotations!=null)
-      aSize = annotations.length+1;
+    public void deleteAnnotation(AlignmentAnnotation aa) {
+        int aSize = 1;
 
-    AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize];
-    int i=0;
-    if (aSize > 1)
-      for (i = 0; i < aSize-1; i++)
-        temp[i] = annotations[i];
+        if (annotations != null) {
+            aSize = annotations.length;
+        }
 
-    temp[i] = aa;
+        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
 
-    annotations = temp;
-  }
-  public AlignmentAnnotation[] getAlignmentAnnotation()
-  {
-    return annotations;
-  }
+        int tIndex = 0;
 
-}
+        for (int i = 0; i < aSize; i++) {
+            if (annotations[i] == aa) {
+                continue;
+            }
 
+            temp[tIndex] = annotations[i];
+            tIndex++;
+        }
+
+        annotations = temp;
+    }
 
+    public void addAnnotation(AlignmentAnnotation aa) {
+        int aSize = 1;
 
+        if (annotations != null) {
+            aSize = annotations.length + 1;
+        }
 
+        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+        int i = 0;
 
+        if (aSize > 1) {
+            for (i = 0; i < (aSize - 1); i++)
+                temp[i] = annotations[i];
+        }
 
+        temp[i] = aa;
 
+        annotations = temp;
+    }
 
+    public AlignmentAnnotation[] getAlignmentAnnotation() {
+        return annotations;
+    }
+}
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 337d879..35297b5 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -16,107 +16,117 @@
 * 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 AlignmentAnnotation
-{
-  public String label;
-  public String description;
-  public Annotation  [] annotations;
-  public boolean isGraph = false;
-  public float graphMin, graphMax;
-  public int windowLength;
-
-  // Graphical hints and tips
-  public boolean editable = false;
-  public boolean hasIcons; //
-  public boolean hasText;
-  public boolean visible = true;
-  public int height=0;
-
-  public AlignmentAnnotation(String label, String description, Annotation [] annotations)
-  {
-    // always editable?
-    editable = true;
-    this.label = label;
-    this.description = description;
-    this.annotations = annotations;
-    for(int i=0; i<annotations.length; i++)
-    {
-      if (annotations[i]!=null &&(
-          annotations[i].secondaryStructure == 'H' ||
-          annotations[i].secondaryStructure == 'E'))
-        hasIcons = true;
-
-      if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)
-        hasText = true;
-    }
-  }
-
-  public AlignmentAnnotation(String label, String description, 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)
-          continue;
-        if(annotations[i].value>max)
-          max = annotations[i].value;
-        if(annotations[i].value<min)
-          min = annotations[i].value;
-      }
+public class AlignmentAnnotation {
+    public String label;
+    public String description;
+    public Annotation[] annotations;
+    public boolean isGraph = false;
+    public float graphMin;
+    public float graphMax;
+    public int windowLength;
+
+    // Graphical hints and tips
+    public boolean editable = false;
+    public boolean hasIcons; //
+    public boolean hasText;
+    public boolean visible = true;
+    public int height = 0;
+
+    public AlignmentAnnotation(String label, String description,
+        Annotation[] annotations) {
+        // always editable?
+        editable = true;
+        this.label = label;
+        this.description = description;
+        this.annotations = annotations;
+
+        for (int i = 0; i < annotations.length; i++) {
+            if ((annotations[i] != null) &&
+                    ((annotations[i].secondaryStructure == 'H') ||
+                    (annotations[i].secondaryStructure == 'E'))) {
+                hasIcons = true;
+            }
+
+            if ((annotations[i] != null) &&
+                    (annotations[i].displayCharacter.length() > 0)) {
+                hasText = true;
+            }
+        }
     }
 
-    graphMin = min;
-    graphMax = max;
-    windowLength = winLength;
-    for(int i=0; i<annotations.length; i++)
-    {
-      if (annotations[i]!=null &&(
-          annotations[i].secondaryStructure == 'H' ||
-          annotations[i].secondaryStructure == 'E'))
-        hasIcons = true;
-
-      if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)
-        hasText = true;
+    public AlignmentAnnotation(String label, String description,
+        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) {
+                    continue;
+                }
+
+                if (annotations[i].value > max) {
+                    max = annotations[i].value;
+                }
+
+                if (annotations[i].value < min) {
+                    min = annotations[i].value;
+                }
+            }
+        }
+
+        graphMin = min;
+        graphMax = max;
+        windowLength = winLength;
+
+        for (int i = 0; i < annotations.length; i++) {
+            if ((annotations[i] != null) &&
+                    ((annotations[i].secondaryStructure == 'H') ||
+                    (annotations[i].secondaryStructure == 'E'))) {
+                hasIcons = true;
+            }
+
+            if ((annotations[i] != null) &&
+                    (annotations[i].displayCharacter.length() > 0)) {
+                hasText = true;
+            }
+        }
     }
-  }
-
-  public String toString()
-  {
-    StringBuffer buffer = new StringBuffer();
-    for(int i=0; i<annotations.length; i++)
-   {
-     if(annotations[i]!=null)
-     {
-       if(isGraph)
-         buffer.append(annotations[i].value);
-       else if(hasIcons)
-         buffer.append(annotations[i].secondaryStructure);
-       else
-         buffer.append(annotations[i].displayCharacter);
-
-     }
-     buffer.append(", ");
-   }
-   if(label.equals("Consensus"))
-   {
-     buffer.append("\n");
-     for (int i = 0; i < annotations.length; i++)
-     {
-       if (annotations[i] != null)
-           buffer.append(annotations[i].description);
-       buffer.append(", ");
-     }
-   }
-   return buffer.toString();
-  }
 
+    public String toString() {
+        StringBuffer buffer = new StringBuffer();
+
+        for (int i = 0; i < annotations.length; i++) {
+            if (annotations[i] != null) {
+                if (isGraph) {
+                    buffer.append(annotations[i].value);
+                } else if (hasIcons) {
+                    buffer.append(annotations[i].secondaryStructure);
+                } else {
+                    buffer.append(annotations[i].displayCharacter);
+                }
+            }
+
+            buffer.append(", ");
+        }
+
+        if (label.equals("Consensus")) {
+            buffer.append("\n");
+
+            for (int i = 0; i < annotations.length; i++) {
+                if (annotations[i] != null) {
+                    buffer.append(annotations[i].description);
+                }
+
+                buffer.append(", ");
+            }
+        }
+
+        return buffer.toString();
+    }
 }
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index e48ff36..8a14a08 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -16,81 +16,101 @@
 * 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.*;
 
+
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
 public interface AlignmentI {
+    public int getHeight();
 
-  public int         getHeight() ;
-  public int         getWidth() ;
-  public int         getMaxIdLength() ;
+    public int getWidth();
 
-  public boolean isAligned();
+    public int getMaxIdLength();
 
-  public Vector      getSequences();
-  public SequenceI   getSequenceAt(int i);
+    public boolean isAligned();
 
-  public void        addSequence(SequenceI seq) ;
-  public void        setSequenceAt(int i,SequenceI seq);
+    public Vector getSequences();
 
-  public void        deleteSequence(SequenceI s) ;
-  public void        deleteSequence(int i) ;
+    public SequenceI getSequenceAt(int i);
 
-  public SequenceI[] getColumns(int start, int end) ;
-  public SequenceI[] getColumns(int seq1, int seq2, int start, int end) ;
+    public void addSequence(SequenceI seq);
 
-  public void        deleteColumns(int start, int end) ;
-  public void        deleteColumns(int seq1, int seq2, int start, int end) ;
+    public void setSequenceAt(int i, SequenceI seq);
 
-  public void        insertColumns(SequenceI[] seqs, int pos) ;
+    public void deleteSequence(SequenceI s);
 
-  public SequenceI   findName(String name) ;
-  public SequenceI   findbyDisplayId(String name);
+    public void deleteSequence(int i);
 
-  public int         findIndex(SequenceI s) ;
+    public SequenceI[] getColumns(int start, int end);
 
-  // Modifying
-  public void        trimLeft(int i) ;
-  public void        trimRight(int i) ;
+    public SequenceI[] getColumns(int seq1, int seq2, int start, int end);
 
-  public void        removeGaps() ;
-  public Vector      removeRedundancy(float threshold, Vector sel) ;
+    public void deleteColumns(int start, int end);
 
+    public void deleteColumns(int seq1, int seq2, int start, int end);
 
-  // Grouping methods
-  public SequenceGroup findGroup(int i) ;
-  public SequenceGroup findGroup(SequenceI s) ;
-  public SequenceGroup [] findAllGroups(SequenceI s);
-  public void          addToGroup(SequenceGroup g, SequenceI s) ;
-  public void          removeFromGroup(SequenceGroup g,SequenceI s) ;
-  public void          addGroup(SequenceGroup sg) ;
-  public void          deleteGroup(SequenceGroup g) ;
-  public Vector        getGroups();
-  public void deleteAllGroups();
+    public void insertColumns(SequenceI[] seqs, int pos);
 
-  public void          addSuperGroup(SuperGroup sg);
-  public void          removeSuperGroup(SuperGroup sg);
-  public SuperGroup    getSuperGroup(SequenceGroup sg);
+    public SequenceI findName(String name);
 
-  // Sorting
-  public void          sortGroups() ;
-  public void          sortByPID(SequenceI s) ;
-  public void          sortByID() ;
+    public SequenceI findbyDisplayId(String name);
 
-  //Annotations
-  public void addAnnotation(AlignmentAnnotation aa);
-  public void deleteAnnotation(AlignmentAnnotation aa);
-  public AlignmentAnnotation [] getAlignmentAnnotation();
+    public int findIndex(SequenceI s);
 
-  public void          setGapCharacter(char gc);
-  public char          getGapCharacter();
+    // Modifying
+    public void trimLeft(int i);
 
-  public Vector        getAAFrequency();
-}
+    public void trimRight(int i);
+
+    public void removeGaps();
+
+    public Vector removeRedundancy(float threshold, Vector sel);
+
+    // Grouping methods
+    public SequenceGroup findGroup(int i);
+
+    public SequenceGroup findGroup(SequenceI s);
+
+    public SequenceGroup[] findAllGroups(SequenceI s);
+
+    public void addToGroup(SequenceGroup g, SequenceI s);
+
+    public void removeFromGroup(SequenceGroup g, SequenceI s);
+
+    public void addGroup(SequenceGroup sg);
+
+    public void deleteGroup(SequenceGroup g);
 
+    public Vector getGroups();
 
+    public void deleteAllGroups();
 
+    public void addSuperGroup(SuperGroup sg);
+
+    public void removeSuperGroup(SuperGroup sg);
+
+    public SuperGroup getSuperGroup(SequenceGroup sg);
+
+    // Sorting
+    public void sortGroups();
+
+    public void sortByPID(SequenceI s);
+
+    public void sortByID();
+
+    //Annotations
+    public void addAnnotation(AlignmentAnnotation aa);
+
+    public void deleteAnnotation(AlignmentAnnotation aa);
+
+    public AlignmentAnnotation[] getAlignmentAnnotation();
+
+    public void setGapCharacter(char gc);
+
+    public char getGapCharacter();
+
+    public Vector getAAFrequency();
+}
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 3e6fd9f..c0da1fc 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -15,12 +15,12 @@
 * 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.*;
-
+*/
+package jalview.datamodel;
+
+import java.util.*;
+
+
 /**
  * <p>Title: </p>
  *
@@ -32,105 +32,94 @@ import java.util.*;
  *
  * @author not attributable
  * @version 1.0
- */
-public class AlignmentOrder
-{
-  public AlignmentOrder()
-  {
-  }
-
-  public void setType(int Type)
-  {
-    this.Type = Type;
-  }
-
-  public int getType()
-  {
-    return Type;
-  }
-
-  public void setName(String Name)
-  {
-    this.Name = Name;
-  }
-
-  public String getName()
-  {
-    return Name;
-  }
-
-  public void setOrder(Vector Order)
-  {
-    this.Order = Order;
-  }
-
-  public Vector getOrder()
-  {
-
-    return Order;
-  }
-// 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)
+ */
+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 static final int FILE = 0;
-  public static final int MSA = 1;
-  public static final int USER = 2;
-
-  private int Type = 0;
-  private String Name;
-  private Vector Order = null;
-
-  /**
-   * AlignmentOrder
-   *
-   * @param anOrder Vector
-   */
-  public AlignmentOrder(Vector anOrder)
-  {
-    Order = anOrder;
-  }
-
-  /**
-   * 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) {
-    Order = new Vector();
-    for (int i=0,ns=orderFrom.length; i<ns; i++)
-      Order.addElement(orderFrom[i]);
-  }
-
-
-
-  /**
-   * 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 static final int FILE = 0;
+    public static final int MSA = 1;
+    public static final int USER = 2;
+    private int Type = 0;
+    private String Name;
+    private Vector Order = null;
+
+    public AlignmentOrder() {
+    }
+
+    /**
+ * AlignmentOrder
+ *
+ * @param anOrder Vector
+ */
+    public AlignmentOrder(Vector anOrder) {
+        Order = anOrder;
+    }
+
+    /**
+ * 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) {
+        Order = new Vector();
+
+        for (int i = 0, ns = orderFrom.length; i < ns; i++)
+            Order.addElement(orderFrom[i]);
+    }
+
+    public void setType(int Type) {
+        this.Type = Type;
+    }
+
+    public int getType() {
+        return Type;
+    }
+
+    public void setName(String Name) {
+        this.Name = Name;
+    }
+
+    public String getName() {
+        return Name;
+    }
+
+    public void setOrder(Vector Order) {
+        this.Order = Order;
+    }
+
+    public Vector getOrder() {
+        return Order;
+    }
+
+    /**
+ * 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
 
-}
+} */
+}
diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index b99ce9f..7858e3f 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -15,30 +15,31 @@
 * 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 Annotation
-{
-  public String displayCharacter="";
-  public String description="";       // currently used as mouse over
-  public char secondaryStructure=' '; // recognises H and E
-  public float value;
-
-  // add visual cues here
-  public Color colour = Color.black;
-
-  public Annotation(String displayChar, String desc, char ss, float val)
-  {
-    displayCharacter = displayChar;
-    description = desc;
-    secondaryStructure = ss;
-    value = val;
-  }
-  public Annotation(String displayChar, String desc, char ss, float val, Color colour) {
-    this(displayChar, desc, ss, val);
-    this.colour = colour;
-  }
-}
+*/
+package jalview.datamodel;
+
+import java.awt.*;
+
+
+public class Annotation {
+    public String displayCharacter = "";
+    public String description = ""; // currently used as mouse over
+    public char secondaryStructure = ' '; // recognises H and E
+    public float value;
+
+    // add visual cues here
+    public Color colour = Color.black;
+
+    public Annotation(String displayChar, String desc, char ss, float val) {
+        displayCharacter = displayChar;
+        description = desc;
+        secondaryStructure = ss;
+        value = val;
+    }
+
+    public Annotation(String displayChar, String desc, char ss, float val,
+        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 cefbc22..850730b 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -15,167 +15,148 @@
 * 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
-{
-
-  Object element;
-  String name;
-  BinaryNode left;
-  BinaryNode right;
-  BinaryNode parent;
-  public int bootstrap;
-
-  public BinaryNode()
-  {
-    left = right = parent = null;
-    bootstrap = 0;
-  }
-
-  public BinaryNode(Object element, BinaryNode parent, String name)
-  {
-    this.element = element;
-    this.parent = parent;
-    this.name = name;
-
-    left = right = null;
-  }
-
-  public Object element()
-  {
-    return element;
-  }
-
-  public Object setElement(Object v)
-  {
-    return element = v;
-  }
-
-  public BinaryNode left()
-  {
-    return left;
-  }
-
-  public BinaryNode setLeft(BinaryNode n)
-  {
-    return left = n;
-  }
-
-  public BinaryNode right()
-  {
-    return right;
-  }
-
-  public BinaryNode setRight(BinaryNode n)
-  {
-    return right = n;
-  }
-
-  public BinaryNode parent()
-  {
-    return parent;
-  }
-
-  public BinaryNode setParent(BinaryNode n)
-  {
-    return parent = n;
-  }
-
-  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)
-    {
-      this.setLeft(leftchild);
-      leftchild.detach();
-      leftchild.setParent(this);
-
-    }
-    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)
-      {
-        this.parent.left = null;
-      }
-      else
-      {
-        if (this.parent.right == this)
-        {
-          this.parent.right = null;
-        }
-      }
-    }
-    this.parent = null;
-    return this;
-  }
-  /**
-   * Traverses up through the tree until a node with a free leftchild is discovered.
-   * @return BinaryNode
-   */
-  public BinaryNode ascendLeft() {
-    BinaryNode c = this;
-    do {
-      c = c.parent();
-    }  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() {
-    BinaryNode c = this;
-    do {
-      c = c.parent();
-    }  while (c!=null && c.right()!=null && !c.right().isLeaf());
-    return c;
-  }
-
-
-  public void setName(String name)
-  {
-    this.name = name;
-  }
-
-  public String getName()
-  {
-    return this.name;
-  }
-
-  public void setBootstrap(int boot)
-  {
-    this.bootstrap = boot;
-  }
-
-  public int getBootstrap()
-  {
-    return bootstrap;
-  }
-}
+*/
+package jalview.datamodel;
+
+public class BinaryNode {
+    Object element;
+    String name;
+    BinaryNode left;
+    BinaryNode right;
+    BinaryNode parent;
+    public int bootstrap;
+
+    public BinaryNode() {
+        left = right = parent = null;
+        bootstrap = 0;
+    }
+
+    public BinaryNode(Object element, BinaryNode parent, String name) {
+        this.element = element;
+        this.parent = parent;
+        this.name = name;
+
+        left = right = null;
+    }
+
+    public Object element() {
+        return element;
+    }
+
+    public Object setElement(Object v) {
+        return element = v;
+    }
+
+    public BinaryNode left() {
+        return left;
+    }
+
+    public BinaryNode setLeft(BinaryNode n) {
+        return left = n;
+    }
+
+    public BinaryNode right() {
+        return right;
+    }
+
+    public BinaryNode setRight(BinaryNode n) {
+        return right = n;
+    }
+
+    public BinaryNode parent() {
+        return parent;
+    }
+
+    public BinaryNode setParent(BinaryNode n) {
+        return parent = n;
+    }
+
+    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) {
+            this.setLeft(leftchild);
+            leftchild.detach();
+            leftchild.setParent(this);
+        }
+
+        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) {
+                this.parent.left = null;
+            } else {
+                if (this.parent.right == this) {
+                    this.parent.right = null;
+                }
+            }
+        }
+
+        this.parent = null;
+
+        return this;
+    }
+
+    /**
+ * Traverses up through the tree until a node with a free leftchild is discovered.
+ * @return BinaryNode
+ */
+    public BinaryNode ascendLeft() {
+        BinaryNode c = this;
+
+        do {
+            c = c.parent();
+        } 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() {
+        BinaryNode c = this;
+
+        do {
+            c = c.parent();
+        } while ((c != null) && (c.right() != null) && !c.right().isLeaf());
+
+        return c;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getName() {
+        return this.name;
+    }
+
+    public void setBootstrap(int boot) {
+        this.bootstrap = boot;
+    }
+
+    public int getBootstrap() {
+        return bootstrap;
+    }
+}
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 63c8d86..a351b04 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -16,96 +16,110 @@
 * 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.io.*;
 import jalview.analysis.PCA;
+
+import jalview.io.*;
+
 import jalview.jbgui.*;
+
 import jalview.schemes.*;
 
 import java.awt.*;
 
+
 public class BinarySequence extends Sequence {
-  int[] binary;
-  double[] dbinary;
-
-  public BinarySequence(SequenceI s) {
-    super(s.getName(),s.getSequence(),s.getStart(),s.getEnd());
-  }
-
-  public BinarySequence(String name, String sequence, int start, int end) {
-    super(name,sequence,start,end);
-  }
-
-  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++) {
-      dbinary[i] = 0.0;
+    int[] binary;
+    double[] dbinary;
+
+    public BinarySequence(SequenceI s) {
+        super(s.getName(), s.getSequence(), s.getStart(), s.getEnd());
+    }
+
+    public BinarySequence(String name, String sequence, int start, int end) {
+        super(name, sequence, start, end);
     }
 
-    for (int i=0; i < getSequence().length(); i++ ) {
-      int aanum = 20;
-      try {
-        aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();
-      } catch (NullPointerException e) {
-        aanum = 20;
-      }
-      if (aanum > 20) {
-        aanum = 20;
-      }
+    public void encode() {
+        // Set all matrix to 0
+        dbinary = new double[getSequence().length() * 21];
 
-      dbinary[i* nores + aanum] = 1.0;
+        int nores = 21;
 
+        for (int i = 0; i < dbinary.length; i++) {
+            dbinary[i] = 0.0;
+        }
+
+        for (int i = 0; i < getSequence().length(); i++) {
+            int aanum = 20;
+
+            try {
+                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
+                                                                         .substring(i,
+                            i + 1))).intValue();
+            } catch (NullPointerException e) {
+                aanum = 20;
+            }
+
+            if (aanum > 20) {
+                aanum = 20;
+            }
+
+            dbinary[(i * nores) + aanum] = 1.0;
+        }
     }
-  }
-
-  public void blosumEncode() {
-
-    // Set all matrix to 0
-    dbinary = new double[getSequence().length() * 21];
-    int nores = 21;
-    //for (int i = 0; i < dbinary.length; i++) {
-    //  dbinary[i] = 0.0;
-    //}
-
-    for (int i=0; i < getSequence().length(); i++ ) {
-      int aanum = 20;
-      try {
-        aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();
-      } catch (NullPointerException e) {
-        aanum = 20;
-      }
-      if (aanum > 20) {
-        aanum = 20;
-      }
-
-      // Do the blosum thing
-      for (int j = 0;j < 20;j++) {
-        dbinary[i * nores + j] = ResidueProperties.getBLOSUM62()[aanum][j];
-      }
 
+    public void blosumEncode() {
+        // Set all matrix to 0
+        dbinary = new double[getSequence().length() * 21];
+
+        int nores = 21;
+
+        //for (int i = 0; i < dbinary.length; i++) {
+        //  dbinary[i] = 0.0;
+        //}
+        for (int i = 0; i < getSequence().length(); i++) {
+            int aanum = 20;
+
+            try {
+                aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
+                                                                         .substring(i,
+                            i + 1))).intValue();
+            } catch (NullPointerException e) {
+                aanum = 20;
+            }
+
+            if (aanum > 20) {
+                aanum = 20;
+            }
+
+            // Do the blosum thing
+            for (int j = 0; j < 20; j++) {
+                dbinary[(i * nores) + j] = ResidueProperties.getBLOSUM62()[aanum][j];
+            }
+        }
     }
-  }
-
-  public String toBinaryString() {
-    String out = "";
-    for (int i=0; i < binary.length;i++) {
-      out += (new Integer(binary[i])).toString();
-      if (i < binary.length-1) {
-        out += " ";
-      }
+
+    public String toBinaryString() {
+        String out = "";
+
+        for (int i = 0; i < binary.length; i++) {
+            out += (new Integer(binary[i])).toString();
+
+            if (i < (binary.length - 1)) {
+                out += " ";
+            }
+        }
+
+        return out;
     }
-    return out;
-  }
 
-  public double[] getDBinary() {
-    return dbinary;
-  }
+    public double[] getDBinary() {
+        return dbinary;
+    }
 
-  public static void printMemory(Runtime rt) {
-    System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.
-  }
+    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 bb18b66..ed119e8 100755
--- a/src/jalview/datamodel/HistoryItem.java
+++ b/src/jalview/datamodel/HistoryItem.java
@@ -16,56 +16,54 @@
 * 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.*;
 
-public class HistoryItem
-{
-  public static final int EDIT = 0;
-  public static final int SORT = 1;
-  public static final int HIDE = 2;
-  public static final int PASTE= 3;
 
-  final int type;
-  Vector sequences;
-  Vector alignIndex;
-  String description;
-  Vector hiddenSeqs;
+public class HistoryItem {
+    public static final int EDIT = 0;
+    public static final int SORT = 1;
+    public static final int HIDE = 2;
+    public static final int PASTE = 3;
+    final int type;
+    Vector sequences;
+    Vector alignIndex;
+    String description;
+    Vector hiddenSeqs;
 
-  public HistoryItem(String description, AlignmentI al, int type)
-  {
-    this.type = type;
-    this.description = description;
-    sequences = new Vector();
-    alignIndex = new Vector();
-    hiddenSeqs = new Vector();
+    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++)
-    {
-      SequenceI seq = al.getSequenceAt(i);
-      sequences.addElement(seq);
-      alignIndex.addElement(i + "");
-      hiddenSeqs.addElement(seq.getSequence().toString());
+        for (int i = 0; i < al.getHeight(); i++) {
+            SequenceI seq = al.getSequenceAt(i);
+            sequences.addElement(seq);
+            alignIndex.addElement(i + "");
+            hiddenSeqs.addElement(seq.getSequence().toString());
+        }
     }
-  }
-
-  public int getType()
-  {return type;}
 
-  public Vector getSequences()
-  {return sequences;}
+    public int getType() {
+        return type;
+    }
 
-  public String getDescription()
-  {return description; }
+    public Vector getSequences() {
+        return sequences;
+    }
 
-  public Vector getHidden()
-  { return hiddenSeqs; }
+    public String getDescription() {
+        return description;
+    }
 
-  public int getAlignIndex(int seq)
-  {
-    return Integer.parseInt(alignIndex.elementAt(seq).toString());
-  }
+    public Vector getHidden() {
+        return hiddenSeqs;
+    }
 
+    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 d7f2b9f..3853af9 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -16,220 +16,241 @@
 * 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 MCview.*;
+
 import jalview.analysis.*;
+
 import java.awt.*;
+
 import java.util.*;
-import MCview.*;
 
 
-public class Sequence implements SequenceI
-{
-  protected String name;
-  protected String sequence;
-  protected String description;
-  protected int start;
-  protected int end;
-  protected String displayId;
-  protected Color color = Color.white;
-  String pdbId;
-
-   public Vector sequenceFeatures = new Vector();
-   public void setSequenceFeatures(Vector v)
-   {
-     sequenceFeatures = v;
-   }
-
-   public Vector getSequenceFeatures()
-   {return sequenceFeatures; }
-
-   public void setPDBId(String id)
-   {
-     pdbId = id;
-   }
-   public String getPDBId()
-   {
-     return pdbId;
-   }
-
-
-  public Sequence(String name, String sequence, int start, int end)
-  {
-
-    this.name     = name;
-    this.sequence = sequence;
-    this.start    = start;
-    this.end      = end;
-
-    setDisplayId();
-
-  }
-
-  public Sequence(String name,String sequence) {
-    this(name,sequence,1,sequence.length());
-  }
-  public Sequence(SequenceI seq) {
-    this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());
-  }
-  public String getDisplayId() {
-    return displayId;
-  }
-  public void setDisplayId() {
-    displayId = name + "/" + start + "-" + end;
-  }
-  public void setName(String name) {
-    this.name = name;
-    setDisplayId();
-  }
-  public String getName() {
-    return this.name;
-  }
-  public void setStart(int start) {
-    this.start = start;
-    setDisplayId();
-  }
-  public int getStart() {
-    return this.start;
-  }
-  public void setEnd(int end) {
-    this.end = end;
-    setDisplayId();
-  }
-  public int getEnd() {
-    return this.end;
-  }
-  public int getLength() {
-    return this.sequence.length();
-  }
-  public void setSequence(String seq) {
-    this.sequence = seq;
-  }
-  public String getSequence() {
-    return this.sequence;
-  }
-  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())
-      return "";
-
-    if(end>=sequence.length())
-      end = sequence.length();
-
-    return this.sequence.substring(start,end);
-  }
-
-  public char getCharAt(int i) {
-    if (i < sequence.length()) {
-      return sequence.charAt(i);
-    } else {
-      return ' ';
-    }
-  }
-  public void setDescription(String desc) {
-    this.description = desc;
-  }
-  public String getDescription() {
-    return this.description;
-  }
-
-  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) {
-
-      char c = sequence.charAt(i);
-
-      if (!jalview.util.Comparison.isGap((c)))
-        j++;
-
-      i++;
-    }
-    if (j == end && j < pos)
-      return end+1;
-    else
-      return i;
-
-  }
-
-  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())
-    {
-      char c = sequence.charAt(j);
-      if (!jalview.util.Comparison.isGap((c)))
-        pos++;
-
-      j++;
-    }
-    return pos;
-  }
-
-  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))) {
-        map[p++]=j;
-      }
-      j++;
-    }
-    return map;
-  }
-
-  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())
-      return;
-    if (j>=sequence.length())
-      sequence = sequence.substring(0,i);
-    else
-      sequence = sequence.substring(0,i) + sequence.substring(j);
-  }
-
-  public void insertCharAt(int i, char c)
-  {
-    insertCharAt(i,c,true);
-  }
-
-  public void insertCharAt(int i,char c,boolean chop) {
-
-    String tmp = new String(sequence);
-
-    if (i < sequence.length()) {
-      sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);
-    } 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()];
-      for (int j=0, k=ch.length; j<k; j++)
-        ch[j] = c;
-      sequence = tmp + String.valueOf(ch);
-    }
-
-  }
-
-  public void        setColor(Color c) {
-    this.color = c;
-  }
-
-  public Color       getColor() {
-    return color;
-  }
+public class Sequence implements SequenceI {
+    protected String name;
+    protected String sequence;
+    protected String description;
+    protected int start;
+    protected int end;
+    protected String displayId;
+    protected Color color = Color.white;
+    String pdbId;
+    public Vector sequenceFeatures = new Vector();
+
+    public Sequence(String name, String sequence, int start, int end) {
+        this.name = name;
+        this.sequence = sequence;
+        this.start = start;
+        this.end = end;
+
+        setDisplayId();
+    }
+
+    public Sequence(String name, String sequence) {
+        this(name, sequence, 1, sequence.length());
+    }
+
+    public Sequence(SequenceI seq) {
+        this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+    }
+
+    public void setSequenceFeatures(Vector v) {
+        sequenceFeatures = v;
+    }
+
+    public Vector getSequenceFeatures() {
+        return sequenceFeatures;
+    }
+
+    public void setPDBId(String id) {
+        pdbId = id;
+    }
+
+    public String getPDBId() {
+        return pdbId;
+    }
+
+    public String getDisplayId() {
+        return displayId;
+    }
+
+    public void setDisplayId() {
+        displayId = name + "/" + start + "-" + end;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+        setDisplayId();
+    }
+
+    public String getName() {
+        return this.name;
+    }
+
+    public void setStart(int start) {
+        this.start = start;
+        setDisplayId();
+    }
+
+    public int getStart() {
+        return this.start;
+    }
+
+    public void setEnd(int end) {
+        this.end = end;
+        setDisplayId();
+    }
+
+    public int getEnd() {
+        return this.end;
+    }
+
+    public int getLength() {
+        return this.sequence.length();
+    }
+
+    public void setSequence(String seq) {
+        this.sequence = seq;
+    }
+
+    public String getSequence() {
+        return this.sequence;
+    }
+
+    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()) {
+            return "";
+        }
+
+        if (end >= sequence.length()) {
+            end = sequence.length();
+        }
+
+        return this.sequence.substring(start, end);
+    }
+
+    public char getCharAt(int i) {
+        if (i < sequence.length()) {
+            return sequence.charAt(i);
+        } else {
+            return ' ';
+        }
+    }
+
+    public void setDescription(String desc) {
+        this.description = desc;
+    }
+
+    public String getDescription() {
+        return this.description;
+    }
+
+    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)) {
+            char c = sequence.charAt(i);
+
+            if (!jalview.util.Comparison.isGap((c))) {
+                j++;
+            }
+
+            i++;
+        }
+
+        if ((j == end) && (j < pos)) {
+            return end + 1;
+        } else {
+            return i;
+        }
+    }
+
+    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())) {
+            char c = sequence.charAt(j);
+
+            if (!jalview.util.Comparison.isGap((c))) {
+                pos++;
+            }
+
+            j++;
+        }
+
+        return pos;
+    }
+
+    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))) {
+                map[p++] = j;
+            }
+
+            j++;
+        }
+
+        return map;
+    }
+
+    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()) {
+            return;
+        }
+
+        if (j >= sequence.length()) {
+            sequence = sequence.substring(0, i);
+        } else {
+            sequence = sequence.substring(0, i) + sequence.substring(j);
+        }
+    }
 
+    public void insertCharAt(int i, char c) {
+        insertCharAt(i, c, true);
+    }
+
+    public void insertCharAt(int i, char c, boolean chop) {
+        String tmp = new String(sequence);
+
+        if (i < sequence.length()) {
+            sequence = tmp.substring(0, i) + String.valueOf(c) +
+                tmp.substring(i);
+        } 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()];
+
+            for (int j = 0, k = ch.length; j < k; j++)
+                ch[j] = c;
+
+            sequence = tmp + String.valueOf(ch);
+        }
+    }
+
+    public void setColor(Color c) {
+        this.color = c;
+    }
+
+    public Color getColor() {
+        return color;
+    }
 }
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index a2856fa..f7d8d89 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -16,85 +16,86 @@
 * 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 SequenceFeature {
-  int begin;
-  int end;
-  String type;
-  String description;
-  String status;
+    int begin;
+    int end;
+    String type;
+    String description;
+    String status;
 
-  public SequenceFeature()
-  {
-  }
+    public SequenceFeature() {
+    }
 
-  public SequenceFeature(String type, int start, int end, String description, String status)
-  {
-    this.type = type;
-    this.begin = start;
-    this.end = end;
-    this.description = description;
-    this.status = status;
-  }
+    public SequenceFeature(String type, int start, int end, String description,
+        String status) {
+        this.type = type;
+        this.begin = start;
+        this.end = end;
+        this.description = description;
+        this.status = status;
+    }
 
-  public int getStart() {
-    return begin;
-  }
-  public int getEnd() {
-    return end;
-  }
-  public String getType() {
-    return type;
-  }
-  public String getDescription() {
-    return description;
-  }
-  public String getStatus()
-  {return status;}
+    public int getStart() {
+        return begin;
+    }
 
+    public int getEnd() {
+        return end;
+    }
 
-/*
-      <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" />
-*/
+    public String getType() {
+        return type;
+    }
 
-}
+    public String getDescription() {
+        return description;
+    }
+
+    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" />
+    */
+}
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index d6ea5dd..0ae9ec2 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -16,272 +16,256 @@
 * 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.schemes.*;
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
-import java.util.Vector;
+
+import jalview.schemes.*;
+
 import java.awt.*;
 
-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(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)
-      startRes = startRes - col;
-    if(endRes>=col)
-    {
-      endRes = endRes - col;
-      if(startRes>endRes)
-        startRes = 0;
+import java.util.Vector;
+
+
+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(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) {
+            startRes = startRes - col;
+        }
+
+        if (endRes >= col) {
+            endRes = endRes - col;
+
+            if (startRes > endRes) {
+                startRes = 0;
+            }
+        } else {
+            // must delete this group!!
+            return false;
+        }
+
+        return true;
+    }
+
+    public boolean adjustForRemoveRight(int col) {
+        if (startRes > col) {
+            // delete this group
+            return false;
+        }
+
+        if (endRes >= col) {
+            endRes = col;
+        }
+
+        return true;
+    }
+
+    public String getName() {
+        return groupName;
+    }
+
+    public void setName(String name) {
+        groupName = name;
+    }
+
+    public Conservation getConservation() {
+        return conserve;
+    }
+
+    public void setConservation(Conservation c) {
+        conserve = c;
+    }
+
+    public void addSequence(SequenceI s) {
+        if (!sequences.contains(s)) {
+            sequences.addElement(s);
+        }
+
+        if (cs != null) {
+            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+        }
+
+        if (cs instanceof ConservationColourScheme) {
+            recalcConservation();
+        }
+    }
+
+    void recalcConservation() {
+        Conservation c = new Conservation(groupName,
+                ResidueProperties.propHash, 3, sequences, 0, getWidth());
+        c.calculate();
+        c.verdict(false, 25);
+
+        ConservationColourScheme ccs = (ConservationColourScheme) cs;
+        ccs.conserve = c;
     }
-    else
-    {
-        // must delete this group!!
-        return false;
+
+    public void addOrRemove(SequenceI s) {
+        if (sequences.contains(s)) {
+            deleteSequence(s);
+        } else {
+            addSequence(s);
+        }
+    }
+
+    public void deleteSequence(SequenceI s) {
+        sequences.removeElement(s);
+
+        if (cs != null) {
+            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+        }
+
+        if (cs instanceof ConservationColourScheme) {
+            recalcConservation();
+        }
+    }
+
+    public int getStartRes() {
+        return startRes;
+    }
+
+    public int getEndRes() {
+        return endRes;
+    }
+
+    public void setStartRes(int i) {
+        startRes = i;
     }
 
-    return true;
-  }
+    public void setEndRes(int i) {
+        endRes = i;
+    }
 
-  public boolean adjustForRemoveRight(int col)
-  {
+    public int getSize() {
+        return sequences.size();
+    }
 
-    if(startRes>col)
-    {
-      // delete this group
-      return false;
+    public SequenceI getSequenceAt(int i) {
+        return (SequenceI) sequences.elementAt(i);
     }
 
-    if(endRes>=col)
-      endRes = col;
-
-    return true;
-  }
-
-
-  public String getName()
-  {
-    return groupName;
-  }
-
-  public void setName(String name)
-  {
-    groupName = name;
-  }
-
-  public Conservation getConservation()
-  {
-    return conserve;
-  }
-
-  public void setConservation(Conservation c)
-  {
-    conserve = c;
-  }
-
-  public void addSequence(SequenceI s)
-  {
-    if(!sequences.contains(s))
-      sequences.addElement(s);
-
-
-    if(cs!=null)
-      cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );
-
-    if(cs instanceof ConservationColourScheme)
-      recalcConservation();
-  }
-
-  void recalcConservation()
-  {
-      Conservation c = new Conservation(groupName,
-                                        ResidueProperties.propHash, 3,
-                                        sequences, 0, getWidth());
-      c.calculate();
-      c.verdict(false, 25);
-      ConservationColourScheme ccs = (ConservationColourScheme)cs;
-      ccs.conserve = c;
-  }
-
-  public void addOrRemove(SequenceI s)
-  {
-    if(sequences.contains(s))
-      deleteSequence(s);
-    else
-      addSequence(s);
-  }
-
-  public void deleteSequence(SequenceI s)
-  {
-    sequences.removeElement(s);
-
-    if(cs!=null)
-      cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );
-
-    if(cs instanceof ConservationColourScheme)
-      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)
-      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();
+    public void setColourText(boolean state) {
+        colourText = state;
     }
-    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(Alignment al) {
-    int sz;
-    java.util.Hashtable orderedSeqs = new java.util.Hashtable();
-    SequenceI[] seqs=new SequenceI[sz=sequences.size()];
-    for(int i=0; i<sz; i++)
-    {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
-      int index = al.findIndex(seq);
-      orderedSeqs.put(index+"", seq);
+
+    public boolean getColourText() {
+        return colourText;
     }
 
-    int index=0;
-    for(int i=0; i<sz; i++) {
-      SequenceI seq = null;
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
-        {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-          break;
+    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) {
+            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();
+            }
         }
-        else
-          index++;
-      }
-      seqs[index] = seq;
+
+        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(Alignment al) {
+        int sz;
+        java.util.Hashtable orderedSeqs = new java.util.Hashtable();
+        SequenceI[] seqs = new SequenceI[sz = sequences.size()];
+
+        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 < sz; i++) {
+            SequenceI seq = null;
+
+            while (seq == null) {
+                if (orderedSeqs.containsKey(index + "")) {
+                    seq = (SequenceI) orderedSeqs.get(index + "");
+                    index++;
+
+                    break;
+                } else {
+                    index++;
+                }
+            }
+
+            seqs[index] = seq;
+        }
+
+        return seqs;
     }
-    return seqs;
-  }
 }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 9c2ab48..f16c009 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -16,62 +16,67 @@
 * 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 {
-  public void        setName(String name);
-  public String      getName();
+    public void setName(String name);
+
+    public String getName();
+
+    public void setStart(int start);
+
+    public int getStart();
+
+    public String getDisplayId();
 
-  public void        setStart(int start);
-  public int         getStart();
+    public void setEnd(int end);
 
-  public String      getDisplayId();
+    public int getEnd();
 
-  public void        setEnd(int end);
-  public int         getEnd();
+    public int getLength();
 
-  public int         getLength();
+    public void setSequence(String sequence);
 
-  public void        setSequence(String sequence);
-  public String      getSequence();
-  public String      getSequence(int start,int end);
-  public char        getCharAt(int i);
+    public String getSequence();
 
-  public void        setDescription(String desc);
-  public String      getDescription();
+    public String getSequence(int start, int end);
 
-  public int         findIndex(int pos);
-  public int         findPosition(int i);
-  public int[]         gapMap();
-  public void       deleteChars(int i, int j);
-  public void       deleteCharAt(int i);
-  public void       insertCharAt(int i, char c);
-  public void       insertCharAt(int i,char c,boolean chop);
+    public char getCharAt(int i);
 
-  public void        setColor(Color c);
-  public Color       getColor();
+    public void setDescription(String desc);
 
-  public Vector     getSequenceFeatures();
-  public void       setSequenceFeatures(Vector v);
+    public String getDescription();
 
-  public void setPDBId(String id);
-  public String getPDBId();
+    public int findIndex(int pos);
 
-  }
+    public int findPosition(int i);
 
+    public int[] gapMap();
 
+    public void deleteChars(int i, int j);
 
+    public void deleteCharAt(int i);
 
+    public void insertCharAt(int i, char c);
 
+    public void insertCharAt(int i, char c, boolean chop);
 
+    public void setColor(Color c);
 
+    public Color getColor();
 
+    public Vector getSequenceFeatures();
 
+    public void setSequenceFeatures(Vector v);
 
+    public void setPDBId(String id);
 
+    public String getPDBId();
+}
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 74776ea..f86c63e 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -16,73 +16,73 @@
 * 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 {
+    public float dist;
+    public int count;
+    public float height;
+    public float ycount;
+    public Color color = Color.black;
+    public boolean dummy = false;
+    private boolean placeholder = false;
+
+    public SequenceNode() {
+        super();
+    }
 
-  public float dist;
-  public int count;
-  public float height;
-  public float ycount;
-  public Color color = Color.black;
-  public boolean dummy = false;
-  private boolean placeholder = false;
+    public SequenceNode(Object val, SequenceNode parent, float dist, String name) {
+        super(val, parent, name);
+        this.dist = dist;
+    }
 
-  public SequenceNode() {
-    super();
-  }
+    public SequenceNode(Object val, SequenceNode parent, String name,
+        float dist, int bootstrap, boolean dummy) {
+        super(val, parent, name);
+        this.dist = dist;
+        this.bootstrap = bootstrap;
+        this.dummy = dummy;
+    }
 
-  public SequenceNode(Object val, SequenceNode parent, float dist,String name) {
-    super(val,parent,name);
-    this.dist = dist;
-  }
-  public SequenceNode(Object val, SequenceNode parent, String name, float dist, int bootstrap, boolean dummy) {
-    super(val,parent,name);
-    this.dist = dist;
-    this.bootstrap = bootstrap;
-    this.dummy = dummy;
-  }
+    /**
+     * @param dummy true if node is created for the representation of polytomous trees
+     */
+    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() {
+        return placeholder;
+    }
 
-  /**
-   * @param dummy true if node is created for the representation of polytomous trees
-   */
+    public boolean setDummy(boolean newstate) {
+        boolean oldstate = dummy;
+        dummy = newstate;
 
-  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()
-  {
-    return placeholder;
-  }
+        return oldstate;
+    }
 
-  public boolean setDummy(boolean newstate) {
-    boolean oldstate = dummy;
-    dummy = newstate;
-    return oldstate;
-  }
+    public void setPlaceholder(boolean Placeholder) {
+        this.placeholder = Placeholder;
+    }
 
-  public void setPlaceholder(boolean Placeholder)
-  {
-    this.placeholder = Placeholder;
-  }
+    /**
+     * 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() {
+        SequenceNode c = this;
 
-  /**
-   * 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.
-   */
+        do {
+            c = (SequenceNode) c.parent();
+        } while ((c != null) && c.dummy);
 
-  public SequenceNode AscendTree() {
-    SequenceNode c = this;
-    do {
-      c = (SequenceNode) c.parent();
-    } while (c!=null && c.dummy);
-    return c;
-  }
+        return c;
+    }
 }
diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 5da4d64..fa91e59 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -16,22 +16,21 @@
 * 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.*;
-import java.awt.*;
 
+import java.awt.*;
 
-public class SequencePoint {
+import java.util.*;
 
-  // SMJS PUBLIC
-  public SequenceI sequence;
-  public float[] coord;
-  // SMJS ENDPUBLIC
 
-  public SequencePoint(SequenceI sequence, float[] coord) {
-    this.sequence = sequence;
-    this.coord = coord;
-  }
+public class SequencePoint {
+    // SMJS PUBLIC
+    public SequenceI sequence;
+    public float[] coord;
 
+    // SMJS ENDPUBLIC
+    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 cd86ef6..ad6f703 100755
--- a/src/jalview/datamodel/SuperGroup.java
+++ b/src/jalview/datamodel/SuperGroup.java
@@ -16,99 +16,88 @@
 * 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.schemes.*;
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
+
+import jalview.schemes.*;
+
 import java.util.*;
 
-public class SuperGroup
-{
-  String groupName;
-  boolean displayBoxes;
-  boolean displayText;
-  boolean colourText;
-  public ColourSchemeI cs;
-  Vector sequenceGroups = new Vector();
-
-  public SuperGroup()
-  {
-    groupName = "Super group";
-    this.displayBoxes = true;
-    this.displayText = true;
-    this.colourText = false;
-    cs = null;
-  }
-
-
-  public SuperGroup(String groupName, ColourSchemeI scheme,
-                       boolean displayBoxes, boolean displayText,
-                       boolean colourText)
-     {
-       this.groupName = groupName;
-       this.displayBoxes = displayBoxes;
-       this.displayText = displayText;
-       this.colourText = colourText;
-       this.cs = scheme;
-     }
-
-  public String getName()
-  {
-    return groupName;
-  }
-
-  public void setName(String name)
-  {
-    groupName = name;
-  }
-
-
-  public void addGroup(SequenceGroup sg)
-  {
-    if(!sequenceGroups.contains(sg))
-      sequenceGroups.addElement(sg);
-  }
-
-  public void addOrRemove(SequenceGroup sg)
-  {
-    if(sequenceGroups.contains(sg))
-      deleteGroup(sg);
-    else
-      addGroup(sg);
-  }
-
-  public void deleteGroup(SequenceGroup sg)
-  {
-    sequenceGroups.removeElement(sg);
-  }
-
-  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++)
-    {
-      SequenceGroup temp = (SequenceGroup)sequenceGroups.elementAt(i);
-      temp.cs = sg.cs;
-      temp.colourText = sg.colourText;
-      temp.displayText = sg.displayText;
-      temp.displayBoxes = sg.displayBoxes;
+
+public class SuperGroup {
+    String groupName;
+    boolean displayBoxes;
+    boolean displayText;
+    boolean colourText;
+    public ColourSchemeI cs;
+    Vector sequenceGroups = new Vector();
+
+    public SuperGroup() {
+        groupName = "Super group";
+        this.displayBoxes = true;
+        this.displayText = true;
+        this.colourText = false;
+        cs = null;
+    }
+
+    public SuperGroup(String groupName, ColourSchemeI scheme,
+        boolean displayBoxes, boolean displayText, boolean colourText) {
+        this.groupName = groupName;
+        this.displayBoxes = displayBoxes;
+        this.displayText = displayText;
+        this.colourText = colourText;
+        this.cs = scheme;
+    }
+
+    public String getName() {
+        return groupName;
     }
-  }
 
+    public void setName(String name) {
+        groupName = name;
+    }
+
+    public void addGroup(SequenceGroup sg) {
+        if (!sequenceGroups.contains(sg)) {
+            sequenceGroups.addElement(sg);
+        }
+    }
 
-  public int getSize()
-  {
-    return sequenceGroups.size();
-  }
+    public void addOrRemove(SequenceGroup sg) {
+        if (sequenceGroups.contains(sg)) {
+            deleteGroup(sg);
+        } else {
+            addGroup(sg);
+        }
+    }
+
+    public void deleteGroup(SequenceGroup sg) {
+        sequenceGroups.removeElement(sg);
+    }
 
-  public SequenceGroup getGroupeAt(int i)
-  {
-    return (SequenceGroup) sequenceGroups.elementAt(i);
-  }
+    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++) {
+            SequenceGroup temp = (SequenceGroup) sequenceGroups.elementAt(i);
+            temp.cs = sg.cs;
+            temp.colourText = sg.colourText;
+            temp.displayText = sg.displayText;
+            temp.displayBoxes = sg.displayBoxes;
+        }
+    }
+
+    public int getSize() {
+        return sequenceGroups.size();
+    }
+
+    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 8cb12d1..9bc4bc0 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,1388 +1,1630 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import java.awt.print.*;
-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.*;
-import java.beans.PropertyChangeEvent;
-
-public class AlignFrame extends GAlignFrame
-{
-  final AlignmentPanel alignPanel;
-  final AlignViewport viewport;
-  public static final int NEW_WINDOW_WIDTH = 700;
-  public static final int NEW_WINDOW_HEIGHT = 500;
-  public String currentFileFormat = "Jalview";
-
-  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();    }
-          });
-
-     }
-   });
-
-  }
-
-  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)
-    {
-      currentFileFormat  = chooser.getSelectedFormat();
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat);
-
-      if (currentFileFormat.equals("Jalview"))
-      {
-        String shortName = title;
-        if(shortName.indexOf(java.io.File.separatorChar)>-1)
-              shortName = shortName.substring(
-                    shortName.lastIndexOf(java.io.File.separatorChar)+1);
-
-        String choice = chooser.getSelectedFile().getPath();
-        Jalview2XML.SaveState(this, choice, 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();
-      }
-      catch(Exception ex){}
-    }
-
-  }
-
-  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();
-  }
-
-  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();
-        }
-      }
-    }
-
-  }
-
-
-
-
-  public void closeMenuItem_actionPerformed(ActionEvent e)
-  {
-    try{
-      this.setClosed(true);
-    }catch(Exception ex){}
-  }
-
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
-  private int treeCount = 0;
-
-  void updateEditMenuBar()
-   {
-     if(historyList.size()>0)
-      {
-        undoMenuItem.setEnabled(true);
-        HistoryItem hi = (HistoryItem)historyList.peek();
-        undoMenuItem.setText("Undo "+hi.getDescription());
-      }
-     else
-     {
-       undoMenuItem.setEnabled(false);
-       undoMenuItem.setText("Undo");
-     }
-
-     if(redoList.size()>0)
-      {
-        redoMenuItem.setEnabled(true);
-        HistoryItem hi = (HistoryItem)redoList.peek();
-        redoMenuItem.setText("Redo "+hi.getDescription());
-      }
-     else
-     {
-       redoMenuItem.setEnabled(false);
-       redoMenuItem.setText("Redo");
-     }
-   }
-
-   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)
-      {
-           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());
-  }
-
-  public void moveSelectedSequences(boolean up)
-  {
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg == null)
-      return;
-
-    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))
-          continue;
-
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i - 1);
-      }
-    }
-    else
-    {
-      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);
-      }
-    }
-
-    alignPanel.repaint();
-  }
-
-
-
-  protected void copy_actionPerformed(ActionEvent e)
-  {
-     if(viewport.getSelectionGroup()==null)
-       return;
-
-     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++)
-     {
-        SequenceI seq = sg.getSequenceAt(i);
-        int index = viewport.alignment.findIndex(seq);
-        orderedSeqs.put(index+"", seq);
-     }
-
-     int index=0;
-     for(int i=0; i<sg.getSize(); i++)
-     {
-       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");
-     }
-     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);
-  }
-
-  void paste(boolean newAlignment)
-  {
-    try{
-      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();
-      }
-
-    }catch(Exception ex){}// could be anything being pasted in here
-
-  }
-
-
-  protected void cut_actionPerformed(ActionEvent e)
-  {
-    copy_actionPerformed(null);
-    delete_actionPerformed(null);
-  }
-
-  protected void delete_actionPerformed(ActionEvent e)
-  {
-    boolean seqsdeleted=false;
-
-    if (viewport.getSelectionGroup() == null)
-      return;
-
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
-
-     SequenceGroup sg = viewport.getSelectionGroup();
-     for (int i=0;i < sg.sequences.size(); i++)
-     {
-       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);
-       }
-     }
-
-     viewport.setSelectionGroup(null);
-     viewport.alignment.deleteGroup(sg);
-     if (seqsdeleted)
-       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-     viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
-     if(viewport.getAlignment().getHeight()<1)
-     try
-     {
-       this.setClosed(true);
-     }catch(Exception ex){}
-   viewport.updateConservation();
-   viewport.updateConsensus();
-   alignPanel.repaint();
- }
-
-
-  protected void deleteGroups_actionPerformed(ActionEvent e)
-  {
-    viewport.alignment.deleteAllGroups();
-    viewport.setSelectionGroup(null);
-    alignPanel.repaint();
-  }
-
-
-
-  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = new SequenceGroup();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
-    sg.setEndRes(viewport.alignment.getWidth());
-    viewport.setSelectionGroup(sg);
-    PaintRefresher.Refresh(null);
-  }
-
-  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setSelectionGroup(null);
-    viewport.getColumnSelection().clear();
-    viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(null);
-  }
-
-  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = viewport.getSelectionGroup();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
-
-    PaintRefresher.Refresh(null);
-  }
-
-  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
-  {
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
-    {
-      addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
-                                     HistoryItem.HIDE));
-      int min = colSel.getMin();
-      viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0,min);
-
-      if(viewport.getSelectionGroup()!=null)
-        viewport.getSelectionGroup().adjustForRemoveLeft(min);
-
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
-        if(!sg.adjustForRemoveLeft(min))
-          viewport.alignment.deleteGroup(sg);
-      }
-
-      alignPanel.repaint();
-    }
-  }
-
-  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
-  {
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
-    {
-      addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
-                                     HistoryItem.HIDE));
-
-      int max = colSel.getMax();
-      viewport.getAlignment().trimRight(max);
-      if(viewport.getSelectionGroup()!=null)
-        viewport.getSelectionGroup().adjustForRemoveRight(max);
-
-      Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
-        if(!sg.adjustForRemoveRight(max))
-          viewport.alignment.deleteGroup(sg);
-      }
-
-
-
-      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();
-  }
-
-  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("Remove Gaps",
-                                   viewport.alignment,
-                                   HistoryItem.HIDE));
-    SequenceI current;
-    int jSize;
-    for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
-    {
-      current = viewport.getAlignment().getSequenceAt(i);
-      jSize = current.getLength();
-      for (int j=0; j < jSize; j++)
-        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
-        {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
-        }
-    }
-    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()-1;
-      for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
-      {
-        current = viewport.getAlignment().getSequenceAt(i);
-
-        if (current.getLength()<Width)
-          current.insertCharAt(Width, viewport.getGapCharacter());
-      }
-      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)
-      ( (ResidueColourScheme) cs).setThreshold(0);
-    else if (cs instanceof ScoreColourScheme)
-      ( (ScoreColourScheme) cs).setThreshold(0);
-
-
-
-    if (viewport.getConservationSelected())
-    {
-      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);
-
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus( viewport.vconsensus );
-      viewport.setGlobalColourScheme(ccs);
-
-      ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
-
-    }
-    else
-    {
-        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-        if (cs != null)
-          cs.setConsensus(viewport.vconsensus);
-        viewport.setGlobalColourScheme(cs);
-    }
-
-
-    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();
-  }
-
-  protected void modifyPID_actionPerformed(ActionEvent e)
-  {
-      if(viewport.getAbovePIDThreshold())
-      {
-        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
-                                   "Background");
-        SliderPanel.showPIDSlider();
-      }
-  }
-
-  protected void modifyConservation_actionPerformed(ActionEvent e)
-  {
-    if(viewport.getConservationSelected())
-    {
-      SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
-                                        "Background");
-      SliderPanel.showConservationSlider();
-    }
-  }
-
-
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.setConservationSelected(conservationMenuItem.isSelected());
-
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setSelected(false);
-
-   ColourSchemeI cs = viewport.getGlobalColourScheme();
-   if(cs instanceof ConservationColourScheme )
-     changeColour( ((ConservationColourScheme)cs).cs );
-    else
-      changeColour( cs );
-
-    modifyConservation_actionPerformed(null);
-  }
-
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)
-  {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
-    conservationMenuItem.setSelected(false);
-    viewport.setConservationSelected(false);
-
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if(cs instanceof ConservationColourScheme )
-        changeColour( ((ConservationColourScheme)cs).cs );
-    else
-        changeColour( cs );
-
-    modifyPID_actionPerformed(null);
-  }
-
-
-
-  public void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    new UserDefinedColours( alignPanel, null);
-  }
-
-  public void PIDColour_actionPerformed(ActionEvent e)
-  {
-    changeColour( new PIDColourScheme() );
-  }
-
-
-  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new Blosum62ColourScheme() );
-  }
-
-
-
-  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();
-  }
-
-  public void sortIDMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
-    AlignmentSorter.sortByID( viewport.getAlignment() );
-    alignPanel.repaint();
-  }
-
-  public void sortGroupMenuItem_actionPerformed(ActionEvent e)
-  {
-    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
-  //  AlignmentSorter.sortByGroup(viewport.getAlignment());
-    AlignmentSorter.sortGroups(viewport.getAlignment());
-    alignPanel.repaint();
-  }
-
-  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);
-
-  }
-
-  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);
-    else
-    {
-      JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(new PairwiseAlignPanel(viewport));
-      Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
-    }
-  }
-
-  public void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-
-    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);
-      return;
-    }
-
-    try{
-      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)
-  {
-    String ltitle;
-    final TreePanel tp;
-    if (viewport.getSelectionGroup() != null &&
-        viewport.getSelectionGroup().getSize() > 3)
-    {
-      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);
-  }
-
-  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()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
-                                       HistoryItem.SORT));
-        // TODO: JBPNote - have to map order entries to curent SequenceI pointers
-        AlignmentSorter.sortBy(viewport.getAlignment(), order);
-        alignPanel.repaint();
-      }
-    });
-  }
-
-  void addTreeMenuItem(final TreePanel treePanel, String title)
-  {
-    final JMenuItem item = new JMenuItem(title);
-
-    treeCount++;
-
-    if (treeCount==1)
-      sort.add(sortByTreeMenu);
-
-    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();
-        }
-      }
-
-    }
-    );
-  }
-
-
-  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();
-
-          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) {
-          jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, false, true);
-        }
-  }
-  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)
-        {
-          // 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();
-
-          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) {
-          jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
-        }
-  }
-
-
-  protected void jpred_actionPerformed(ActionEvent e)
-{
-    SequenceI seq=null;
-    SequenceI[] msa=null;
-
-    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);
-        }
-      }
-    }
-    if (msa!=null) {
-      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");
-    }
-  }
-  protected void msaAlignMenuItem_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();
-
-        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) {
-        MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, false, true);
-      }
-  }
-    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");
-    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");
-        ShowNewickTree(fin, choice);
-      }
-      catch (Exception ex)
-      {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                                      "Problem reading tree file",
-                                      ex.getMessage(),
-                                      JOptionPane.WARNING_MESSAGE);
-        ex.printStackTrace();
-      }
-    }
-  }
-
-  public void ShowNewickTree(NewickFile nf, String title)
-  {
-    try{
-      nf.parse();
-      if (nf.getTree() != null)
-      {
-        TreePanel tp = new TreePanel(viewport,
-                                     viewport.getAlignment().getSequences(),
-                                     nf, "FromFile", title);
-        Desktop.addInternalFrame(tp, title, 600, 500);
-        addTreeMenuItem(tp, title);
-        viewport.setCurrentTree(tp.getTree());
-      }
-     }catch(Exception ex){ex.printStackTrace();}
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.beans.*;
+import java.util.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.event.*;
+import java.awt.print.*;
+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
+{
+  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()
+        {
+          public void run()
+          {
+            alignPanel.requestFocus();
+          }
+        });
+      }
+    });
+  }
+
+  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)
+    {
+      currentFileFormat = chooser.getSelectedFormat();
+      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+                                    currentFileFormat);
+
+      if (currentFileFormat.equals("Jalview"))
+      {
+        String shortName = title;
+
+        if (shortName.indexOf(java.io.File.separatorChar) > -1)
+        {
+          shortName = shortName.substring(shortName.lastIndexOf(
+              java.io.File.separatorChar) + 1);
+        }
+
+        String choice = chooser.getSelectedFile().getPath();
+        Jalview2XML.SaveState(this, choice, 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();
+      }
+      catch (Exception ex)
+      {
+      }
+    }
+  }
+
+  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
+    {
+      this.setClosed(true);
+    }
+    catch (Exception ex)
+    {
+    }
+  }
+
+  void updateEditMenuBar()
+  {
+    if (historyList.size() > 0)
+    {
+      undoMenuItem.setEnabled(true);
+
+      HistoryItem hi = (HistoryItem) historyList.peek();
+      undoMenuItem.setText("Undo " + hi.getDescription());
+    }
+    else
+    {
+      undoMenuItem.setEnabled(false);
+      undoMenuItem.setText("Undo");
+    }
+
+    if (redoList.size() > 0)
+    {
+      redoMenuItem.setEnabled(true);
+
+      HistoryItem hi = (HistoryItem) redoList.peek();
+      redoMenuItem.setText("Redo " + hi.getDescription());
+    }
+    else
+    {
+      redoMenuItem.setEnabled(false);
+      redoMenuItem.setText("Redo");
+    }
+  }
+
+  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)
+    {
+      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());
+  }
+
+  public void moveSelectedSequences(boolean up)
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
+
+    if (sg == null)
+    {
+      return;
+    }
+
+    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))
+        {
+          continue;
+        }
+
+        viewport.alignment.getSequences().setElementAt(temp, i);
+        viewport.alignment.getSequences().setElementAt(seq, i - 1);
+      }
+    }
+    else
+    {
+      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);
+      }
+    }
+
+    alignPanel.repaint();
+  }
+
+  protected void copy_actionPerformed(ActionEvent e)
+  {
+    if (viewport.getSelectionGroup() == null)
+    {
+      return;
+    }
+
+    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++)
+    {
+      SequenceI seq = sg.getSequenceAt(i);
+      int index = viewport.alignment.findIndex(seq);
+      orderedSeqs.put(index + "", seq);
+    }
+
+    int index = 0;
+
+    for (int i = 0; i < sg.getSize(); i++)
+    {
+      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");
+    }
+
+    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);
+  }
+
+  void paste(boolean newAlignment)
+  {
+    try
+    {
+      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();
+      }
+    }
+    catch (Exception ex)
+    {
+    }
+
+    // could be anything being pasted in here
+  }
+
+  protected void cut_actionPerformed(ActionEvent e)
+  {
+    copy_actionPerformed(null);
+    delete_actionPerformed(null);
+  }
+
+  protected void delete_actionPerformed(ActionEvent e)
+  {
+    boolean seqsdeleted = false;
+
+    if (viewport.getSelectionGroup() == null)
+    {
+      return;
+    }
+
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+                                   HistoryItem.HIDE));
+
+    SequenceGroup sg = viewport.getSelectionGroup();
+
+    for (int i = 0; i < sg.sequences.size(); i++)
+    {
+      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);
+      }
+    }
+
+    viewport.setSelectionGroup(null);
+    viewport.alignment.deleteGroup(sg);
+
+    if (seqsdeleted)
+    {
+      viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+    }
+
+    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
+
+    if (viewport.getAlignment().getHeight() < 1)
+    {
+      try
+      {
+        this.setClosed(true);
+      }
+      catch (Exception ex)
+      {
+      }
+    }
+
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
+  }
+
+  protected void deleteGroups_actionPerformed(ActionEvent e)
+  {
+    viewport.alignment.deleteAllGroups();
+    viewport.setSelectionGroup(null);
+    alignPanel.repaint();
+  }
+
+  public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = new SequenceGroup();
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
+    {
+      sg.addSequence(viewport.getAlignment().getSequenceAt(i));
+    }
+
+    sg.setEndRes(viewport.alignment.getWidth());
+    viewport.setSelectionGroup(sg);
+    PaintRefresher.Refresh(null);
+  }
+
+  public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setSelectionGroup(null);
+    viewport.getColumnSelection().clear();
+    viewport.setSelectionGroup(null);
+    PaintRefresher.Refresh(null);
+  }
+
+  public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = viewport.getSelectionGroup();
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
+    {
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));
+    }
+
+    PaintRefresher.Refresh(null);
+  }
+
+  public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+  {
+    ColumnSelection colSel = viewport.getColumnSelection();
+
+    if (colSel.size() > 0)
+    {
+      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
+                                     HistoryItem.HIDE));
+
+      int min = colSel.getMin();
+      viewport.getAlignment().trimLeft(min);
+      colSel.compensateForEdit(0, min);
+
+      if (viewport.getSelectionGroup() != null)
+      {
+        viewport.getSelectionGroup().adjustForRemoveLeft(min);
+      }
+
+      Vector groups = viewport.alignment.getGroups();
+
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+
+        if (!sg.adjustForRemoveLeft(min))
+        {
+          viewport.alignment.deleteGroup(sg);
+        }
+      }
+
+      alignPanel.repaint();
+    }
+  }
+
+  public void remove2RightMenuItem_actionPerformed(ActionEvent e)
+  {
+    ColumnSelection colSel = viewport.getColumnSelection();
+
+    if (colSel.size() > 0)
+    {
+      addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
+                                     HistoryItem.HIDE));
+
+      int max = colSel.getMax();
+      viewport.getAlignment().trimRight(max);
+
+      if (viewport.getSelectionGroup() != null)
+      {
+        viewport.getSelectionGroup().adjustForRemoveRight(max);
+      }
+
+      Vector groups = viewport.alignment.getGroups();
+
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+
+        if (!sg.adjustForRemoveRight(max))
+        {
+          viewport.alignment.deleteGroup(sg);
+        }
+      }
+
+      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();
+  }
+
+  public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
+                                   HistoryItem.HIDE));
+
+    SequenceI current;
+    int jSize;
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
+    {
+      current = viewport.getAlignment().getSequenceAt(i);
+      jSize = current.getLength();
+
+      for (int j = 0; j < jSize; j++)
+      {
+        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
+        {
+          current.deleteCharAt(j);
+          j--;
+          jSize--;
+        }
+      }
+    }
+
+    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() - 1;
+
+    for (int i = 0; i < viewport.getAlignment().getSequences().size();
+         i++)
+    {
+      current = viewport.getAlignment().getSequenceAt(i);
+
+      if (current.getLength() < Width)
+      {
+        current.insertCharAt(Width, viewport.getGapCharacter());
+      }
+    }
+
+    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)
+    {
+      ( (ResidueColourScheme) cs).setThreshold(0);
+    }
+    else if (cs instanceof ScoreColourScheme)
+    {
+      ( (ScoreColourScheme) cs).setThreshold(0);
+    }
+
+    if (viewport.getConservationSelected())
+    {
+      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);
+
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      ccs.setConsensus(viewport.vconsensus);
+      viewport.setGlobalColourScheme(ccs);
+
+      ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
+                                                  "Background");
+    }
+    else
+    {
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      if (cs != null)
+      {
+        cs.setConsensus(viewport.vconsensus);
+      }
+
+      viewport.setGlobalColourScheme(cs);
+    }
+
+    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();
+  }
+
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+    if (viewport.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(alignPanel,
+                                     viewport.getGlobalColourScheme(),
+                                     "Background");
+      SliderPanel.showPIDSlider();
+    }
+  }
+
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+    if (viewport.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(alignPanel,
+                                        viewport.globalColourScheme,
+                                        "Background");
+      SliderPanel.showConservationSlider();
+    }
+  }
+
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
+
+    viewport.setAbovePIDThreshold(false);
+    abovePIDThreshold.setSelected(false);
+
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
+
+    if (cs instanceof ConservationColourScheme)
+    {
+      changeColour( ( (ConservationColourScheme) cs).cs);
+    }
+    else
+    {
+      changeColour(cs);
+    }
+
+    modifyConservation_actionPerformed(null);
+  }
+
+  public void abovePIDThreshold_actionPerformed(ActionEvent e)
+  {
+    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+
+    conservationMenuItem.setSelected(false);
+    viewport.setConservationSelected(false);
+
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
+
+    if (cs instanceof ConservationColourScheme)
+    {
+      changeColour( ( (ConservationColourScheme) cs).cs);
+    }
+    else
+    {
+      changeColour(cs);
+    }
+
+    modifyPID_actionPerformed(null);
+  }
+
+  public void userDefinedColour_actionPerformed(ActionEvent e)
+  {
+    new UserDefinedColours(alignPanel, null);
+  }
+
+  public void PIDColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new PIDColourScheme());
+  }
+
+  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new Blosum62ColourScheme());
+  }
+
+  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();
+  }
+
+  public void sortIDMenuItem_actionPerformed(ActionEvent e)
+  {
+    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+                                   HistoryItem.SORT));
+    AlignmentSorter.sortByID(viewport.getAlignment());
+    alignPanel.repaint();
+  }
+
+  public void sortGroupMenuItem_actionPerformed(ActionEvent e)
+  {
+    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+                                   HistoryItem.SORT));
+
+    //  AlignmentSorter.sortByGroup(viewport.getAlignment());
+    AlignmentSorter.sortGroups(viewport.getAlignment());
+    alignPanel.repaint();
+  }
+
+  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);
+  }
+
+  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);
+    }
+    else
+    {
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(new PairwiseAlignPanel(viewport));
+      Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+    }
+  }
+
+  public void PCAMenuItem_actionPerformed(ActionEvent e)
+  {
+    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);
+
+      return;
+    }
+
+    try
+    {
+      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)
+  {
+    String ltitle;
+    final TreePanel tp;
+
+    if ( (viewport.getSelectionGroup() != null) &&
+        (viewport.getSelectionGroup().getSize() > 3))
+    {
+      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);
+  }
+
+  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()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+                                       HistoryItem.SORT));
+
+        // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+        AlignmentSorter.sortBy(viewport.getAlignment(), order);
+        alignPanel.repaint();
+      }
+    });
+  }
+
+  void addTreeMenuItem(final TreePanel treePanel, String title)
+  {
+    final JMenuItem item = new JMenuItem(title);
+
+    treeCount++;
+
+    if (treeCount == 1)
+    {
+      sort.add(sortByTreeMenu);
+    }
+
+    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();
+        }
+      }
+    });
+  }
+
+  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();
+
+      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)
+    {
+      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
+          title, msa, false, true);
+    }
+  }
+
+  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))
+    {
+      // 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();
+
+      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)
+    {
+      jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
+          title, msa, true, true);
+    }
+  }
+
+  protected void jpred_actionPerformed(ActionEvent e)
+  {
+    SequenceI seq = null;
+    SequenceI[] msa = null;
+
+    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);
+        }
+      }
+    }
+
+    if (msa != null)
+    {
+      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");
+    }
+  }
+
+  protected void msaAlignMenuItem_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();
+
+      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)
+    {
+      MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
+                                                  false, true);
+    }
+  }
+
+  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");
+
+    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");
+        ShowNewickTree(fin, choice);
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "Problem reading tree file",
+                                      ex.getMessage(),
+                                      JOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+    }
+  }
+
+  public void ShowNewickTree(NewickFile nf, String title)
+  {
+    try
+    {
+      nf.parse();
+
+      if (nf.getTree() != null)
+      {
+        TreePanel tp = new TreePanel(viewport,
+                                     viewport.getAlignment().getSequences(), nf,
+                                     "FromFile",
+                                     title);
+        Desktop.addInternalFrame(tp, title, 600, 500);
+        addTreeMenuItem(tp, title);
+        viewport.setCurrentTree(tp.getTree());
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  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 1f5ec79..bd43a97 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,90 +1,86 @@
 /*
-* 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.gui;
 
+import java.util.*;
+
 import java.awt.*;
+
 import jalview.analysis.*;
-import jalview.analysis.NJTree;
+import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.util.*;
-import jalview.bin.Cache;
 
 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 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;
-
+  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 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.endRes = al.getWidth() - 1;
     this.startSeq = 0;
-    this.endSeq = al.getHeight()-1;
+    this.endSeq = al.getHeight() - 1;
 
     updateFromPreferences();
-
   }
 
   public void updateFromPreferences()
@@ -95,20 +91,30 @@ public class AlignViewport
     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)
+
+    if ( (fontName != null) && (fontStyle != null) && (fontSize != null))
     {
       int style = 0;
-      if(fontStyle.equals("bold"))
+
+      if (fontStyle.equals("bold"))
+      {
         style = 1;
-      else if(fontStyle.equals("italic"))
+      }
+      else if (fontStyle.equals("italic"))
+      {
         style = 2;
+      }
+
       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
     }
     else
+    {
       setFont(font);
+    }
 
     alignment.setGapCharacter(Preferences.gapSymbol);
 
@@ -116,49 +122,55 @@ public class AlignViewport
     // as Blosum and Clustal require this to be done
     updateConservation();
     updateConsensus();
-    if(Preferences.defaultColour!=null)
+
+    if (Preferences.defaultColour != null)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour);
-      if(globalColourScheme instanceof UserColourScheme)
+      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 Vector vconsensus;
-  AlignmentAnnotation consensus;
-  AlignmentAnnotation conservation;
-  AlignmentAnnotation quality;
+      if (globalColourScheme != null)
+      {
+        globalColourScheme.setConsensus(vconsensus);
+      }
+    }
+  }
 
-  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+  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);
+        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];
+    Annotation[] annotations = new Annotation[alWidth];
+    Annotation[] qannotations = new Annotation[alWidth];
     String sequence = cons.getConsSequence().getSequence();
-    float minR,minG,minB, maxR,maxG,maxB;
+    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
+    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();
@@ -167,108 +179,140 @@ public class AlignViewport
     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 = Integer.parseInt(sequence.charAt(i) + "");
+          value = 11;
         }
-      catch (Exception ex)
+
+        if (sequence.charAt(i) == '+')
         {
-          if (sequence.charAt(i) == '*') value = 11;
-          if (sequence.charAt(i) == '+') value = 10;
+          value = 10;
         }
-      float vprop = value-min;
-      vprop/=max;
-      annotations[i] = new Annotation(sequence.charAt(i) + "",
-                                      "", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+      }
+
+      float vprop = value - min;
+      vprop /= max;
+      annotations[i] = new Annotation(sequence.charAt(i) + "", "", ' ',
+                                      value,
+                                      new Color(minR + (maxR * vprop),
+                                                minG + (maxG * vprop),
+                                                minB + (maxB * vprop)));
+
       // Quality calc
-      value = ((Double) cons.quality.get(i)).floatValue();
+      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));
+      vprop /= qmax;
+      qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
+                                       value,
+                                       new Color(minR + (maxR * vprop),
+                                                 minG + (maxG * vprop),
+                                                 minB + (maxB * vprop)));
     }
 
-    if(conservation==null)
+    if (conservation == null)
     {
       conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than "+ConsPercGaps+"% gaps",
-                                             annotations,
-                                             0f, // cons.qualityRange[0].floatValue(),
+                                             "Conservation of total alignment less than " +
+                                             ConsPercGaps + "% gaps",
+                                             annotations, 0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
                                              1);
-      if(showConservation)
-      alignment.addAnnotation(conservation);
+
+      if (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)
+                                        cons.qualityRange[1].floatValue(), 1);
+
+      if (showQuality)
+      {
         alignment.addAnnotation(quality);
+      }
     }
-    else {
+    else
+    {
       conservation.annotations = annotations;
       quality.annotations = qannotations;
       quality.graphMax = cons.qualityRange[1].floatValue();
     }
-
-
   }
 
   public void updateConsensus()
   {
-    Annotation [] annotations = new Annotation[alignment.getWidth()];
+    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();
+    if (vconsensus == null)
+    {
+      vconsensus = alignment.getAAFrequency();
+    }
     else
     {
-        Vector temp = alignment.getAAFrequency();
-        vconsensus.clear();
-        Enumeration e = temp.elements();
-        while(e.hasMoreElements())
-        {
-          vconsensus.add(e.nextElement());
-        }
+      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++)
+
+    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 = "+ ";
-        }
+      hash = (Hashtable) vconsensus.elementAt(i);
+
+      float value = Float.parseFloat(hash.get("maxCount").toString());
+      value /= Float.parseFloat(hash.get("size").toString());
+
+      value *= 100;
 
-        mouseOver += (int)value+"%";
-        annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+      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(consensus==null)
-     {
-       consensus = new AlignmentAnnotation("Consensus",
-                                           "PID", annotations, 0f, 100f, 1);
-       if(showIdentity)
-         alignment.addAnnotation(consensus);
-     }
-     else
-       consensus.annotations = annotations;
+    if (consensus == null)
+    {
+      consensus = new AlignmentAnnotation("Consensus", "PID",
+                                          annotations, 0f, 100f, 1);
 
+      if (showIdentity)
+      {
+        alignment.addAnnotation(consensus);
+      }
+    }
+    else
+    {
+      consensus.annotations = annotations;
+    }
   }
 
-
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -279,42 +323,44 @@ public class AlignViewport
     selectionGroup = sg;
   }
 
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
 
- public boolean getConservationSelected()
- {
-   return conservationColourSelected;
- }
-
- public void setConservationSelected(boolean b)
- {
-   conservationColourSelected = b;
- }
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
 
- public boolean getAbovePIDThreshold()
- {
-   return abovePIDThreshold;
- }
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
 
- public void setAbovePIDThreshold(boolean b)
- {
-   abovePIDThreshold = b;
- }
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
 
-  public int getStartRes() {
+  public int getStartRes()
+  {
     return startRes;
   }
 
-  public int getEndRes() {
+  public int getEndRes()
+  {
     return endRes;
   }
 
-  public int getStartSeq() {
+  public int getStartSeq()
+  {
     return startSeq;
   }
 
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
-     globalColourScheme = cs;
+    globalColourScheme = cs;
   }
 
   public ColourSchemeI getGlobalColourScheme()
@@ -322,91 +368,134 @@ public class AlignViewport
     return globalColourScheme;
   }
 
-
-  public void setStartRes(int res) {
+  public void setStartRes(int res)
+  {
     this.startRes = res;
   }
-  public void setStartSeq(int seq) {
+
+  public void setStartSeq(int seq)
+  {
     this.startSeq = seq;
   }
-  public void setEndRes(int res) {
-    if (res > alignment.getWidth()-1) {
+
+  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;
+      res = alignment.getWidth() - 1;
     }
-    if (res < 0) {
+
+    if (res < 0)
+    {
       res = 0;
     }
+
     this.endRes = res;
   }
-  public void setEndSeq(int seq) {
-    if (seq > alignment.getHeight()) {
+
+  public void setEndSeq(int seq)
+  {
+    if (seq > alignment.getHeight())
+    {
       seq = alignment.getHeight();
     }
-    if (seq < 0) {
+
+    if (seq < 0)
+    {
       seq = 0;
     }
+
     this.endSeq = seq;
   }
-  public int getEndSeq() {
+
+  public int getEndSeq()
+  {
     return endSeq;
   }
 
-  public void setFont(Font f) {
+  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() {
+  public Font getFont()
+  {
     return font;
   }
-  public void setCharWidth(int w) {
+
+  public void setCharWidth(int w)
+  {
     this.charWidth = w;
   }
-  public int getCharWidth() {
+
+  public int getCharWidth()
+  {
     return charWidth;
   }
-  public void setCharHeight(int h) {
+
+  public void setCharHeight(int h)
+  {
     this.charHeight = h;
   }
-  public int getCharHeight() {
+
+  public int getCharHeight()
+  {
     return charHeight;
   }
-  public void setChunkWidth(int w) {
+
+  public void setChunkWidth(int w)
+  {
     this.chunkWidth = w;
   }
-  public int getChunkWidth() {
+
+  public int getChunkWidth()
+  {
     return chunkWidth;
   }
-  public void setChunkHeight(int h) {
+
+  public void setChunkHeight(int h)
+  {
     this.chunkHeight = h;
   }
-  public int getChunkHeight() {
+
+  public int getChunkHeight()
+  {
     return chunkHeight;
   }
-  public AlignmentI getAlignment() {
+
+  public AlignmentI getAlignment()
+  {
     return alignment;
   }
-  public void setAlignment(AlignmentI align) {
+
+  public void setAlignment(AlignmentI align)
+  {
     this.alignment = align;
   }
 
-  public void setWrapAlignment(boolean state) {
+  public void setWrapAlignment(boolean state)
+  {
     wrapAlignment = state;
   }
-  public void setShowText(boolean state) {
+
+  public void setShowText(boolean state)
+  {
     showText = state;
   }
 
-  public void setRenderGaps(boolean state){
+  public void setRenderGaps(boolean state)
+  {
     renderGaps = state;
   }
 
-
   public boolean getColourText()
   {
     return showColourText;
@@ -417,79 +506,117 @@ public class AlignViewport
     showColourText = state;
   }
 
-  public void setShowBoxes(boolean state) {
+  public void setShowBoxes(boolean state)
+  {
     showBoxes = state;
   }
 
-  public boolean getWrapAlignment() {
-      return wrapAlignment;
+  public boolean getWrapAlignment()
+  {
+    return wrapAlignment;
   }
-  public boolean getShowText() {
+
+  public boolean getShowText()
+  {
     return showText;
   }
-  public boolean getShowBoxes() {
+
+  public boolean getShowBoxes()
+  {
     return showBoxes;
   }
 
-  public char getGapCharacter() {
+  public char getGapCharacter()
+  {
     return getAlignment().getGapCharacter();
   }
-  public void setGapCharacter(char gap) {
-    if (getAlignment() != null) {
+
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
+    {
       getAlignment().setGapCharacter(gap);
     }
   }
-  public void setThreshold(int thresh) {
+
+  public void setThreshold(int thresh)
+  {
     threshold = thresh;
   }
-  public int getThreshold() {
+
+  public int getThreshold()
+  {
     return threshold;
   }
-  public void setIncrement(int inc) {
+
+  public void setIncrement(int inc)
+  {
     increment = inc;
   }
-  public int getIncrement() {
+
+  public int getIncrement()
+  {
     return increment;
   }
-  public int getIndex(int y) {
-    int y1     = 0;
+
+  public int getIndex(int y)
+  {
+    int y1 = 0;
     int starty = getStartSeq();
-    int endy   = getEndSeq();
+    int endy = getEndSeq();
 
-    for (int i = starty; i <= endy; i++) {
-      if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {
+    for (int i = starty; i <= endy; i++)
+    {
+      if ( (i < alignment.getHeight()) &&
+          (alignment.getSequenceAt(i) != null))
+      {
         int y2 = y1 + getCharHeight();
 
-        if (y>=y1 && y <=y2) {
+        if ( (y >= y1) && (y <= y2))
+        {
           return i;
         }
-        y1  = y2;
-      } else {
+
+        y1 = y2;
+      }
+      else
+      {
         return -1;
       }
     }
+
     return -1;
   }
 
-  public ColumnSelection getColumnSelection() {
+  public ColumnSelection getColumnSelection()
+  {
     return colSel;
   }
 
-  public void resetSeqLimits(int height) {
-    setEndSeq(height/getCharHeight());
+  public void resetSeqLimits(int height)
+  {
+    setEndSeq(height / getCharHeight());
   }
-  public void setCurrentTree(NJTree tree) {
-      currentTree = tree;
+
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
   }
-  public NJTree getCurrentTree() {
+
+  public NJTree getCurrentTree()
+  {
     return currentTree;
   }
 
   public void setColourAppliesToAllGroups(boolean b)
-  {   colourAppliesToAllGroups = b; }
+  {
+    colourAppliesToAllGroups = b;
+  }
 
   public boolean getColourAppliesToAllGroups()
-  {return colourAppliesToAllGroups; }
+  {
+    return colourAppliesToAllGroups;
+  }
 
   public boolean getShowFullId()
   {
@@ -502,38 +629,59 @@ public class AlignViewport
   }
 
   public boolean getShowAnnotation()
-  {   return showAnnotation;  }
+  {
+    return showAnnotation;
+  }
 
   public void setShowAnnotation(boolean b)
-  {    showAnnotation = b;  }
+  {
+    showAnnotation = b;
+  }
 
   public boolean getScaleAboveWrapped()
-  { return scaleAboveWrapped;}
+  {
+    return scaleAboveWrapped;
+  }
 
   public boolean getScaleLeftWrapped()
-  { return scaleLeftWrapped; }
+  {
+    return scaleLeftWrapped;
+  }
 
   public boolean getScaleRightWrapped()
-  { return scaleRightWrapped; }
+  {
+    return scaleRightWrapped;
+  }
 
   public void setScaleAboveWrapped(boolean b)
-  { scaleAboveWrapped = b; }
+  {
+    scaleAboveWrapped = b;
+  }
 
   public void setScaleLeftWrapped(boolean b)
-  { scaleLeftWrapped = b; }
+  {
+    scaleLeftWrapped = b;
+  }
 
   public void setScaleRightWrapped(boolean b)
-  { scaleRightWrapped = b; }
-  // JBPNote Prolly only need this in the applet version.
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
-  public void addPropertyChangeListener(java.beans.PropertyChangeListener listener) {
+  {
+    scaleRightWrapped = b;
+  }
+
+  public void addPropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
     changeSupport.addPropertyChangeListener(listener);
   }
 
-  public void removePropertyChangeListener(java.beans.PropertyChangeListener listener) {
+  public void removePropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
     changeSupport.removePropertyChangeListener(listener);
   }
-  public void firePropertyChange(String prop, Object oldvalue, Object newvalue) {
+
+  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 7a8a811..1a48af6 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,46 +1,45 @@
 /*
-* 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.gui;
 
-import jalview.jbgui.GAlignmentPanel;
-import jalview.schemes.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import java.io.*;
+import javax.imageio.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.awt.print.*;
-import java.io.*;
 import java.awt.image.*;
-import org.jibble.epsgraphics.*;
-import javax.imageio.*;
+import java.awt.print.*;
 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
+public class AlignmentPanel
+    extends GAlignmentPanel implements AdjustmentListener, Printable
 {
-
-  AlignViewport     av;
+  AlignViewport av;
   OverviewPanel overviewPanel;
-  SeqPanel   seqPanel;
-  IdPanel    idPanel;
+  SeqPanel seqPanel;
+  IdPanel idPanel;
   IdwidthAdjuster idwidthAdjuster;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
@@ -49,13 +48,15 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   // 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);
+    this.av = av;
+    seqPanel = new SeqPanel(av, this);
+    idPanel = new IdPanel(av, this);
 
     scalePanel = new ScalePanel(av, this);
 
@@ -66,7 +67,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     annotationPanel = new AnnotationPanel(this);
     alabels = new AnnotationLabels(this);
 
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
+                                                 getPreferredSize());
     annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
     annotationScroller.setViewportView(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
@@ -81,27 +83,31 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
-   setFocusable(true);
-   addKeyListener(new KeyAdapter()
-   {
-     public void keyPressed(KeyEvent evt)
-     {
-       switch(evt.getKeyCode())
-       {
-         case  27: // escape key
-           av.setSelectionGroup(null);
-           repaint();
-           break;
-
-        case KeyEvent.VK_DOWN:
-          alignFrame.moveSelectedSequences(false);
-          break;
-        case KeyEvent.VK_UP:
-          alignFrame.moveSelectedSequences(true);
-          break;
-       }
-     }
-   });
+    setFocusable(true);
+    addKeyListener(new KeyAdapter()
+    {
+      public void keyPressed(KeyEvent evt)
+      {
+        switch (evt.getKeyCode())
+        {
+          case 27: // escape key
+            av.setSelectionGroup(null);
+            repaint();
+
+            break;
+
+          case KeyEvent.VK_DOWN:
+            alignFrame.moveSelectedSequences(false);
+
+            break;
+
+          case KeyEvent.VK_UP:
+            alignFrame.moveSelectedSequences(true);
+
+            break;
+        }
+      }
+    });
   }
 
   public void fontChanged()
@@ -110,11 +116,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     // 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()));
+    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);
@@ -122,11 +131,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     repaint();
   }
 
-
   Dimension calculateIdWidth()
   {
     Graphics g = this.getGraphics();
-    if(g==null)
+
+    if (g == null)
     {
       javax.swing.JFrame f = new javax.swing.JFrame();
       f.addNotify();
@@ -136,70 +145,83 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     FontMetrics fm = g.getFontMetrics(av.font);
     AlignmentI al = av.getAlignment();
 
-       int i   = 0;
-       int idWidth = 0;
-       String id;
-       while (i < al.getHeight() && al.getSequenceAt(i) != null)
-       {
-         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++;
-       }
-
-       // Also check annotation label widths
-       i=0;
-       if(al.getAlignmentAnnotation()!=null)
-       {
-         fm = g.getFontMetrics(alabels.getFont());
-         while (i < al.getAlignmentAnnotation().length)
-         {
-           String label = al.getAlignmentAnnotation()[i].label;
-           if (fm.stringWidth(label) > idWidth)
-             idWidth = fm.stringWidth(label);
-           i++;
-         }
-       }
-
-       return new Dimension(idWidth, 12);
-  }
+    int i = 0;
+    int idWidth = 0;
+    String id;
 
+    while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
+    {
+      SequenceI s = al.getSequenceAt(i);
 
- public void highlightSearchResults(int [] results)
- {
-   seqPanel.seqCanvas.highlightSearchResults( results );
+      if (av.getShowFullId())
+      {
+        id = s.getDisplayId();
+      }
+      else
+      {
+        id = s.getName();
+      }
 
-   // do we need to scroll the panel?
-   if(results!=null)
+      if (fm.stringWidth(id) > idWidth)
+      {
+        idWidth = fm.stringWidth(id);
+      }
+
+      i++;
+    }
+
+    // Also check annotation label widths
+    i = 0;
+
+    if (al.getAlignmentAnnotation() != 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]);
+      fm = g.getFontMetrics(alabels.getFont());
+
+      while (i < al.getAlignmentAnnotation().length)
+      {
+        String label = al.getAlignmentAnnotation()[i].label;
+
+        if (fm.stringWidth(label) > idWidth)
+        {
+          idWidth = fm.stringWidth(label);
+        }
+
+        i++;
+      }
     }
 
- }
+    return new Dimension(idWidth, 12);
+  }
+
+  public void highlightSearchResults(int[] results)
+  {
+    seqPanel.seqCanvas.highlightSearchResults(results);
 
+    // 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;
 
- public OverviewPanel getOverviewPanel()
- {
-   return overviewPanel;
- }
+      if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
+          ( (av.getStartSeq() > results[0]) ||
+           (av.getEndSeq() < results[0])))
+      {
+        setScrollValues(start, results[0]);
+      }
+    }
+  }
 
- public void setOverviewPanel(OverviewPanel op)
- {
-   overviewPanel = op;
- }
+  public OverviewPanel getOverviewPanel()
+  {
+    return overviewPanel;
+  }
 
+  public void setOverviewPanel(OverviewPanel op)
+  {
+    overviewPanel = op;
+  }
 
   public void setAnnotationVisible(boolean b)
   {
@@ -207,7 +229,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     annotationScroller.setVisible(b);
   }
 
-
   public void setWrapAlignment(boolean wrap)
   {
     scalePanelHolder.setVisible(!wrap);
@@ -220,112 +241,130 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     idSpaceFillerPanel1.setVisible(!wrap);
 
     repaint();
-
   }
 
-
   public void setColourScheme()
   {
     ColourSchemeI cs = av.getGlobalColourScheme();
 
-    if(av.getConservationSelected())
+    if (av.getConservationSelected())
     {
+      Alignment al = (Alignment) av.getAlignment();
+      Conservation c = new Conservation("All",
+                                        ResidueProperties.propHash, 3,
+                                        al.getSequences(), 0,
+                                        al.getWidth());
 
-       Alignment al = (Alignment)av.getAlignment();
-       Conservation c = new Conservation("All",
-                            ResidueProperties.propHash, 3, al.getSequences(), 0,
-                            al.getWidth() );
-
-       c.calculate();
-       c.verdict(false, av.ConsPercGaps);
-       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+      c.calculate();
+      c.verdict(false, av.ConsPercGaps);
 
-       av.setGlobalColourScheme( ccs );
+      ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
+      av.setGlobalColourScheme(ccs);
     }
 
     repaint();
   }
 
-
-  int hextent = 0;
-  int vextent = 0;
-
   // return value is true if the scroll is valid
   public boolean scrollUp(boolean up)
   {
-    if(up)
+    if (up)
     {
-      if(vscroll.getValue()<1)
+      if (vscroll.getValue() < 1)
+      {
         return false;
-      fastPaint  = false;
+      }
+
+      fastPaint = false;
       vscroll.setValue(vscroll.getValue() - 1);
     }
     else
     {
-     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
-       return false;
-      fastPaint  = false;
+      if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+      {
+        return false;
+      }
+
+      fastPaint = false;
       vscroll.setValue(vscroll.getValue() + 1);
     }
+
     fastPaint = true;
+
     return true;
   }
 
   public boolean scrollRight(boolean right)
   {
-
     if (right)
     {
       if (hscroll.getValue() < 1)
+      {
         return false;
+      }
+
       fastPaint = false;
       hscroll.setValue(hscroll.getValue() - 1);
     }
     else
     {
-      if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+      if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+      {
         return false;
+      }
+
       fastPaint = false;
       hscroll.setValue(hscroll.getValue() + 1);
     }
+
     fastPaint = true;
+
     return true;
   }
 
-
   public void setScrollValues(int x, int y)
   {
-    av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
+                 1);
 
-    hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
-    vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
+    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
 
-    if(hextent > av.alignment.getWidth())
+    if (hextent > av.alignment.getWidth())
+    {
       hextent = av.alignment.getWidth();
-    if(vextent > av.alignment.getHeight())
+    }
+
+    if (vextent > av.alignment.getHeight())
+    {
       vextent = av.alignment.getHeight();
+    }
 
-    if(hextent+x  >  av.getAlignment().getWidth())
-      x =  av.getAlignment().getWidth()- hextent;
+    if ( (hextent + x) > av.getAlignment().getWidth())
+    {
+      x = av.getAlignment().getWidth() - hextent;
+    }
 
-    if(vextent+y > av.getAlignment().getHeight())
+    if ( (vextent + y) > av.getAlignment().getHeight())
+    {
       y = av.getAlignment().getHeight() - vextent;
+    }
 
-    if(y<0)
+    if (y < 0)
+    {
       y = 0;
+    }
 
-    if(x<0)
-      x=0;
-
-    hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
-    vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
-
-
+    if (x < 0)
+    {
+      x = 0;
+    }
 
+    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
+    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
   }
 
-
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     int oldX = av.getStartRes();
@@ -335,30 +374,38 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+      av.setEndRes( (x +
+                     (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
     }
 
     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 );
+        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());
+        av.setEndSeq(offy +
+                     (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
       }
     }
 
-    if(overviewPanel!=null)
+    if (overviewPanel != null)
+    {
       overviewPanel.setBoxPosition();
+    }
 
-    if(av.getWrapAlignment() || !fastPaint)
+    if (av.getWrapAlignment() || !fastPaint)
+    {
       repaint();
+    }
     else
     {
       idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
@@ -366,16 +413,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
                                    av.getStartSeq() - oldY);
 
       scalePanel.repaint();
+
       if (av.getShowAnnotation())
+      {
         annotationPanel.fastPaint(av.getStartRes() - oldX);
+      }
     }
-
   }
 
-
   public void paintComponent(Graphics g)
   {
     invalidate();
+
     Dimension d = idPanel.idCanvas.getPreferredSize();
     idPanelHolder.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
@@ -383,7 +432,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+      int max = av.alignment.getWidth() /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);
@@ -392,226 +442,270 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
-
-
-
   }
 
-  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
+  public int print(Graphics pg, PageFormat pf, int pi)
+      throws PrinterException
   {
-    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
+    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
 
     int pwidth = (int) pf.getImageableWidth();
     int pheight = (int) pf.getImageableHeight();
 
     if (av.getWrapAlignment())
-      return printWrappedAlignment(pg, pwidth,pheight, pi);
+    {
+      return printWrappedAlignment(pg, pwidth, pheight, pi);
+    }
     else
-      return printUnwrapped(pg,pwidth, pheight,pi);
+    {
+      return printUnwrapped(pg, pwidth, pheight, pi);
+    }
   }
 
-  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+  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 idWidth = calculateIdWidth().width + 4;
-      FontMetrics fm = getFontMetrics(av.getFont());
-      int scaleHeight = av.charHeight + fm.getDescent();
+    pg.setColor(Color.white);
+    pg.fillRect(0, 0, pwidth, pheight);
+    pg.setFont(av.getFont());
 
-      pg.setColor(Color.white);
-      pg.fillRect(0, 0, pwidth, pheight);
-      pg.setFont(av.getFont());
+    ////////////////////////////////////
+    /// How many sequences and residues can we fit on a printable page?
+    int totalRes = (pwidth - idWidth) / av.getCharWidth();
 
-      ////////////////////////////////////
-      /// How many sequences and residues can we fit on a printable page?
-      int totalRes = (pwidth - idWidth) / av.getCharWidth();
+    int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
+        1;
 
-      int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - 1;
+    int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
 
-      int pagesWide = av.getAlignment().getWidth() / totalRes + 1;
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int startRes;
 
-      /////////////////////////////
-      /// Only print these sequences and residues on this page
-      int startRes, endRes, startSeq, endSeq;
-      startRes = (pi % pagesWide) * totalRes;
-      endRes = startRes + totalRes - 1;
-      if (endRes > av.getAlignment().getWidth()-1)
-        endRes = av.getAlignment().getWidth()-1;
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int endRes;
 
-      startSeq = (pi / pagesWide) * totalSeq;
-      endSeq = startSeq + totalSeq;
-      if (endSeq > av.getAlignment().getHeight())
-        endSeq = av.getAlignment().getHeight();
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int startSeq;
 
-      int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int endSeq;
+    startRes = (pi % pagesWide) * totalRes;
+    endRes = (startRes + totalRes) - 1;
 
-      if (av.showAnnotation)
-        pagesHigh += annotationPanel.getHeight();
+    if (endRes > (av.getAlignment().getWidth() - 1))
+    {
+      endRes = av.getAlignment().getWidth() - 1;
+    }
+
+    startSeq = (pi / pagesWide) * totalSeq;
+    endSeq = startSeq + totalSeq;
 
-      pagesHigh /= pheight;
+    if (endSeq > av.getAlignment().getHeight())
+    {
+      endSeq = av.getAlignment().getHeight();
+    }
 
-      if (pi >= pagesWide * pagesHigh)
-        return Printable.NO_SUCH_PAGE;
+    int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
 
-        //draw Scale
-      pg.translate(idWidth, 0);
-      scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
-      pg.translate( -idWidth, scaleHeight);
-      ////////////////
-      // Draw the ids
-      Color currentColor = null;
-      Color currentTextColor = null;
-      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;
-        }
+    if (av.showAnnotation)
+    {
+      pagesHigh += annotationPanel.getHeight();
+    }
 
-        pg.setColor(currentColor);
-        pg.fillRect(0,
-                    jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
-            av.getCharHeight()),
-                    idWidth,
-                    av.getCharHeight());
+    pagesHigh /= pheight;
+
+    if (pi >= (pagesWide * pagesHigh))
+    {
+      return Printable.NO_SUCH_PAGE;
+    }
 
-        pg.setColor(currentTextColor);
+    //draw Scale
+    pg.translate(idWidth, 0);
+    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
+    pg.translate( -idWidth, scaleHeight);
 
-        String string = av.getAlignment().getSequenceAt(i).getName();
-        if (av.getShowFullId())
-          string = av.getAlignment().getSequenceAt(i).getDisplayId();
+    ////////////////
+    // Draw the ids
+    Color currentColor = null;
+    Color currentTextColor = null;
 
-        pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
-                      (startSeq, i, av.getCharHeight()) + av.getCharHeight() -
-                      (av.getCharHeight() / 5));
+    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 main sequence panel
-      pg.translate(idWidth, 0);
-      seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
-                                   startRes, startSeq, 0);
+      pg.setColor(currentColor);
+      pg.fillRect(0,
+                  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
+          av.getCharHeight()), idWidth, av.getCharHeight());
 
+      pg.setColor(currentTextColor);
 
-      if (av.showAnnotation && endSeq == av.alignment.getHeight())
+      String string = av.getAlignment().getSequenceAt(i).getName();
+
+      if (av.getShowFullId())
       {
-        pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
-        alabels.drawComponent( (Graphics2D) pg);
-        pg.translate(idWidth, 0);
-        annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes+1);
+        string = av.getAlignment().getSequenceAt(i).getDisplayId();
       }
 
-      return Printable.PAGE_EXISTS;
+      pg.drawString(string, 0,
+                    (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,
+          av.getCharHeight()) + av.getCharHeight()) -
+                    (av.getCharHeight() / 5));
+    }
 
-  }
+    // 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()))
+    {
+      pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);
+      alabels.drawComponent( (Graphics2D) pg);
+      pg.translate(idWidth, 0);
+      annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
+                                    1);
+    }
 
-  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+    return Printable.PAGE_EXISTS;
+  }
+
+  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
+                                   int pi)
+      throws PrinterException
   {
-      int idWidth = calculateIdWidth().width + 4;
+    int idWidth = calculateIdWidth().width + 4;
 
-      int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth);
-      int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
-          ( (av.alignment.getWidth()
-             / resWidth) + 1) * av.charHeight;
+    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
+        idWidth);
+    int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *
+        ( (av.alignment.getWidth() / resWidth) +
+         1) * av.charHeight;
 
+    pg.setColor(Color.white);
+    pg.fillRect(0, 0, pwidth, pheight);
+    pg.setFont(av.getFont());
 
-      pg.setColor(Color.white);
-      pg.fillRect(0, 0, pwidth, pheight);
-      pg.setFont(av.getFont());
+    ////////////////
+    // Draw the ids
+    pg.setColor(Color.black);
 
-      ////////////////
-      // Draw the ids
-      pg.setColor(Color.black);
+    pg.translate(0, -pi * pheight);
 
-      pg.translate(0, -pi * pheight);
+    pg.setClip(0, pi * pheight, pwidth, pheight);
 
-      pg.setClip(0,pi*pheight,pwidth, pheight);
+    int ypos = 2 * av.charHeight;
 
-      int ypos = 2 * av.charHeight;
-      do
+    do
+    {
+      for (int i = 0; i < av.alignment.getHeight(); i++)
       {
-        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,
-                        AlignmentUtil.getPixelHeight(0, i, av.charHeight) +
-                        ypos +
-                        av.charHeight - (av.charHeight / 5));
+        SequenceI s = av.alignment.getSequenceAt(i);
+        String string = s.getName();
 
+        if (av.getShowFullId())
+        {
+          string = s.getDisplayId();
         }
 
-        ypos += (av.alignment.getHeight() + 2) * av.charHeight;
-
+        pg.drawString(string, 0,
+                      (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
+                       av.charHeight) - (av.charHeight / 5));
       }
-      while (ypos < totalHeight);
-
-      pg.translate(idWidth, 0);
 
-      seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
-
-      if (pi * pheight < totalHeight)
-        return Printable.PAGE_EXISTS;
-      else
-        return Printable.NO_SUCH_PAGE;
+      ypos += ( (av.alignment.getHeight() + 2) * av.charHeight);
+    }
+    while (ypos < totalHeight);
 
+    pg.translate(idWidth, 0);
 
+    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 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;
+      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
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"),
-              new String[]{"eps"},
-              new String[]{"Encapsulated Postscript"},
-              "Encapsulated Postscript");
+      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;
+      }
 
-      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);
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                    chooser.getSelectedFile().getParent());
 
-        if (av.getWrapAlignment())
-          printWrappedAlignment(pg, width, height, 0);
-        else
-          printUnwrapped(pg, width, height, 0);
+      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+      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();
+      pg.flush();
+      pg.close();
     }
     catch (Exception ex)
     {
@@ -621,64 +715,76 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   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;
-      }
+    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;
+    }
 
     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.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;
+      }
+
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                    chooser.getSelectedFile().getParent());
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 
-      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
-      Graphics2D png = (Graphics2D)bi.getGraphics();
+      BufferedImage bi = new BufferedImage(width, height,
+                                           BufferedImage.TYPE_INT_RGB);
+      Graphics2D png = (Graphics2D) bi.getGraphics();
 
-      png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
+      png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                           RenderingHints.VALUE_ANTIALIAS_ON);
 
-        if (av.getWrapAlignment())
-          printWrappedAlignment(png, width, height, 0);
-        else
-          printUnwrapped(png, width, height, 0);
+      if (av.getWrapAlignment())
+      {
+        printWrappedAlignment(png, width, height, 0);
+      }
+      else
+      {
+        printUnwrapped(png, width, height, 0);
+      }
 
-        ImageIO.write(bi, "png", out);
-        out.close();
+      ImageIO.write(bi, "png", out);
+      out.close();
     }
     catch (Exception ex)
     {
       ex.printStackTrace();
     }
   }
-
 }
 
-class Preview extends JFrame
+class Preview
+    extends JFrame
 {
-
   public Preview(Image image)
   {
     setResizable(true);
@@ -691,22 +797,25 @@ class Preview extends JFrame
   }
 }
 
-class PreviewPanel extends JPanel
+class PreviewPanel
+    extends JPanel
 {
   Image image;
+
   public PreviewPanel(Image image)
   {
     this.image = image;
   }
+
   public void paintComponent(Graphics g)
   {
-    if(image!=null)
-      g.drawImage(image,0,0,this);
+    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 f2603ea..1b9fd8f 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,44 +1,45 @@
-
 /*
-* 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.gui;
 
-import javax.swing.*;
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
 import java.awt.image.*;
+import javax.swing.*;
+
 import jalview.datamodel.*;
-import jalview.io.FormatAdapter;
 
-public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener
+public class AnnotationLabels
+    extends JPanel implements MouseListener,
+    MouseMotionListener, ActionListener
 {
-  boolean active = false;
-  Image image;
-  AlignmentPanel ap ;
-  boolean resizing = false;
-  int oldY, mouseX;
   static String ADDNEW = "Add New Row";
   static String HIDE = "Hide This Row";
   static String DELETE = "Delete This Row";
-  static String SHOWALL="Show All Hidden Rows";
-  static String OUTPUT_TEXT="Show Values In Textbox";
+  static String 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;
 
@@ -48,8 +49,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, MouseMoti
 
     java.net.URL url = getClass().getResource("/images/idwidth.gif");
     Image temp = null;
+
     if (url != null)
+    {
       temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+    }
 
     try
     {
@@ -57,9 +61,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, MouseMoti
       mt.addImage(temp, 0);
       mt.waitForID(0);
     }
-    catch (Exception ex) {}
+    catch (Exception ex)
+    {
+    }
 
-    BufferedImage bi = new BufferedImage(temp.getHeight(this), temp.getWidth(this),
+    BufferedImage bi = new BufferedImage(temp.getHeight(this),
+                                         temp.getWidth(this),
                                          BufferedImage.TYPE_INT_RGB);
     Graphics2D g = (Graphics2D) bi.getGraphics();
     g.rotate(Math.toRadians(90));
@@ -80,126 +87,175 @@ public class AnnotationLabels extends JPanel implements MouseListener, MouseMoti
   {
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
-    if(evt.getActionCommand().equals(ADDNEW))
+    if (evt.getActionCommand().equals(ADDNEW))
     {
-      String label = JOptionPane.showInputDialog(this, "Label for annotation");
-      if(label==null)
+      String label = JOptionPane.showInputDialog(this,
+                                                 "Label for annotation");
+
+      if (label == null)
+      {
         label = "";
-      ap.av.alignment.addAnnotation(new AlignmentAnnotation
-                                      (label,
-                                       "New description",
-                                       new Annotation[ap.av.alignment.getWidth()]));
+      }
+
+      ap.av.alignment.addAnnotation(new AlignmentAnnotation(label,
+          "New description",
+          new Annotation[ap.av.alignment.getWidth()]));
+    }
+    else if (evt.getActionCommand().equals(HIDE))
+    {
+      aa[selectedRow].visible = false;
+
+      if (aa[selectedRow].label.equals("Conservation"))
+      {
+        ap.av.showConservation = false;
+      }
+
+      if (aa[selectedRow].label.equals("Quality"))
+      {
+        ap.av.showQuality = false;
+      }
+
+      if (aa[selectedRow].label.equals("Consensus"))
+      {
+        ap.av.showIdentity = false;
+      }
+    }
+    else if (evt.getActionCommand().equals(DELETE))
+    {
+      ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+    }
+    else if (evt.getActionCommand().equals(SHOWALL))
+    {
+      for (int i = 0; i < aa.length; i++)
+      {
+        aa[i].visible = true;
+      }
+    }
+    else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+      Desktop.addInternalFrame(cap,
+                               ap.alignFrame.getTitle() + " - " +
+                               aa[selectedRow].label, 500,
+                               100);
+      cap.setText(aa[selectedRow].toString());
     }
-   else if(evt.getActionCommand().equals(HIDE))
-   {
-     aa[selectedRow].visible = false;
-     if(aa[selectedRow].label.equals("Conservation"))
-       ap.av.showConservation = false;
-     if(aa[selectedRow].label.equals("Quality"))
-       ap.av.showQuality = false;
-     if(aa[selectedRow].label.equals("Consensus"))
-       ap.av.showIdentity = false;
-   }
-   else if(evt.getActionCommand().equals(DELETE))
-   {
-     ap.av.alignment.deleteAnnotation(aa[selectedRow]);
-   }
-   else if(evt.getActionCommand().equals(SHOWALL))
-   {
-       for(int i=0; i<aa.length; i++)
-         aa[i].visible = true;
-   }
-   else if(evt.getActionCommand().equals(OUTPUT_TEXT))
-   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-     Desktop.addInternalFrame(cap, ap.alignFrame.getTitle()+" - "+ aa[selectedRow].label, 500, 100);
-     cap.setText( aa[selectedRow].toString() );
-   }
-
-   ap.annotationPanel.adjustPanelHeight();
-   ap.repaint();
 
+    ap.annotationPanel.adjustPanelHeight();
+    ap.repaint();
   }
 
   public void mousePressed(MouseEvent evt)
   {
     int y = evt.getY() - scrollOffset;
 
-      AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-       if(aa==null || aa.length==0)
-       {
-            JPopupMenu pop = new JPopupMenu("Annotations");
-            JMenuItem item = new JMenuItem(ADDNEW);
-            item.addActionListener(this);
-            pop.add(item);
-            pop.show(this, evt.getX(), evt.getY());
-            return;
-       }
-
-       int height = 0;
-       for (int i = 0; i < aa.length; i++)
-       {
-         if(!aa[i].visible)
-           continue;
-
-         height += aa[i].height;
-         if(y<height)
-         {
-           selectedRow = i;
-           break;
-         }
-       }
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
+    if ( (aa == null) || (aa.length == 0))
+    {
       JPopupMenu pop = new JPopupMenu("Annotations");
       JMenuItem item = new JMenuItem(ADDNEW);
       item.addActionListener(this);
       pop.add(item);
-      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());
 
+      return;
+    }
+
+    int height = 0;
+
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (!aa[i].visible)
+      {
+        continue;
+      }
+
+      height += aa[i].height;
+
+      if (y < height)
+      {
+        selectedRow = i;
+
+        break;
+      }
+    }
+
+    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());
+
     oldY = evt.getY();
   }
 
-  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 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.annotationScroller.getPreferredSize();
     int dif = evt.getY() - oldY;
 
     dif /= ap.av.charHeight;
     dif *= ap.av.charHeight;
 
-    if(d.height-dif>20)
+    if ( (d.height - dif) > 20)
     {
-      ap.annotationScroller.setPreferredSize(new Dimension(d.width,d.height - dif));
+      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.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+          d.width, d.height - dif));
       ap.repaint();
     }
+
     ap.addNotify();
   }
 
-  public void mouseMoved(MouseEvent evt)   {}
-  public void mouseClicked(MouseEvent evt) {}
+  public void mouseMoved(MouseEvent evt)
+  {
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
 
   public void paintComponent(Graphics g1)
   {
-    Graphics2D g = (Graphics2D)g1;
-    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
+    Graphics2D g = (Graphics2D) g1;
+    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                       RenderingHints.VALUE_ANTIALIAS_ON);
 
     drawComponent(g);
   }
@@ -208,48 +264,56 @@ public class AnnotationLabels extends JPanel implements MouseListener, MouseMoti
   {
     FontMetrics fm = g.getFontMetrics(g.getFont());
     g.setColor(Color.white);
-    g.fillRect(0,0, getWidth(), getHeight());
+    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)
-       continue;
-
-     x = getWidth() - 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;
-   }
-
-   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);
-   }
+    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)
+        {
+          continue;
+        }
+
+        x = getWidth() - 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;
+        }
+      }
+    }
 
+    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 41bbb43..449c449 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,59 +1,55 @@
 /*
-* 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.gui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
-import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 import java.awt.image.*;
+import javax.swing.*;
 
-public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
-{
-  AlignViewport av;
-  AlignmentPanel ap;
-  int activeRow =-1;
+import jalview.datamodel.*;
 
-  ArrayList activeRes;
-  static String HELIX ="Helix";
-  static String SHEET ="Sheet";
-  static String LABEL ="Label";
-  static String REMOVE="Remove Annotation";
-  static String COLOUR="Colour";
+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;
+  ArrayList activeRes;
   BufferedImage image;
   Graphics2D gg;
   FontMetrics fm;
-  int imgWidth=0;
-
+  int imgWidth = 0;
   boolean fastPaint = false;
 
-  public static int GRAPH_HEIGHT = 40;
-
-
-
   public AnnotationPanel(AlignmentPanel ap)
   {
     this.ap = ap;
@@ -63,13 +59,12 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
     addMouseMotionListener(this);
     adjustPanelHeight();
 
-
-    ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener( this );
+    ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    ap.alabels.setScrollOffset( -evt.getValue() );
+    ap.alabels.setScrollOffset( -evt.getValue());
   }
 
   public void adjustPanelHeight()
@@ -77,148 +72,199 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
     int height = 0;
-    if(aa!=null)
-    for (int i = 0; i < aa.length; i++)
+
+    if (aa != null)
     {
-      if(!aa[i].visible)
-        continue;
+      for (int i = 0; i < aa.length; i++)
+      {
+        if (!aa[i].visible)
+        {
+          continue;
+        }
 
-      aa[i].height = 0;
+        aa[i].height = 0;
 
-      if(aa[i].hasText)
-        aa[i].height += av.charHeight;
-      if (aa[i].hasIcons)
-        aa[i].height += 16;
+        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].isGraph)
+        {
+          aa[i].height += GRAPH_HEIGHT;
+        }
 
-      if(aa[i].height==0)
-        aa[i].height = 20;
-      height += aa[i].height;
+        if (aa[i].height == 0)
+        {
+          aa[i].height = 20;
+        }
+
+        height += aa[i].height;
+      }
+    }
+    else
+    {
+      height = 20;
     }
-  else height=20;
-    this.setPreferredSize(new Dimension(1, height));
 
+    this.setPreferredSize(new Dimension(1, height));
   }
 
   public void addEditableColumn(int i)
   {
-    if(activeRow==-1)
+    if (activeRow == -1)
     {
-      AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-      for(int j=0; j<aa.length; j++)
-        if(aa[j].editable)
+      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+      for (int j = 0; j < aa.length; j++)
+      {
+        if (aa[j].editable)
         {
           activeRow = j;
+
           break;
         }
+      }
     }
 
-    if(activeRes==null)
+    if (activeRes == null)
     {
       activeRes = new ArrayList();
       activeRes.add(String.valueOf(i));
+
       return;
     }
 
     activeRes.add(String.valueOf(i));
-
   }
 
-
   public void actionPerformed(ActionEvent evt)
   {
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    Annotation[] anot = aa[activeRow].annotations;
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-    Annotation [] anot = aa[activeRow].annotations;
-
-    if(evt.getActionCommand().equals(REMOVE))
+    if (evt.getActionCommand().equals(REMOVE))
     {
-      for(int i=0; i<activeRes.size(); i++)
+      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))
+    else if (evt.getActionCommand().equals(LABEL))
     {
-      String label = JOptionPane.showInputDialog(this, "Enter Label ", "Enter label", JOptionPane.QUESTION_MESSAGE );
-      if(label==null)
+      String label = JOptionPane.showInputDialog(this, "Enter Label ",
+                                                 "Enter label",
+                                                 JOptionPane.QUESTION_MESSAGE);
+
+      if (label == null)
+      {
         label = "";
+      }
 
-      if(label.length()>0 && !aa[activeRow].hasText)
-       aa[activeRow].hasText = true;
+      if ( (label.length() > 0) && !aa[activeRow].hasText)
+      {
+        aa[activeRow].hasText = true;
+      }
 
-      for(int i=0; i<activeRes.size(); i++)
+      for (int i = 0; i < activeRes.size(); i++)
       {
         int index = Integer.parseInt(activeRes.get(i).toString());
-        if(anot[index]==null)
-          anot[index] = new Annotation(label, "", ' ',0);
+
+        if (anot[index] == null)
+        {
+          anot[index] = new Annotation(label, "", ' ', 0);
+        }
+
         anot[index].displayCharacter = label;
       }
     }
-    else if(evt.getActionCommand().equals(COLOUR))
+    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)
-         anot[index] = new Annotation("", "", ' ', 0);
-       anot[index].colour = col;
-     }
+      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)
+        {
+          anot[index] = new Annotation("", "", ' ', 0);
+        }
+
+        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";
-    }
+      char type = 0;
+      String symbol = "\u03B1";
 
-    if(!aa[activeRow].hasIcons)
-      aa[activeRow].hasIcons = true;
+      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)
-       label="";
+      String label = JOptionPane.showInputDialog(
+          "Enter a label for the structure?",
+          symbol);
 
-    if(label.length()>0 && !aa[activeRow].hasText)
-       aa[activeRow].hasText = true;
+      if (label == null)
+      {
+        label = "";
+      }
 
-    for(int i=0; i<activeRes.size(); i++)
-    {
-      int index = Integer.parseInt(activeRes.get(i).toString());
-      if (anot[index] == null)
+      if ( (label.length() > 0) && !aa[activeRow].hasText)
       {
-        anot[index] = new Annotation(label, "", type, 0);
+        aa[activeRow].hasText = true;
       }
 
-        anot[ index ].secondaryStructure = type;
-        anot[ index ].displayCharacter = label;
-    }
+      for (int i = 0; i < activeRes.size(); i++)
+      {
+        int index = Integer.parseInt(activeRes.get(i).toString());
+
+        if (anot[index] == null)
+        {
+          anot[index] = new Annotation(label, "", type, 0);
+        }
+
+        anot[index].secondaryStructure = type;
+        anot[index].displayCharacter = label;
+      }
     }
 
     adjustPanelHeight();
     activeRes = null;
     repaint();
-    return;
-
 
+    return;
   }
 
   public void mousePressed(MouseEvent evt)
   {
     if (SwingUtilities.isRightMouseButton(evt))
     {
-      if(activeRes==null)
+      if (activeRes == null)
+      {
         return;
+      }
 
       JPopupMenu pop = new JPopupMenu("Structure type");
       JMenuItem item = new JMenuItem(HELIX);
@@ -237,371 +283,481 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
       item.addActionListener(this);
       pop.add(item);
       pop.show(this, evt.getX(), evt.getY());
+
       return;
     }
 
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-    if(aa==null)
+    if (aa == null)
+    {
       return;
+    }
 
     int height = 0;
     activeRow = -1;
-    for(int i=0; i<aa.length; i++)
+
+    for (int i = 0; i < aa.length; i++)
     {
-      height+= aa[i].height;
+      height += aa[i].height;
 
-      if(evt.getY()<height)
+      if (evt.getY() < height)
       {
-        if(!aa[i].editable)
+        if (!aa[i].editable)
         {
           activeRes = null;
+
           continue;
         }
 
         activeRow = i;
+
         break;
       }
     }
 
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-
-    if(evt.isControlDown() || evt.isAltDown())
+    if (evt.isControlDown() || evt.isAltDown())
+    {
       addEditableColumn(res);
-
-    else if(evt.isShiftDown())
+    }
+    else if (evt.isShiftDown())
     {
-
-      if(activeRes==null)
-        activeRes=new ArrayList();
+      if (activeRes == null)
+      {
+        activeRes = new ArrayList();
+      }
       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);
+        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 ArrayList();
-        activeRes.add( String.valueOf(res) );
+      activeRes = new ArrayList();
+      activeRes.add(String.valueOf(res));
     }
 
     repaint();
-
   }
+
   public void mouseReleased(MouseEvent evt)
-  {  }
+  {
+  }
+
   public void mouseEntered(MouseEvent evt)
-  {  }
+  {
+  }
+
   public void mouseExited(MouseEvent evt)
-  {  }
+  {
+  }
+
   public void mouseDragged(MouseEvent evt)
-  {  }
+  {
+  }
+
   public void mouseMoved(MouseEvent evt)
   {
     ToolTipManager.sharedInstance().registerComponent(this);
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
-    if(aa==null)
+
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+    if (aa == null)
+    {
       return;
+    }
 
     int row = -1;
-    int height=0;
-    for(int i=0; i<aa.length; i++)
-    {
+    int height = 0;
 
-      if( aa[i].visible )
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (aa[i].visible)
+      {
         height += aa[i].height;
+      }
 
-      if(evt.getY()<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)
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+    if ( (row > -1) && (res < aa[row].annotations.length) &&
+        (aa[row].annotations[res] != null))
     {
       this.setToolTipText(aa[row].annotations[res].description);
-      StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
-                                           "  " +
+
+      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 mouseClicked(MouseEvent evt)
+  {
+  }
 
   public void paintComponent(Graphics g)
   {
     g.setColor(Color.white);
-    g.fillRect(0,0,getWidth(), getHeight());
+    g.fillRect(0, 0, getWidth(), getHeight());
 
-    if(fastPaint)
+    if (fastPaint)
     {
       g.drawImage(image, 0, 0, this);
       fastPaint = false;
+
       return;
     }
 
-    imgWidth = (av.endRes-av.startRes+1) *av.charWidth;
+    imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
-    image = new BufferedImage(imgWidth,
-                                ap.annotationPanel.getHeight(),
-                                BufferedImage.TYPE_INT_RGB);
-      gg = (Graphics2D) image.getGraphics();
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                          RenderingHints.VALUE_ANTIALIAS_ON);
+    image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+                              BufferedImage.TYPE_INT_RGB);
+    gg = (Graphics2D) image.getGraphics();
+    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                        RenderingHints.VALUE_ANTIALIAS_ON);
 
-      gg.setFont(av.getFont());
-      fm = gg.getFontMetrics();
-
-    drawComponent( gg, av.startRes, av.endRes+1);
-    g.drawImage( image, 0, 0, this);
+    gg.setFont(av.getFont());
+    fm = gg.getFontMetrics();
 
+    drawComponent(gg, av.startRes, av.endRes + 1);
+    g.drawImage(image, 0, 0, this);
   }
 
   public void fastPaint(int horizontal)
-{
-  if( horizontal == 0
-     || av.alignment.getAlignmentAnnotation()==null
-     || av.alignment.getAlignmentAnnotation().length<1
-    )
   {
-    repaint();
-    return;
-  }
+    if ( (horizontal == 0) ||
+        (av.alignment.getAlignmentAnnotation() == null) ||
+        (av.alignment.getAlignmentAnnotation().length < 1))
+    {
+      repaint();
 
-  gg.copyArea( 0,0, imgWidth, getHeight(), -horizontal*av.charWidth, 0 );
-  int sr=av.startRes, er=av.endRes+1, transX=0;
+      return;
+    }
 
-  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;
-  }
+    gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
 
+    int sr = av.startRes;
+    int er = av.endRes + 1;
+    int transX = 0;
 
-  gg.translate(transX, 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;
+    }
 
-  drawComponent(gg, sr, er);
+    gg.translate(transX, 0);
 
-  gg.translate( -transX, 0 );
+    drawComponent(gg, sr, er);
 
-  fastPaint = true;
-  repaint();
-}
+    gg.translate( -transX, 0);
 
+    fastPaint = true;
+    repaint();
+  }
 
   public void drawComponent(Graphics2D g, int startRes, int endRes)
   {
     g.setColor(Color.white);
-    g.fillRect(0,0,(endRes-startRes) *av.charWidth, getHeight());
-    if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)
+    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+
+    if ( (av.alignment.getAlignmentAnnotation() == null) ||
+        (av.alignment.getAlignmentAnnotation().length < 1))
     {
       g.setColor(Color.white);
-      g.fillRect(0,0,getWidth(), getHeight());
+      g.fillRect(0, 0, getWidth(), getHeight());
       g.setColor(Color.black);
-      g.drawString("Alignment has no annotations",20,15);
+      g.drawString("Alignment has no annotations", 20, 15);
+
       return;
     }
 
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    int j, x=0, y=0;
-    char [] lastSS = new char[aa.length];
-    int  [] lastSSX= new int[aa.length] ;
-    int iconOffset = av.charHeight/2;
+    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++)
+    //\u03B2 \u03B1
+    for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
-      if(!row.visible)
+
+      if (!row.visible)
+      {
         continue;
+      }
 
-      if(row.isGraph)
+      if (row.isGraph)
       {
         // this is so that we draw the characters below the graph
         y += row.height;
-        if(row.hasText)
+
+        if (row.hasText)
+        {
           y -= av.charHeight;
+        }
+      }
+
+      if (row.hasText)
+      {
+        iconOffset = av.charHeight / 2;
       }
-      if(row.hasText)
-        iconOffset = av.charHeight/2;
       else
+      {
         iconOffset = 0;
+      }
 
-      for(j=startRes; j<endRes; j++)
+      for (j = startRes; j < endRes; j++)
       {
-        if(row.annotations.length<=j || row.annotations[j]==null)
-        validRes = false;
-       else
-         validRes = true;
-
-       x = (j-startRes)*av.charWidth;
+        if ( (row.annotations.length <= j) ||
+            (row.annotations[j] == null))
+        {
+          validRes = false;
+        }
+        else
+        {
+          validRes = true;
+        }
 
+        x = (j - startRes) * av.charWidth;
 
-       if(activeRow==i)
-       {
+        if (activeRow == i)
+        {
+          g.setColor(Color.red);
 
-         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(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)
+          {
+            if ( (row.annotations[0].secondaryStructure == 'H') ||
+                (row.annotations[0].secondaryStructure == 'E'))
+            {
+              g.drawString(row.annotations[j].displayCharacter,
+                           x, y + iconOffset + 2);
+            }
+          }
+          else if ( ( (row.annotations[j].secondaryStructure == 'H') ||
+                     (row.annotations[j].secondaryStructure == 'E')) &&
+                   ( (row.annotations[j - 1] == null) ||
+                    (row.annotations[j].secondaryStructure != row.annotations[j -
+                     1].secondaryStructure)))
+          {
+            g.drawString(row.annotations[j].displayCharacter, x,
+                         y + iconOffset + 2);
+          }
 
+          if (!row.hasIcons)
+          {
+            g.drawString(row.annotations[j].displayCharacter,
+                         x + charOffset, y + iconOffset + 2);
+          }
+        }
 
-       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)
+        if (row.hasIcons)
+        {
+          if (!validRes ||
+              (row.annotations[j].secondaryStructure != lastSS[i]))
           {
-            if (row.annotations[0].secondaryStructure == 'H'
-                || row.annotations[0].secondaryStructure == 'E')
-              g.drawString(row.annotations[j].displayCharacter, x,
-                           y + iconOffset + 2);
+            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 + 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;
           }
-         else if( (row.annotations[j].secondaryStructure=='H'
-               || row.annotations[j].secondaryStructure=='E') &&
-               (row.annotations[j-1]==null ||
-                row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))
+        }
 
-        g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);
+        if (validRes && row.isGraph)
+        {
+          g.setColor(new Color(0, 0, 180));
 
-        if(!row.hasIcons)
-            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);
-             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 );
-       }
+          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);
+        }
       }
 
-      x+=av.charWidth;
+      x += av.charWidth;
 
-      if(row.hasIcons)
-      switch (lastSS[i])
+      if (row.hasIcons)
       {
-        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;
+        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 && row.hasText)
+      {
+        y += av.charHeight;
       }
 
-       if(row.isGraph && row.hasText)
-         y+=av.charHeight;
-       if(!row.isGraph)
-          y+=aa[i].height;
+      if (!row.isGraph)
+      {
+        y += aa[i].height;
+      }
     }
   }
 
   // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)
+  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));
+    g.fillRect(0, 0, width, y);
+    g.setColor(new Color(0, 0, 180));
+
     int x = 0;
-    for(int j=0; j<aa.annotations.length; j++)
+
+    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 );
+
+      int height = (int) ( (aa.annotations[j].value / aa.graphMax) *
+                          GRAPH_HEIGHT);
       g.fillRect(x, y - height, av.charWidth, height);
-      x+=av.charWidth;
+      x += av.charWidth;
     }
   }
 }
diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index 5761184..fc11698 100755
--- a/src/jalview/gui/ColumnSelection.java
+++ b/src/jalview/gui/ColumnSelection.java
@@ -1,22 +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.gui;
 
 import java.util.*;
@@ -24,70 +23,95 @@ import java.util.*;
 /**
  * NOTE: Columns are zero based.
  */
-public class ColumnSelection{
+public class ColumnSelection
+{
   Vector selected = new Vector();
 
-  public void addElement(int col) {
+  public void addElement(int col)
+  {
     selected.addElement(new Integer(col));
   }
 
-  public void clear() {
+  public void clear()
+  {
     selected.removeAllElements();
   }
 
-  public void removeElement(int col) {
+  public void removeElement(int col)
+  {
     Integer colInt = new Integer(col);
-    if (selected.contains(colInt)) {
+
+    if (selected.contains(colInt))
+    {
       selected.removeElement(colInt);
-    } else {
-      System.err.println("WARNING: Tried to remove Integer NOT in ColumnSelection");
+    }
+    else
+    {
+      System.err.println(
+          "WARNING: Tried to remove Integer NOT in ColumnSelection");
     }
   }
 
-  public boolean contains(int col) {
+  public boolean contains(int col)
+  {
     return selected.contains(new Integer(col));
   }
 
-  public int columnAt(int i) {
-    return ((Integer)selected.elementAt(i)).intValue();
+  public int columnAt(int i)
+  {
+    return ( (Integer) selected.elementAt(i)).intValue();
   }
 
-  public int size() {
+  public int size()
+  {
     return selected.size();
   }
 
-  public int getMax() {
+  public int getMax()
+  {
     int max = -1;
 
-    for (int i=0;i<selected.size();i++) {
-      if (columnAt(i) > max) {
+    for (int i = 0; i < selected.size(); i++)
+    {
+      if (columnAt(i) > max)
+      {
         max = columnAt(i);
       }
     }
+
     return max;
   }
 
-  public int getMin() {
+  public int getMin()
+  {
     int min = 1000000000;
 
-    for (int i=0;i<selected.size();i++) {
-      if (columnAt(i) < min) {
+    for (int i = 0; i < selected.size(); i++)
+    {
+      if (columnAt(i) < min)
+      {
         min = columnAt(i);
       }
     }
+
     return min;
   }
 
-  public Vector asVector() {
+  public Vector asVector()
+  {
     return selected;
   }
 
-  public void compensateForEdit(int start, int change) {
-    for (int i=0; i < size();i++) {
+  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);
+      {
+        selected.setElementAt(new Integer(temp - change), i);
+      }
     }
   }
 }
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 262fc41..175a609 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,115 +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
-*/
-
-package jalview.gui;
-
-import jalview.jbgui.GCutAndPasteTransfer;
-import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.datatransfer.*;
-import jalview.datamodel.Alignment;
-import jalview.io.FormatAdapter;
-import jalview.datamodel.SequenceI;
-import javax.swing.JOptionPane;
-import jalview.io.IdentifyFile;
-
-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)
-      return;
-    try{
-      textarea.setText( (String) contents.getTransferData(DataFlavor.
-          stringFlavor));
-    }catch(Exception ex){}
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-      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);
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try{
-      this.setClosed(true);
-    }catch(Exception ex){}
-  }
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import 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
+{
+  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)
+    {
+      return;
+    }
+
+    try
+    {
+      textarea.setText( (String) contents.getTransferData(
+          DataFlavor.stringFlavor));
+    }
+    catch (Exception ex)
+    {
+    }
+  }
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    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);
+    }
+  }
+
+  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 fca0acc..e239a10 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,57 +1,61 @@
 /*
-* 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.gui;
 
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.datamodel.*;
-import javax.swing.*;
 import java.awt.*;
-import java.awt.event.*;
+import java.awt.datatransfer.*;
 import java.awt.dnd.*;
+import java.awt.event.*;
 import javax.swing.*;
-import java.awt.datatransfer.*;
-import jalview.bin.Cache;
 
+import jalview.datamodel.*;
+import jalview.io.*;
 
-public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener
+public class Desktop
+    extends jalview.jbgui.GDesktop implements DropTargetListener
 {
   public static JDesktopPane desktop;
   static int openFrameCount = 0;
-  static final int xOffset = 30, yOffset = 30;
+  static final int xOffset = 30;
+  static final int yOffset = 30;
 
   public Desktop()
   {
-    Image image =null;
-    try{
+    Image image = null;
+
+    try
+    {
       java.net.URL url = getClass().getResource("/images/logo.gif");
-      if(url!=null)
+
+      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){}
+    }
+    catch (Exception ex)
+    {
+    }
 
     setTitle("Jalview 2005");
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
@@ -60,11 +64,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListene
     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() );
-
+    desktop.setDesktopManager(new DefaultDesktopManager());
 
     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
     String x = jalview.bin.Cache.getProperty("SCREEN_X");
@@ -72,311 +74,396 @@ public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListene
     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)
+    if ( (x != null) && (y != null) && (width != null) && (height != null))
     {
-      setBounds( Integer.parseInt(x), Integer.parseInt(y),
-                 Integer.parseInt(width), Integer.parseInt(height));
+      setBounds(Integer.parseInt(x), Integer.parseInt(y),
+                Integer.parseInt(width), Integer.parseInt(height));
     }
     else
-      setBounds( (int)(screenSize.width-900)/2,
-           (int)(screenSize.height-650)/2,
-          900 ,
-          650);
+    {
+      setBounds( (int) (screenSize.width - 900) / 2,
+                (int) (screenSize.height - 650) / 2, 900, 650);
+    }
 
-this.addWindowListener(new WindowAdapter()
-{
-public void windowClosing(WindowEvent evt)
-{
- 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() + "");
-}
-});
-setVisible(true);
+    this.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        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() + "");
+      }
+    });
+    setVisible(true);
 
-this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 
-/////////Add a splashscreen on startup
-   /////////Add a splashscreen on startup
+    /////////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));
+    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)
+
+  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 )
+  public static void addInternalFrame(final JInternalFrame frame,
+                                      String title, int w, int h,
+                                      boolean resizable)
   {
-   desktop.add(frame);
-   openFrameCount++;
-   try {
-       frame.setSelected(true);
-   } catch (java.beans.PropertyVetoException e) {}
-   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()
+    desktop.add(frame);
+    openFrameCount++;
+
+    try
+    {
+      frame.setSelected(true);
+    }
+    catch (java.beans.PropertyVetoException e)
+    {
+    }
+
+    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){};
+        try
+        {
+          frame.setSelected(true);
+          frame.setIcon(false);
+        }
+        catch (java.beans.PropertyVetoException ex)
+        {
+        }
+
+        ;
       }
     });
 
-   frame.setVisible(true);
-   windowMenu.add(menuItem);
- }
+    frame.setVisible(true);
+    windowMenu.add(menuItem);
+  }
 
- public void dragEnter(DropTargetDragEvent evt){}
- public void dragExit(DropTargetEvent evt){}
- public void dragOver(DropTargetDragEvent evt){}
- public void dropActionChanged(DropTargetDragEvent evt){}
- public void drop(DropTargetDropEvent evt)
-{
-   Transferable t = evt.getTransferable();
-   if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
-     return;
-
-   evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-   try{
-     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";
-       if(file.endsWith(".jar"))
-                Jalview2XML.LoadJalviewAlign(file);
+  public void dragEnter(DropTargetDragEvent evt)
+  {
+  }
+
+  public void dragExit(DropTargetEvent evt)
+  {
+  }
+
+  public void dragOver(DropTargetDragEvent evt)
+  {
+  }
+
+  public void dropActionChanged(DropTargetDragEvent evt)
+  {
+  }
+
+  public void drop(DropTargetDropEvent evt)
+  {
+    Transferable t = evt.getTransferable();
+
+    if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+    {
+      return;
+    }
+
+    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+
+    try
+    {
+      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";
+
+        if (file.endsWith(".jar"))
+        {
+          Jalview2XML.LoadJalviewAlign(file);
+        }
+        else
+        {
+          String format = jalview.io.IdentifyFile.Identify(file,
+              protocol);
+          LoadFile(file, protocol, format);
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  public void inputLocalFileMenuItem_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"
+    }, 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)
+    {
+      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 = jalview.io.IdentifyFile.Identify(file, protocol);
-        LoadFile(file, protocol, format);
+        String format = IdentifyFile.Identify(choice, "File");
+        jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+        LoadFile(choice, "File", format);
       }
-     }
+    }
+  }
 
-   }catch(Exception ex){ex.printStackTrace();}
+  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)
+    {
+      return;
+    }
 
- public void inputLocalFileMenuItem_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"}
-       ,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)
-   {
-     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);
-     }
-   }
- }
-
- public void LoadFile(String file, String protocol,  String format)
- {
-   LoadingThread loader = new LoadingThread(file, protocol, format);
-   loader.start();
- }
-
- class LoadingThread extends Thread
- {
-   String file, protocol, format;
-
-   public LoadingThread(String file, String protocol,  String format)
-   {
-     this.file = file;
-     this.protocol = protocol;
-     this.format = format;
-   }
-   public void run()
-   {
-     SequenceI [] sequences = null;
-
-     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{
-           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);
-
-   }
- }
-
-
- 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)
-     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;
-   }
+    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);
- }
+  }
 
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
- {
-   CutAndPasteTransfer cap = new CutAndPasteTransfer();
-   cap.setForInput();
-   Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
- }
+  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_actionPerformed(ActionEvent e)
- {
-   if(jalview.bin.Jalview.applet!=null)
-     jalview.bin.Jalview.applet.destroy();
+  /*
+   * Exit the program
+   */
+  public void quit_actionPerformed(ActionEvent e)
+  {
+    if (jalview.bin.Jalview.applet != null)
+    {
+      jalview.bin.Jalview.applet.destroy();
+    }
     else
+    {
       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
-   {
+    }
+  }
+
+  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
+    {
       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);
+      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.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();
- }
-
- 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");
-   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);
-   }
-
- }
-
-
- 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)
-   {
-     String choice =  chooser.getSelectedFile().getAbsolutePath();
-     jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
-     Jalview2XML.LoadJalviewAlign(choice);
-   }
- }
-}
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  protected void preferences_actionPerformed(ActionEvent e)
+  {
+    Preferences pref = 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");
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save State");
+
+    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);
+    }
+  }
 
+  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)
+    {
+      String choice = chooser.getSelectedFile().getAbsolutePath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                    chooser.getSelectedFile().getParent());
+      Jalview2XML.LoadJalviewAlign(choice);
+    }
+  }
+
+  class LoadingThread
+      extends Thread
+  {
+    String file;
+    String protocol;
+    String format;
+
+    public LoadingThread(String file, String protocol, String format)
+    {
+      this.file = file;
+      this.protocol = protocol;
+      this.format = format;
+    }
+
+    public void run()
+    {
+      SequenceI[] sequences = null;
+
+      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
+        {
+          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);
+      }
+    }
+  }
+}
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 1dd434d..e80d01a 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,35 +1,34 @@
 /*
-* 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.gui;
 
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.*;
 import java.util.*;
 
+import java.awt.*;
+
+import jalview.datamodel.*;
+
 public class FeatureRenderer
 {
   AlignViewport av;
-
   SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
+  SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
 
@@ -38,48 +37,60 @@ public class FeatureRenderer
     this.av = av;
   }
 
-
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)
+  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() )
+
+    while (e.hasMoreElements())
     {
-      SequenceFeature sf = (SequenceFeature)e.nextElement();
-      if(sf.getStart()>seq.getEnd())
+      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;
+      int fstart = seq.findIndex(sf.getStart()) - 1;
+      int fend = seq.findIndex(sf.getEnd()) - 1;
 
-      if(   (fstart<=end && fend>=start)  )
+      if ( ( (fstart <= end) && (fend >= start)))
       {
-        if(fstart<0) // fix for if the feature we have starts before the sequence start,
-          fstart = 0;// but the feature end is still valid!!
+        if (fstart < 0)
+        { // fix for if the feature we have starts before the sequence start,
+          fstart = 0; // but the feature end is still valid!!
+        }
 
-        if(fstart==fend)
+        if (fstart == fend)
         {
           g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
+          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);
-
+          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) )
+
+            if (jalview.util.Comparison.isGap(s))
+            {
               continue;
+            }
 
             g.setColor(Color.blue);
-            g.fillRect( (i-start) * width, y1, width, height);
+            g.fillRect( (i - start) * width, y1, width, height);
 
             g.setColor(Color.white);
 
@@ -87,13 +98,11 @@ public class FeatureRenderer
             int charOffset = (width - fm.charWidth(s)) / 2;
             int pady = height / 5;
             g.drawString(String.valueOf(s),
-                         charOffset + x1 + width * (i-start),
-                         y1 + height - pady);
+                         charOffset + x1 + (width * (i - start)),
+                         (y1 + height) - pady);
           }
         }
       }
-
     }
-   }
-
+  }
 }
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index d20cb65..af1888c 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,42 +1,44 @@
 /*
-* 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.gui;
 
-import jalview.jbgui.GFinder;
-import jalview.datamodel.*;
+import java.util.*;
+
+import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
-import java.util.*;
-import java.awt.*;
 
-public class Finder extends GFinder
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+
+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;
@@ -52,16 +54,17 @@ public class Finder extends GFinder
         SwingUtilities.invokeLater(new Runnable()
         {
           public void run()
-          {   textfield.requestFocus();      }
-       });
-     }
-
-     public void internalFrameClosing(InternalFrameEvent evt)
-     {
-       cancel_actionPerformed(null);
-     }
-});
+          {
+            textfield.requestFocus();
+          }
+        });
+      }
 
+      public void internalFrameClosing(InternalFrameEvent evt)
+      {
+        cancel_actionPerformed(null);
+      }
+    });
   }
 
   public void textfield_actionPerformed(ActionEvent e)
@@ -76,213 +79,257 @@ public class Finder extends GFinder
 
   public void findAll_actionPerformed(ActionEvent e)
   {
-    resIndex=0;
-    seqIndex=0;
+    resIndex = 0;
+    seqIndex = 0;
     doSearch(true);
   }
 
   public void cancel_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-      ap.highlightSearchResults( null );
-      ap.idPanel.highlightSearchResults( null );
-     // frame.setClosed(true);
-    }catch(Exception ex){ }
-  }
+      ap.highlightSearchResults(null);
+      ap.idPanel.highlightSearchResults(null);
 
+      // frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {
+    }
+  }
 
   public void createNewGroup_actionPerformed(ActionEvent e)
   {
+    Color[] newColors = new Color[24];
 
-   Color [] newColors = new Color[24];
-   for(int i=0; i<24; i++)
-     newColors[i] = new Color(60,160,115);
-
-   jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
-   String searchString = textfield.getText();
+    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();
 
+    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
-    for(int i=0; i<searchResults.size(); i+=3)
+    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  );
+      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);
       av.alignment.addGroup(sg);
-      searchGroup.addGroup( sg );
-
+      searchGroup.addGroup(sg);
     }
 
     ap.av.alignment.addSuperGroup(searchGroup);
-    ap.highlightSearchResults( null );
+    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);
+    com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
     searchResults = new Vector();
-    int [] allResults = null;
+
+    int[] allResults = null;
 
     Sequence seq;
-    String item=null;
+    String item = null;
     boolean found = false;
 
     ////// is the searchString a residue number?
-    try{
+    try
+    {
       int res = Integer.parseInt(searchString);
       found = true;
 
-      if(av.getSelectionGroup().getSize()>0)
-        seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
+      if (av.getSelectionGroup().getSize() > 0)
+      {
+        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+      }
       else
-        seq = (Sequence)av.getAlignment().getSequenceAt(0);
+      {
+        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 ) );
+      searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));
+      searchResults.add(Integer.toString(seq.findIndex(res) - 1));
+      searchResults.add(Integer.toString(seq.findIndex(res) - 1));
+    }
+    catch (NumberFormatException ex)
+    {
+    }
 
-    }catch(NumberFormatException ex){}
     ///////////////////////////////////////////////
+    Color[] newColors = new Color[24];
 
+    for (int i = 0; i < 24; i++)
+    {
+      newColors[i] = new Color(60, 160, 115);
+    }
 
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+        newColors);
 
-    Color [] newColors = new Color[24];
-    for(int i=0; i<24; i++)
-      newColors[i] = new Color(60,160,115);
-
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
-
-    searchGroup = new SuperGroup(searchString, ucs , true, true, false);
+    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
     int end = av.alignment.getHeight();
 
     SequenceGroup selection = av.getSelectionGroup();
-    if(selection!=null)
-     if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
-      selection = null;
 
-    while( !found && seqIndex<end)
+    if (selection != null)
     {
-      seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
+      if ( (selection.getSize() < 1) ||
+          ( (selection.getEndRes() - selection.getStartRes()) < 2))
+      {
+        selection = null;
+      }
+    }
 
+    while (!found && (seqIndex < end))
+    {
+      seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 
-      if(selection!=null && !selection.sequences.contains(seq))
+      if ( (selection != null) && !selection.sequences.contains(seq))
       {
         seqIndex++;
-        resIndex=0;
+        resIndex = 0;
+
         continue;
       }
 
       item = seq.getSequence().toUpperCase();
 
-      if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
-          item = item.substring(0, selection.getEndRes()+1);
+      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;
+      int insertCount = 0;
       Vector spaces = new Vector();
 
-      for (int j=0; j < item.length(); j++)
+      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));
-         }
+        if (!jalview.util.Comparison.isGap(item.charAt(j)))
+        {
+          noGaps.append(item.charAt(j));
+          spaces.add(new Integer(insertCount));
+        }
         else
-           insertCount++;
+        {
+          insertCount++;
+        }
       }
 
-
-
-      for(int r = resIndex; r<noGaps.length(); r++)
+      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 (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)
+
+      if (!found)
       {
         seqIndex++;
         resIndex = 0;
       }
     }
 
-
     Vector idMatch = new Vector();
-    for(int id = 0; id<av.alignment.getHeight(); 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 (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)
+    if (searchResults.size() > 0)
     {
       allResults = new int[searchResults.size()];
-      for(int i=0; i<searchResults.size(); i++)
+
+      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;
+      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 );
+    ap.highlightSearchResults(allResults);
 
     if (findAll)
     {
-      String message =  (searchResults.size()/3) + " matches found.";
+      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 d781d72..b911d7d 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -1,34 +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.gui;
 
-import jalview.jbgui.GFontChooser;
-import jalview.gui.*;
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
-import javax.swing.event.*;
-import jalview.bin.Cache;
 
+import jalview.bin.*;
+import jalview.jbgui.*;
 
-public class FontChooser extends GFontChooser
+public class FontChooser
+    extends GFontChooser
 {
   AlignmentPanel ap;
   Font oldFont;
@@ -39,37 +37,50 @@ public class FontChooser extends GFontChooser
   {
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Change Font", 480,100, false);
+    Desktop.addInternalFrame(frame, "Change Font", 480, 100, false);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
     this.ap = ap;
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-    for(int i=0; i<fonts.length; i++)
+
+    String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
+        .getAvailableFontFamilyNames();
+
+    for (int i = 0; i < fonts.length; i++)
+    {
       fontName.addItem(fonts[i]);
+    }
 
-    for(int i=1; i<31; i++)
-      fontSize.addItem(i+"");
+    for (int i = 1; i < 31; i++)
+    {
+      fontSize.addItem(i + "");
+    }
 
-   fontStyle.addItem("plain");
-   fontStyle.addItem("bold");
-   fontStyle.addItem("italic");
+    fontStyle.addItem("plain");
+    fontStyle.addItem("bold");
+    fontStyle.addItem("italic");
 
-   oldFont = ap.av.getFont();
-   fontName.setSelectedItem(oldFont.getName());
-   fontSize.setSelectedItem(oldFont.getSize()+"");
-   fontStyle.setSelectedIndex(oldFont.getStyle());
+    oldFont = ap.av.getFont();
+    fontName.setSelectedItem(oldFont.getName());
+    fontSize.setSelectedItem(oldFont.getSize() + "");
+    fontStyle.setSelectedIndex(oldFont.getStyle());
 
-   init = false;
+    init = false;
   }
 
   protected void ok_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       frame.setClosed(true);
-    }catch(Exception ex){}
-
-   if(ap.getOverviewPanel()!=null)
-     ap.getOverviewPanel().updateOverviewImage();
+    }
+    catch (Exception ex)
+    {
+    }
+
+    if (ap.getOverviewPanel() != null)
+    {
+      ap.getOverviewPanel().updateOverviewImage();
+    }
   }
 
   protected void cancel_actionPerformed(ActionEvent e)
@@ -77,48 +88,62 @@ public class FontChooser extends GFontChooser
     ap.av.setFont(oldFont);
     ap.repaint();
     fontName.setSelectedItem(oldFont.getName());
-    fontSize.setSelectedItem(oldFont.getSize()+"");
+    fontSize.setSelectedItem(oldFont.getSize() + "");
     fontStyle.setSelectedIndex(oldFont.getStyle());
-    try{
+
+    try
+    {
       frame.setClosed(true);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
   }
 
   void changeFont()
   {
     Font newFont = new Font(fontName.getSelectedItem().toString(),
                             fontStyle.getSelectedIndex(),
-                            Integer.parseInt(fontSize.getSelectedItem().toString())
-                            );
+                            Integer.parseInt(fontSize.getSelectedItem().
+                                             toString()));
     ap.av.setFont(newFont);
     ap.fontChanged();
   }
 
   protected void fontName_actionPerformed(ActionEvent e)
   {
-    if(init) return;
+    if (init)
+    {
+      return;
+    }
+
     changeFont();
   }
 
   protected void fontSize_actionPerformed(ActionEvent e)
   {
-    if(init) return;
+    if (init)
+    {
+      return;
+    }
+
     changeFont();
   }
 
   protected void fontStyle_actionPerformed(ActionEvent e)
   {
-    if(init) return;
+    if (init)
+    {
+      return;
+    }
+
     changeFont();
   }
 
   public void defaultButton_actionPerformed(ActionEvent e)
   {
     Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
-    Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex()+"");
+    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 c523060..e30be30 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,113 +1,139 @@
 /*
-* 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.gui;
 
 import java.awt.*;
-import java.awt.Graphics2D.*;
 import java.awt.image.*;
 import javax.swing.*;
-import jalview.datamodel.*;
+
 import jalview.analysis.*;
-public class IdCanvas extends JPanel
+import jalview.datamodel.*;
+
+public class IdCanvas
+    extends JPanel
 {
   protected AlignViewport av;
-
-  protected boolean showScores  = true;
-
-  protected int     maxIdLength = -1;
-  protected String  maxIdStr    = null;
+  protected boolean showScores = true;
+  protected int maxIdLength = -1;
+  protected String maxIdStr = null;
   BufferedImage image;
   Graphics2D gg;
-  int imgHeight=0;
+  int imgHeight = 0;
   boolean fastPaint = false;
-
   java.util.Vector searchResults;
 
   public IdCanvas(AlignViewport av)
   {
     setLayout(new BorderLayout());
-    this.av         = av;
+    this.av = av;
     PaintRefresher.Register(this);
   }
 
-  public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
+  public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
+                           int ypos)
+  {
+    int charHeight = av.getCharHeight();
 
-      if(searchResults!=null && searchResults.contains(s))
-      {
-        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);
-      }
+    if ( (searchResults != null) && searchResults.contains(s))
+    {
+      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);
+    }
 
-      String string = s.getName();
-      if(av.getShowFullId())
-        string = s.getDisplayId();
+    String string = s.getName();
 
-      gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight-   (charHeight/5));
+    if (av.getShowFullId())
+    {
+      string = s.getDisplayId();
+    }
 
+    gg.drawString(string, 0,
+                  (AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +
+                   charHeight) - (charHeight / 5));
   }
 
   public void fastPaint(int vertical)
   {
-    if(gg==null)
-    {  repaint(); return;}
+    if (gg == null)
+    {
+      repaint();
 
-    gg.copyArea( 0,0, getWidth(), imgHeight, 0, -vertical*av.charHeight );
+      return;
+    }
 
-    int ss=av.startSeq, es=av.endSeq, transY = 0;
-    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(es > av.endSeq)
-         es = av.endSeq;
-     }
+    gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
 
+    int ss = av.startSeq;
+    int es = av.endSeq;
+    int transY = 0;
 
+    if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
 
-        gg.translate(0, transY);
+      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 (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
 
-        drawIds(ss, es);
+    gg.translate(0, transY);
 
-        gg.translate( 0, -transY );
+    drawIds(ss, es);
 
+    gg.translate(0, -transY);
 
-      fastPaint = true;
-      repaint();
+    fastPaint = true;
+    repaint();
   }
 
   public void paintComponent(Graphics g)
@@ -119,70 +145,74 @@ public class IdCanvas extends JPanel
     {
       fastPaint = false;
       g.drawImage(image, 0, 0, this);
+
       return;
     }
 
     imgHeight = getHeight();
-    imgHeight -= imgHeight % av.charHeight;
+    imgHeight -= (imgHeight % av.charHeight);
 
-    if (imgHeight<1)
+    if (imgHeight < 1)
+    {
       return;
+    }
 
-    image = new BufferedImage(getWidth(), imgHeight, BufferedImage.TYPE_INT_RGB);
+    image = new BufferedImage(getWidth(), imgHeight,
+                              BufferedImage.TYPE_INT_RGB);
     gg = (Graphics2D) image.getGraphics();
+
     //Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
     gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                         RenderingHints.VALUE_ANTIALIAS_ON);
+
     Font italic = new Font(av.getFont().getName(), Font.ITALIC,
                            av.getFont().getSize());
     gg.setFont(italic);
 
-    drawIds( av.getStartSeq(), av.endSeq);
+    drawIds(av.getStartSeq(), av.endSeq);
 
     g.drawImage(image, 0, 0, this);
   }
 
   void drawIds(int starty, int endy)
   {
-    Color currentColor     = Color.white;
+    Color currentColor = Color.white;
     Color currentTextColor = Color.black;
 
     if (av.getWrapAlignment())
     {
+      int rowSize = av.getEndRes() - av.getStartRes();
 
-          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
+      // 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
     {
-
       //Now draw the id strings
       for (int i = starty; i < endy; i++)
       {
         // Selected sequence colours
-
-        if(searchResults!=null && searchResults.contains(av.alignment.getSequenceAt(i)))
+        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)))
+        }
+        else if ( (av.getSelectionGroup() != null) &&
+                 av.getSelectionGroup().sequences.contains(
+                     av.alignment.getSequenceAt(i)))
         {
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
@@ -197,23 +227,26 @@ public class IdCanvas extends JPanel
 
         gg.fillRect(0,
                     AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                    getWidth(),
-                    av.charHeight);
+                    getWidth(), av.charHeight);
 
         gg.setColor(currentTextColor);
+
         String string = av.alignment.getSequenceAt(i).getName();
-        if(av.getShowFullId())
+
+        if (av.getShowFullId())
+        {
           string = av.alignment.getSequenceAt(i).getDisplayId();
+        }
+
         gg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +
-                      av.charHeight - (av.charHeight / 5));
+                      (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());
+      gg.fillRect(getWidth() - 4, 0, 4, getHeight());
     }
-
   }
 
   public void setHighlighted(java.util.Vector found)
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 4236cf8..4efef45 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,46 +1,45 @@
 /*
-* 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.gui;
 
 import java.awt.*;
 import java.awt.event.*;
-
-import jalview.datamodel.*;
-
 import javax.swing.*;
 
-public class IdPanel extends JPanel implements MouseListener, MouseMotionListener {
+import jalview.datamodel.*;
 
-  protected IdCanvas       idCanvas;
-  protected AlignViewport  av;
+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 offy;
+  int width;
   int lastid = -1;
   boolean mouseDragging = false;
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
-    this.av         = av;
+    this.av = av;
     alignPanel = parent;
     idCanvas = new IdCanvas(av);
     setLayout(new BorderLayout());
@@ -49,24 +48,36 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
     addMouseMotionListener(this);
   }
 
-  public void mouseMoved(MouseEvent e) {}
-
+  public void mouseMoved(MouseEvent e)
+  {
+  }
 
-  public void mouseDragged(MouseEvent e) {
+  public void mouseDragged(MouseEvent e)
+  {
     mouseDragging = true;
 
     int y = e.getY();
-    if(av.getWrapAlignment())
-      y-=2*av.charHeight;
+
+    if (av.getWrapAlignment())
+    {
+      y -= (2 * av.charHeight);
+    }
+
     int seq = av.getIndex(y);
 
-    if(seq<0)
+    if (seq < 0)
+    {
       return;
+    }
 
     if (seq < lastid)
+    {
       selectSeqs(lastid - 1, seq);
+    }
     else if (seq > lastid)
+    {
       selectSeqs(lastid + 1, seq);
+    }
 
     lastid = seq;
     alignPanel.repaint();
@@ -76,95 +87,128 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
   {
     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+[swall-id:" + 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();
-       }
-    }
+      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+[swall-id:" +
+            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 mouseEntered(MouseEvent e)
   {
-    if(scrollThread!=null)
+    if (scrollThread != null)
+    {
       scrollThread.running = false;
+    }
   }
 
-  public void mouseExited (MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
-    if(av.getWrapAlignment())
+    if (av.getWrapAlignment())
+    {
       return;
+    }
 
-    if(mouseDragging && e.getY()<0 && av.getStartSeq()>0)
+    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
     {
       scrollThread = new ScrollThread(true);
     }
 
-    if(mouseDragging && e.getY()>=getHeight() && av.alignment.getHeight()>av.getEndSeq())
+    if (mouseDragging && (e.getY() >= getHeight()) &&
+        (av.alignment.getHeight() > av.getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
   }
 
-
-  public void mousePressed(MouseEvent e) {
+  public void mousePressed(MouseEvent e)
+  {
     if (e.getClickCount() == 2)
+    {
       return;
+    }
 
     int y = e.getY();
-    if(av.getWrapAlignment())
-      y-=2*av.charHeight;
+
+    if (av.getWrapAlignment())
+    {
+      y -= (2 * av.charHeight);
+    }
 
     int seq = av.getIndex(y);
+
     if (seq == -1)
+    {
       return;
+    }
 
     if (javax.swing.SwingUtilities.isRightMouseButton(e))
     {
       jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-          (Sequence)av.getAlignment().getSequenceAt(seq));
+          (Sequence) av.getAlignment().getSequenceAt(seq));
       pop.show(this, e.getX(), y);
+
       return;
     }
 
-    if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)
+    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));
+      SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(
+          seq));
       selection.setStartRes(0);
-      selection.setEndRes(av.alignment.getWidth()-1);
-      for (int i =0; i< sg.getSize(); i++)
+      selection.setEndRes(av.alignment.getWidth() - 1);
+
+      for (int i = 0; i < sg.getSize(); i++)
+      {
         selection.addSequence(sg.getSequenceAt(i));
+      }
 
       av.setSelectionGroup(selection);
+
       return;
     }
 
-    if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))
+    if ( (av.getSelectionGroup() == null) ||
+        (!e.isControlDown() && (av.getSelectionGroup() != null)))
+    {
       av.setSelectionGroup(new SequenceGroup());
+    }
 
     av.getSelectionGroup().setStartRes(0);
-    av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
+    av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
 
-    if(e.isShiftDown() && lastid!=-1)
+    if (e.isShiftDown() && (lastid != -1))
+    {
       selectSeqs(lastid, seq);
+    }
     else
+    {
       selectSeq(seq);
+    }
 
     alignPanel.repaint();
   }
@@ -172,48 +216,56 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
   void selectSeq(int seq)
   {
     lastid = seq;
+
     SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
     av.getSelectionGroup().addOrRemove(pickedSeq);
   }
 
-  void selectSeqs(int start, int end) {
-
+  void selectSeqs(int start, int end)
+  {
     lastid = start;
-    if (end < start)
-     {
-       int tmp = start;
-       start = end;
-       end   = tmp;
-       lastid = end;
-     }
-
-     for (int i = start; i <= end; i++)
-        av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));
 
-   }
+    if (end < start)
+    {
+      int tmp = start;
+      start = end;
+      end = tmp;
+      lastid = end;
+    }
 
+    for (int i = start; i <= end; i++)
+    {
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));
+    }
+  }
 
   public void mouseReleased(MouseEvent e)
   {
-    if(scrollThread!=null)
+    if (scrollThread != null)
+    {
       scrollThread.running = false;
+    }
 
     mouseDragging = false;
     PaintRefresher.Refresh(this);
   }
 
-  public void highlightSearchResults( java.util.Vector found )
+  public void highlightSearchResults(java.util.Vector found)
   {
-    idCanvas.setHighlighted( found );
+    idCanvas.setHighlighted(found);
 
-    if(found == null)
+    if (found == null)
+    {
       return;
+    }
 
-    int index = av.alignment.findIndex( (SequenceI)found.get(0));
+    int index = av.alignment.findIndex( (SequenceI) found.get(0));
 
     // do we need to scroll the panel?
-    if(av.getStartSeq()>index || av.getEndSeq()<index)
-        alignPanel.setScrollValues( av.getStartRes(), index);
+    if ( (av.getStartSeq() > index) || (av.getEndSeq() < index))
+    {
+      alignPanel.setScrollValues(av.getStartRes(), index);
+    }
   }
 
   // this class allows scrolling off the bottom of the visible alignment
@@ -222,6 +274,7 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
   {
     boolean running = false;
     boolean up = true;
+
     public ScrollThread(boolean up)
     {
       this.up = up;
@@ -236,34 +289,45 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
     public void run()
     {
       running = true;
+
       while (running)
       {
-        if(alignPanel.scrollUp(up))
+        if (alignPanel.scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
           int seq = av.getStartSeq();
-          if(!up)
+
+          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 ead38dc..5599a6d 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -1,80 +1,110 @@
 /*
-* 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.gui;
 
-import javax.swing.*;
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
 
-
-public class IdwidthAdjuster extends JPanel implements MouseListener, MouseMotionListener
+public class IdwidthAdjuster
+    extends JPanel implements MouseListener,
+    MouseMotionListener
 {
   boolean active = false;
-  int oldX=0;
+  int oldX = 0;
   Image image;
-  AlignmentPanel ap ;
+  AlignmentPanel ap;
 
   public IdwidthAdjuster(AlignmentPanel ap)
   {
     this.ap = ap;
+
     java.net.URL url = getClass().getResource("/images/idwidth.gif");
-       if (url != null)
-         image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+
+    if (url != null)
+    {
+      image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+    }
 
     addMouseListener(this);
     addMouseMotionListener(this);
   }
 
   public void mousePressed(MouseEvent evt)
-  { oldX = evt.getX(); }
+  {
+    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 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)
+    if ( ( (d.width + dif) > 20) || (dif > 0))
     {
-      ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,d.height));
+      ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,
+          d.height));
       ap.repaint();
     }
 
     oldX = evt.getX();
   }
 
-  public void mouseMoved(MouseEvent evt)   {}
-  public void mouseClicked(MouseEvent evt) {}
+  public void mouseMoved(MouseEvent evt)
+  {
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
 
   public void paintComponent(Graphics g)
   {
     g.setColor(Color.white);
-    g.fillRect(0,0, getWidth(), getHeight());
-    if(active)
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    if (active)
     {
-      if(image!=null)
-        g.drawImage(image, getWidth()-20, 2, this);
+      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 89a7bfc..bfd97f0 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,119 +1,143 @@
 /*
-* 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.gui;
 
 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.*;
-import javax.swing.JInternalFrame;
-import java.net.URL;
-import jalview.io.SequenceFeatureFetcher;
-
 
 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{
-        FileOutputStream fos = new FileOutputStream(statefile);
-        JarOutputStream jout = new JarOutputStream(fos);
-        //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-        ////////////////////////////////////////////////////
-        PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
-
-        Vector shortNames = new Vector();
-        //REVERSE ORDER
-        for (int i = frames.length-1; i > -1; i--)
+    long creation = System.currentTimeMillis();
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+    if (frames == null)
+    {
+      return;
+    }
+
+    try
+    {
+      FileOutputStream fos = new FileOutputStream(statefile);
+      JarOutputStream jout = new JarOutputStream(fos);
+
+      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+      ////////////////////////////////////////////////////
+      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+          "UTF-8"));
+
+      Vector shortNames = new Vector();
+
+      //REVERSE ORDER
+      for (int i = frames.length - 1; i > -1; i--)
+      {
+        if (frames[i] instanceof AlignFrame)
         {
-          if (frames[i] instanceof AlignFrame)
-          {
-            AlignFrame af = (AlignFrame) frames[i];
+          AlignFrame af = (AlignFrame) frames[i];
 
-            String shortName = af.getTitle();
+          String shortName = af.getTitle();
 
-            if(shortName.indexOf(File.separatorChar)>-1)
-              shortName = shortName.substring(
-                    shortName.lastIndexOf(File.separatorChar)+1);
+          if (shortName.indexOf(File.separatorChar) > -1)
+          {
+            shortName = shortName.substring(shortName.lastIndexOf(
+                File.separatorChar) + 1);
+          }
 
-            int count=1;
-            while( shortNames.contains(shortName) )
-            {
-              if(shortName.endsWith("_"+(count-1)))
-                shortName = shortName.substring(0, shortName.lastIndexOf("_"));
+          int count = 1;
 
-              shortName = shortName.concat("_"+count);
-              count++;
+          while (shortNames.contains(shortName))
+          {
+            if (shortName.endsWith("_" + (count - 1)))
+            {
+              shortName = shortName.substring(0,
+                                              shortName.lastIndexOf("_"));
             }
-            shortNames.addElement(shortName);
 
-            if(!shortName.endsWith(".xml"))
-              shortName = shortName+".xml";
+            shortName = shortName.concat("_" + count);
+            count++;
+          }
+
+          shortNames.addElement(shortName);
+
+          if (!shortName.endsWith(".xml"))
+          {
+            shortName = shortName + ".xml";
+          }
 
-            SaveState( af, creation, shortName, jout, out);
-           }
+          SaveState(af, creation, shortName, jout, out);
         }
-        out.close();
-        jout.close();
       }
-      catch(Exception ex){ex.printStackTrace();}
+
+      out.close();
+      jout.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
   }
 
   // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-  public static void SaveState( AlignFrame af, String jarFile, String fileName)
+  public static void SaveState(AlignFrame af, String jarFile, String fileName)
   {
-    try{
+    try
+    {
       FileOutputStream fos = new FileOutputStream(jarFile);
       JarOutputStream jout = new JarOutputStream(fos);
+
       //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
       ////////////////////////////////////////////////////
-      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
+      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+          "UTF-8"));
 
       SaveState(af, System.currentTimeMillis(), fileName, jout, out);
       out.close();
       jout.close();
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
   }
 
-  public static void SaveState( AlignFrame af, long timeStamp,
-      String fileName, JarOutputStream jout, PrintWriter out)
+  public static void SaveState(AlignFrame af, long timeStamp,
+                               String fileName, JarOutputStream jout,
+                               PrintWriter out)
   {
-
     Vector seqids = new Vector();
     Vector userColours = new Vector();
 
     AlignViewport av = af.viewport;
 
     JalviewModel object = new JalviewModel();
-    object.setVamsasModel( new VamsasModel() );
+    object.setVamsasModel(new VamsasModel());
 
-    object.setCreationDate( new java.util.Date(timeStamp) );
+    object.setCreationDate(new java.util.Date(timeStamp));
 
     jalview.datamodel.AlignmentI jal = af.viewport.alignment;
 
@@ -121,19 +145,19 @@ public class Jalview2XML
     Sequence vamsasSeq;
     JalviewModelSequence jms = new JalviewModelSequence();
 
-    vamsasSet.setGapChar(jal.getGapCharacter()+"");
+    vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
     JSeq jseq;
 
-
     //SAVE SEQUENCES
     int id = 0;
-    for(int i=0; i<jal.getHeight(); i++)
+
+    for (int i = 0; i < jal.getHeight(); i++)
     {
       seqids.add(jal.getSequenceAt(i));
 
-      vamsasSeq = new Sequence( );
-      vamsasSeq.setId(id+"");
+      vamsasSeq = new Sequence();
+      vamsasSeq.setId(id + "");
       vamsasSeq.setName(jal.getSequenceAt(i).getName());
       vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
 
@@ -143,7 +167,7 @@ public class Jalview2XML
 
       jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
 
-      jseq.setId( id );
+      jseq.setId(id);
 
       jms.addJSeq(jseq);
       vamsasSet.addSequence(vamsasSeq);
@@ -151,22 +175,24 @@ public class Jalview2XML
     }
 
     //SAVE TREES
-    if(af.viewport.currentTree!=null)
+    if (af.viewport.currentTree != null)
     {
       object.getVamsasModel().addTree(af.viewport.currentTree.toString());
     }
 
     //SAVE ANNOTATIONS
-    if(jal.getAlignmentAnnotation()!=null)
+    if (jal.getAlignmentAnnotation() != null)
     {
+      jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 
-      jalview.datamodel.AlignmentAnnotation [] aa = jal.getAlignmentAnnotation();
-      for(int i=0; i<aa.length; i++)
+      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;}
+        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);
@@ -175,127 +201,154 @@ public class Jalview2XML
 
         AnnotationElement ae;
 
-        for(int a=0; a<aa[i].annotations.length; a++)
+        for (int a = 0; a < aa[i].annotations.length; a++)
         {
-          if(aa[i]==null || aa[i].annotations[a]==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+"");
+          ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
+                                   "");
           an.addAnnotationElement(ae);
         }
 
         vamsasSet.addAnnotation(an);
       }
-
     }
 
     //SAVE GROUPS
-    if(jal.getGroups()!=null)
+    if (jal.getGroups() != null)
     {
-      JGroup [] groups = new JGroup[jal.getGroups().size()];
-      for(int i=0; i<groups.length; i++)
+      JGroup[] groups = new JGroup[jal.getGroups().size()];
+
+      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);
+        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());
+        {
+          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));
+        {
+          groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+                                                  jms));
+        }
         else
-          groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
+        {
+          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++)
+        for (int s = 0; s < sg.getSize(); s++)
         {
-          jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(s);
+          jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.
+              getSequenceAt(s);
           int index = seqids.indexOf(seq);
           groups[i].addSeq(index);
         }
-
       }
-      jms.setJGroup(groups);
 
+      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
-   view.setBgColour( ColourSchemeProperty.getColourName
-                     ( av.getGlobalColourScheme()));
-
-   ColourSchemeI cs = av.getGlobalColourScheme();
-   if(cs instanceof ConservationColourScheme)
-     view.setConsThreshold( ((ConservationColourScheme)cs).inc);
-
-   if (cs instanceof ResidueColourScheme)
-     view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
-  else if (cs instanceof ScoreColourScheme)
-     view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());
-
-
-   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 );
+    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
+    {
+      view.setBgColour(ColourSchemeProperty.getColourName(
+          av.getGlobalColourScheme()));
+    }
+
+    ColourSchemeI cs = av.getGlobalColourScheme();
+
+    if (cs instanceof ConservationColourScheme)
+    {
+      view.setConsThreshold( ( (ConservationColourScheme) cs).inc);
+    }
+
+    if (cs instanceof ResidueColourScheme)
+    {
+      view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
+    }
+    else if (cs instanceof ScoreColourScheme)
+    {
+      view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());
+    }
+
+    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";
+      if (!fileName.endsWith(".xml"))
+      {
+        fileName = fileName + ".xml";
+      }
 
-     JarEntry entry = new JarEntry(fileName);
-     jout.putNextEntry(entry);
+      JarEntry entry = new JarEntry(fileName);
+      jout.putNextEntry(entry);
 
       object.marshal(out);
     }
@@ -309,194 +362,245 @@ public class Jalview2XML
                                     Vector userColours,
                                     JalviewModelSequence jms)
   {
-    String id=null;
-    jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)cs;
+    String id = null;
+    jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
+        cs;
+
     if (!userColours.contains(ucs))
     {
       userColours.add(ucs);
-      java.awt.Color [] colours = ucs.getColours();
+
+      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.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);
+        jalview.binding.Colour col = new jalview.binding.Colour();
+        col.setRGB(jalview.util.Format.getHexString(colours[i]));
+        jbucs.addColour(col);
       }
-      id = "ucs"+userColours.indexOf(ucs);
+
+      id = "ucs" + userColours.indexOf(ucs);
       uc.setId(id);
       uc.setUserColourScheme(jbucs);
       jms.addUserColours(uc);
     }
+
     return id;
   }
 
-  static jalview.schemes.UserColourScheme GetUserColourScheme(JalviewModelSequence jms, String id)
+  static jalview.schemes.UserColourScheme GetUserColourScheme(
+      JalviewModelSequence jms, String id)
   {
-    UserColours [] uc = jms.getUserColours();
-    UserColours colours=null;
-    for(int i=0; i<uc.length; i++)
+    UserColours[] uc = jms.getUserColours();
+    UserColours colours = null;
+
+    for (int i = 0; i < uc.length; i++)
     {
-       if(uc[i].getId().equals(id))
-       {  colours = uc[i]; break;  }
+      if (uc[i].getId().equals(id))
+      {
+        colours = uc[i];
+
+        break;
+      }
     }
-    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) );
+    int csize = colours.getUserColourScheme().getColourCount();
+    java.awt.Color[] newColours = new java.awt.Color[csize];
 
-    return  new jalview.schemes.UserColourScheme(newColours);
+    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);
   }
 
-
   public static void LoadJalviewAlign(String file)
   {
     JalviewModel object = new JalviewModel();
-    try{
-      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 
+    try
+    {
+      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       URL url = null;
-      if( file.startsWith("http://"))
-       url = new URL(file);
+
+      if (file.startsWith("http://"))
+      {
+        url = new URL(file);
+      }
 
       JarInputStream jin = null;
-      JarEntry jarentry=null;
+      JarEntry jarentry = null;
       int entryCount = 1;
-      do{
+
+      do
+      {
         if (url != null)
+        {
           jin = new JarInputStream(url.openStream());
+        }
         else
+        {
           jin = new JarInputStream(new FileInputStream(file));
+        }
 
-        for(int i=0; i<entryCount; i++)
+        for (int i = 0; i < entryCount; i++)
+        {
           jarentry = jin.getNextJarEntry();
+        }
 
-        if(jarentry!=null)
+        if (jarentry != null)
         {
           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
           object = (JalviewModel) object.unmarshal(in);
           LoadFromObject(object);
           entryCount++;
         }
-      }while(jarentry!=null);
-
+      }
+      while (jarentry != null);
     }
-    catch(Exception ex)
-    {   System.err.println("Exception whilst loading jalview XML file : "+ex+"\n");
-     ex.printStackTrace(); return; }
+    catch (Exception ex)
+    {
+      System.err.println("Exception whilst loading jalview XML file : " +
+                         ex + "\n");
+      ex.printStackTrace();
 
+      return;
+    }
   }
 
   static void LoadFromObject(JalviewModel object)
   {
-     Vector seqids = new Vector();
-     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
-     Sequence [] vamsasSeq = vamsasSet.getSequence();
-
-     JalviewModelSequence jms = object.getJalviewModelSequence();
-     //////////////////////////////////
-     //LOAD SEQUENCES
-     jalview.datamodel.Sequence [] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
-     JSeq [] JSEQ = object.getJalviewModelSequence().getJSeq();
-     for(int i=0; i<vamsasSeq.length; i++)
-     {
-       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
-                                                 vamsasSeq[i].getSequence());
-
-       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]);
-     }
-
-     /////////////////////////////////
-     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
-     /////////////////////////////////
-
-     //////////////////////////////////
-     //LOAD ANNOTATIONS
-     if(vamsasSet.getAnnotation()!=null)
-     {
-       Annotation[] an = vamsasSet.getAnnotation();
-       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 VIEWPORT
-      Viewport[] views = jms.getViewport();
-      Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
-
-      AlignFrame af = new AlignFrame(al);
-    //  af.changeColour() );
+    Vector seqids = new Vector();
+    SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+    Sequence[] vamsasSeq = vamsasSet.getSequence();
+
+    JalviewModelSequence jms = object.getJalviewModelSequence();
+
+    //////////////////////////////////
+    //LOAD SEQUENCES
+    jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[
+        vamsasSeq.length];
+    JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+
+    for (int i = 0; i < vamsasSeq.length; i++)
+    {
+      jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
+                                                vamsasSeq[i].getSequence());
+
+      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]);
+    }
+
+    /////////////////////////////////
+    jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
+
+    /////////////////////////////////
+    //////////////////////////////////
+    //LOAD ANNOTATIONS
+    if (vamsasSet.getAnnotation() != null)
+    {
+      Annotation[] an = vamsasSet.getAnnotation();
+
+      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 VIEWPORT
+    Viewport[] views = jms.getViewport();
+    Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+
+    AlignFrame af = new AlignFrame(al);
+
+    //  af.changeColour() );
     /////////////////////////
     //LOAD GROUPS
-    if (jms.getJGroupCount()>0)
+    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 (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());
-       }
-
-        jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup
-                (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()));
-        int [] ids = groups[i].getSeq();
-        for(int s=0; s<ids.length; s++)
-            sg.addSequence( (jalview.datamodel.SequenceI)seqids.elementAt( ids[s] ));
-
-        if(groups[i].getConsThreshold()!=0)
+        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());
+          }
+        }
+
+        jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
+            SequenceGroup(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()));
+
+        int[] ids = groups[i].getSeq();
+
+        for (int s = 0; s < ids.length; s++)
+        {
+          sg.addSequence( (jalview.datamodel.SequenceI) seqids.elementAt(
+              ids[s]));
+        }
+
+        if (groups[i].getConsThreshold() != 0)
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
-              ResidueProperties.propHash, 3,
-              sg.sequences, 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);
@@ -504,33 +608,34 @@ public class Jalview2XML
           sg.cs = cs;
         }
 
-
         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() );
+    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.viewport.setColourText( view.getShowColourText() );
-    af.viewport.setConservationSelected( view.getConservationSelected());
-    af.viewport.setShowFullId( view.getShowFullId());
-    af.viewport.setFont( new java.awt.Font( view.getFontName(),
-                                            view.getFontStyle(),
-                                            view.getFontSize()));
+    af.viewport.showIdentity = view.getShowIdentity();
+    af.viewport.setAbovePIDThreshold(view.getPidSelected());
+    af.viewport.setColourText(view.getShowColourText());
+    af.viewport.setConservationSelected(view.getConservationSelected());
+    af.viewport.setShowFullId(view.getShowFullId());
+    af.viewport.setFont(new java.awt.Font(view.getFontName(),
+                                          view.getFontStyle(), view.getFontSize()));
     af.alignPanel.fontChanged();
 
     af.sequenceFeatures_actionPerformed(null);
-    af.viewport.setRenderGaps( view.getRenderGaps() );
+    af.viewport.setRenderGaps(view.getRenderGaps());
 
-    af.viewport.setWrapAlignment( view.getWrapAlignment() );
-    if(view.getWrapAlignment())
+    af.viewport.setWrapAlignment(view.getWrapAlignment());
+
+    if (view.getWrapAlignment())
     {
       af.alignPanel.setWrapAlignment(view.getWrapAlignment());
     }
@@ -540,51 +645,67 @@ public class Jalview2XML
       af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
     }
 
-    af.viewport.setShowBoxes( view.getShowBoxes() );
-    af.viewport.setShowText( view.getShowText() );
+    af.viewport.setShowBoxes(view.getShowBoxes());
+    af.viewport.setShowText(view.getShowText());
 
-    ColourSchemeI cs=null;
-    if(view.getBgColour()!=null)
-    {
+    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.setGlobalColourScheme(cs);
 
     af.viewport.setColourAppliesToAllGroups(false);
     af.changeColour(af.viewport.getGlobalColourScheme());
     af.viewport.setColourAppliesToAllGroups(true);
 
     System.out.println(view.getShowSequenceFeatures());
-    if( view.getShowSequenceFeatures() );
+
+    if (view.getShowSequenceFeatures())
     {
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, af.alignPanel);
+      ;
+    }
+
+    {
+      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al,
+          af.alignPanel);
     }
 
     //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE
-    if(object.getVamsasModel().getTreeCount()>0)
+    if (object.getVamsasModel().getTreeCount() > 0)
     {
-      try{
+      try
+      {
         af.ShowNewickTree(new jalview.io.NewickFile(
-            (String)object.getVamsasModel().getTree(0)), "Tree");
-      }catch(Exception ex){ex.printStackTrace();}
+            (String) object.getVamsasModel().getTree(0)), "Tree");
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
     }
-
   }
 }
-
-
-
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index a55af89..244d884 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,41 +1,43 @@
 /*
-* 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.gui;
 
-import javax.swing.*;
+import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
-import java.awt.*;
+import javax.swing.*;
 
-public class OverviewPanel extends JPanel implements Runnable
+public class OverviewPanel
+    extends JPanel implements Runnable
 {
   BufferedImage miniMe;
   AlignViewport av;
   AlignmentPanel ap;
   float scalew = 1f;
   float scaleh = 1f;
-
-  int width, sequencesHeight;
-  int graphHeight=30;
-  int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1;
-
+  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)
@@ -45,50 +47,61 @@ public class OverviewPanel extends JPanel implements Runnable
     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())
+    float initialScale = (float) av.alignment.getWidth() /
+        (float) av.alignment.getHeight();
+
+    if (av.alignment.getWidth() > av.alignment.getHeight())
     {
       // wider
       width = 400;
-      sequencesHeight = (int)(400f/initialScale);
+      sequencesHeight = (int) (400f / initialScale);
     }
     else
     {
       // taller
-      width = (int)(400f*initialScale);
+      width = (int) (400f * initialScale);
       sequencesHeight = 300;
-      if(width<120)
+
+      if (width < 120)
+      {
         width = 120;
+      }
     }
 
     addComponentListener(new ComponentAdapter()
-   {
-
-       public void componentResized(ComponentEvent evt)
-       {
-         if( getWidth()!=width || getHeight()!=sequencesHeight+graphHeight)
-         {
-           updateOverviewImage();
-         }
-       }
-   });
+    {
+      public void componentResized(ComponentEvent evt)
+      {
+        if ( (getWidth() != width) ||
+            (getHeight() != (sequencesHeight + graphHeight)))
+        {
+          updateOverviewImage();
+        }
+      }
+    });
 
     addMouseMotionListener(new MouseMotionAdapter()
-           {
-             public void mouseDragged(MouseEvent evt)
-             { doMouseDragged(evt);}
-           });
+    {
+      public void mouseDragged(MouseEvent evt)
+      {
+        doMouseDragged(evt);
+      }
+    });
 
     addMouseListener(new MouseAdapter()
     {
       public void mousePressed(MouseEvent evt)
-      { doMousePressed(evt);}
+      {
+        doMousePressed(evt);
+      }
+
       public void mouseReleased(MouseEvent evt)
-      { doMouseReleased(evt);}
+      {
+        doMouseReleased(evt);
+      }
     });
 
     updateOverviewImage();
-
   }
 
   public void doMousePressed(MouseEvent evt)
@@ -105,9 +118,12 @@ public class OverviewPanel extends JPanel implements Runnable
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    if(!resizing)
-    ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),
-                        (int)(boxY/scaleh/av.getCharHeight()) );
+
+    if (!resizing)
+    {
+      ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
+                         (int) (boxY / scaleh / av.getCharHeight()));
+    }
   }
 
   public void doMouseDragged(MouseEvent evt)
@@ -115,34 +131,46 @@ public class OverviewPanel extends JPanel implements Runnable
     boxX = evt.getX();
     boxY = evt.getY();
     checkValid();
-    if(!resizing)
-    ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()),
-                        (int)(boxY/scaleh/av.getCharHeight()) );
+
+    if (!resizing)
+    {
+      ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),
+                         (int) (boxY / scaleh / av.getCharHeight()));
+    }
   }
 
   void checkValid()
   {
     if (boxY < 0)
+    {
       boxY = 0;
+    }
 
-    if (boxY > sequencesHeight - boxHeight)
-      boxY = sequencesHeight - boxHeight+1;
+    if (boxY > (sequencesHeight - boxHeight))
+    {
+      boxY = sequencesHeight - boxHeight + 1;
+    }
 
     if (boxX < 0)
+    {
       boxX = 0;
+    }
 
-    if (boxX > width - boxWidth)
+    if (boxX > (width - boxWidth))
+    {
       boxX = width - boxWidth;
+    }
   }
 
   public void updateOverviewImage()
   {
-    if(resizing)
+    if (resizing)
     {
       return;
     }
 
     resizing = true;
+
     Thread thread = new Thread(this);
     thread.start();
     repaint();
@@ -151,18 +179,19 @@ public class OverviewPanel extends JPanel implements Runnable
   public void run()
   {
     miniMe = null;
+
     int alwidth = av.alignment.getWidth();
     int alheight = av.alignment.getHeight();
 
-    if(getWidth()>0 && getHeight()>0)
+    if ( (getWidth() > 0) && (getHeight() > 0))
     {
       width = getWidth();
       sequencesHeight = getHeight() - graphHeight;
     }
 
-    setPreferredSize (new Dimension(width, sequencesHeight+graphHeight));
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
 
-    int fullsizeWidth  = alwidth * av.getCharWidth();
+    int fullsizeWidth = alwidth * av.getCharWidth();
     int fullsizeHeight = alheight * av.getCharHeight();
 
     scalew = (float) width / (float) fullsizeWidth;
@@ -172,70 +201,85 @@ public class OverviewPanel extends JPanel implements Runnable
                                BufferedImage.TYPE_INT_RGB);
 
     Graphics mg = miniMe.getGraphics();
-    BufferedImage consensus = new BufferedImage(fullsizeWidth,
-                                           60,
-                                           BufferedImage.TYPE_3BYTE_BGR);
+    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);
-
+                 sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);
 
     boolean oldRenderGaps = av.renderGaps;
-    try{
-    // We'll have to draw the full size alignment in chunks, as an image of the
-    // whole alignment requires too much memory
 
+    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();
+      int maxSize = 2000 / av.getFont().getSize();
       BufferedImage block;
-      int blockx=0, blocky=0, blockw=0, blockh=0, eRes=0, eSeq=0;
+      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++)
+
+      for (int sRes = 0, chunkx = 0; sRes < alwidth;
+           sRes += maxSize, chunkx++)
       {
-          eSeq = 0;
-          eRes+=maxSize;
-          if(eRes>alwidth)
-            eRes = alwidth;
+        eSeq = 0;
+        eRes += maxSize;
 
-          for(int sSeq=0, chunky=0; sSeq<alheight; sSeq+=maxSize, chunky++)
-          {
-            eSeq+=maxSize;
-            if(eSeq>alheight)
-              eSeq = alheight;
+        if (eRes > alwidth)
+        {
+          eRes = alwidth;
+        }
 
-            blocky = 0;
-            blockx = (int)((float)sRes/(float)alwidth * width);
+        for (int sSeq = 0, chunky = 0; sSeq < alheight;
+             sSeq += maxSize, chunky++)
+        {
+          eSeq += maxSize;
 
-            block = new BufferedImage((eRes-sRes)*av.charWidth,
-              (eSeq-sSeq)*av.charHeight,
-              BufferedImage.TYPE_3BYTE_BGR);
-            g = block.getGraphics();
+          if (eSeq > alheight)
+          {
+            eSeq = alheight;
+          }
 
-           ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq, 0);
+          blocky = 0;
+          blockx = (int) ( (float) sRes / (float) alwidth * width);
 
-           blockh = (int)( (float)(eSeq-sSeq)/(float)alheight *  sequencesHeight  )+1 ;
-           blockw = (int)( (float)(eRes-sRes)/(float)alwidth  *   width )+1;
+          block = new BufferedImage( (eRes - sRes) * av.charWidth,
+                                    (eSeq - sSeq) * av.charHeight,
+                                    BufferedImage.TYPE_3BYTE_BGR);
+          g = block.getGraphics();
 
-           blocky += (int) ((float)sSeq/(float)alheight* sequencesHeight);
+          ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq,
+                                          sRes, sSeq, 0);
 
-           mg.drawImage(block,  blockx,
-                              blocky ,
-                            blockx + blockw,
-                            blocky + blockh,
+          blockh = (int) ( (float) (eSeq - sSeq) / (float) alheight *
+                          sequencesHeight) +
+              1;
+          blockw = (int) ( (float) (eRes - sRes) / (float) alwidth * width) +
+              1;
 
-                         0, 0, block.getWidth(),block.getHeight(), this);
+          blocky += (int) ( (float) sSeq / (float) alheight * sequencesHeight);
 
-          block = null;
-          }
+          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!");   }
-
+    }
+    catch (OutOfMemoryError error)
+    {
+      System.err.println(
+          "Out of memory when trying to calculate the overview window image!");
+    }
 
     av.setRenderGaps(oldRenderGaps);
     resizing = false;
@@ -245,35 +289,37 @@ public class OverviewPanel extends JPanel implements Runnable
 
   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();
+    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.fillRect(0, 0, getWidth(), getHeight());
     g.setColor(Color.black);
 
-    if(resizing)
+    if (resizing)
     {
       g.setFont(new Font("Verdana", Font.BOLD, 15));
-      g.drawString("Recalculating", 5, sequencesHeight/2);
-      g.drawString("Overview.....", 5, sequencesHeight/2 +20);
+      g.drawString("Recalculating", 5, sequencesHeight / 2);
+      g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
     }
     else
     {
-      if(miniMe!=null)
-        g.drawImage(miniMe, 0,0,this);
+      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.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
     }
   }
-
 }
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 8f3ff73..ebde9cb 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,120 +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.gui;
 
-import jalview.datamodel.*;
-import jalview.analysis.PCA;
-import jalview.jbgui.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
 
-public class PCAPanel extends GPCAPanel implements Runnable
+public class PCAPanel
+    extends GPCAPanel implements Runnable
 {
   PCA pca;
   int top;
   RotatableCanvas rc;
   AlignViewport av;
 
-  public void run()
+  public PCAPanel(AlignViewport av, SequenceI[] s)
   {
-    // do stuff
-  }
-
-  public PCAPanel(AlignViewport av, SequenceI[] s) {
-
     this.av = av;
-    if(av.getSelectionGroup()!=null && av.getSelectionGroup().getSize()>3)
+
+    if ( (av.getSelectionGroup() != null) &&
+        (av.getSelectionGroup().getSize() > 3))
     {
       s = new Sequence[av.getSelectionGroup().getSize()];
-      for(int i=0; i<s.length; i++)
+
+      for (int i = 0; i < s.length; i++)
+      {
         s[i] = av.getSelectionGroup().getSequenceAt(i);
+      }
     }
 
-
-    if(s==null)
+    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???
+    //////////////////////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)
+    int ii = 0;
+
+    while ( (ii < s.length) && (s[ii] != null))
     {
       ii++;
     }
 
     double[][] comps = new double[ii][ii];
 
-    for (int i=0; i < ii; i++ )
+    for (int i = 0; i < ii; i++)
     {
       if (pca.getEigenvalue(i) > 1e-4)
       {
-        comps[i]  = pca.component(i);
+        comps[i] = pca.component(i);
       }
     }
 
     //////////////////
-
     xCombobox.setSelectedIndex(0);
     yCombobox.setSelectedIndex(1);
     zCombobox.setSelectedIndex(2);
 
-    top = pca.getM().rows-1;
+    top = pca.getM().rows - 1;
 
     Vector points = new Vector();
-    float[][] scores = pca.getComponents(top-1,top-2,top-3,100);
+    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
-    for (int i =0; i < pca.getM().rows; i++ )
+    for (int i = 0; i < pca.getM().rows; i++)
     {
-      SequencePoint sp = new SequencePoint(s[i],scores[i]);
+      SequencePoint sp = new SequencePoint(s[i], scores[i]);
       points.addElement(sp);
     }
 
-    rc = new RotatableCanvas(av,points,pca.getM().rows);
+    rc = new RotatableCanvas(av, points, pca.getM().rows);
 
     //rc.printPoints();
-
     add(rc, BorderLayout.CENTER);
   }
 
+  public void run()
+  {
+    // do stuff
+  }
 
   void doDimensionChange()
   {
-    if(top==0)
+    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];
+    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;
@@ -137,5 +147,4 @@ public class PCAPanel extends GPCAPanel implements Runnable
   {
     doDimensionChange();
   }
-
 }
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 12545af..6bec8fd 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,54 +1,62 @@
 /*
-* 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.gui;
-import java.awt.*;
+
 import java.util.*;
 
+import java.awt.*;
+
 public class PaintRefresher
 {
   static Vector components = new Vector();
 
   public static void Register(Component c)
   {
-    if(!components.contains(c))
+    if (!components.contains(c))
+    {
       components.add(c);
+    }
     else
+    {
       components.remove(c);
+    }
   }
 
   public static void Refresh(Component c)
   {
     Component temp;
     Enumeration e = components.elements();
-    while( e.hasMoreElements() )
+
+    while (e.hasMoreElements())
     {
-      temp = (Component)e.nextElement();
+      temp = (Component) e.nextElement();
 
-      if(!temp.isValid())
-        components.removeElement( temp );
-      else if( temp == c )
-           continue;
+      if (!temp.isValid())
+      {
+        components.removeElement(temp);
+      }
+      else if (temp == c)
+      {
+        continue;
+      }
 
       temp.repaint();
     }
-
   }
-
 }
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 2825467..69789b9 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,98 +1,118 @@
 /*
-* 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.gui;
 
-import jalview.datamodel.*;
-import jalview.jbgui.GPairwiseAlignPanel;
-import jalview.analysis.*;
-import java.awt.event.*;
-import javax.swing.*;
 import java.util.*;
 
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
 
-public class PairwiseAlignPanel extends GPairwiseAlignPanel
+public class PairwiseAlignPanel
+    extends GPairwiseAlignPanel
 {
-    Vector sequences = new Vector();
-    AlignViewport av;
+  Vector sequences = new Vector();
+  AlignViewport av;
+
+  public PairwiseAlignPanel(AlignViewport av)
+  {
+    super();
+    this.av = av;
 
-    public PairwiseAlignPanel(AlignViewport av)
+    Vector selsubset = new Vector();
+
+    for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++)
     {
-      super();
-      this.av = av;
-      Vector selsubset = new Vector();
-      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));
-      float scores[][] = new float[selsubset.size()][selsubset.size()];
-      double totscore = 0;
-      int count = selsubset.size();
-
-      int acount = 0;
-      for (int i = 1; i < count; i++)
+      if (av.getAlignment().getSequences().contains(av.getSelectionGroup()
+          .getSequenceAt(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()));
-        }
+        selsubset.add(av.getSelectionGroup().getSequenceAt(i));
       }
-      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");
+    }
+
+    float[][] scores = new float[selsubset.size()][selsubset.size()];
+    double totscore = 0;
+    int count = selsubset.size();
 
+    int acount = 0;
+
+    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");
 
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
+      for (int i = 0; i < count; i++)
+      {
+        jalview.util.Format.print(System.out, "%s \n",
+                                  ("" + i) + " " +
+                                  ( (SequenceI) selsubset.elementAt(i)).getName());
+      }
 
-      Sequence [] seq = new Sequence[sequences.size()];
+      System.out.println("\n");
 
-      for (int i=0;i<sequences.size();i++)
-       seq[i] = (Sequence) sequences.elementAt(i);
+      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");
+    }
+  }
 
-      AlignFrame af = new AlignFrame(new Alignment(seq));
-      Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-                               AlignFrame.NEW_WINDOW_WIDTH,
-                               AlignFrame.NEW_WINDOW_HEIGHT);
+  protected void viewInEditorButton_actionPerformed(ActionEvent e)
+  {
+    Sequence[] seq = new Sequence[sequences.size()];
 
-  }
+    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 7133e44..7576173 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,41 +1,43 @@
 /*
-* 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.gui;
 
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
 import java.awt.*;
-import javax.swing.*;
 import java.awt.event.*;
-import jalview.io.*;
+import javax.swing.*;
+
 import MCview.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
 
-public class PopupMenu extends JPopupMenu
+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 hydrophobicityColour = new
+      JRadioButtonMenuItem();
   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
@@ -46,8 +48,6 @@ public class PopupMenu extends JPopupMenu
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-
-
   AlignmentPanel ap;
   JMenu sequenceMenu = new JMenu();
   JMenuItem sequenceName = new JMenuItem();
@@ -69,7 +69,6 @@ public class PopupMenu extends JPopupMenu
     //
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
-
     this.ap = ap;
     sequence = seq;
 
@@ -89,57 +88,96 @@ public class PopupMenu extends JPopupMenu
     colours.add(BLOSUM62Colour);
 
     try
-    {     jbInit();   }
-    catch(Exception e)
-    {    e.printStackTrace();    }
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
 
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg!=null)
+
+    if (sg != null)
     {
       groupName.setText(sg.getName());
-      if(sg.cs instanceof ZappoColourScheme)
+
+      if (sg.cs instanceof ZappoColourScheme)
+      {
         zappoColour.setSelected(true);
-      else if(sg.cs instanceof TaylorColourScheme)
+      }
+      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))
+    if (!ap.av.alignment.getGroups().contains(sg))
+    {
       unGroupMenuItem.setVisible(false);
+    }
     else
+    {
       groupMenu.insertSeparator(3);
+    }
 
-    if(seq==null)
-       sequenceMenu.setVisible(false);
-
+    if (seq == null)
+    {
+      sequenceMenu.setVisible(false);
+    }
   }
-  private void jbInit() throws Exception
+
+  private void jbInit()
+      throws Exception
   {
     groupMenu.setText("Group");
     groupMenu.setText("Define");
@@ -356,24 +394,24 @@ public class PopupMenu extends JPopupMenu
       }
     });
     conservationMenuItem.setText("Conservation");
-   conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-   {
-     public void actionPerformed(ActionEvent e)
-     {
-       conservationMenuItem_actionPerformed(e);
-     }
-   });
-
-
-
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed(e);
+      }
+    });
   }
 
   void refresh()
   {
     SequenceGroup sg = getGroup();
-    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
-    if( superG !=null)
-      superG.setSuperGroupProperties( sg );
+    SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
+
+    if (superG != null)
+    {
+      superG.setSuperGroupProperties(sg);
+    }
 
     ap.seqPanel.repaint();
   }
@@ -381,7 +419,8 @@ public class PopupMenu extends JPopupMenu
   protected void clustalColour_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg.sequences,
+                                     ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -397,7 +436,6 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
-
   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
     getGroup().cs = new HydrophobicColourScheme();
@@ -434,24 +472,28 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
-
-
   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());
+
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+          getGroup().getName());
+
       if (sg.cs instanceof ResidueColourScheme)
-        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
+      {
+        ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
+      }
       else if (sg.cs instanceof ScoreColourScheme)
+      {
         ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+      }
 
       SliderPanel.showPIDSlider();
-
-
     }
     else // remove PIDColouring
     {
@@ -461,13 +503,11 @@ public class PopupMenu extends JPopupMenu
     }
 
     refresh();
-
   }
 
-
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    new UserDefinedColours( ap, getGroup());
+    new UserDefinedColours(ap, getGroup());
   }
 
   protected void PIDColour_actionPerformed(ActionEvent e)
@@ -475,7 +515,7 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+                                             ap.av.alignment.getWidth()));
     refresh();
   }
 
@@ -486,34 +526,32 @@ public class PopupMenu extends JPopupMenu
     sg.cs = new Blosum62ColourScheme();
 
     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+                                             ap.av.alignment.getWidth()));
 
     refresh();
   }
 
-
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
     getGroup().cs = null;
     refresh();
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = getGroup();
 
-    if(conservationMenuItem.isSelected())
+    if (conservationMenuItem.isSelected())
     {
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3,
+                                        sg.sequences, 0,
+                                        ap.av.alignment.getWidth());
 
-        Conservation c = new Conservation("Group",
-                                          ResidueProperties.propHash, 3,
-                                          sg.sequences, 0,
-                                          ap.av.alignment.getWidth());
-
-        c.calculate();
-        c.verdict(false, ap.av.ConsPercGaps);
-        ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
 
+      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
       sg.cs = ccs;
 
@@ -522,45 +560,48 @@ public class PopupMenu extends JPopupMenu
     }
     else // remove ConservationColouring
     {
-        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-        sg.cs = ccs.cs;
+      ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
+      sg.cs = ccs.cs;
     }
 
-     refresh();
+    refresh();
   }
 
-
   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)
+    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);
   }
 
-
   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() );
+    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());
   }
 
   SequenceGroup getGroup()
@@ -576,47 +617,47 @@ public class PopupMenu extends JPopupMenu
   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);
+    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 != null)
     {
       sequence.setName(s);
       ap.repaint();
     }
-
   }
 
   void unGroupMenuItem_actionPerformed(ActionEvent e)
   {
-     SequenceGroup sg = ap.av.getSelectionGroup();
-     ap.av.alignment.deleteGroup(sg);
-     ap.av.setSelectionGroup(null);
-     ap.repaint();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    ap.repaint();
   }
 
   void pdbMenuItem_actionPerformed(ActionEvent e)
   {
-    if(sequence.getPDBId()==null)
+    if (sequence.getPDBId() == null)
+    {
       return;
+    }
 
     try
     {
       EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
+      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);
+      Desktop.addInternalFrame(frame,
+                               sequence.getName() + " " + sequence.getPDBId(),
+                               400, 400);
     }
     catch (Exception ex)
     {
@@ -627,9 +668,14 @@ public class PopupMenu extends JPopupMenu
   protected void outline_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = getGroup();
-    Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
-    if(col!=null)
+    Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+                                         Color.BLUE);
+
+    if (col != null)
+    {
       sg.setOutlineColour(col);
+    }
+
     ap.repaint();
   }
 
@@ -650,5 +696,4 @@ public class PopupMenu extends JPopupMenu
     getGroup().setColourText(showColourText.isSelected());
     refresh();
   }
-
 }
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 4708ced..b16ae32 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,127 +1,69 @@
 /*
-* 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.gui;
 
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.io.*;
-
-import jalview.bin.Cache;
-import javax.swing.*;
-import java.awt.event.ActionEvent;
 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
+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";
-
+  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 static void initPreferences()
-  {
-  String string = Cache.getProperty("SHOW_FULL_ID");
-  if(string!=null)
-    showFullId = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("SHOW_FULLSCREEN");
-  if(string!=null)
-    showFullscreen = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("SHOW_ANNOTATIONS");
-      if(string!=null)
-    showAnnotation = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("SHOW_CONSERVATION");
-      if(string!=null)
-    showConservation = Boolean.valueOf(string).booleanValue();
-  string = Cache.getProperty("SHOW_QUALITY");
-      if(string!=null)
-    showQuality = Boolean.valueOf(string).booleanValue();
-  string = Cache.getProperty("SHOW_IDENTITY");
-      if(string!=null)
-    showIdentity = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("GAP_SYMBOL");
-      if(string!=null)
-    gapSymbol = string.charAt(0);
-
-  string = Cache.getProperty("SHOW_FULL_ID");
-    if(string!=null)
-      showFullId = Boolean.valueOf(string).booleanValue();
-
-    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;
-  }
-
   public Preferences()
   {
     initPreferences();
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Preferences", 480,390 );
+    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();
+
+    if (string != null)
+    {
+      value = Boolean.valueOf(string).booleanValue();
+    }
 
     fullScreen.setSelected(value);
     annotations.setSelected(showAnnotation);
@@ -134,43 +76,158 @@ public class Preferences extends GPreferences
     quality.setSelected(showQuality);
     identity.setSelected(showIdentity);
 
-    for(int i=0; i<12; i++)
-      colour.addItem( ColourSchemeProperty.getColourName(i) );
+    for (int i = 0; i < 12; i++)
+    {
+      colour.addItem(ColourSchemeProperty.getColourName(i));
+    }
 
     string = Cache.getProperty("DEFAULT_COLOUR");
-    if(string!=null)
-      colour.setSelectedItem( string );
+
+    if (string != null)
+    {
+      colour.setSelectedItem(string);
+    }
     else
-      colour.setSelectedIndex( 11 );
+    {
+      colour.setSelectedIndex(11);
+    }
 
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-    for(int i=0; i<fonts.length; i++)
+    String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
+        .getAvailableFontFamilyNames();
+
+    for (int i = 0; i < fonts.length; i++)
+    {
       fontNameCB.addItem(fonts[i]);
+    }
+
+    for (int i = 1; i < 31; i++)
+    {
+      fontSizeCB.addItem(i + "");
+    }
+
+    fontStyleCB.addItem("plain");
+    fontStyleCB.addItem("bold");
+    fontStyleCB.addItem("italic");
+
+    fontNameCB.setSelectedItem(fontName);
+    fontSizeCB.setSelectedItem(fontSize);
+    fontStyleCB.setSelectedItem(fontStyle);
+
+    gapSymbolCB.addItem("-");
+    gapSymbolCB.addItem(".");
+
+    gapSymbolCB.setSelectedItem(gapSymbol + "");
+
+    startupCheckbox.setSelected(showStartupFile);
+    startupFileTextfield.setText(startupFile);
+  }
+
+  public static void initPreferences()
+  {
+    String string = Cache.getProperty("SHOW_FULL_ID");
 
-    for(int i=1; i<31; i++)
-      fontSizeCB.addItem(i+"");
+    if (string != null)
+    {
+      showFullId = Boolean.valueOf(string).booleanValue();
+    }
+
+    string = Cache.getProperty("SHOW_FULLSCREEN");
+
+    if (string != null)
+    {
+      showFullscreen = Boolean.valueOf(string).booleanValue();
+    }
+
+    string = Cache.getProperty("SHOW_ANNOTATIONS");
+
+    if (string != null)
+    {
+      showAnnotation = Boolean.valueOf(string).booleanValue();
+    }
+
+    string = Cache.getProperty("SHOW_CONSERVATION");
+
+    if (string != null)
+    {
+      showConservation = Boolean.valueOf(string).booleanValue();
+    }
+
+    string = Cache.getProperty("SHOW_QUALITY");
+
+    if (string != null)
+    {
+      showQuality = Boolean.valueOf(string).booleanValue();
+    }
+
+    string = Cache.getProperty("SHOW_IDENTITY");
+
+    if (string != null)
+    {
+      showIdentity = Boolean.valueOf(string).booleanValue();
+    }
+
+    string = Cache.getProperty("GAP_SYMBOL");
+
+    if (string != null)
+    {
+      gapSymbol = string.charAt(0);
+    }
+
+    string = Cache.getProperty("SHOW_FULL_ID");
+
+    if (string != null)
+    {
+      showFullId = Boolean.valueOf(string).booleanValue();
+    }
+
+    string = Cache.getProperty("FONT_NAME");
 
-   fontStyleCB.addItem("plain");
-   fontStyleCB.addItem("bold");
-   fontStyleCB.addItem("italic");
+    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");
 
-   fontNameCB.setSelectedItem(fontName);
-   fontSizeCB.setSelectedItem(fontSize);
-   fontStyleCB.setSelectedItem(fontStyle);
+    if (string != null)
+    {
+      defaultColour = string;
+    }
 
-   gapSymbolCB.addItem("-");
-   gapSymbolCB.addItem(".");
+    string = Cache.getProperty("STARTUP_FILE");
 
-   gapSymbolCB.setSelectedItem( gapSymbol+"" );
+    if (string != null)
+    {
+      startupFile = string;
+    }
 
-   startupCheckbox.setSelected(showStartupFile);
-   startupFileTextfield.setText(startupFile);
+    string = Cache.getProperty("SHOW_STARTUP_FILE");
 
+    if (string != null)
+    {
+      showStartupFile = Boolean.valueOf(string).booleanValue();
+    }
+
+    preferencesLoaded = true;
   }
 
   public void ok_actionPerformed(ActionEvent e)
   {
-    showFullId =  fullID.isSelected() ;
+    showFullId = fullID.isSelected();
     showFullscreen = fullScreen.isSelected();
     showAnnotation = annotations.isSelected();
     showConservation = conservation.isSelected();
@@ -185,15 +242,16 @@ public class Preferences extends GPreferences
     showStartupFile = startupCheckbox.isSelected();
 
     Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));
-    Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString( showFullscreen ) );
+    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("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("GAP_SYMBOL", gapSymbol + "");
 
     Cache.setProperty("FONT_NAME", fontName);
     Cache.setProperty("FONT_STYLE", fontStyle);
@@ -202,36 +260,52 @@ public class Preferences extends GPreferences
     Cache.setProperty("STARTUP_FILE", startupFile);
     Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));
 
-
-
-    try    {
+    try
+    {
       frame.setClosed(true);
-    }    catch (Exception ex)  {}
-
+    }
+    catch (Exception ex)
+    {
+    }
   }
 
   public void startupFileTextfield_mouseClicked()
   {
-    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() );
-   }
+    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{
+    try
+    {
       frame.setClosed(true);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
   }
 
   public void annotations_actionPerformed(ActionEvent e)
@@ -240,5 +314,4 @@ public class Preferences extends GPreferences
     quality.setEnabled(annotations.isSelected());
     identity.setEnabled(annotations.isSelected());
   }
-
 }
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index e4ef46e..44aa447 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,30 +1,31 @@
 /*
-* 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.gui;
 
-import jalview.jbgui.*;
-import jalview.datamodel.*;
-import java.awt.event.*;
 import java.util.*;
+
+import java.awt.event.*;
 import javax.swing.event.*;
 
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+
 public class RedundancyPanel
     extends GSliderPanel
 {
@@ -49,7 +50,6 @@ public class RedundancyPanel
     slider.setMinimum(0);
     slider.setMaximum(100);
     slider.setValue(100);
-
   }
 
   public void applyButton_actionPerformed(ActionEvent e)
@@ -57,19 +57,24 @@ public class RedundancyPanel
     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())) {
-      af.addHistoryItem((HistoryItem) historyList.firstElement());
+    historyList.push(it = new HistoryItem("Remove redundancy",
+                                          ap.av.alignment, HistoryItem.HIDE));
+
+    if ( (historyList.size() == 1) ||
+        !af.historyList.contains(historyList.firstElement()))
+    {
+      af.addHistoryItem( (HistoryItem) historyList.firstElement());
       af.updateEditMenuBar();
     }
+
     undoButton.setEnabled(true);
+
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg != null && sg.getSize() >= 1)
-    {
 
+    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)))
@@ -77,32 +82,36 @@ public class RedundancyPanel
           sg.deleteSequence( (SequenceI) del.elementAt(i));
         }
       }
-
     }
     else
     {
       Vector s = new Vector();
       int i = 0;
+
       while (i < ap.av.alignment.getHeight())
       {
         s.addElement(ap.av.alignment.getSequenceAt(i));
         i++;
       }
+
       del = ap.av.alignment.removeRedundancy(threshold, s);
     }
 
     // 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++) {
+    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());
+        sq.deleteChars(0, sq.getLength());
       }
+    }
 
     ap.av.firePropertyChange("alignment", null,
                              ap.av.getAlignment().getSequences());
     ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
+
     if (ap.av.getAlignment().getHeight() < 1)
     {
       try
@@ -110,22 +119,25 @@ public class RedundancyPanel
         af.setClosed(true);
       }
       catch (Exception ex)
-      {}
+      {
+      }
     }
+
     ap.av.updateConservation();
     ap.av.updateConsensus();
     af.updateEditMenuBar();
     ap.repaint();
-
   }
 
   public void undoButton_actionPerformed(ActionEvent e)
   {
     HistoryItem hi = (HistoryItem) historyList.pop();
     af.restoreHistoryItem(hi);
+
     if (historyList.size() == 0)
     {
       undoButton.setEnabled(false);
+
       if (af.historyList.contains(hi))
       {
         af.historyList.remove(hi);
@@ -133,6 +145,7 @@ public class RedundancyPanel
       }
     }
   }
+
   public void valueField_actionPerformed(ActionEvent e)
   {
     try
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 0d5025e..0fc83c3 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,119 +1,112 @@
 /*
-* 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.gui;
 
-import jalview.math.*;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
-import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.math.*;
+import jalview.util.*;
 
-public class RotatableCanvas extends JPanel implements MouseListener,
-                                                       MouseMotionListener,
-                                                       KeyListener
-                                                       //RubberbandListener,
-                                                       //SequenceSelectionListener
+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);
+  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[] 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) {
+  //  Controller    controller;
+  public RotatableCanvas(AlignViewport av, Vector points, int npoint)
+  {
     this.points = points;
     this.npoint = npoint;
     this.av = av;
     ToolTipManager.sharedInstance().registerComponent(this);
     PaintRefresher.Register(this);
-//
+
+    //
     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++) {
+    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++) {
-      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);
+    //Initialize the matrices to identity
+    for (int i = 0; i < 3; i++)
+    {
+      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);
         }
       }
     }
@@ -127,62 +120,74 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     scale = findScale();
 
     //    System.out.println("Scale factor = " + scale);
-
     addMouseListener(this);
     addKeyListener(this);
-   // if (getParent() != null) {
-   //   getParent().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;
+    //   rubberband  = new RubberbandRectangle(this);
+    //  rubberband.setActive(true);
+    //   rubberband.addListener(this);
   }
 
-  public void removeNotify() {
-    controller.removeListener(this);
-    super.removeNotify();
-  }*/
-
-  public void initAxes() {
-    for (int i = 0; i < 3; i++) {
-      for (int j=0; j < 3; j++) {
-        if (i != j) {
+  /* 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++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
+        {
           axes[i][j] = 0;
-        } else {
+        }
+        else
+        {
           axes[i][j] = 1;
         }
       }
     }
   }
 
-  public void findWidth() {
+  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]) {
+        if (sp.coord[i] >= max[i])
+        {
           max[i] = sp.coord[i];
         }
-        if (sp.coord[i] <= min[i]) {
+
+        if (sp.coord[i] <= min[i])
+        {
           min[i] = sp.coord[i];
         }
       }
@@ -191,7 +196,6 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     //    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]);
@@ -199,186 +203,253 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     maxwidth = width[0];
 
     if (width[1] > width[0])
+    {
       maxwidth = width[1];
+    }
+
     if (width[2] > width[1])
+    {
       maxwidth = width[2];
+    }
 
     //System.out.println("Maxwidth = " + maxwidth);
   }
 
-  public float findScale() {
-    int dim, width, height;
-    if (getWidth() != 0) {
+  public float findScale()
+  {
+    int dim;
+    int width;
+    int height;
+
+    if (getWidth() != 0)
+    {
       width = getWidth();
       height = getHeight();
-    } else {
+    }
+    else
+    {
       width = prefsize.width;
       height = prefsize.height;
     }
 
-    if (width < height) {
+    if (width < height)
+    {
       dim = width;
-    } else {
+    }
+    else
+    {
       dim = height;
     }
 
-    return (float)(dim*scalefactor/(2*maxwidth));
+    return (float) ( (dim * scalefactor) / (2 * maxwidth));
   }
 
-  public void findCentre() {
+  public void findCentre()
+  {
     //Find centre coordinate
     findWidth();
 
-    centre[0] = (max[0] + min[0])/2;
-    centre[1] = (max[1] + min[1])/2;
-    centre[2] = (max[2] + min[2])/2;
+    centre[0] = (max[0] + min[0]) / 2;
+    centre[1] = (max[1] + min[1]) / 2;
+    centre[2] = (max[2] + min[2]) / 2;
 
     //    System.out.println("Centre x " + centre[0]);
     //System.out.println("Centre y " + centre[1]);
     //System.out.println("Centre z " + centre[2]);
   }
 
-  public Dimension getPreferredSize() {
-    if (prefsize != null) {
+  public Dimension getPreferredSize()
+  {
+    if (prefsize != null)
+    {
       return prefsize;
-    } else {
-      return new Dimension(400,400);
+    }
+    else
+    {
+      return new Dimension(400, 400);
     }
   }
 
-  public Dimension getMinimumSize() {
+  public Dimension getMinimumSize()
+  {
     return getPreferredSize();
   }
 
-  public void paintComponent(Graphics g) {
+  public void paintComponent(Graphics g)
+  {
     //Only create the image at the beginning -
-    if ((img == null) || (prefsize.width != getWidth()) || (prefsize.height != getHeight())) {
+    if ( (img == null) || (prefsize.width != getWidth()) ||
+        (prefsize.height != getHeight()))
+    {
       prefsize.width = getWidth();
       prefsize.height = getHeight();
 
       scale = findScale();
 
       //      System.out.println("New scale = " + scale);
-      img = createImage(getWidth(),getHeight());
+      img = createImage(getWidth(), getHeight());
       ig = img.getGraphics();
-
     }
 
+    drawBackground(ig, Color.black);
+    drawScene(ig);
 
-      drawBackground(ig,Color.black);
-      drawScene(ig);
-      if (drawAxes == true)
-      {
-        drawAxes(ig);
-      }
-
+    if (drawAxes == true)
+    {
+      drawAxes(ig);
+    }
 
-    g.drawImage(img,0,0,this);
+    g.drawImage(img, 0, 0, this);
   }
 
-  public void drawAxes(Graphics g) {
-
+  public void drawAxes(Graphics g)
+  {
     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));
+
+    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)));
     }
   }
 
-  public void drawBackground(Graphics g, Color col) {
+  public void drawBackground(Graphics g, Color col)
+  {
     g.setColor(col);
-    g.fillRect(0,0,prefsize.width,prefsize.height);
+    g.fillRect(0, 0, prefsize.width, prefsize.height);
   }
 
-
-  public void drawScene(Graphics g) {
+  public void drawScene(Graphics g)
+  {
     boolean darker = false;
 
-    int halfwidth = getWidth()/2;
-    int halfheight = getHeight()/2;
+    int halfwidth = getWidth() / 2;
+    int halfheight = getHeight() / 2;
 
-    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;
+    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);
+      {
+        g.setColor(Color.white);
+      }
       else
-          g.setColor(sp.sequence.getColor());
-
+      {
+        g.setColor(sp.sequence.getColor());
+      }
 
       if (av.getSelectionGroup() != null)
       {
-        if (av.getSelectionGroup().sequences.contains(((SequencePoint)points.elementAt(i)).sequence))
+        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.fillRect(x - 3, y - 3, 6, 6);
       g.setColor(Color.red);
     }
-//    //Now the rectangle
-//    if (rectx2 != -1 && recty2 != -1) {
-//      g.setColor(Color.white);
-//
-//      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
-//    }
+
+    //    //Now the rectangle
+    //    if (rectx2 != -1 && recty2 != -1) {
+    //      g.setColor(Color.white);
+    //
+    //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
+    //    }
   }
 
-  public Dimension minimumsize() {
+  public Dimension minimumsize()
+  {
     return prefsize;
   }
 
-  public Dimension preferredsize() {
+  public Dimension preferredsize()
+  {
     return prefsize;
   }
 
-  public void keyTyped(KeyEvent evt) { }
-  public void keyReleased(KeyEvent evt) { }
+  public void keyTyped(KeyEvent evt)
+  {
+  }
 
-  public void keyPressed(KeyEvent evt) {
+  public void keyReleased(KeyEvent evt)
+  {
+  }
+
+  public void keyPressed(KeyEvent evt)
+  {
     requestFocus();
-    if (evt.getKeyCode() == KeyEvent.VK_UP) {
-      scalefactor = (float)(scalefactor * 1.1);
+
+    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);
+    }
+    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+    {
+      scalefactor = (float) (scalefactor * 0.9);
       scale = findScale();
-    } else if (evt.getKeyChar() == 's') {
+    }
+    else if (evt.getKeyChar() == 's')
+    {
       System.err.println("DEBUG: Rectangle selection"); // log.debug
-      if (rectx2 != -1 && recty2 != -1) {
-        rectSelect(rectx1,recty1,rectx2,recty2);
 
+      if ( (rectx2 != -1) && (recty2 != -1))
+      {
+        rectSelect(rectx1, recty1, rectx2, recty2);
       }
     }
+
     repaint();
   }
 
-  public void printPoints() {
-    for (int i=0; i < npoint; i++) {
-      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]);
+  public void printPoints()
+  {
+    for (int i = 0; i < npoint; i++)
+    {
+      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) { }
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+  }
 
-  public void mousePressed(MouseEvent evt) {
+  public void mouseReleased(MouseEvent evt)
+  {
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
     int x = evt.getX();
     int y = evt.getY();
 
@@ -397,7 +468,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     rectx2 = -1;
     recty2 = -1;
 
-    SequenceI found = findPoint(x,y);
+    SequenceI found = findPoint(x, y);
 
     if (found != null)
     {
@@ -408,49 +479,59 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       }
       else
       {
-          av.setSelectionGroup(new SequenceGroup());
-          av.getSelectionGroup().addOrRemove(found);
-          av.getSelectionGroup().setEndRes(av.alignment.getWidth());
-
+        av.setSelectionGroup(new SequenceGroup());
+        av.getSelectionGroup().addOrRemove(found);
+        av.getSelectionGroup().setEndRes(av.alignment.getWidth());
       }
     }
+
     repaint();
   }
 
- // private void fireSequenceSelectionEvent(Selection sel) {
- //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
+  // 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
-     this.setToolTipText(null);
- }
-
-  public void mouseDragged(MouseEvent evt) {
+    SequenceI found = findPoint(evt.getX(), evt.getY());
+
+    if (found != null)
+    {
+      this.setToolTipText(found.getName());
+    }
+    else
+    {
+      this.setToolTipText(null);
+    }
+  }
+
+  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();
-    } else {
+    if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
+    {
+      //      rectx2 = evt.getX();
+      //      recty2 = evt.getY();
+    }
+    else
+    {
       rotmat.setIdentity();
 
-      rotmat.rotate((float)(my-omy),'x');
-      rotmat.rotate((float)(mx-omx),'y');
+      rotmat.rotate( (float) (my - omy), 'x');
+      rotmat.rotate( (float) (mx - omx), 'y');
 
-      for (int i = 0; i < npoint; i++) {
-        SequencePoint sp = (SequencePoint)points.elementAt(i);
+      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 apply the rotation matrix
-        sp.coord= rotmat.vectorMultiply(sp.coord);
+        sp.coord = rotmat.vectorMultiply(sp.coord);
 
         //Now translate back again
         sp.coord[0] += centre[0];
@@ -458,26 +539,34 @@ public class RotatableCanvas extends JPanel implements MouseListener,
         sp.coord[2] += centre[2];
       }
 
-      for (int i=0; i < 3; i++) {
+      for (int i = 0; i < 3; i++)
+      {
         axes[i] = rotmat.vectorMultiply(axes[i]);
       }
+
       omx = mx;
       omy = my;
 
       paint(this.getGraphics());
     }
-
   }
 
-  public void rectSelect(int x1, int y1, int x2, int y2) {
+  public void rectSelect(int x1, int y1, int x2, int y2)
+  {
     boolean changedSel = false;
-    for (int i=0; i < npoint; i++) {
-      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) {
+    for (int i = 0; i < npoint; i++)
+    {
+      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;
@@ -486,54 +575,62 @@ public class RotatableCanvas extends JPanel implements MouseListener,
         }
       }
     }
-   // 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;
+  public SequenceI findPoint(int x, int y)
+  {
+    int halfwidth = getWidth() / 2;
+    int halfheight = getHeight() / 2;
 
     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;
-
+    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 ) {
+      if ( (Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+      {
         found = i;
       }
     }
-    if (found != -1) {
-      return ((SequencePoint)points.elementAt(found)).sequence;
-    } else {
+
+    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());
 
-    Rubberband rb = (Rubberband)evt.getSource();
+  /*  public boolean handleRubberbandEvent(RubberbandEvent evt) {
+      System.out.println("Rubberband handler called in RotatableCanvas with " +
+                         evt.getBounds());
 
-    // Clear the current selection (instance variable)
-    //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {
-    //   clearSelection();
-    //}
+      Rubberband rb = (Rubberband)evt.getSource();
 
-    if (rb.getComponent() == this) {
-      Rectangle bounds = evt.getBounds();
-      rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);
-    }
+      // Clear the current selection (instance variable)
+      //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {
+      //   clearSelection();
+      //}
 
-    redrawneeded = true;
-    paint(this.getGraphics());
+      if (rb.getComponent() == this) {
+        Rectangle bounds = evt.getBounds();
+   rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);
+      }
 
-    return true;
-  }*/
+      redrawneeded = true;
+      paint(this.getGraphics());
 
+      return true;
+    }*/
 }
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index de0a7b1..250998f 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,43 +1,41 @@
 /*
-* 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.gui;
 
-import jalview.datamodel.*;
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 
-public class ScalePanel extends JPanel
-{
+import jalview.datamodel.*;
 
+public class ScalePanel
+    extends JPanel
+{
   protected int offy = 4;
-  public    int width;
-
+  public int width;
   protected AlignViewport av;
   AlignmentPanel ap;
-
   boolean stretchingGroup = false;
 
   public ScalePanel(AlignViewport av, AlignmentPanel ap)
   {
-    this.av         = av;
+    this.av = av;
     this.ap = ap;
 
     addMouseListener(new MouseAdapter()
@@ -46,11 +44,11 @@ public class ScalePanel extends JPanel
       {
         doMousePressed(evt);
       }
+
       public void mouseReleased(MouseEvent evt)
       {
         doMouseReleased(evt);
       }
-
     });
     addMouseMotionListener(new MouseMotionAdapter()
     {
@@ -59,71 +57,90 @@ public class ScalePanel extends JPanel
         doMouseDragged(evt);
       }
     });
-
   }
 
-
-  public void doMousePressed(MouseEvent evt) {
+  public void doMousePressed(MouseEvent evt)
+  {
     int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
+    int res = (x / av.getCharWidth()) + av.getStartRes();
     SequenceGroup sg = null;
 
     if (av.getColumnSelection().contains(res))
+    {
       av.getColumnSelection().removeElement(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));
+      }
 
       sg.setStartRes(res);
       sg.setEndRes(res);
 
       ap.annotationPanel.addEditableColumn(res);
     }
+
     av.setSelectionGroup(sg);
     ap.repaint();
   }
 
   public void doMouseReleased(MouseEvent evt)
   {
-    if(!stretchingGroup)
+    if (!stretchingGroup)
+    {
       return;
+    }
 
     int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
+    int res = (x / av.getCharWidth()) + av.getStartRes();
 
-   if (! av.getColumnSelection().contains(res))
-     av.getColumnSelection().addElement(res);
+    if (!av.getColumnSelection().contains(res))
+    {
+      av.getColumnSelection().addElement(res);
+    }
 
-   SequenceGroup sg = av.getSelectionGroup();
+    SequenceGroup sg = av.getSelectionGroup();
 
-   if(res>sg.getStartRes())
-     sg.setEndRes(res);
-   else if(res<sg.getStartRes())
-     sg.setStartRes(res);
+    if (res > sg.getStartRes())
+    {
+      sg.setEndRes(res);
+    }
+    else if (res < sg.getStartRes())
+    {
+      sg.setStartRes(res);
+    }
 
-   stretchingGroup = false;
-   ap.repaint();
+    stretchingGroup = false;
+    ap.repaint();
   }
 
   public void doMouseDragged(MouseEvent evt)
   {
     int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
+    int res = (x / av.getCharWidth()) + av.getStartRes();
 
     SequenceGroup sg = av.getSelectionGroup();
-    if(sg!=null)
+
+    if (sg != null)
     {
       stretchingGroup = true;
+
       if (res > sg.getStartRes())
+      {
         sg.setEndRes(res);
+      }
       else if (res < sg.getStartRes())
+      {
         sg.setStartRes(res);
+      }
 
-       ap.annotationPanel.addEditableColumn(res);
+      ap.annotationPanel.addEditableColumn(res);
       ap.repaint();
     }
   }
@@ -133,59 +150,66 @@ public class ScalePanel extends JPanel
     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)
+  // scalewidth will normally be screenwidth,
+  public void drawScale(Graphics g, int startx, int endx, int width,
+                        int height)
   {
-    Graphics2D gg = (Graphics2D)g;
+    Graphics2D gg = (Graphics2D) g;
     gg.setFont(av.getFont());
-    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
+    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                        RenderingHints.VALUE_ANTIALIAS_ON);
 
     //Fill in the background
     gg.setColor(Color.white);
-    gg.fillRect(0,0,width, height);
+    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++)
+    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());
-    }
+      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;
+
+    int scalestartx = (startx / 10) * 10;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = av.charHeight -fm.getDescent();
+    int y = av.charHeight - fm.getDescent();
 
-    if(scalestartx%10==0)
-      scalestartx+=5;
+    if ( (scalestartx % 10) == 0)
+    {
+      scalestartx += 5;
+    }
 
-    for (int i=scalestartx;i < endx; i+= 5)
+    for (int i = scalestartx; i < endx; i += 5)
     {
-      if(i%10==0)
+      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);
+        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);
-
-
+      {
+        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 d40f971..1194d08 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,64 +1,61 @@
 /*
-* 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.gui;
 
 import java.awt.*;
 import java.awt.image.*;
 import javax.swing.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
 
-public class SeqCanvas extends JComponent
+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;
-
-
-    public SeqCanvas(AlignViewport av)
-    {
-	this.av         = av;
-       fr = new FeatureRenderer(av);
-       sr = new SequenceRenderer(av);
-       setLayout(new BorderLayout());
-       PaintRefresher.Register(this);
-
-    }
+  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);
+  }
 
-  void drawNorthScale(Graphics g, int startx, int endx,int ypos) {
-    int scalestartx = startx - startx % 10 + 10;
+  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  {
+    int scalestartx = startx - (startx % 10) + 10;
 
     g.setColor(Color.black);
 
@@ -67,131 +64,154 @@ public class SeqCanvas extends JComponent
     {
       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);
+                   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);
     }
   }
 
   void drawWestScale(Graphics g, int startx, int endx, int ypos)
   {
     FontMetrics fm = getFontMetrics(av.getFont());
-    ypos+= av.charHeight;
-      // EAST SCALE
+    ypos += av.charHeight;
+
+    // EAST SCALE
     for (int i = 0; i < av.alignment.getHeight(); i++)
     {
       SequenceI seq = av.alignment.getSequenceAt(i);
       int index = startx;
       int value = -1;
+
       while (index < endx)
       {
         if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
         {
           index++;
+
           continue;
         }
 
         value = av.alignment.getSequenceAt(i).findPosition(index);
+
         break;
       }
-      if(value!=-1)
+
+      if (value != -1)
       {
-        int x = LABEL_WEST - fm.stringWidth(value+"");
-        g.drawString(value + "", x,  ypos +  i*av.charHeight - av.charHeight/5);
+        int x = LABEL_WEST - fm.stringWidth(value + "");
+        g.drawString(value + "", x,
+                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
       }
     }
   }
 
   void drawEastScale(Graphics g, int startx, int endx, int ypos)
-{
-    ypos+= av.charHeight;
-    // EAST SCALE
-  for (int i = 0; i < av.alignment.getHeight(); i++)
   {
-    SequenceI seq = av.alignment.getSequenceAt(i);
-    int index = endx;
-    int value = -1;
-    while (index > startx)
-    {
-      if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-      {
-        index--;
-        continue;
-      }
+    ypos += av.charHeight;
 
-      value = av.alignment.getSequenceAt(i).findPosition(index);
-      break;
-    }
-    if(value!=-1)
-       g.drawString(value + "", 0,  ypos +  i*av.charHeight - av.charHeight/5);
-  }
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = endx;
+      int value = -1;
 
-}
+      while (index > startx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index--;
 
+          continue;
+        }
 
+        value = av.alignment.getSequenceAt(i).findPosition(index);
 
+        break;
+      }
 
+      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)
+  public void fastPaint(int horizontal, int vertical)
+  {
+    if ( ( (horizontal == 0) && (vertical == 0)) || (gg == null))
+    {
       return;
+    }
 
     gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
                 -vertical * av.charHeight);
 
-    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
-        transX = 0, 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
+
+      if (ss < av.startSeq)
+      { // ie scrolling too fast, more than a page at a time
         ss = av.startSeq;
+      }
       else
-        transY = imgHeight - vertical * av.charHeight;
+      {
+        transY = imgHeight - (vertical * av.charHeight);
+      }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if(es > av.endSeq)
+
+      if (es > av.endSeq)
+      {
         es = av.endSeq;
+      }
     }
 
-
     gg.translate(transX, transY);
 
     gg.setColor(Color.white);
-    gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight);
+    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.
- */
-
+  /**
+   * 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.
+   */
   public void paintComponent(Graphics g)
   {
     g.setColor(Color.white);
@@ -201,44 +221,50 @@ public void fastPaint(int horizontal, int vertical)
     {
       g.drawImage(img, 0, 0, this);
       fastPaint = false;
+
       return;
     }
 
     // this draws the whole of the alignment
-      imgWidth  = getWidth();
-      imgHeight = getHeight();
+    imgWidth = getWidth();
+    imgHeight = getHeight();
 
-      imgWidth -= imgWidth%av.charWidth;
-      imgHeight-= imgHeight%av.charHeight;
+    imgWidth -= (imgWidth % av.charWidth);
+    imgHeight -= (imgHeight % av.charHeight);
 
-      if(imgWidth<1 || imgHeight<1)
-        return;
+    if ( (imgWidth < 1) || (imgHeight < 1))
+    {
+      return;
+    }
 
-      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);
+    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);
 
-      gg.setColor(Color.white);
-      gg.fillRect(0,0,imgWidth,imgHeight);
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
 
-    chunkWidth  =   getWrappedCanvasWidth( getWidth() );
-    chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    chunkWidth = getWrappedCanvasWidth(getWidth());
+    chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
     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);
+    {
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,
+                av.startRes, av.startSeq, 0);
+    }
 
     g.drawImage(img, 0, 0, this);
-
   }
 
-  int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
     FontMetrics fm = getFontMetrics(av.getFont());
@@ -246,161 +272,199 @@ public void fastPaint(int horizontal, int vertical)
     LABEL_EAST = 0;
     LABEL_WEST = 0;
 
-    if(av.scaleRightWrapped)
-      LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
+    }
 
-    if(av.scaleLeftWrapped)
-      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
+    }
 
-    return  (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
+    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
   }
 
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
+                               int startRes)
   {
-      AlignmentI al = av.getAlignment();
+    AlignmentI al = av.getAlignment();
+
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    int LABEL_EAST = 0;
+
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+    }
 
-      FontMetrics fm = getFontMetrics(av.getFont());
+    int LABEL_WEST = 0;
 
-      int LABEL_EAST = 0;
-      if(av.scaleRightWrapped)
-        LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );
-      int LABEL_WEST = 0;
-      if(av.scaleLeftWrapped)
-        LABEL_WEST = fm.stringWidth(al.getWidth()+"0");
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
+    }
 
+    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
-      int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
-      int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
+    av.endRes = av.startRes + cWidth;
 
-      av.endRes = av.startRes + cWidth;
+    int endx = (startRes + cWidth) - 1;
+    int ypos = 2 * av.charHeight;
 
-      int  endx   = startRes+cWidth-1;
-      int  ypos  = 2*av.charHeight;
+    while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
+    {
+      g.setColor(Color.black);
 
-      while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )
+      if (av.scaleLeftWrapped)
       {
-        g.setColor(Color.black);
+        drawWestScale(g, startRes, endx, ypos);
+      }
 
-        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);
+      }
 
-        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);
 
-        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();
+      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);
 
-  synchronized public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
+      ypos += cHeight;
+      startRes += cWidth;
+      endx = (startRes + cWidth) - 1;
+
+      if (endx > al.getWidth())
+      {
+        endx = al.getWidth();
+      }
+    }
+  }
 
-    Graphics2D g = (Graphics2D)g1;
+  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);
 
-
     SequenceI nextSeq;
 
     /// First draw the sequences
     /////////////////////////////
-    for (int i = y1 ; i < y2 ;i++)
+    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);
-     }
+      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);
+      }
     }
+
     //
     /////////////////////////////////////
-
     // Now outline any areas if necessary
     /////////////////////////////////////
     SequenceGroup group = av.getSelectionGroup();
     java.util.Vector groups = av.alignment.getGroups();
 
-    int sx = -1, sy = -1, ex = -1;
+    int sx = -1;
+    int sy = -1;
+    int ex = -1;
     int groupIndex = -1;
-    if (group == null && groups.size() > 0)
+
+    if ( (group == null) && (groups.size() > 0))
     {
       group = (SequenceGroup) groups.elementAt(0);
       groupIndex = 0;
     }
 
     if (group != null)
+    {
       do
       {
         int oldY = -1;
         int i = 0;
         boolean inGroup = false;
-        int top=-1, bottom =-1;
+        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)))
+          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)))
-              bottom = sy + av.charHeight ;
+            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)))
+              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.setStroke(new BasicStroke(1,
+                                            BasicStroke.CAP_BUTT,
+                                            BasicStroke.JOIN_ROUND, 3f,
+                                            new float[]
+                                            {5f, 3f}, 0f));
                 g.setColor(Color.RED);
               }
               else
@@ -414,21 +478,21 @@ public void fastPaint(int horizontal, int vertical)
           {
             if (inGroup)
             {
-              g.drawLine(sx, oldY, sx, sy );
-              g.drawLine(sx+ex, oldY, sx+ex, sy );
+              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;
+                top = -1;
               }
+
               if (bottom != -1)
               {
                 g.drawLine(sx, bottom, sx + ex, bottom);
                 bottom = -1;
               }
 
-
               inGroup = false;
             }
           }
@@ -436,83 +500,89 @@ public void fastPaint(int horizontal, int vertical)
 
         if (inGroup)
         {
-
-          if(top!=-1)
+          if (top != -1)
           {
             g.drawLine(sx, top, sx + ex, top);
-            top =-1;
+            top = -1;
+          }
+
+          if (bottom != -1)
+          {
+            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+            bottom = -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 );
+
+          sy = offset +
+              AlignmentUtil.getPixelHeight(starty, i, 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());
-
+    }
 
     /// Highlight search Results once all sequences have been drawn
     //////////////////////////////////////////////////////////
-    if(displaySearch)
+    if (displaySearch)
     {
-      for(int r=0; r<searchResults.length; r+=3)
+      for (int r = 0; r < searchResults.length; r += 3)
       {
         int searchSeq = searchResults[r];
 
-        if (searchSeq >= y1 && searchSeq < y2)
+        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;
-          if(searchStart<x1)
+
+          if (searchStart < x1)
+          {
             searchStart = x1;
-          if(searchEnd > x2)
+          }
+
+          if (searchEnd > x2)
+          {
             searchEnd = x2;
+          }
 
-          ssr.drawHighlightedText(seq,
-                                  searchStart,
-                                  searchEnd,
+          ssr.drawHighlightedText(seq, searchStart, searchEnd,
                                   (searchStart - startx) * av.charWidth,
                                   offset +
-                                  AlignmentUtil.getPixelHeight(starty, searchSeq,
-              av.charHeight),
-                                  av.charWidth,
-                                  av.charHeight);
+                                  AlignmentUtil.getPixelHeight(starty,
+              searchSeq,
+              av.charHeight), av.charWidth, av.charHeight);
         }
       }
     }
-
   }
 
-
-
-  public void highlightSearchResults(int [] results)
+  public void highlightSearchResults(int[] results)
   {
     // results are in the order sequence, startRes, endRes
-    if(results==null)
+    if (results == null)
+    {
       displaySearch = false;
+    }
     else
+    {
       displaySearch = true;
+    }
 
     searchResults = results;
 
     repaint();
   }
-
-
 }
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 44cf4d4..f4d77c3 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,147 +1,188 @@
 /*
-* 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.gui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import jalview.datamodel.*;
 import javax.swing.*;
-import java.util.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
 import jalview.schemes.*;
-import jalview.analysis.Conservation;
 
-public class SeqPanel extends JPanel
+public class SeqPanel
+    extends JPanel
 {
-
-  public    SeqCanvas         seqCanvas;
-  public    AlignmentPanel    ap;
-
+  public SeqCanvas seqCanvas;
+  public AlignmentPanel ap;
   protected int lastres;
   protected int startseq;
-  int startEdit=-1;
-  int endEdit=-1;
-
+  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) {
-    this.av         = avp;
+  public SeqPanel(AlignViewport avp, AlignmentPanel p)
+  {
+    this.av = avp;
 
-    seqCanvas  = new SeqCanvas(avp);
+    seqCanvas = new SeqCanvas(avp);
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
     ap = p;
 
-    addMouseMotionListener( new MouseMotionAdapter()
+    addMouseMotionListener(new MouseMotionAdapter()
     {
       public void mouseMoved(MouseEvent evt)
       {
-       if(av.getWrapAlignment())
-         return;
-        doMouseMoved(evt);    }
+        if (av.getWrapAlignment())
+        {
+          return;
+        }
+
+        doMouseMoved(evt);
+      }
 
       public void mouseDragged(MouseEvent evt)
       {
-        if(av.getWrapAlignment())
-         return;
-        if( editingSeqs )
+        if (av.getWrapAlignment())
+        {
+          return;
+        }
+
+        if (editingSeqs)
+        {
           doMouseDragged(evt);
+        }
         else
+        {
           doMouseDraggedDefineMode(evt);
+        }
       }
     });
 
-    addMouseListener( new MouseAdapter()
+    addMouseListener(new MouseAdapter()
     {
       public void mouseReleased(MouseEvent evt)
       {
-        if(av.getWrapAlignment())
-         return;
-        if(editingSeqs)
+        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 (av.getWrapAlignment())
         {
-          if(evt.isAltDown() || evt.isControlDown())
+          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);
+        {
+          return;
+        }
 
+        doMouseExitedDefineMode(evt);
       }
+
       public void mouseEntered(MouseEvent evt)
       {
         if (av.getWrapAlignment() || editingSeqs)
+        {
           return;
+        }
+
         doMouseEnteredDefineMode(evt);
       }
-
     });
     repaint();
   }
 
-
-  public void doMouseReleased(MouseEvent evt) {
-
-    if(seqEditOccurred>-1)
+  public void doMouseReleased(MouseEvent evt)
+  {
+    if (seqEditOccurred > -1)
+    {
       editOccurred(seqEditOccurred);
+    }
 
     startseq = -1;
-    lastres  = -1;
+    lastres = -1;
     seqEditOccurred = -1;
-    editingSeqs  = false;
+    editingSeqs = false;
     groupEditing = false;
 
     ap.repaint();
   }
 
-  public void doMousePressed(MouseEvent evt) {
-
-    ap.alignFrame.addHistoryItem( new HistoryItem(
-        "Edit Sequence",av.alignment, HistoryItem.EDIT));
+  public void doMousePressed(MouseEvent evt)
+  {
+    ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+                                                 av.alignment, HistoryItem.EDIT));
 
     int seq;
     int res;
@@ -149,11 +190,11 @@ public class SeqPanel extends JPanel
     int x = evt.getX();
     int y = evt.getY();
 
-    res = x/av.getCharWidth() + av.getStartRes();
-    seq = y/av.getCharHeight() + av.getStartSeq();
+    res = (x / av.getCharWidth()) + av.getStartRes();
+    seq = (y / av.getCharHeight()) + av.getStartSeq();
 
-    if (seq < av.getAlignment().getHeight() &&
-        res < av.getAlignment().getSequenceAt(seq).getLength())
+    if ( (seq < av.getAlignment().getHeight()) &&
+        (res < av.getAlignment().getSequenceAt(seq).getLength()))
     {
       startseq = seq;
       lastres = res;
@@ -172,189 +213,232 @@ public class SeqPanel extends JPanel
 
   public void doMouseMoved(MouseEvent evt)
   {
-    int res=0, seq=0;
+    int res = 0;
+    int seq = 0;
     int x = evt.getX();
     int y = evt.getY();
-    if(av.wrapAlignment)
+
+    if (av.wrapAlignment)
     {
-      y -= 2*av.charHeight;
-      int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
+      y -= (2 * av.charHeight);
 
+      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
-      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();
+      res = (int) ( (y / chunkHeight) * (getWidth() / av.charWidth)) +
+          (x / av.getCharWidth()) + av.getStartRes();
 
       y %= chunkHeight;
-      seq =     y / av.getCharHeight() + av.getStartSeq();
-
+      seq = (y / av.getCharHeight()) + av.getStartSeq();
     }
     else
     {
-      res = x / av.getCharWidth()  + av.getStartRes();
-      seq = y / av.getCharHeight() + av.getStartSeq();
+      res = (x / av.getCharWidth()) + av.getStartRes();
+      seq = (y / av.getCharHeight()) + av.getStartSeq();
     }
 
-
-    if(seq>=av.getAlignment().getHeight())
+    if (seq >= av.getAlignment().getHeight())
+    {
       return;
+    }
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    if(res>sequence.getLength())
+
+    if (res > sequence.getLength())
+    {
       return;
+    }
 
-    Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
+    Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
+                                                  "");
     String aa = "";
-    if(obj!=null)
-         aa = obj.toString();
 
-    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
-    if(aa!="")
-      text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
+    if (obj != null)
+    {
+      aa = obj.toString();
+    }
+
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                                         sequence.getName());
+
+    if (aa != "")
+    {
+      text.append("  Residue: " + aa + " (" +
+                  av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+    }
 
     ap.alignFrame.statusBar.setText(text.toString());
 
     // use aa to see if the mouse pointer is on a
-    if(  av.showSequenceFeatures)
+    if (av.showSequenceFeatures)
     {
       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 ( (sf.getStart() <= sequence.findPosition(res)) &&
+            (sf.getEnd() >= sequence.findPosition(res)))
         {
-          if(sbuffer.length()>0)
+          if (sbuffer.length() > 0)
+          {
             sbuffer.append("; ");
+          }
+
           sbuffer.append(sf.getType() + " " + sf.getDescription());
-          if(sf.getStatus().length()>0)
-            sbuffer.append(" ("+sf.getStatus()+")");
-        }
 
+          if (sf.getStatus().length() > 0)
+          {
+            sbuffer.append(" (" + sf.getStatus() + ")");
+          }
+        }
       }
 
       ToolTipManager.sharedInstance().registerComponent(this);
       this.setToolTipText(sbuffer.toString());
     }
-
-
   }
 
-  public void doMouseDragged(MouseEvent evt) {
-
+  public void doMouseDragged(MouseEvent evt)
+  {
     // If we're dragging we're editing
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
     if (res < 0)
+    {
       res = 0;
+    }
 
-    if (lastres == -1 || lastres == res)
+    if ( (lastres == -1) || (lastres == res))
+    {
       return;
+    }
 
     boolean dragRight = true;
-    if (res < av.getAlignment().getWidth() && res < lastres)
-      dragRight = false;
 
+    if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+    {
+      dragRight = false;
+    }
 
     if (res != lastres)
     {
-        // Group editing
-        if (groupEditing)
+      // Group editing
+      if (groupEditing)
+      {
+        SequenceGroup sg = av.getSelectionGroup();
+
+        if (sg == null)
         {
-          SequenceGroup sg = av.getSelectionGroup();
-          if(sg==null)
-          {
-            lastres=-1;
-            return;
-          }
+          lastres = -1;
 
-            // drag to right
-            if(dragRight)
-                sg.setEndRes(sg.getEndRes() + (res-lastres));
+          return;
+        }
 
-            // drag to left
-            else
+        // 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++)
             {
-               /// Are we able to delete?
-               // ie are all columns blank?
-               boolean deleteAllowed = false;
-              for (int s = 0; s < sg.getSize(); s++)
+              if (seq.getSequence().length() <= j)
               {
-                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;
-                }
+                continue;
               }
 
-              if(!deleteAllowed)
+              if (!jalview.util.Comparison.isGap(
+                  seq.getSequence().charAt(j)))
               {
-                lastres = -1;
-                return;
+                // Not a gap, block edit not valid
+                res = j + 1;
+                deleteAllowed = false;
+
+                continue;
               }
 
-              sg.setEndRes(sg.getEndRes() - (lastres-res));
+              deleteAllowed = true;
             }
+          }
 
+          if (!deleteAllowed)
+          {
+            lastres = -1;
 
-            for (int i = 0; i < sg.getSize(); i++)
-            {
-              SequenceI s = sg.getSequenceAt(i);
-              int k = av.alignment.findIndex(s);
+            return;
+          }
+
+          sg.setEndRes(sg.getEndRes() - (lastres - res));
+        }
 
-              // drag to right
-              if (dragRight)
-                for (int j = lastres; j < res; j++)
-                  insertChar(j, k);
+        for (int i = 0; i < sg.getSize(); i++)
+        {
+          SequenceI s = sg.getSequenceAt(i);
+          int k = av.alignment.findIndex(s);
 
-              // drag to left
-              else
+          // 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)
               {
-                for (int j = res; j < lastres; j++)
-                {
-                  if(s.getLength()>j)
-                    deleteChar(res, k);
-                }
+                deleteChar(res, k);
               }
             }
+          }
         }
-        else /////Editing a single sequence///////////
+      }
+      else /////Editing a single sequence///////////
+      {
+        if ( (res < av.getAlignment().getWidth()) && (res > lastres))
         {
-          if (res < av.getAlignment().getWidth() && res > lastres)
+          // dragging to the right
+          for (int j = lastres; j < res; j++)
           {
-            // dragging to the right
-            for (int j = lastres; j < res; j++)
-              insertChar(j, startseq);
+            insertChar(j, startseq);
           }
-          else if (res < av.getAlignment().getWidth() && res < lastres)
+        }
+        else if ( (res < av.getAlignment().getWidth()) &&
+                 (res < lastres))
+        {
+          // dragging to the left
+          for (int j = lastres; j > res; j--)
           {
-            // dragging to the left
-            for (int j = lastres; j > res; j--)
+            if (jalview.util.Comparison.isGap(
+                av.alignment.getSequenceAt(startseq)
+                .getSequence().charAt(res)))
             {
-              if( jalview.util.Comparison.isGap(
-                av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
-
               deleteChar(res, startseq);
-              else
-              {
-
-                break;
-              }
+            }
+            else
+            {
+              break;
             }
           }
-
         }
+      }
     }
 
     endEdit = res;
@@ -362,30 +446,31 @@ public class SeqPanel extends JPanel
     repaint();
   }
 
-  public void drawChars(int seqstart, int seqend, int start) {
-    seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
+  public void drawChars(int seqstart, int seqend, int start)
+  {
+    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
+                        seqend, av.getStartRes(), av.getStartSeq(), 0);
     repaint();
   }
 
   public void insertChar(int j, int seq)
   {
     av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
-    seqEditOccurred=seq;
+    seqEditOccurred = seq;
   }
 
   public void deleteChar(int j, int seq)
   {
     av.alignment.getSequenceAt(seq).deleteCharAt(j);
-    seqEditOccurred=seq;
+    seqEditOccurred = seq;
 
     av.alignment.getWidth();
     repaint();
   }
 
-
   void editOccurred(int i)
   {
-    if(endEdit==startEdit)
+    if (endEdit == startEdit)
     {
       ap.alignFrame.historyList.pop();
       ap.alignFrame.updateEditMenuBar();
@@ -396,11 +481,13 @@ public class SeqPanel extends JPanel
 
     // Y O Y CLUSTALX
     ColourSchemeI cs = av.getGlobalColourScheme();
-    if(cs instanceof ConservationColourScheme)
+
+    if (cs instanceof ConservationColourScheme)
     {
-      ConservationColourScheme ccs =  (ConservationColourScheme) cs;
-      if(ccs.cs instanceof ClustalxColourScheme)
-     {
+      ConservationColourScheme ccs = (ConservationColourScheme) cs;
+
+      if (ccs.cs instanceof ClustalxColourScheme)
+      {
         Conservation c = new Conservation("All",
                                           ResidueProperties.propHash, 3,
                                           av.alignment.getSequences(), 0,
@@ -408,135 +495,151 @@ public class SeqPanel extends JPanel
         c.calculate();
         c.verdict(false, av.ConsPercGaps);
 
-        ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;
-        cxs.resetClustalX(av.alignment.getSequences(),  av.alignment.getWidth());
+        ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
+        cxs.resetClustalX(av.alignment.getSequences(),
+                          av.alignment.getWidth());
         ccs = new ConservationColourScheme(c, cxs);
         av.setGlobalColourScheme(ccs);
-     }
+      }
     }
 
-    if(cs instanceof ClustalxColourScheme)
+    if (cs instanceof ClustalxColourScheme)
     {
-      ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),
-                                    av.alignment.getWidth());
+      ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
+                                                 av.alignment.getWidth());
       av.setGlobalColourScheme(cs);
     }
-
   }
 
-//////////////////////////////////////////
-/////Everything below this is for defining the boundary of the rubberband
-//////////////////////////////////////////
-  int oldSeq = -1;
   public void doMousePressedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
     oldSeq = seq;
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
-    if(sequence==null || res>sequence.getLength())
+    if ( (sequence == null) || (res > sequence.getLength()))
+    {
       return;
+    }
 
     stretchGroup = av.getSelectionGroup();
 
-    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;
-
-       SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
-
-       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;
-           }
-     }
-
-    if(stretchGroup==null)
+    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;
+
+      SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+
+      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;
+          }
+        }
+      }
+    }
+
+    if (stretchGroup == null)
     {
       // define a new group here
       SequenceGroup sg = new SequenceGroup();
       sg.setStartRes(res);
       sg.setEndRes(res);
-      sg.addSequence( sequence );
-      av.setSelectionGroup( sg );
+      sg.addSequence(sequence);
+      av.setSelectionGroup(sg);
       stretchGroup = sg;
 
-      if(av.getConservationSelected())
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
-      if(av.getAbovePIDThreshold())
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
+      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))
+    else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-        jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
-        pop.show(this, evt.getX(), evt.getY());
+      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
+      pop.show(this, evt.getX(), evt.getY());
 
-    // edit the properties of existing group
+      // edit the properties of existing group
     }
 
-    if(stretchGroup!=null && stretchGroup.getEndRes()==res)
+    if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
+    {
       // Edit end res position of selected group
       changeEndRes = true;
-
-   else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
+    }
+    else if ( (stretchGroup != null) && (stretchGroup.getStartRes() == res))
+    {
       // Edit end res position of selected group
       changeStartRes = true;
+    }
 
     stretchGroup.getWidth();
 
     repaint();
-
   }
 
-  boolean changeEndSeq = false;
-  boolean changeStartSeq = false;
-  boolean changeEndRes = false;
-  boolean changeStartRes = false;
-  SequenceGroup stretchGroup = null;
-
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
     mouseDragging = false;
 
-    if(stretchGroup==null)
+    if (stretchGroup == null)
+    {
       return;
+    }
 
-    if(stretchGroup.cs instanceof ClustalxColourScheme)
+    if (stretchGroup.cs instanceof ClustalxColourScheme)
     {
-      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
+      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,
+                                                 av.alignment.getWidth());
       repaint();
     }
-
-    else if(stretchGroup.cs instanceof ConservationColourScheme)
+    else if (stretchGroup.cs instanceof ConservationColourScheme)
     {
-       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
-       stretchGroup.cs = ccs;
-       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
+      ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
+      stretchGroup.cs = ccs;
+      SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                                        stretchGroup.getName());
 
-       repaint();
+      repaint();
     }
     else
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
-
+    {
+      SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                                     stretchGroup.getName());
+    }
 
     changeEndRes = false;
     changeStartRes = false;
@@ -544,58 +647,75 @@ public class SeqPanel extends JPanel
     ap.idPanel.repaint();
   }
 
-
-  boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
 
-    if(stretchGroup==null)
+    if (stretchGroup == null)
+    {
       return;
+    }
 
-    if(res>av.alignment.getWidth())
-      res = av.alignment.getWidth()-1;
-
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
 
-    if(stretchGroup.getEndRes()==res)
+    if (stretchGroup.getEndRes() == res)
+    {
       // Edit end res position of selected group
       changeEndRes = true;
-
-    else if(stretchGroup.getStartRes()==res)
+    }
+    else if (stretchGroup.getStartRes() == res)
+    {
       // Edit start res position of selected group
       changeStartRes = true;
+    }
 
-
-    if(res<av.getStartRes())
+    if (res < av.getStartRes())
+    {
       res = av.getStartRes();
-    else if(res>av.getEndRes())
+    }
+    else if (res > av.getEndRes())
+    {
       res = av.getEndRes();
+    }
 
-    if(changeEndRes)
+    if (changeEndRes)
     {
-      if(res>stretchGroup.getStartRes()-1)
-        stretchGroup.setEndRes( res );
+      if (res > (stretchGroup.getStartRes() - 1))
+      {
+        stretchGroup.setEndRes(res);
+      }
     }
-    else if(changeStartRes)
+    else if (changeStartRes)
     {
-      if(res<stretchGroup.getEndRes()+1)
-        stretchGroup.setStartRes( res );
+      if (res < (stretchGroup.getEndRes() + 1))
+      {
+        stretchGroup.setStartRes(res);
+      }
     }
 
     int dragDirection = 0;
+
     if (y > oldSeq)
+    {
       dragDirection = 1;
+    }
     else if (y < oldSeq)
+    {
       dragDirection = -1;
+    }
 
-    while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
+    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);
 
       oldSeq += dragDirection;
+
       Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
       if (stretchGroup.sequences.contains(nextSeq))
@@ -605,15 +725,22 @@ public class SeqPanel extends JPanel
       }
       else
       {
-       if(seq!=null)
-        stretchGroup.addSequence(seq);
+        if (seq != null)
+        {
+          stretchGroup.addSequence(seq);
+        }
+
         stretchGroup.addSequence(nextSeq);
       }
     }
+
     oldSeq = y;
     mouseDragging = true;
-    if(scrollThread!=null)
+
+    if (scrollThread != null)
+    {
       scrollThread.setEvent(evt);
+    }
 
     repaint();
   }
@@ -621,23 +748,31 @@ public class SeqPanel extends JPanel
   public void doMouseEnteredDefineMode(MouseEvent e)
   {
     if (scrollThread != null)
+    {
       scrollThread.running = false;
+    }
   }
 
   public void doMouseExitedDefineMode(MouseEvent e)
   {
     if (av.getWrapAlignment())
+    {
       return;
+    }
 
-    if(mouseDragging)
+    if (mouseDragging)
+    {
       scrollThread = new ScrollThread();
-
+    }
   }
+
   // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread extends Thread
+  class ScrollThread
+      extends Thread
   {
     MouseEvent evt;
     boolean running = false;
+
     public ScrollThread()
     {
       start();
@@ -656,23 +791,31 @@ public class SeqPanel extends JPanel
     public void run()
     {
       running = true;
+
       while (running)
       {
-        if(evt!=null)
+        if (evt != null)
         {
-
-          if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+          if (mouseDragging && (evt.getY() < 0) &&
+              (av.getStartSeq() > 0))
+          {
             running = ap.scrollUp(true);
+          }
 
-          if (mouseDragging && evt.getY() >= getHeight() &&
-              av.alignment.getHeight() > av.getEndSeq())
+          if (mouseDragging && (evt.getY() >= getHeight()) &&
+              (av.alignment.getHeight() > av.getEndSeq()))
+          {
             running = ap.scrollUp(false);
+          }
 
-          if (mouseDragging && evt.getX() < 0)
+          if (mouseDragging && (evt.getX() < 0))
+          {
             running = ap.scrollRight(true);
-
-          else if (mouseDragging && evt.getX() >= getWidth())
+          }
+          else if (mouseDragging && (evt.getX() >= getWidth()))
+          {
             running = ap.scrollRight(false);
+          }
         }
 
         try
@@ -680,15 +823,9 @@ public class SeqPanel extends JPanel
           Thread.sleep(75);
         }
         catch (Exception ex)
-        {}
+        {
+        }
       }
     }
+  }
 }
-
-
-
-}
-
-
-
-
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 2c98754..896fda5 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,27 +1,27 @@
 /*
-* 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.gui;
 
+import java.awt.*;
+
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.awt.*;
 
 public class SequenceRenderer
 {
@@ -29,7 +29,7 @@ public class SequenceRenderer
   FontMetrics fm;
   boolean renderGaps = true;
   SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
+  SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
 
@@ -38,7 +38,6 @@ public class SequenceRenderer
     this.av = av;
   }
 
-
   public void renderGaps(boolean b)
   {
     renderGaps = b;
@@ -47,18 +46,25 @@ public class SequenceRenderer
   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)
-       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
-   else
-       resBoxColour = Color.white;
+    if (cs != null)
+    {
+      resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+    }
+    else
+    {
+      resBoxColour = Color.white;
+    }
   }
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)
+  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
+                           int start, int end, int x1, int y1, int width,
+                           int height)
   {
     allGroups = sg;
 
@@ -67,145 +73,182 @@ public class SequenceRenderer
     drawBoxes(seq, start, end, x1, y1, (int) width, height);
 
     fm = g.getFontMetrics();
-    drawText(seq,start,end,x1,y1,(int)width,height);
-
+    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;
+  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;
 
     Color tempColour = null;
-    while (i <= end && i < length)
+
+    while ( (i <= end) && (i < length))
     {
-      if(inCurrentSequenceGroup(i))
+      if (inCurrentSequenceGroup(i))
       {
-        if( currentSequenceGroup.getDisplayBoxes())
-             getBoxColour(currentSequenceGroup.cs, seq, i);
+        if (currentSequenceGroup.getDisplayBoxes())
+        {
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+        }
         else
-             resBoxColour = Color.white;
+        {
+          resBoxColour = Color.white;
+        }
+      }
+      else if (av.getShowBoxes())
+      {
+        getBoxColour(av.getGlobalColourScheme(), seq, i);
       }
-      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);
+        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++;
     }
 
-
-     graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+    graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
+                      height);
   }
 
-  public void drawText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
+  public void drawText(SequenceI seq, int start, int end, int x1, int y1,
+                       int width, int height)
   {
-    int pady = height/5;
-    int charOffset=0;
+    int pady = height / 5;
+    int charOffset = 0;
     char s;
-    // Need to find the sequence position here.
 
+    // Need to find the sequence position here.
+    String sequence = seq.getSequence();
 
-    String sequence  = seq.getSequence();
     for (int i = start; i <= end; i++)
     {
-        graphics.setColor(Color.black);
+      graphics.setColor(Color.black);
 
-        if(i<sequence.length())
-          s = sequence.charAt(i);
-        else
-          s = ' ';
+      if (i < sequence.length())
+      {
+        s = sequence.charAt(i);
+      }
+      else
+      {
+        s = ' ';
+      }
 
-        if(!renderGaps && jalview.util.Comparison.isGap(s))
-          continue;
+      if (!renderGaps && jalview.util.Comparison.isGap(s))
+      {
+        continue;
+      }
 
+      if (inCurrentSequenceGroup(i))
+      {
+        if (!currentSequenceGroup.getDisplayText())
+        {
+          continue;
+        }
 
-        if (inCurrentSequenceGroup(i))
+        if (currentSequenceGroup.getColourText())
         {
-          if(!currentSequenceGroup.getDisplayText())
-            continue;
-
-            if (currentSequenceGroup.getColourText())
-            {
-              getBoxColour(currentSequenceGroup.cs, seq, i);
-              graphics.setColor(resBoxColour.darker());
-            }
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+          graphics.setColor(resBoxColour.darker());
         }
-        else
+      }
+      else
+      {
+        if (!av.getShowText())
         {
-          if(!av.getShowText())
-            continue;
-
-          if(av.getColourText())
-           {
-             getBoxColour(av.getGlobalColourScheme(), seq, i);
-             if(av.getShowBoxes())
-              graphics.setColor(resBoxColour.darker());
-            else
-              graphics.setColor(resBoxColour);
-           }
+          continue;
         }
 
-          charOffset =  (width - fm.charWidth(s))/2;
-          graphics.drawString(String.valueOf(s),
-                              charOffset + x1 + width * (i - start),
-                              y1 + height - pady);
+        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);
+    }
   }
 
   boolean inCurrentSequenceGroup(int res)
   {
-    if(allGroups ==null)
+    if (allGroups == null)
+    {
       return false;
+    }
 
-    for(int i=0; i<allGroups.length; i++)
-      if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)
+    for (int i = 0; i < allGroups.length; i++)
+    {
+      if ( (allGroups[i].getStartRes() <= res) &&
+          (allGroups[i].getEndRes() >= res))
       {
-         currentSequenceGroup = allGroups[i];
-         return true;
+        currentSequenceGroup = allGroups[i];
+
+        return true;
       }
+    }
 
     return false;
   }
 
-  public void drawHighlightedText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
+  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+                                  int y1, int width, int height)
   {
-    int pady = height/5;
-    int charOffset=0;
+    int pady = height / 5;
+    int charOffset = 0;
     graphics.setColor(Color.BLACK);
-    graphics.fillRect(x1,y1,width*(end-start+1),height);
+    graphics.fillRect(x1, y1, width * (end - start + 1), height);
     graphics.setColor(Color.white);
 
-    char s='~';
+    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);
+      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);
+      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 97c5e10..f95f84b 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,47 +1,84 @@
 /*
-* 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.gui;
 
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.datamodel.*;
+import java.util.*;
+
 import java.awt.event.*;
-import javax.swing.event.*;
 import javax.swing.*;
-import java.util.*;
+import javax.swing.event.*;
+
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
 
-public class SliderPanel extends GSliderPanel
+public class SliderPanel
+    extends GSliderPanel
 {
+  static JInternalFrame conservationSlider;
+  static JInternalFrame PIDSlider;
   AlignmentPanel ap;
   boolean forConservation = true;
   ColourSchemeI cs;
 
-  static JInternalFrame conservationSlider;
-  static JInternalFrame PIDSlider;
+  public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
+                     ColourSchemeI cs)
+  {
+    this.ap = ap;
+    this.cs = cs;
+    forConservation = forConserve;
+    undoButton.setVisible(false);
+    applyButton.setVisible(false);
 
-  public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs, String 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);
+    }
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      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;
+    ConservationColourScheme ccs = (ConservationColourScheme) cs;
 
-    if(conservationSlider == null)
+    if (conservationSlider == null)
     {
       sp = new SliderPanel(ap, ccs.inc, true, cs);
       conservationSlider = new JInternalFrame();
@@ -50,175 +87,169 @@ public class SliderPanel extends GSliderPanel
     }
     else
     {
-        sp = (SliderPanel)conservationSlider.getContentPane();
-        sp.cs = cs;
+      sp = (SliderPanel) conservationSlider.getContentPane();
+      sp.cs = cs;
     }
 
-    conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");
-    if(ap.av.alignment.getGroups()!=null)
-      sp.setAllGroupsCheckEnabled( true );
+    conservationSlider.setTitle("Conservation Colour Increment  (" +
+                                source + ")");
+
+    if (ap.av.alignment.getGroups() != null)
+    {
+      sp.setAllGroupsCheckEnabled(true);
+    }
     else
-      sp.setAllGroupsCheckEnabled( false);
+    {
+      sp.setAllGroupsCheckEnabled(false);
+    }
 
     return sp.getValue();
   }
 
   public static void showConservationSlider()
   {
-    try{
+    try
+    {
       PIDSlider.setClosed(true);
       PIDSlider = null;
-    }catch(Exception ex){}
-
+    }
+    catch (Exception ex)
+    {
+    }
 
-    if(!conservationSlider.isVisible())
+    if (!conservationSlider.isVisible())
     {
-      Desktop.addInternalFrame(conservationSlider, conservationSlider.getTitle(), 420, 90, false);
+      Desktop.addInternalFrame(conservationSlider,
+                               conservationSlider.getTitle(), 420, 90, false);
       conservationSlider.addInternalFrameListener(new javax.swing.event.
                                                   InternalFrameAdapter()
       {
-        public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)
+        public void internalFrameClosed(
+            javax.swing.event.InternalFrameEvent e)
         {
           conservationSlider = null;
         }
       });
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
-
   }
 
-  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
-   {
-     SliderPanel pid = null;
-
-     int threshold = 50;
-     if (cs instanceof ResidueColourScheme)
-       threshold = ( ( (ResidueColourScheme) cs).getThreshold());
-     else if (cs instanceof ScoreColourScheme)
-       threshold = ( ( (ScoreColourScheme) cs).getThreshold());
-
-
-     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;
-     }
-     PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
-
-     if (ap.av.alignment.getGroups() != null)
-       pid.setAllGroupsCheckEnabled(true);
-     else
-       pid.setAllGroupsCheckEnabled(false);
-
-     return pid.getValue();
-
-   }
-
-   public static void showPIDSlider()
-   {
-     try{
-       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);
+  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
+                                       String source)
+  {
+    SliderPanel pid = null;
+
+    int threshold = 50;
+
+    if (cs instanceof ResidueColourScheme)
+    {
+      threshold = ( ( (ResidueColourScheme) cs).getThreshold());
+    }
+    else if (cs instanceof ScoreColourScheme)
+    {
+      threshold = ( ( (ScoreColourScheme) cs).getThreshold());
     }
 
-   }
+    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;
+    }
 
+    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
 
-  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)
+    if (ap.av.alignment.getGroups() != null)
     {
-      label.setText("Enter value to increase conservation visibility");
-      slider.setMinimum(0);
-      slider.setMaximum(50);
+      pid.setAllGroupsCheckEnabled(true);
     }
     else
     {
-      label.setText("Enter % identity above which to colour residues");
-      slider.setMinimum(0);
-      slider.setMaximum(100);
+      pid.setAllGroupsCheckEnabled(false);
     }
 
+    return pid.getValue();
+  }
 
+  public static void showPIDSlider()
+  {
+    try
+    {
+      conservationSlider.setClosed(true);
+      conservationSlider = null;
+    }
+    catch (Exception ex)
+    {
+    }
 
-    slider.addChangeListener( new ChangeListener()
+    if (!PIDSlider.isVisible())
     {
-      public void stateChanged(ChangeEvent evt)
+      Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
+                               false);
+      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+      PIDSlider.addInternalFrameListener(new javax.swing.event.
+                                         InternalFrameAdapter()
       {
-        valueField.setText( slider.getValue()+"" );
-        valueChanged( slider.getValue() );
-      }
-    });
-
-    slider.setValue(value);
-    valueField.setText(value+"");
+        public void internalFrameClosed(
+            javax.swing.event.InternalFrameEvent e)
+        {
+          PIDSlider = null;
+        }
+      });
+      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
   }
 
   public void valueChanged(int i)
   {
-    if(cs == null)
+    if (cs == null)
+    {
       return;
+    }
 
     ColourSchemeI toChange = null;
     Vector allGroups = null;
     int groupIndex = 0;
 
-    if(allGroupsCheck.isSelected())
+    if (allGroupsCheck.isSelected())
     {
       allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size()-1;
+      groupIndex = allGroups.size() - 1;
     }
     else
+    {
       toChange = cs;
+    }
 
-
-    while( groupIndex > -1 )
+    while (groupIndex > -1)
     {
-      if(allGroups!=null)
-        toChange = ((SequenceGroup)allGroups.get(groupIndex)).cs;
+      if (allGroups != null)
+      {
+        toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;
+      }
 
       if (forConservation)
       {
         if (toChange instanceof ConservationColourScheme)
+        {
           ( (ConservationColourScheme) toChange).inc = i;
+        }
       }
       else
       {
-          ( (ResidueColourScheme) toChange).setThreshold(i);
+        ( (ResidueColourScheme) toChange).setThreshold(i);
       }
 
       groupIndex--;
     }
 
     ap.seqPanel.seqCanvas.repaint();
-
   }
 
   public void setAllGroupsCheckEnabled(boolean b)
@@ -226,16 +257,16 @@ public class SliderPanel extends GSliderPanel
     allGroupsCheck.setEnabled(b);
   }
 
-
   public void valueField_actionPerformed(ActionEvent e)
   {
-    try{
+    try
+    {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
     }
-    catch(Exception ex)
+    catch (Exception ex)
     {
-      valueField.setText( slider.getValue()+"" );
+      valueField.setText(slider.getValue() + "");
     }
   }
 
@@ -243,10 +274,9 @@ public class SliderPanel extends GSliderPanel
   {
     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 794bbb8..6edab5d 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -1,66 +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.gui;
 
-import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
+import javax.swing.*;
 
-public class SplashScreen extends JPanel implements Runnable
+public class SplashScreen
+    extends JPanel implements Runnable
 {
   boolean visible = true;
   JInternalFrame iframe;
   Image image;
+  int fontSize = 11;
+  int yoffset = 30;
 
   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)
+    {
+      public void mousePressed(MouseEvent evt)
       {
         try
-        {   closeSplash();  }
+        {
+          closeSplash();
+        }
         catch (Exception ex)
-        {}
+        {
+        }
       }
-      });
+    });
   }
 
-
   public void run()
   {
-    long startTime =  System.currentTimeMillis()/1000;
+    long startTime = System.currentTimeMillis() / 1000;
 
-    while( visible )
+    while (visible)
     {
-      if( System.currentTimeMillis()/1000 - startTime > 5)
+      if ( ( (System.currentTimeMillis() / 1000) - startTime) > 5)
+      {
         visible = false;
+      }
 
-      try{
+      try
+      {
         Thread.sleep(1000);
       }
-      catch(Exception ex){}
+      catch (Exception ex)
+      {
+      }
     }
+
     closeSplash();
   }
 
@@ -71,29 +83,36 @@ public class SplashScreen extends JPanel implements Runnable
       iframe.setClosed(true);
     }
     catch (Exception ex)
-    {}
-
+    {
+    }
   }
 
-  int fontSize = 11;
-  int yoffset = 30;
   public void paintComponent(Graphics g)
   {
     g.setColor(Color.white);
-    g.fillRect(0,0,getWidth(),getHeight());
+    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);
-    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.setFont(new Font("Verdana", Font.BOLD, fontSize + 6));
 
-  }
+    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));
+  }
 }
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 5ebf323..12416ae 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,68 +1,65 @@
 /*
-* 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.gui;
 
+import java.util.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.util.*;
-import jalview.schemes.*;
-import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
 import java.awt.print.*;
+import javax.swing.*;
 
-public class TreeCanvas extends JPanel implements MouseListener, Runnable, Printable
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.*;
+
+public class TreeCanvas
+    extends JPanel implements MouseListener, Runnable,
+    Printable
 {
+  public static final String PLACEHOLDER = " * ";
   NJTree tree;
   JScrollPane scrollPane;
   AlignViewport av;
-  public static final String PLACEHOLDER=" * ";
   Font font;
-  int  fontSize = 12;
-
+  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;
+  int labelLength = -1;
 
   //RubberbandRectangle rubberband;
-
-  Vector    listeners;
-
+  Vector listeners;
   Hashtable nameHash = new Hashtable();
   Hashtable nodeHash = new Hashtable();
 
-  public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, String label)
+  public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,
+                    String label)
   {
     this.av = av;
-    this.tree     = tree;
+    this.tree = tree;
     scrollPane = scroller;
     addMouseListener(this);
     tree.findHeight(tree.getTopNode());
@@ -70,10 +67,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
 
     PaintRefresher.Register(this);
   }
+
   public void TreeSelectionChanged(Sequence sequence)
- {
+  {
     SequenceGroup selected = av.getSelectionGroup();
-    if(selected == null)
+
+    if (selected == null)
     {
       selected = new SequenceGroup();
       av.setSelectionGroup(selected);
@@ -82,205 +81,259 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
     selected.setEndRes(av.alignment.getWidth());
     selected.addOrRemove(sequence);
 
-
     PaintRefresher.Refresh(this);
     repaint();
- }
-
-
+  }
 
-  public void setTree(NJTree tree) {
+  public void setTree(NJTree tree)
+  {
     this.tree = tree;
     tree.findHeight(tree.getTopNode());
   }
 
-    public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
-    if (node == null) {
+  public void drawNode(Graphics g, SequenceNode node, float chunk,
+                       float scale, int width, int offx, int offy)
+  {
+    if (node == null)
+    {
       return;
     }
 
-    if (node.left() == null && node.right() == null) {
+    if ( (node.left() == null) && (node.right() == null))
+    {
       // Drawing leaf node
-
       float height = node.height;
-      float dist   = node.dist;
+      float dist = node.dist;
 
-      int xstart = (int)((height-dist)*scale) + offx;
-      int xend =   (int)(height*scale)        + offx;
+      int xstart = (int) ( (height - dist) * scale) + offx;
+      int xend = (int) (height * scale) + offx;
 
-      int ypos = (int)(node.ycount * chunk) + offy;
+      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());
-
+        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);
-
+      {
+        g.setColor(Color.black);
+      }
 
       // Draw horizontal line
-      g.drawLine(xstart,ypos,xend,ypos);
+      g.drawLine(xstart, ypos, xend, ypos);
 
       String nodeLabel = "";
-      if (showDistances && node.dist > 0) {
+
+      if (showDistances && (node.dist > 0))
+      {
         nodeLabel = new Format("%5.2f").form(node.dist);
       }
-      if (showBootstrap) {
-        if (showDistances) {
+
+      if (showBootstrap)
+      {
+        if (showDistances)
+        {
           nodeLabel = nodeLabel + " : ";
         }
+
         nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
       }
-      if (! nodeLabel.equals("")) {
-      g.drawString(nodeLabel,xstart,ypos - 10);
+
+      if (!nodeLabel.equals(""))
+      {
+        g.drawString(nodeLabel, xstart, ypos - 10);
       }
 
-      String name    = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER+node.getName()) : node.getName();
+      String name = (markPlaceholders && node.isPlaceholder())
+          ? (PLACEHOLDER + node.getName()) : node.getName();
       FontMetrics fm = g.getFontMetrics(font);
-      int charWidth  = fm.stringWidth(name) + 3;
+      int charWidth = fm.stringWidth(name) + 3;
       int charHeight = fm.getHeight();
 
-      Rectangle rect = new Rectangle(xend+20,ypos-charHeight,
-                                     charWidth,charHeight);
+      Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,
+                                     charWidth, charHeight);
 
-      nameHash.put((SequenceI)node.element(),rect);
+      nameHash.put( (SequenceI) node.element(), rect);
 
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
-      if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {
+
+      if ( (selected != null) &&
+          selected.sequences.contains( (SequenceI) node.element()))
+      {
         g.setColor(Color.gray);
 
-        g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);
+        g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,
+                   charHeight);
         g.setColor(Color.white);
       }
-      g.drawString(name,xend+10,ypos);
+
+      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);
+    }
+    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;
+      float dist = node.dist;
 
-      int xstart = (int)((height-dist)*scale) + offx;
-      int xend   = (int)(height       *scale) + offx;
-      int ypos   = (int)(node.ycount  *chunk) + offy;
+      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());
+      g.setColor( ( (SequenceNode) node).color.darker());
 
       // Draw horizontal line
-      g.drawLine(xstart,ypos,xend,ypos);
-      g.fillRect(xend-2, ypos-2, 4,4);
+      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;
+      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);
+      Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
+      nodeHash.put(node, pos);
 
-      g.drawLine((int)(height*scale) + offx, ystart,
-                 (int)(height*scale) + offx, yend);
+      g.drawLine( (int) (height * scale) + offx, ystart,
+                 (int) (height * scale) + offx, yend);
 
-      if (showDistances && node.dist > 0) {
-        g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
+      if (showDistances && (node.dist > 0))
+      {
+        g.drawString(new Format("%5.2f").form(node.dist), xstart,
+                     ypos - 5);
       }
-
     }
   }
-  public Object findElement(int x, int y) {
-       Enumeration keys = nameHash.keys();
 
-    while (keys.hasMoreElements()) {
-            Object ob = keys.nextElement();
-            Rectangle rect = (Rectangle)nameHash.get(ob);
+  public Object findElement(int x, int y)
+  {
+    Enumeration keys = nameHash.keys();
 
-            if (x >= rect.x && x <= (rect.x + rect.width) &&
-              y >= rect.y && y <= (rect.y + rect.height)) {
-              return ob;
-            }
-  }
-  keys = nodeHash.keys();
+    while (keys.hasMoreElements())
+    {
+      Object ob = keys.nextElement();
+      Rectangle rect = (Rectangle) nameHash.get(ob);
 
-    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;
+      }
+    }
 
-            if (x >= rect.x && x <= (rect.x + rect.width) &&
-              y >= rect.y && y <= (rect.y + rect.height)) {
-              return ob;
-            }
+    keys = nodeHash.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;
+      }
     }
-      return null;
 
+    return null;
   }
 
-  public void pickNodes(Rectangle pickBox) {
-    int width  = getWidth();
+  public void pickNodes(Rectangle pickBox)
+  {
+    int width = getWidth();
     int height = getHeight();
 
     SequenceNode top = tree.getTopNode();
 
-    float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()
-;
-    if (top.count == 0) {
-      top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
+    float wscale = (float) ( (width * .8) - (offx * 2)) / tree.getMaxHeight();
+
+    if (top.count == 0)
+    {
+      top.count = ( (SequenceNode) top.left()).count +
+          ( (SequenceNode) top.right()).count;
     }
-    float chunk = (float)(height-offy*2)/top.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) {
+  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+                       float scale, int width, int offx, int offy)
+  {
+    if (node == null)
+    {
       return;
     }
 
-    if (node.left() == null && node.right() == null) {
+    if ( (node.left() == null) && (node.right() == null))
+    {
       float height = node.height;
-      float dist   = node.dist;
+      float dist = node.dist;
 
-      int xstart = (int)((height-dist)*scale) + offx;
-      int xend   = (int)(height*scale) + offx;
+      int xstart = (int) ( (height - dist) * scale) + offx;
+      int xend = (int) (height * scale) + offx;
 
-      int ypos = (int)(node.ycount * chunk) + offy;
+      int ypos = (int) (node.ycount * chunk) + offy;
 
-      if (pickBox.contains(new Point(xend,ypos))) {
-        if (node.element() instanceof SequenceI) {
-          SequenceI seq = (SequenceI)node.element();
+      if (pickBox.contains(new Point(xend, ypos)))
+      {
+        if (node.element() instanceof SequenceI)
+        {
+          SequenceI seq = (SequenceI) node.element();
           SequenceGroup sg = av.getSelectionGroup();
-          if(sg!=null)
+
+          if (sg != null)
+          {
             sg.addOrRemove(seq);
+          }
         }
       }
-    } else {
-      pickNode(pickBox,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
-      pickNode(pickBox,(SequenceNode)node.right(),chunk,scale,width,offx,offy);
+    }
+    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)
+    {
       return;
+    }
 
-    if (node.left() == null && node.right() == null)
+    if ( (node.left() == null) && (node.right() == null))
     {
       node.color = c;
 
       if (node.element() instanceof SequenceI)
-          ((SequenceI)node.element()).setColor(c);
-    } else
+      {
+        ( (SequenceI) node.element()).setColor(c);
+      }
+    }
+    else
     {
       node.color = c;
-      setColor((SequenceNode)node.left(),c);
-      setColor((SequenceNode)node.right(),c);
+      setColor( (SequenceNode) node.left(), c);
+      setColor( (SequenceNode) node.right(), c);
     }
   }
 
@@ -297,6 +350,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
     PageFormat pf = printJob.pageDialog(printJob.defaultPage());
 
     printJob.setPrintable(this, pf);
+
     if (printJob.printDialog())
     {
       try
@@ -310,216 +364,259 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
     }
   }
 
-
-  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
+  public int print(Graphics pg, PageFormat pf, int pi)
+      throws PrinterException
   {
-
     pg.setFont(font);
-    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
+    pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+
     int pwidth = (int) pf.getImageableWidth();
     int pheight = (int) pf.getImageableHeight();
 
     int noPages = getHeight() / pheight;
-    if(pi>noPages)
-      return Printable.NO_SUCH_PAGE;
 
+    if (pi > noPages)
+    {
+      return Printable.NO_SUCH_PAGE;
+    }
 
     if (pwidth > getWidth())
-        pwidth = getWidth();
+    {
+      pwidth = getWidth();
+    }
 
-    if(fitToWindow)
+    if (fitToWindow)
     {
       if (pheight > getHeight())
+      {
         pheight = getHeight();
+      }
 
       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 = 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;
     }
 
     draw(pg, pwidth, pheight);
 
     return Printable.PAGE_EXISTS;
-
   }
 
   public void paintComponent(Graphics g)
   {
-
-    font = new Font("Verdana",Font.PLAIN,fontSize);
+    font = new Font("Verdana", Font.PLAIN, fontSize);
     g.setFont(font);
 
     FontMetrics fm = g.getFontMetrics(font);
 
-    if(nameHash.size()==0)
+    if (nameHash.size() == 0)
+    {
       repaint();
+    }
 
-
-    if( fitToWindow || (!fitToWindow && scrollPane.getHeight() > fm.getHeight() * nameHash.size()+offy ) )
-     {
-         draw(g,scrollPane.getWidth(),scrollPane.getHeight());
-         setPreferredSize(null);
-     }
+    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());
-     }
+    {
+      setPreferredSize(new Dimension(scrollPane.getWidth(),
+                                     fm.getHeight() * nameHash.size()));
+      draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
+    }
 
     scrollPane.revalidate();
   }
-    public int getFontSize() {
-        return fontSize;
-    }
-    public void setFontSize(int fontSize) {
-        this.fontSize = fontSize;
-        repaint();
-    }
-  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);
+  public int getFontSize()
+  {
+    return fontSize;
+  }
 
+  public void setFontSize(int fontSize)
+  {
+    this.fontSize = fontSize;
+    repaint();
+  }
 
-      labelLength = g2.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar
+  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);
 
-      float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();
+    labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
 
-      SequenceNode top = tree.getTopNode();
+    float wscale = (float) (width - labelLength - (offx * 2)) /
+        tree.getMaxHeight();
 
-      if (top.count == 0) {
-          top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
-      }
-      float chunk = (float)(height-offy*2)/top.count ;
+    SequenceNode top = tree.getTopNode();
 
-      drawNode(g2,tree.getTopNode(),chunk,wscale,width,offx,offy);
+    if (top.count == 0)
+    {
+      top.count = ( (SequenceNode) top.left()).count +
+          ( (SequenceNode) top.right()).count;
+    }
 
-      if (threshold != 0)
-      {
-        if(av.getCurrentTree() == tree)
-          g2.setColor(Color.red);
-        else
-          g2.setColor(Color.gray);
+    float chunk = (float) (height - (offy * 2)) / top.count;
 
-          int x = (int)(    threshold * (float)(getWidth()-labelLength - 2*offx) +offx   ) ;
+    drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
 
-          g2.drawLine(x,0,x,getHeight());
+    if (threshold != 0)
+    {
+      if (av.getCurrentTree() == tree)
+      {
+        g2.setColor(Color.red);
       }
-
-  }
-
-  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)
+      else
       {
-          TreeSelectionChanged((Sequence)ob);
-          repaint();
-          return;
-
-      } else if (ob instanceof SequenceNode) {
-          SequenceNode tmpnode = (SequenceNode)ob;
-          tree.swapNodes(tmpnode);
-          tree.reCount(tree.getTopNode());
-          tree.findHeight(tree.getTopNode());
-      } else {
-          // Find threshold
+        g2.setColor(Color.gray);
+      }
 
-          if (tree.getMaxHeight() != 0) {
-              threshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);
+      int x = (int) ( (threshold * (float) (getWidth() - labelLength -
+                                            (2 * offx))) + offx);
 
-              tree.getGroups().removeAllElements();
-              tree.groupNodes(tree.getTopNode(),threshold);
-              setColor(tree.getTopNode(),Color.black);
+      g2.drawLine(x, 0, x, getHeight());
+    }
+  }
 
-              av.setSelectionGroup(null);
-              av.alignment.deleteAllGroups();
+  public void mouseReleased(MouseEvent e)
+  {
+  }
 
-              for (int i=0; i < tree.getGroups().size(); i++)
-              {
+  public void mouseEntered(MouseEvent e)
+  {
+  }
 
-                  Color col = new Color((int)(Math.random()*255),
-                                        (int)(Math.random()*255),
-                                        (int)(Math.random()*255));
-                  setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());
+  public void mouseExited(MouseEvent e)
+  {
+  }
 
-                  Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
-                  SequenceGroup sg = null;
-                  for (int j = 0; j < l.size(); j++)
-                  {
-                    SequenceNode sn = (SequenceNode) l.elementAt(j);
-                    if(sg==null)
-                       sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());
+  public void mouseClicked(MouseEvent e)
+  {
+  }
 
-                    sg.addSequence( (Sequence) sn.element());
-                  }
+  public void mousePressed(MouseEvent e)
+  {
+    av.setCurrentTree(tree);
 
-                  if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
-                  {
-                    ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();
-                    Conservation c = new Conservation("Group",
-                                                      ResidueProperties.propHash, 3,
-                                                      sg.sequences, sg.getStartRes(),
-                                                      sg.getEndRes());
+    int x = e.getX();
+    int y = e.getY();
 
-                    c.calculate();
-                    c.verdict(false, av.ConsPercGaps);
-                    ccs = new ConservationColourScheme(c, ccs.cs);
+    Object ob = findElement(x, y);
 
-                    sg.cs = ccs;
+    if (ob instanceof SequenceI)
+    {
+      TreeSelectionChanged( (Sequence) ob);
+      repaint();
 
-                  }
+      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());
+          SequenceGroup sg = null;
+
+          for (int j = 0; j < l.size(); j++)
+          {
+            SequenceNode sn = (SequenceNode) l.elementAt(j);
+
+            if (sg == null)
+            {
+              sg = new SequenceGroup("TreeGroup",
+                                     av.getGlobalColourScheme(), true, true,
+                                     false, 0, av.alignment.getWidth());
+            }
 
+            sg.addSequence( (Sequence) sn.element());
+          }
 
+          if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
+          {
+            ConservationColourScheme ccs = (ConservationColourScheme) av.
+                getGlobalColourScheme();
+            Conservation c = new Conservation("Group",
+                                              ResidueProperties.propHash, 3,
+                                              sg.sequences,
+                                              sg.getStartRes(), sg.getEndRes());
 
-                  av.alignment.addGroup(sg);
+            c.calculate();
+            c.verdict(false, av.ConsPercGaps);
+            ccs = new ConservationColourScheme(c, ccs.cs);
 
-              }
+            sg.cs = ccs;
           }
-      }
 
-      PaintRefresher.Refresh(this);
-      repaint();
+          av.alignment.addGroup(sg);
+        }
+      }
+    }
 
+    PaintRefresher.Refresh(this);
+    repaint();
   }
 
-    public void setShowDistances(boolean state) {
-        this.showDistances = state;
-        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();
-    }
+  public void setShowBootstrap(boolean state)
+  {
+    this.showBootstrap = state;
+    repaint();
+  }
 
+  public void setMarkPlaceholders(boolean state)
+  {
+    this.markPlaceholders = state;
+    repaint();
+  }
 }
-
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index a574795..2a8c9b4 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.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
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.jbgui.GTreePanel;
-import jalview.io.*;
-import java.awt.event.*;
-import java.util.*;
 import java.io.*;
-import javax.swing.*;
-import java.awt.*;
-import java.awt.image.*;
-import org.jibble.epsgraphics.*;
+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
+public class TreePanel
+    extends GTreePanel
 {
   SequenceI[] seq;
   String type;
@@ -45,12 +45,8 @@ public class TreePanel extends GTreePanel
   TreeCanvas treeCanvas;
   NJTree tree;
 
-  public NJTree getTree()
-  {
-    return tree;
-  }
-
-  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
+  public TreePanel(AlignViewport av, Vector seqVector, String type,
+                   String pwtype, int s, int e)
   {
     super();
 
@@ -61,12 +57,16 @@ public class TreePanel extends GTreePanel
     end = e;
 
     String longestName = "";
-    seq = new Sequence [seqVector.size()];
-    for (int i=0;i < seqVector.size();i++)
+    seq = new Sequence[seqVector.size()];
+
+    for (int i = 0; i < seqVector.size(); i++)
     {
       seq[i] = (Sequence) seqVector.elementAt(i);
-      if(seq[i].getName().length()>longestName.length())
+
+      if (seq[i].getName().length() > longestName.length())
+      {
         longestName = seq[i].getName();
+      }
     }
 
     tree = new NJTree(seq, type, pwtype, start, end);
@@ -77,108 +77,145 @@ public class TreePanel extends GTreePanel
     tree.reCount(tree.getTopNode());
     tree.findHeight(tree.getTopNode());
     scrollPane.setViewportView(treeCanvas);
-
   }
-  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 TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
                    String type, String pwtype)
+  {
+    super();
+
+    // These are probably only  arbitrary strings reflecting source of tree
+    this.type = type;
+    this.pwtype = pwtype;
+
+    start = 0;
+    end = seqVector.size();
+
+    String longestName = "";
+    seq = new Sequence[seqVector.size()];
+
+    for (int i = 0; i < seqVector.size(); i++)
     {
-      super();
-      // These are probably only  arbitrary strings reflecting source of tree
-      this.type = type;
-      this.pwtype = pwtype;
+      seq[i] = (Sequence) seqVector.elementAt(i);
+    }
+
+    // This constructor matches sequence names to treenodes and sets up the tree layouts.
+    tree = new NJTree(seq, newtree);
+
+    // Now have to calculate longest name based on the leaves
+    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+    boolean has_placeholders = false;
 
-      start = 0;
-      end = seqVector.size();
+    for (int i = 0; i < leaves.size(); i++)
+    {
+      SequenceNode lf = (SequenceNode) leaves.elementAt(i);
 
-      String longestName = "";
-      seq = new Sequence [seqVector.size()];
-      for (int i=0;i < seqVector.size();i++)
+      if (lf.isPlaceholder())
       {
-        seq[i] = (Sequence) seqVector.elementAt(i);
+        has_placeholders = true;
       }
-      // This constructor matches sequence names to treenodes and sets up the tree layouts.
-      tree = new NJTree(seq, newtree);
-      // Now have to calculate longest name based on the leaves
-      Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
-      boolean has_placeholders = false;
-      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();
+
+      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
     }
 
+    tree.reCount(tree.getTopNode());
+    tree.findHeight(tree.getTopNode());
 
-    public void textbox_actionPerformed(ActionEvent e)
-    {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    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
+  }
 
-      StringBuffer buffer = new StringBuffer();
+  public NJTree getTree()
+  {
+    return tree;
+  }
 
-      if(type.equals("AV"))
-        buffer.append("Average distance tree using ");
-      else
-        buffer.append("Neighbour joining tree using ");
+  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);
+  }
 
-      if(pwtype.equals("BL"))
-       buffer.append("BLOSUM62");
-      else
-        buffer.append("PID");
+  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();
+  }
 
-      Desktop.addInternalFrame(cap,buffer.toString(), 500, 100);
-      jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-      cap.setText(  fout.print(false,true) );
+  public void textbox_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
 
-    }
+    StringBuffer buffer = new StringBuffer();
 
+    if (type.equals("AV"))
+    {
+      buffer.append("Average distance tree using ");
+    }
+    else
+    {
+      buffer.append("Neighbour joining tree using ");
+    }
 
-    public void saveAsNewick_actionPerformed(ActionEvent e)
+    if (pwtype.equals("BL"))
+    {
+      buffer.append("BLOSUM62");
+    }
+    else
     {
+      buffer.append("PID");
+    }
 
-  JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty("LAST_DIRECTORY"));
+    Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+    cap.setText(fout.print(false, true));
+  }
+
+  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");
+
     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{
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      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 )  );
+        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) {
+      catch (Exception ex)
+      {
         ex.printStackTrace();
       }
     }
@@ -186,7 +223,6 @@ public class TreePanel extends GTreePanel
 
   protected void printMenu_actionPerformed(ActionEvent e)
   {
-
     //Putting in a thread avoids Swing painting problems
     treeCanvas.startPrinting();
   }
@@ -197,29 +233,33 @@ public class TreePanel extends GTreePanel
     repaint();
   }
 
-
   protected void fontSize_actionPerformed(ActionEvent e)
   {
-    if( treeCanvas==null )
-     return;
-
-   String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);
-
-   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);
-   if(selection!=null)
-   {
-     fontSize.setText("Font Size - " + selection);
-
-     int i = Integer.parseInt(selection.toString());
-     treeCanvas.setFontSize(i);
-   }
-    scrollPane.setViewportView(treeCanvas);
+    if (treeCanvas == null)
+    {
+      return;
+    }
+
+    String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +
+                                               1);
+
+    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);
 
+    if (selection != null)
+    {
+      fontSize.setText("Font Size - " + selection);
+
+      int i = Integer.parseInt(selection.toString());
+      treeCanvas.setFontSize(i);
+    }
+
+    scrollPane.setViewportView(treeCanvas);
   }
 
   protected void distanceMenu_actionPerformed(ActionEvent e)
@@ -233,37 +273,46 @@ public class TreePanel extends GTreePanel
   }
 
   protected void placeholdersMenu_actionPerformed(ActionEvent e)
-    {
-      treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+  {
+    treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
   }
 
   protected void epsTree_actionPerformed(ActionEvent e)
   {
-    int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();
+    int width = treeCanvas.getWidth();
+    int height = treeCanvas.getHeight();
+
     try
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"),
-              new String[]{"eps"},
-              new String[]{"Encapsulated Postscript"},
-              "Encapsulated Postscript");
+      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);
+      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();
+      pg.flush();
+      pg.close();
     }
     catch (Exception ex)
     {
@@ -272,14 +321,18 @@ public class TreePanel extends GTreePanel
   }
 
   protected void pngTree_actionPerformed(ActionEvent e)
- {
-  int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();
+  {
+    int width = treeCanvas.getWidth();
+    int height = treeCanvas.getHeight();
+
     try
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-          jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-          new String[] {"png"},
-          new String[] {"Portable network graphics"},
+          jalview.bin.Cache.getProperty(
+              "LAST_DIRECTORY"), new String[]
+          {"png"},
+          new String[]
+          {"Portable network graphics"},
           "Portable network graphics");
 
       chooser.setFileView(new jalview.io.JalviewFileView());
@@ -287,24 +340,29 @@ public class TreePanel extends GTreePanel
       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());
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 
-      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+      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();
+      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 f0cf6c1..18382fb 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,39 +1,39 @@
 /*
-* 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.gui;
 
-import jalview.jbgui.GUserDefinedColours;
-import jalview.datamodel.*;
-import jalview.io.*;
-import javax.swing.*;
+import java.io.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
+import javax.swing.*;
 import javax.swing.event.*;
-import jalview.schemes.*;
-import java.io.*;
-import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
 
-public class UserDefinedColours extends GUserDefinedColours implements ChangeListener
+public class UserDefinedColours
+    extends GUserDefinedColours implements ChangeListener
 {
-
   AlignmentPanel ap;
   SequenceGroup seqGroup;
   JButton selectedButton;
@@ -41,55 +41,66 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
   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"))
-      frame.setSize(450,560);
+    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);
+    }
+
+    if (sg != null)
+    {
+      frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");
+    }
 
     colorChooser.getSelectionModel().addChangeListener(this);
 
     this.ap = ap;
     seqGroup = sg;
 
+    if (seqGroup != null)
+    {
+      oldColourScheme = seqGroup.cs;
+    }
+    else
+    {
+      oldColourScheme = ap.av.getGlobalColourScheme();
+    }
 
-      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]);
+    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)
-     selectedButton.setBackground( colorChooser.getColor() );
- }
+  public void stateChanged(ChangeEvent evt)
+  {
+    if (selectedButton != null)
+    {
+      selectedButton.setBackground(colorChooser.getColor());
+    }
+  }
 
   public void colourButtonPressed(MouseEvent e)
   {
-     selectedButton = (JButton)e.getSource();
-     colorChooser.setColor(selectedButton.getBackground());
+    selectedButton = (JButton) e.getSource();
+    colorChooser.setColor(selectedButton.getBackground());
   }
 
   void makeButton(String label, String aa)
@@ -97,15 +108,18 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
     final JButton button = new JButton();
     Color col = Color.white;
 
-
-    try{
+    try
+    {
       col = oldColourScheme.findColour(aa, -1);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
 
-    button.setBackground(  col );
-    oldColours.addElement( col );
-    button.setText( label );
-    button.setForeground( col.darker().darker().darker() );
+    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()
     {
@@ -118,167 +132,207 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
     buttonPanel.add(button, null);
   }
 
-
   protected void okButton_actionPerformed(ActionEvent e)
   {
     applyButton_actionPerformed(null);
-    try{
+
+    try
+    {
       frame.setClosed(true);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
   }
 
   protected void applyButton_actionPerformed(ActionEvent e)
   {
-    Color [] newColours = new Color[24];
-    for(int i=0; i<24; i++)
+    Color[] newColours = new Color[24];
+
+    for (int i = 0; i < 24; i++)
     {
-          JButton button = (JButton)buttonPanel.getComponent(i);
-          newColours[i] = button.getBackground();
+      JButton button = (JButton) buttonPanel.getComponent(i);
+      newColours[i] = button.getBackground();
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
     ucs.setThreshold(0);
 
-    if(seqGroup!=null)
+    if (seqGroup != null)
     {
       seqGroup.cs = ucs;
       ap.repaint();
     }
     else
+    {
       ap.alignFrame.changeColour(ucs);
-
+    }
   }
 
   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");
+    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)
     {
       File choice = chooser.getSelectedFile();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",  choice.getParent());
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice.getPath());
+      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]);
       }
-
     }
   }
 
   public static UserColourScheme loadDefaultColours()
   {
-    if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
-      return loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
+    if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)
+    {
+      return loadDefaultColours(jalview.bin.Cache.getProperty(
+          "USER_DEFINED_COLOUR"));
+    }
     else
+    {
       return null;
+    }
   }
 
   public static UserColourScheme loadDefaultColours(String file)
   {
-      UserColourScheme ucs = null;
-      Color cols[] = loadColours(file);
-      if(cols!=null)
-      {
-        ucs = new UserColourScheme(cols);
-        ucs.setThreshold(0);
-      }
-      return ucs;
+    UserColourScheme ucs = null;
+    Color[] cols = loadColours(file);
+
+    if (cols != null)
+    {
+      ucs = new UserColourScheme(cols);
+      ucs.setThreshold(0);
+    }
+
+    return ucs;
   }
 
-  static Color [] loadColours(String file)
+  static Color[] loadColours(String file)
   {
-    Color [] newColours=null;
+    Color[] newColours = null;
+
     try
     {
-      InputStreamReader in = new InputStreamReader(
-          new FileInputStream(file), "UTF-8");
+      InputStreamReader in = new InputStreamReader(new FileInputStream(
+          file), "UTF-8");
 
-      jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
-      ucs = (jalview.binding.JalviewUserColours)ucs.unmarshal(in);
+      jalview.binding.JalviewUserColours ucs = new jalview.binding.
+          JalviewUserColours();
+      ucs = (jalview.binding.JalviewUserColours) ucs.unmarshal(in);
 
       newColours = new Color[ucs.getColourCount()];
-      for (int i = 0; i < 24; i++)
-        newColours[i] = new Color(Integer.parseInt(ucs.getColour(i).getRGB(), 16));
 
+      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);}
+    {
+      System.out.println("Error loading UserColourFile " + file);
+    }
 
     return newColours;
   }
 
   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");
+    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("Save colour scheme");
     chooser.setToolTipText("Save");
+
     int value = chooser.showSaveDialog(this);
+
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);
-      jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
 
-      try{
+      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++)
+            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);
+          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();}
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
     }
-
   }
 
   protected void cancelButton_actionPerformed(ActionEvent e)
   {
+    Color[] newColours = new Color[24];
 
-    Color [] newColours = new Color[24];
-    for(int i=0; i<24; i++)
+    for (int i = 0; i < 24; i++)
     {
-          newColours[i] = (Color)oldColours.elementAt(i);
-          buttonPanel.getComponent(i).setBackground(newColours[i]);
+      newColours[i] = (Color) oldColours.elementAt(i);
+      buttonPanel.getComponent(i).setBackground(newColours[i]);
     }
 
-    UserColourScheme ucs = new UserColourScheme( newColours );
+    UserColourScheme ucs = new UserColourScheme(newColours);
 
     if (seqGroup != null)
+    {
       seqGroup.cs = ucs;
+    }
     else
+    {
       ap.av.setGlobalColourScheme(ucs);
+    }
 
     ap.repaint();
 
-    try{
+    try
+    {
       frame.setClosed(true);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
   }
-
-
 }
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 9e980c5..0a098e5 100755
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.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.gui;
 
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
-import jalview.jbgui.GWebserviceInfo;
 
-public class WebserviceInfo extends GWebserviceInfo
-{
+import jalview.jbgui.*;
 
+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;
@@ -36,17 +36,9 @@ public class WebserviceInfo extends GWebserviceInfo
   int currentStatus = STATE_QUEUING;
   Image image;
   int angle = 0;
-
-  String title="";
+  String title = "";
   jalview.ws.WSClientI thisService;
   boolean serviceIsCancellable;
-  public jalview.ws.WSClientI getthisService() {
-    return thisService;
-  }
-  public void setthisService(jalview.ws.WSClientI newservice) {
-    thisService = newservice;
-    serviceIsCancellable = newservice.isCancellable();
-  }
 
   public WebserviceInfo(String title, String info)
   {
@@ -58,6 +50,17 @@ public class WebserviceInfo extends GWebserviceInfo
     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();
@@ -66,20 +69,24 @@ public class WebserviceInfo extends GWebserviceInfo
 
     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
     {
       mt.waitForID(0);
     }
     catch (Exception ex)
-    {}
-
+    {
+    }
 
     AnimatedPanel ap = new AnimatedPanel();
     titlePanel.add(ap, BorderLayout.CENTER);
+
     Thread thread = new Thread(ap);
     thread.start();
   }
@@ -90,97 +97,130 @@ public class WebserviceInfo extends GWebserviceInfo
   }
 
   public String getInfoText()
-  {   return infoText.getText();  }
+  {
+    return infoText.getText();
+  }
 
   public void setInfoText(String text)
-  {   infoText.setText(text);     }
+  {
+    infoText.setText(text);
+  }
 
   public void appendInfoText(String text)
-  {  infoText.append(text);  }
+  {
+    infoText.append(text);
+  }
 
   public String getProgressText()
-  {   return progressText.getText();  }
+  {
+    return progressText.getText();
+  }
 
   public void setProgressText(String text)
-  {   progressText.setText(text);   }
+  {
+    progressText.setText(text);
+  }
 
   public void appendProgressText(String text)
-  {   progressText.append(text);  }
+  {
+    progressText.append(text);
+  }
 
   protected void cancel_actionPerformed(ActionEvent e)
   {
     if (!serviceIsCancellable)
+    {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "This job cannot be cancelled." ,
-                                            "Cancel job"
-                                            ,JOptionPane.WARNING_MESSAGE);
+                                            "This job cannot be cancelled.",
+                                            "Cancel job",
+                                            JOptionPane.WARNING_MESSAGE);
+    }
     else
+    {
       thisService.cancelJob();
+    }
   }
 
-
-  class AnimatedPanel extends JPanel implements Runnable
+  class AnimatedPanel
+      extends JPanel implements Runnable
   {
-    long startTime=0;
+    long startTime = 0;
+
     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();
+      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)
+        {
+        }
       }
-      catch (Exception ex)
-      {}
+
       angle = 0;
       cancel.setEnabled(false);
-
     }
 
-   synchronized public void  paintComponent(Graphics g1)
+    synchronized public void paintComponent(Graphics g1)
     {
       Graphics2D g = (Graphics2D) g1;
       g.setColor(Color.white);
       g.fillRect(0, 0, getWidth(), getHeight());
+
       if (image != null)
       {
         g.rotate(Math.toRadians(angle), 28, 28);
         g.drawImage(image, 10, 10, this);
         g.rotate( -Math.toRadians(angle), 28, 28);
       }
+
       g.setFont(new Font("Arial", Font.BOLD, 12));
       g.setColor(Color.black);
-      switch(currentStatus)
+
+      switch (currentStatus)
       {
         case STATE_QUEUING:
           g.drawString(title.concat(" - queuing"), 60, 30);
+
           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);
+          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 0dfef6a..04ddff3 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -16,102 +16,103 @@
 * 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 java.io.*;
+
 import java.util.*;
 
+
 public abstract class AlignFile extends FileParse {
-  int noSeqs    = 0;
-  int maxLength = 0;
-
-  Vector    seqs;
-  Vector    headers;
-
-  long start;
-  long end;
-
-  public AlignFile()
-  {}
-
-  public AlignFile(String inStr) {
-    initData();
-System.out.println("is this ever called??");
-    try{
-      parse();
-    }catch(Exception ex){}
-  }
-
-/**
- * Constructor which parses the data from a file of some specified type.
- * @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 {
-    super(inFile,type);
-
-    initData();
-
-    parse();
-
-  }
-
-/**
- * Return the seqs Vector
- */
-  public Vector getSeqs() {
-    return seqs;
-  }
-
-/**
- * Return the Sequences in the seqs Vector as an array of Sequences
- */
-  public SequenceI [] getSeqsAsArray() {
-    SequenceI [] s = new SequenceI[seqs.size()];
-    for (int i=0;i < seqs.size();i++) {
-      s[i] = (SequenceI)seqs.elementAt(i);
+    int noSeqs = 0;
+    int maxLength = 0;
+    Vector seqs;
+    Vector headers;
+    long start;
+    long end;
+
+    public AlignFile() {
+    }
+
+    public AlignFile(String inStr) {
+        initData();
+        System.out.println("is this ever called??");
+
+        try {
+            parse();
+        } catch (Exception ex) {
+        }
     }
-    return s;
-  }
-
-
-/**
- * Initialise objects to store sequence data in.
- */
-  protected void initData() {
-    seqs    = new Vector();
-    headers = new Vector();
-  }
-
-  protected void setSeqs(SequenceI [] s) {
-    seqs = new Vector();
-    for (int i=0; i<s.length; i++) {
-      seqs.addElement(s[i]);
+
+    /**
+     * Constructor which parses the data from a file of some specified type.
+     * @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 {
+        super(inFile, type);
+
+        initData();
+
+        parse();
     }
-  }
 
-  // Checks whether sequence is valid aa characters
-  protected boolean isValidProteinSequence(String sequence)
-  {
-    for (int i = 0; i < sequence.length(); i++)
-      if (!jalview.schemes.ResidueProperties.aaHash.containsKey(String.valueOf(sequence.charAt(i))))
-        return false;
+    /**
+     * Return the seqs Vector
+     */
+    public Vector getSeqs() {
+        return seqs;
+    }
 
-    return true;
-  }
+    /**
+     * Return the Sequences in the seqs Vector as an array of Sequences
+     */
+    public SequenceI[] getSeqsAsArray() {
+        SequenceI[] s = new SequenceI[seqs.size()];
 
+        for (int i = 0; i < seqs.size(); i++) {
+            s[i] = (SequenceI) seqs.elementAt(i);
+        }
 
-/**
- * This method must be implemented to parse the contents of the file.
- */
-  public abstract void parse() throws IOException;
+        return s;
+    }
+
+    /**
+     * Initialise objects to store sequence data in.
+     */
+    protected void initData() {
+        seqs = new Vector();
+        headers = new Vector();
+    }
+
+    protected void setSeqs(SequenceI[] s) {
+        seqs = new Vector();
+
+        for (int i = 0; i < s.length; i++) {
+            seqs.addElement(s[i]);
+        }
+    }
+
+    // Checks whether sequence is valid aa characters
+    protected boolean isValidProteinSequence(String sequence) {
+        for (int i = 0; i < sequence.length(); i++)
+            if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
+                        String.valueOf(sequence.charAt(i)))) {
+                return false;
+            }
+
+        return true;
+    }
 
+    /**
+     * This method must be implemented to parse the contents of the file.
+     */
+    public abstract void parse() throws IOException;
 
-/**
- * Print out in alignment file format the Sequences in the seqs Vector.
- */
-  public abstract String print();
+    /**
+     * Print out in alignment file format the Sequences in the seqs Vector.
+     */
+    public abstract String print();
 }
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 7961810..687eef9 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -16,160 +16,168 @@
 * 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 java.io.*;
+
 import java.util.*;
 
+
 public class BLCFile extends AlignFile {
+    Vector titles;
 
-  Vector titles;
-
-  public BLCFile()
-  {}
-
-  public BLCFile(String inStr) {
-    super(inStr);
-  }
-
-  public void initData() {
-    super.initData();
-    titles = new Vector();
-  }
-
-  public BLCFile(String inFile, String type) throws IOException {
-    super(inFile,type);
-  }
-
-
-  public void parse()
-  {
-    boolean idsFound=false;
-    Vector ids = new Vector();
-    StringBuffer seqstrings [];
-    Vector starts = new Vector();
-    Vector ends = new Vector();
-
-   String line=null;
-   try{
-     do{
-      line = nextLine();
-
-      // seek end of ids
-      if (line.indexOf("*") > -1)
-      {
-        idsFound=true;
-        break;
-      }
-
-      int abracket = line.indexOf(">");
-
-      if (abracket > -1)
-      {
-
-        if(line.indexOf(" ")>-1)//
-        {
-          ///Colur it be this format?
-          //>54402046         0             1   137   137:
-          // or this??
-          //     1   >L1H14       30539  343
-          try{
-            ids.addElement(line.substring(abracket + 1,
-                                          line.indexOf(" ", abracket + 1)));
-
-
-            // remove p Value
-            line = line.substring(abracket + 1);
-            line = line.substring(line.indexOf(" ") + 1);
-            line = line.trim();
-            line = line.substring(line.indexOf(" ") + 1);
-            line = line.trim();
-            int value = Integer.parseInt(line.substring(0, line.indexOf(" ")));
-            starts.addElement(value+"");
-            line = line.substring(line.indexOf(" ") + 1);
-            line = line.trim();
-            value = Integer.parseInt(line.substring(0, line.indexOf(" ")));
-            ends.addElement(value+"");
-
-          }catch(Exception ex)
-          {
-            System.err.println("Error during blockfile read.");
-            ex.printStackTrace();
-            starts.addElement("0");
-            ends.addElement("0");
-          }
+    public BLCFile() {
+    }
 
-        }
-        else
-        {
-          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));
-        }
-      }
-    }while(!idsFound);
-
-    int starCol = line.indexOf("*");
-    seqstrings = new StringBuffer[ids.size()];
-    for(int i=0; i<ids.size(); i++)
-    {
-      if(seqstrings[i]==null)
-        seqstrings[i] = new StringBuffer();
+    public BLCFile(String inStr) {
+        super(inStr);
+    }
+
+    public BLCFile(String inFile, String type) throws IOException {
+        super(inFile, type);
     }
 
-    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));
-      }
+    public void initData() {
+        super.initData();
+        titles = new Vector();
     }
 
-    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);
+    public void parse() {
+        boolean idsFound = false;
+        Vector ids = new Vector();
+        StringBuffer[] seqstrings;
+        Vector starts = new Vector();
+        Vector ends = new Vector();
+
+        String line = null;
+
+        try {
+            do {
+                line = nextLine();
+
+                // seek end of ids
+                if (line.indexOf("*") > -1) {
+                    idsFound = true;
+
+                    break;
+                }
+
+                int abracket = line.indexOf(">");
+
+                if (abracket > -1) {
+                    if (line.indexOf(" ") > -1) //
+                     {
+                        ///Colur it be this format?
+                        //>54402046         0             1   137   137:
+                        // or this??
+                        //     1   >L1H14       30539  343
+                        try {
+                            ids.addElement(line.substring(abracket + 1,
+                                    line.indexOf(" ", abracket + 1)));
+
+                            // remove p Value
+                            line = line.substring(abracket + 1);
+                            line = line.substring(line.indexOf(" ") + 1);
+                            line = line.trim();
+                            line = line.substring(line.indexOf(" ") + 1);
+                            line = line.trim();
+
+                            int value = Integer.parseInt(line.substring(0,
+                                        line.indexOf(" ")));
+                            starts.addElement(value + "");
+                            line = line.substring(line.indexOf(" ") + 1);
+                            line = line.trim();
+                            value = Integer.parseInt(line.substring(0,
+                                        line.indexOf(" ")));
+                            ends.addElement(value + "");
+                        } catch (Exception ex) {
+                            System.err.println("Error during blockfile read.");
+                            ex.printStackTrace();
+                            starts.addElement("0");
+                            ends.addElement("0");
+                        }
+                    } else {
+                        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));
+                    }
+                }
+            } while (!idsFound);
+
+            int starCol = line.indexOf("*");
+            seqstrings = new StringBuffer[ids.size()];
+
+            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)) {
+                        seqstrings[i].append(line.charAt(i + starCol));
+                    }
+                }
+            }
+
+            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) {
+            ex.printStackTrace();
+        }
     }
 
-   }catch(Exception ex){ex.printStackTrace();}
-  }
-
-  public String print() {
-    return print(getSeqsAsArray());
-  }
-  public static String print(SequenceI[] s) {
-    StringBuffer out = new StringBuffer();
-
-    int i=0;
-    int max = -1;
-    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) { max = s[i].getSequence().length();}
-      i++;
+    public String print() {
+        return print(getSeqsAsArray());
     }
 
-      out.append("* iteration 1\n");
-      for (int j = 0; j < max; j++) {
-        i=0;
-        while (i < s.length && s[i] != null) {
-          if(s[i].getSequence().length()>j )
-            out.append(s[i].getSequence().substring(j,j+1));
-          else
-            out.append("-");
-          i++;
+    public static String print(SequenceI[] s) {
+        StringBuffer out = new StringBuffer();
+
+        int i = 0;
+        int max = -1;
+
+        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) {
+                max = s[i].getSequence().length();
+            }
+
+            i++;
         }
-        out.append("\n");
-      }
-    out.append("*\n");
-    return out.toString();
 
-  }
+        out.append("* iteration 1\n");
+
+        for (int j = 0; j < max; j++) {
+            i = 0;
+
+            while ((i < s.length) && (s[i] != null)) {
+                if (s[i].getSequence().length() > j) {
+                    out.append(s[i].getSequence().substring(j, j + 1));
+                } else {
+                    out.append("-");
+                }
+
+                i++;
+            }
+
+            out.append("\n");
+        }
+
+        out.append("*\n");
+
+        return out.toString();
+    }
 }
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 9b56526..b0d46b2 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -16,183 +16,200 @@
 * 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.*;
 
+
 public class ClustalFile extends AlignFile {
+    Vector ids;
 
-  Vector ids;
-
-  public ClustalFile()
-  {}
-
-  public ClustalFile(String inStr) {
-    super(inStr);
-  }
-
-
-  public void initData() {
-    super.initData();
-    ids = new Vector();
-  }
-
-  public ClustalFile(String inFile, String type) throws IOException {
-    super(inFile,type);
-  }
-
-  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());
-	      }
-	    }
-	  }
-	}
-      }
-    } catch (IOException e) {
-      System.err.println("Exception parsing clustal file " + e);
-      e.printStackTrace();
+    public ClustalFile() {
     }
 
-    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));
+    public ClustalFile(String inStr) {
+        super(inStr);
+    }
+
+    public ClustalFile(String inFile, String type) throws IOException {
+        super(inFile, type);
+    }
 
-          }
-          Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-                                         seqhash.get(headers.elementAt(i).toString()).toString(),start,end);
+    public void initData() {
+        super.initData();
+        ids = new Vector();
+    }
 
-          seqs.addElement(newSeq);
+    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());
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        } catch (IOException e) {
+            System.err.println("Exception parsing clustal file " + e);
+            e.printStackTrace();
+        }
 
-        } else {
-          System.err.println("Clustal File Reader: Can't find sequence for " + headers.elementAt(i));
+        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));
+                }
+            }
         }
-      }
     }
 
-  }
+    public String print() {
+        return print(getSeqsAsArray());
+    }
+
+    public static String print(SequenceI[] s) {
+        StringBuffer out = new StringBuffer("CLUSTAL\n\n");
 
-  public String print() {
-    return print(getSeqsAsArray());
-  }
-  public static String print(SequenceI[] s) {
+        int max = 0;
+        int maxid = 0;
 
-    StringBuffer out = new StringBuffer("CLUSTAL\n\n");
+        int i = 0;
 
-    int max = 0;
-    int maxid = 0;
+        while ((i < s.length) && (s[i] != null)) {
+            String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +
+                s[i].getEnd();
 
-    int i = 0;
+            if (s[i].getSequence().length() > max) {
+                max = s[i].getSequence().length();
+            }
 
-    while (i < s.length && s[i] != null) {
-      String tmp = s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd();
+            if (tmp.length() > maxid) {
+                maxid = tmp.length();
+            }
 
-      if (s[i].getSequence().length() > max) {
-        max = s[i].getSequence().length();
-      }
-      if (tmp.length() > maxid) {
-        maxid = tmp.length();
-      }
-      i++;
-    }
+            i++;
+        }
 
-    if (maxid < 15) {
-      maxid = 15;
-    }
-    maxid++;
-    int len = 60;
-    int nochunks =  max / len + 1;
-
-    for (i = 0; i < nochunks; i++) {
-      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()) + " ");
-        int start = i*len;
-        int end = start + len;
-
-        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));
+        if (maxid < 15) {
+            maxid = 15;
         }
-        out.append("\n");
-        j++;
-      }
-      out.append("\n");
 
-    }
+        maxid++;
+
+        int len = 60;
+        int nochunks = (max / len) + 1;
 
-    return out.toString();
-  }
+        for (i = 0; i < nochunks; i++) {
+            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()) + " ");
 
+                int start = i * len;
+                int end = start + len;
+
+                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));
+                    }
+                }
+
+                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 3c6e5f9..5b21bfe 100755
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -16,166 +16,160 @@
 * 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 org.apache.axis.client.*;
-
-import java.io.*;
-
-import javax.activation.DataHandler;
 import org.apache.axis.AxisFault;
+import org.apache.axis.client.*;
 import org.apache.axis.encoding.XMLType;
-import javax.xml.rpc.ParameterMode;
-import javax.xml.namespace.QName;
-import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;
 import org.apache.axis.encoding.ser.JAFDataHandlerDeserializerFactory;
+import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;
 
+import java.io.*;
 
-public class EBIFetchClient
-{
-  Call call;
-  String format = "default";
-  String style = "raw";
-
-  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){}
-  }
-
-
-  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){return null;}
-  }
+import javax.activation.DataHandler;
 
-  public String [] getSupportedFormats()
-  {
-      try{
-        call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
-        call.setReturnType(XMLType.SOAP_ARRAY);
-        return (String[]) call.invoke(new Object[] {});
+import javax.xml.namespace.QName;
+import javax.xml.rpc.ParameterMode;
 
-      }catch(Exception ex){ return null; }
-   }
 
-   public String [] getSupportedStyles()
-   {
-        try{
-          call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
-          call.setReturnType(XMLType.SOAP_ARRAY);
-          return (String[]) call.invoke(new Object[] {});
+public class EBIFetchClient {
+    Call call;
+    String format = "default";
+    String style = "raw";
 
-         }catch(Exception ex){return null;}
+    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) {
+        }
     }
 
-    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{
-        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)
-          format = f;
-
-        if (s != null)
-          style = s;
-
-        return (String[]) call.invoke(new Object[] {ids, format, style});
-
-      }catch(Exception ex){return null;}
+    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) {
+            return null;
+        }
     }
 
-    public String fetchDataFile(String arg, String f, String s)
-    {
-
-      if (f != null)
-        format = f;
+    public String[] getSupportedFormats() {
+        try {
+            call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
+            call.setReturnType(XMLType.SOAP_ARRAY);
 
-      if (s != null)
-        style = s;
-
-
-      call.setOperationName(new QName("urn:Dbfetch", "fetchDataFile"));
-      call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);
-      call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
-      call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
-
-      QName qnameAttachment = new QName("urn:Dbfetch", "DataHandler");
-      call.registerTypeMapping(javax.activation.DataSource.class,
-                               qnameAttachment,
-                               JAFDataHandlerSerializerFactory.class,
-                               JAFDataHandlerDeserializerFactory.class);
+            return (String[]) call.invoke(new Object[] {  });
+        } catch (Exception ex) {
+            return null;
+        }
+    }
 
-      call.setReturnType(qnameAttachment);
+    public String[] getSupportedStyles() {
+        try {
+            call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
+            call.setReturnType(XMLType.SOAP_ARRAY);
 
-      try{
-        Object ret = call.invoke(new Object[]
-                                 {arg, format, style});
+            return (String[]) call.invoke(new Object[] {  });
+        } catch (Exception ex) {
+            return null;
+        }
+    }
 
-        if (null == ret)
-        {
-          System.err.println("Received null ");
-          throw new AxisFault("", "Received null", null, null);
+    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 {
+            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) {
+                format = f;
+            }
+
+            if (s != null) {
+                style = s;
+            }
+
+            return (String[]) call.invoke(new Object[] { ids, format, style });
+        } catch (Exception ex) {
+            return null;
         }
-        if (ret instanceof String)
-        {
-          System.err.println("Received problem response from server: " + ret);
-          throw new AxisFault("", (String) ret, null, null);
+    }
+
+    public String fetchDataFile(String arg, String f, String s) {
+        if (f != null) {
+            format = f;
         }
-        if (! (ret instanceof DataHandler))
-        {
-          //The wrong type of object that what was expected.
-          System.err.println("Received problem response from server:" +
-                             ret.getClass().getName());
-          throw new AxisFault("", "Received problem response from server:" +
-                              ret.getClass().getName(), null, null);
 
+        if (s != null) {
+            style = s;
         }
-        //Still here, so far so good.
-        DataHandler rdh = (DataHandler) ret;
 
-        //From here we'll just treat the data resource as file.
-        String receivedfileName = rdh.getName(); //Get the filename.
+        call.setOperationName(new QName("urn:Dbfetch", "fetchDataFile"));
+        call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);
+        call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
+        call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
 
-        if (receivedfileName == null)
-        {
-          System.err.println("Could not get the file name.");
-          throw new AxisFault("", "Could not get the file name.", null, null);
+        QName qnameAttachment = new QName("urn:Dbfetch", "DataHandler");
+        call.registerTypeMapping(javax.activation.DataSource.class,
+            qnameAttachment, JAFDataHandlerSerializerFactory.class,
+            JAFDataHandlerDeserializerFactory.class);
+
+        call.setReturnType(qnameAttachment);
+
+        try {
+            Object ret = call.invoke(new Object[] { arg, format, style });
+
+            if (null == ret) {
+                System.err.println("Received null ");
+                throw new AxisFault("", "Received null", null, null);
+            }
+
+            if (ret instanceof String) {
+                System.err.println("Received problem response from server: " +
+                    ret);
+                throw new AxisFault("", (String) ret, null, null);
+            }
+
+            if (!(ret instanceof DataHandler)) {
+                //The wrong type of object that what was expected.
+                System.err.println("Received problem response from server:" +
+                    ret.getClass().getName());
+                throw new AxisFault("",
+                    "Received problem response from server:" +
+                    ret.getClass().getName(), null, null);
+            }
+
+            //Still here, so far so good.
+            DataHandler rdh = (DataHandler) ret;
+
+            //From here we'll just treat the data resource as file.
+            String receivedfileName = rdh.getName(); //Get the filename.
+
+            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")) {
+                return receivedfileName;
+            } else if (arg.equalsIgnoreCase("interpro")) {
+                return receivedfileName;
+            } else {
+                System.err.println(receivedfileName);
+            }
+        } catch (Exception ex) {
+            ex.printStackTrace();
         }
-        if (arg.equalsIgnoreCase("medline"))
-        {
-          return receivedfileName;
-        }
-        else if (arg.equalsIgnoreCase("interpro"))
-        {
-          return receivedfileName;
-        }
-        else
-          System.err.println(receivedfileName);
-      }catch(Exception ex)
-      {
-        ex.printStackTrace();
-      }
-
-      return "ERROR";
-    }
-
 
+        return "ERROR";
+    }
 }
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 7910340..7e7e06b 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -16,160 +16,167 @@
 * 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.analysis.*;
 
+import jalview.datamodel.*;
+
 import java.io.*;
+
 import java.util.*;
 
+
 public class FastaFile extends AlignFile {
+    public FastaFile() {
+    }
 
-  public FastaFile()
-  {}
-
-  public FastaFile(String inStr) {
-    super(inStr);
-  }
-
-  public FastaFile(String inFile, String type) throws IOException {
-    super(inFile,type);
-  }
-
-  public void parse() throws IOException
-  {
-
-    String       id    = "";
-    StringBuffer seq   = new StringBuffer();
-    int          count = 0;
-    boolean      flag  = false;
-
-    int          sstart = 0;
-    int          send   = 0;
-
-    String line;
-
-      while ((line = nextLine()) != null) {
-
-	if (line.length() > 0) {
-
-	  // Do we have an id line?
-
-	  if (line.substring(0,1).equals(">")) {
-
-	    if (count != 0) {
-	      if (sstart != 0) {
-		seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),sstart,send));
-	      } else {
-		seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),1,seq.length()));
-	      }
-	    }
-
-	    count++;
-
-	    StringTokenizer str = new StringTokenizer(line," ");
-
-	    id = str.nextToken();
-	    id = id.substring(1);
-            com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex("[A-Za-z-]+/[A-Za-z-]+\\|(\\w+)\\|(.+)");
-            if (dbId.search(id))
-               {
-                 String dbid = dbId.stringMatched(1);
-                 String idname = dbId.stringMatched(2);
-                 if (idname.length()>0 && idname.indexOf("_") > -1)
-                 {
-                   id = idname; // just use friendly name // JBPNote: we may lose uniprot standardised ID here.
-                 }
-                 else
-                 {
-                   id = dbid; // use dbid to ensure sensible queries
-                 }
-
-               }
-	    if (id.indexOf("/") > 0 ) {
-
-	      StringTokenizer st = new StringTokenizer(id,"/");
-	      if (st.countTokens() == 2) {
-		id = st.nextToken();
-		String tmp = st.nextToken();
-
-		st = new StringTokenizer(tmp,"-");
-
-		if (st.countTokens() == 2) {
-		  sstart = Integer.valueOf(st.nextToken()).intValue();
-		  send   = Integer.valueOf(st.nextToken()).intValue();
-		}
-	      }
-	    }
-
-	    seq = new StringBuffer();
-
-	  } else {
-	    seq = seq.append(line);
-	  }
-	}
-      }
-      if (count > 0) {
-
-        if(!isValidProteinSequence(seq.toString().toUpperCase()))
-          throw new IOException("Invalid protein sequence");
-
-	if (sstart != 0) {
-	  seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),sstart,send));
-	} else {
-	  seqs.addElement(new Sequence(id,seq.toString().toUpperCase(),1,seq.length()));
-	}
-      }
-
-  }
-
-  public static String print(SequenceI[] s) {
-    return print(s,72);
-  }
-  public static String print(SequenceI[] s, int len) {
-    return print(s,len,true);
-  }
-
-  public static String print(SequenceI[] s, int len,boolean gaps) {
-    return print(s,len,gaps,true);
-  }
-
-  public static String print(SequenceI[] s, int len,boolean gaps, boolean displayId) {
-    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());
-      }
-      // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +
-      out.append(">" + ((displayId) ? s[i].getDisplayId() : s[i].getName())+"\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");
+    public FastaFile(String inStr) {
+        super(inStr);
+    }
+
+    public FastaFile(String inFile, String type) throws IOException {
+        super(inFile, type);
+    }
+
+    public void parse() throws IOException {
+        String id = "";
+        StringBuffer seq = new StringBuffer();
+        int count = 0;
+        boolean flag = false;
+
+        int sstart = 0;
+        int send = 0;
+
+        String line;
+
+        while ((line = nextLine()) != null) {
+            if (line.length() > 0) {
+                // Do we have an id line?
+                if (line.substring(0, 1).equals(">")) {
+                    if (count != 0) {
+                        if (sstart != 0) {
+                            seqs.addElement(new Sequence(id,
+                                    seq.toString().toUpperCase(), sstart, send));
+                        } else {
+                            seqs.addElement(new Sequence(id,
+                                    seq.toString().toUpperCase(), 1,
+                                    seq.length()));
+                        }
+                    }
+
+                    count++;
+
+                    StringTokenizer str = new StringTokenizer(line, " ");
+
+                    id = str.nextToken();
+                    id = id.substring(1);
+
+                    com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(
+                            "[A-Za-z-]+/[A-Za-z-]+\\|(\\w+)\\|(.+)");
+
+                    if (dbId.search(id)) {
+                        String dbid = dbId.stringMatched(1);
+                        String idname = dbId.stringMatched(2);
+
+                        if ((idname.length() > 0) &&
+                                (idname.indexOf("_") > -1)) {
+                            id = idname; // just use friendly name // JBPNote: we may lose uniprot standardised ID here.
+                        } else {
+                            id = dbid; // use dbid to ensure sensible queries
+                        }
+                    }
+
+                    if (id.indexOf("/") > 0) {
+                        StringTokenizer st = new StringTokenizer(id, "/");
+
+                        if (st.countTokens() == 2) {
+                            id = st.nextToken();
+
+                            String tmp = st.nextToken();
+
+                            st = new StringTokenizer(tmp, "-");
+
+                            if (st.countTokens() == 2) {
+                                sstart = Integer.valueOf(st.nextToken())
+                                                .intValue();
+                                send = Integer.valueOf(st.nextToken()).intValue();
+                            }
+                        }
+                    }
+
+                    seq = new StringBuffer();
+                } else {
+                    seq = seq.append(line);
+                }
+            }
+        }
+
+        if (count > 0) {
+            if (!isValidProteinSequence(seq.toString().toUpperCase())) {
+                throw new IOException("Invalid protein sequence");
+            }
+
+            if (sstart != 0) {
+                seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),
+                        sstart, send));
+            } else {
+                seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),
+                        1, seq.length()));
+            }
         }
-      }
-      i++;
     }
-    return out.toString();
-  }
 
-  public String print() {
-    return print(getSeqsAsArray());
-  }
-}
+    public static String print(SequenceI[] s) {
+        return print(s, 72);
+    }
 
+    public static String print(SequenceI[] s, int len) {
+        return print(s, len, true);
+    }
+
+    public static String print(SequenceI[] s, int len, boolean gaps) {
+        return print(s, len, gaps, true);
+    }
+
+    public static String print(SequenceI[] s, int len, boolean gaps,
+        boolean displayId) {
+        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());
+            }
+
+            // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +
+            out.append(">" +
+                ((displayId) ? s[i].getDisplayId() : s[i].getName()) + "\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++;
+        }
+
+        return out.toString();
+    }
+
+    public String print() {
+        return print(getSeqsAsArray());
+    }
+}
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index ea86ae0..0c46a17 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -16,50 +16,48 @@
 * 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;
+import java.net.*;
 
-  public FileParse() {}
 
-  public FileParse(String fileStr, String type) throws MalformedURLException, IOException
-  {
+public class FileParse {
+    public File inFile;
+    public int fileSize;
+    public int noLines;
+    protected String type;
+    protected BufferedReader dataIn;
 
-    this.type = type;
+    public FileParse() {
+    }
 
-    if (type.equals("File")) {
-      this.inFile = new File(fileStr);
-      this.fileSize = (int)inFile.length();
+    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));
+        }
+    }
 
-      dataIn = new BufferedReader(new FileReader( fileStr ));
+    public String nextLine() throws IOException {
+        String next = dataIn.readLine();
 
-    } 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();
-    if (next != null) {
-      noLines++;
+        return next;
     }
-    return next;
-  }
-
 }
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 0382cee..e59c191 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -16,90 +16,90 @@
 * 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 java.util.Vector;
-public class FormatAdapter
-{
-
-  public static Vector formats = new Vector();
-  static{
-    formats.addElement("FASTA");
-    formats.addElement("MSF");
-    formats.addElement("PileUp");
-    formats.addElement("CLUSTAL");
-    formats.addElement("BLC");
-    formats.addElement("PIR");
-    formats.addElement("PFAM");
-  }
-
-  public static SequenceI[] readFile(String inFile, String type, String format)
-  {
-
-    try
-    {
-      AlignFile afile = null;
-      if (format.equals("FASTA"))
-        afile = new FastaFile(inFile, type);
-      else if (format.equals("MSF"))
-        afile = new MSFfile(inFile, type);
-      else if (format.equals("PileUp"))
-              afile = new PileUpfile(inFile, type);
-      else if (format.equals("CLUSTAL"))
-        afile = new ClustalFile(inFile, type);
-      else if (format.equals("BLC"))
-        afile = new BLCFile(inFile, type);
-      else if (format.equals("PIR"))
-        afile = new PIRFile(inFile, type);
-      else if (format.equals("PFAM"))
-        afile = new PfamFile(inFile, type);
-
-      return afile.getSeqsAsArray();
-    }
-    catch (Exception e)  {
-    System.err.println("Failed to read alignment using the '"+format+"' reader.");
-    e.printStackTrace();
-    }
 
-    return null;
-  }
-
-
-  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
-    {
-      AlignFile afile = null;
-      if (format.equals("FASTA"))
-        afile = new FastaFile();
-      else if (format.equals("MSF"))
-        afile = new MSFfile();
-      else if (format.equals("PileUp"))
-        afile = new PileUpfile();
-      else if (format.equals("CLUSTAL"))
-        afile = new ClustalFile();
-      else if (format.equals("BLC"))
-        afile = new BLCFile();
-      else if (format.equals("PIR"))
-        afile = new PIRFile();
-      else if (format.equals("PFAM"))
-        afile = new PfamFile();
-
-      afile.setSeqs(s);
-      return afile.print();
+
+public class FormatAdapter {
+    public static Vector formats = new Vector();
+
+    static {
+        formats.addElement("FASTA");
+        formats.addElement("MSF");
+        formats.addElement("PileUp");
+        formats.addElement("CLUSTAL");
+        formats.addElement("BLC");
+        formats.addElement("PIR");
+        formats.addElement("PFAM");
     }
-    catch (Exception e)  {
-      System.err.println("Failed to write alignment as a '"+format+"' file\n");
-      e.printStackTrace();
+
+    public static SequenceI[] readFile(String inFile, String type, String format) {
+        try {
+            AlignFile afile = null;
+
+            if (format.equals("FASTA")) {
+                afile = new FastaFile(inFile, type);
+            } else if (format.equals("MSF")) {
+                afile = new MSFfile(inFile, type);
+            } else if (format.equals("PileUp")) {
+                afile = new PileUpfile(inFile, type);
+            } else if (format.equals("CLUSTAL")) {
+                afile = new ClustalFile(inFile, type);
+            } else if (format.equals("BLC")) {
+                afile = new BLCFile(inFile, type);
+            } else if (format.equals("PIR")) {
+                afile = new PIRFile(inFile, type);
+            } else if (format.equals("PFAM")) {
+                afile = new PfamFile(inFile, type);
+            }
+
+            return afile.getSeqsAsArray();
+        } catch (Exception e) {
+            System.err.println("Failed to read alignment using the '" + format +
+                "' reader.");
+            e.printStackTrace();
+        }
+
+        return null;
     }
 
-    return null;
-  }
+    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 {
+            AlignFile afile = null;
+
+            if (format.equals("FASTA")) {
+                afile = new FastaFile();
+            } else if (format.equals("MSF")) {
+                afile = new MSFfile();
+            } else if (format.equals("PileUp")) {
+                afile = new PileUpfile();
+            } else if (format.equals("CLUSTAL")) {
+                afile = new ClustalFile();
+            } else if (format.equals("BLC")) {
+                afile = new BLCFile();
+            } else if (format.equals("PIR")) {
+                afile = new PIRFile();
+            } else if (format.equals("PFAM")) {
+                afile = new PfamFile();
+            }
+
+            afile.setSeqs(s);
+
+            return afile.print();
+        } catch (Exception e) {
+            System.err.println("Failed to write alignment as a '" + format +
+                "' file\n");
+            e.printStackTrace();
+        }
+
+        return null;
+    }
 }
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 290dee7..54b9595 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -16,237 +16,252 @@
 * 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.gui.*;
 import jalview.datamodel.*;
+
+import jalview.gui.*;
+
 import jalview.schemes.*;
+
 import java.awt.*;
-import javax.swing.*;
+
 import java.io.*;
-import java.util.*;
 
+import java.util.*;
 
-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>");
-
-
-        if(av.getWrapAlignment())
-           drawWrappedAlignment(out);
-        else
-           drawUnwrappedAlignment(out);
-
-        out.println("\n</body>\n</html>");
-        out.close();
-        jalview.util.BrowserLauncher.openURL( "file:///"+choice );
-      }
-      catch(Exception ex){ex.printStackTrace();}
-    }
-  }
+import javax.swing.*;
 
-  void drawUnwrappedAlignment(PrintWriter out)
-  {
 
-    out.println("<table border=\"1\"><tr><td>\n");
-    out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
+public class HTMLOutput {
+    AlignViewport av;
+    SequenceRenderer sr;
+    Color color;
 
+    public HTMLOutput(AlignViewport av) {
+        this.av = av;
+        sr = new SequenceRenderer(av);
 
-    //////////////
-    SequenceGroup [] groups;
-    SequenceI seq;
-    ColourSchemeI cs = null;
-    AlignmentI alignment = av.getAlignment();
-    String r,g,b;
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"), new String[] { "html" },
+                new String[] { "HTML files" }, "HTML files");
 
-  // 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>");
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save as HTML");
+        chooser.setToolTipText("Save");
 
-    out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");
-    out.println("</tr>");
+        int value = chooser.showSaveDialog(null);
 
-    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()+"&nbsp;&nbsp;</td>");
-      else
-        out.println("<tr><td nowrap>"+seq.getName()+"&nbsp;&nbsp;</td>");
+        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; ");
+                }
 
-      for (int res = 0; res < seq.getLength(); res++)
-      {
-        cs = av.getGlobalColourScheme();
+                if (av.getFont().getStyle() == Font.ITALIC) {
+                    out.print("font-style: italic; ");
+                }
 
-        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;
-             }
-         }
+                out.println("text-align: center; }");
 
+                out.println("-->");
+                out.println("</style>");
+                out.println("<BODY>");
 
-        color = sr.getResidueBoxColour(cs, seq, res);
+                if (av.getWrapAlignment()) {
+                    drawWrappedAlignment(out);
+                } else {
+                    drawUnwrappedAlignment(out);
+                }
 
-        if(color.getRGB()<-1)
-        {
-          out.println("<td bgcolor=\"#"
-                      + jalview.util.Format.getHexString(color)
-                      + "\">"+seq.getCharAt(res)+"</td>");
+                out.println("\n</body>\n</html>");
+                out.close();
+                jalview.util.BrowserLauncher.openURL("file:///" + choice);
+            } catch (Exception ex) {
+                ex.printStackTrace();
+            }
         }
-        else
-          out.println("<td>"+seq.getCharAt(res)+"</td>");
-
-      }
-
-      out.println("</tr>");
     }
-    //////////////
-    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,g,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++)
-              {
+
+    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>");
+
+        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() +
+                    "&nbsp;&nbsp;</td>");
+            } 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;
-                     }
-                 }
+
+                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);
 
-                if(color.getRGB()<-1)
-                {
-                  r = Integer.toHexString(color.getRed());
-                  if(r.length()<2)
-                    r = "0"+r;
-                  g = Integer.toHexString(color.getGreen());
-                  if(g.length()<2)
-                    g = "0"+g;
-                  b = Integer.toHexString(color.getBlue());
-                  if(b.length()<2)
-                    b = "0"+b;
-                  out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");
+                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>");
+        }
+
+        //////////////
+        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>");
                 }
-                else
-                  out.println("<td>"+seq.getCharAt(res)+"</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;
 
-         out.println("</tr>");
+                                break;
+                            }
+                    }
 
-       }
-       if(endRes<al.getWidth())
-           out.println("<tr><td height=\"5\"></td></tr>");
+                    color = sr.getResidueBoxColour(cs, seq, res);
 
+                    if (color.getRGB() < -1) {
+                        r = Integer.toHexString(color.getRed());
 
+                        if (r.length() < 2) {
+                            r = "0" + r;
+                        }
 
-     }
+                        g = Integer.toHexString(color.getGreen());
 
-    out.println("</table>");
-    out.println("</table>");
+                        if (g.length() < 2) {
+                            g = "0" + g;
+                        }
 
+                        b = Integer.toHexString(color.getBlue());
 
+                        if (b.length() < 2) {
+                            b = "0" + b;
+                        }
 
-  }
+                        out.println("<td bgcolor=\"#" + r + g + b + "\">" +
+                            seq.getCharAt(res) + "</td>");
+                    } else {
+                        out.println("<td>" + seq.getCharAt(res) + "</td>");
+                    }
+                }
+
+                out.println("</tr>");
+            }
 
+            if (endRes < al.getWidth()) {
+                out.println("<tr><td height=\"5\"></td></tr>");
+            }
+        }
 
+        out.println("</table>");
+        out.println("</table>");
+    }
 }
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index f1cf1e0..2442b4b 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -16,83 +16,84 @@
 * 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 IdentifyFile
-{
-  public static String Identify(String file, String protocol)
-  {
-    String reply = "PFAM";
-    try{
-
-      BufferedReader reader = null;
-
-      if(protocol.equals("File"))
-        reader = new BufferedReader(new FileReader(file));
-
-      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"))
-        reader = new BufferedReader( new StringReader(file) );
-
-
-      String data;
-      while( (data=reader.readLine())!=null)
-      {
-        data = data.toUpperCase();
-        if(data.indexOf("#")==0 || data.length()<1)
-          continue;
-
-        if(data.indexOf("PILEUP")>-1)
-        {
-          reply = "PileUp";
-          break;
-        }
-        if((data.indexOf("//")==0)
-           || ((data.indexOf("!!")>-1)
-           && (data.indexOf("!!")<data.indexOf("_MULTIPLE_ALIGNMENT "))))
-        {
-          reply = "MSF";
-          break;
-        }
-        else if(data.indexOf("CLUSTAL")>-1)
-        {
-          reply = "CLUSTAL";
-          break;
-        }
-        else if(data.indexOf(">P1;")>-1 || data.indexOf(">DL;")>-1)
-        {
-          reply = "PIR";
-          break;
-        }
-        else if(data.indexOf(">")>-1)
-        {
-          // could be BLC file, read next line to confirm
-          data = reader.readLine();
-          if(data.indexOf(">")>-1)
-            reply = "BLC";
-          else
-            reply = "FASTA";
-
-            break;
-        }
-      }
-      reader.close();
-    }
-    catch(Exception ex){
-      System.err.println("File Identification failed!\n"+ex);}
 
-    return reply;
-  }
+public class IdentifyFile {
+    public static String Identify(String file, String protocol) {
+        String reply = "PFAM";
+
+        try {
+            BufferedReader reader = null;
+
+            if (protocol.equals("File")) {
+                reader = new BufferedReader(new FileReader(file));
+            }
+            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")) {
+                reader = new BufferedReader(new StringReader(file));
+            }
+
+            String data;
 
+            while ((data = reader.readLine()) != null) {
+                data = data.toUpperCase();
 
+                if ((data.indexOf("#") == 0) || (data.length() < 1)) {
+                    continue;
+                }
+
+                if (data.indexOf("PILEUP") > -1) {
+                    reply = "PileUp";
+
+                    break;
+                }
+
+                if ((data.indexOf("//") == 0) ||
+                        ((data.indexOf("!!") > -1) &&
+                        (data.indexOf("!!") < data.indexOf(
+                            "_MULTIPLE_ALIGNMENT ")))) {
+                    reply = "MSF";
+
+                    break;
+                } else if (data.indexOf("CLUSTAL") > -1) {
+                    reply = "CLUSTAL";
+
+                    break;
+                } else if ((data.indexOf(">P1;") > -1) ||
+                        (data.indexOf(">DL;") > -1)) {
+                    reply = "PIR";
+
+                    break;
+                } else if (data.indexOf(">") > -1) {
+                    // could be BLC file, read next line to confirm
+                    data = reader.readLine();
+
+                    if (data.indexOf(">") > -1) {
+                        reply = "BLC";
+                    } else {
+                        reply = "FASTA";
+                    }
+
+                    break;
+                }
+            }
+
+            reader.close();
+        } catch (Exception ex) {
+            System.err.println("File Identification failed!\n" + ex);
+        }
+
+        return reply;
+    }
 }
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 38addf7..12be9de 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -15,299 +15,286 @@
 * 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
-*/
-
+*/
+
 /**
  * PredFile.java
  * JalviewX / Vamsas Project
  * JPred.seq.concise reader
- */
-
-package jalview.io;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-import java.io.*;
-import java.util.*;
-
-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 void setQuerySeqPosition(int QuerySeqPosition)
-  {
-    this.QuerySeqPosition = QuerySeqPosition;
-  }
-
-  public int getQuerySeqPosition()
-  {
-    return QuerySeqPosition;
-  }
-  public Hashtable getScores() {
-    return Scores;
-  }
-  public Hashtable getSymscores() {
-    return Symscores;
-  }
-
-  public JPredFile(String inStr)
-  {
-    super(inStr);
-  }
-
-  public void initData()
-  {
-
-    super.initData();
-    Scores = new Hashtable();
-    ids = null;
-    conf = null;
-  }
-
-  public JPredFile(String inFile, String type)
-      throws IOException
-  {
-
-    super(inFile, type);
-  }
+ */
+package jalview.io;
+
+import jalview.datamodel.*;
+
+import jalview.util.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+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) {
+        super(inStr);
+    }
+
+    public JPredFile(String inFile, String type) throws IOException {
+        super(inFile, type);
+    }
+
+    public void setQuerySeqPosition(int QuerySeqPosition) {
+        this.QuerySeqPosition = QuerySeqPosition;
+    }
+
+    public int getQuerySeqPosition() {
+        return QuerySeqPosition;
+    }
+
+    public Hashtable getScores() {
+        return Scores;
+    }
+
+    public Hashtable getSymscores() {
+        return Symscores;
+    }
+
+    public void initData() {
+        super.initData();
+        Scores = new Hashtable();
+        ids = null;
+        conf = null;
+    }
+
+    /**
+ * parse a JPred concise file into a sequence-alignment like object.
+ */
+    public void parse() throws IOException {
+        // JBPNote log.System.out.println("all read in ");
+        String line;
+        QuerySeqPosition = -1;
+        noSeqs = 0;
+
+        Vector seq_entries = new Vector();
+        Vector ids = new Vector();
+        Hashtable Symscores = new Hashtable();
+
+        while ((line = nextLine()) != null) {
+            // Concise format allows no comments or non comma-formatted data
+            StringTokenizer str = new StringTokenizer(line, ":");
+            String id = "";
+
+            if (!str.hasMoreTokens()) {
+                continue;
+            }
+
+            id = str.nextToken();
+
+            String seqsym = str.nextToken();
+            StringTokenizer symbols = new StringTokenizer(seqsym, ",");
+
+            // decide if we have more than just alphanumeric symbols
+            int numSymbols = symbols.countTokens();
+
+            if (numSymbols == 0) {
+                continue;
+            }
+
+            if (seqsym.length() != (2 * numSymbols)) {
+                // Set of scalars for some property
+                if (Scores.containsKey(id)) {
+                    int i = 1;
+
+                    while (Scores.containsKey(id + "_" + i)) {
+                        i++;
+                    }
+
+                    id = id + "_" + i;
+                }
+
+                Vector scores = new Vector();
+
+                // Typecheck from first entry
+                int i = 0;
+                String ascore = "dead";
+
+                try {
+                    // store elements as floats...
+                    while (symbols.hasMoreTokens()) {
+                        ascore = symbols.nextToken();
+
+                        Float score = new Float(ascore);
+                        scores.addElement((Object) score);
+                    }
+
+                    Scores.put(id, scores);
+                } catch (Exception e) {
+                    // or just keep them as strings
+                    i = scores.size();
+
+                    for (int j = 0; j < i; j++) {
+                        scores.set(j,
+                            (Object) ((Float) scores.get(j)).toString());
+                    }
+
+                    scores.addElement((Object) ascore);
+
+                    while (symbols.hasMoreTokens()) {
+                        ascore = symbols.nextToken();
+                        scores.addElement((Object) ascore);
+                    }
+
+                    Scores.put(id, scores);
+                }
+            } 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++) {
+                    conf.set(i, (Object) symbols.nextToken());
+                }
+            } else {
+                // Sequence or a prediction string (rendered as sequence)
+                StringBuffer newseq = new StringBuffer();
+
+                for (int i = 0; i < numSymbols; i++) {
+                    newseq.append(symbols.nextToken());
+                }
+
+                if (id.indexOf(";") > -1) {
+                    seq_entries.addElement(newseq);
+
+                    int i = 1;
+                    String name = id.substring(id.indexOf(";") + 1);
+
+                    while (ids.lastIndexOf(name) > -1) {
+                        name = id.substring(id.indexOf(";") + 1) + "_" + 1;
+                    }
+
+                    ids.addElement(name);
+
+                    noSeqs++;
+                } else {
+                    if (id.equals("JNETPRED")) {
+                        id = "Predicted Secondary Structure";
+                    }
+
+                    seq_entries.addElement(newseq.toString());
+                    ids.addElement(id);
+                    Symscores.put((Object) id,
+                        (Object) new Integer(ids.size() - 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++) {
+            // 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())) {
+                throw new IOException(
+                    "JPredConcise: Not a valid protein sequence - (" +
+                    ids.elementAt(i).toString() + ")");
+            }
+
+            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 = seqs.size();
+            }
+
+            seqs.addElement(newSeq);
+        }
+    }
+
+    /**
+ * print
+ *
+ * @return String
+   */
+    public String print() {
+        return "Not Supported";
+    }
+
+    public static void main(String[] args) {
+        try {
+            JPredFile blc = new JPredFile(args[0], "File");
+
+            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) {
+            System.err.println("Exception " + e);
+            e.printStackTrace();
+        }
+    }
+}
+
+
+/*
+ StringBuffer out = new StringBuffer();
+
+ out.append("START PRED\n");
+ for (int i = 0; i < s[0].sequence.length(); i++)
+ {
+  out.append(s[0].sequence.substring(i, i + 1) + " ");
+  out.append(s[1].sequence.substring(i, i + 1) + " ");
+  out.append(s[1].score[0].elementAt(i) + " ");
+  out.append(s[1].score[1].elementAt(i) + " ");
+  out.append(s[1].score[2].elementAt(i) + " ");
+  out.append(s[1].score[3].elementAt(i) + " ");
+
+  out.append("\n");
+ }
+ out.append("END PRED\n");
+ return out.toString();
+ }
 
-  /**
-   * parse a JPred concise file into a sequence-alignment like object.
-   */
-  public void parse()
-      throws IOException
+    public static void main(String[] args)
+ {
+  try
   {
-    // JBPNote log.System.out.println("all read in ");
-    String line;
-    QuerySeqPosition = -1;
-    noSeqs = 0;
-    Vector seq_entries = new Vector();
-    Vector ids = new Vector();
-    Hashtable Symscores = new Hashtable();
-    while ( (line = nextLine()) != null)
+    BLCFile blc = new BLCFile(args[0], "File");
+    DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
+    for (int i = 0; i < blc.seqs.size(); i++)
     {
-      // Concise format allows no comments or non comma-formatted data
-      StringTokenizer str = new StringTokenizer(line, ":");
-      String id = "";
-      if (!str.hasMoreTokens())
-      {
-        continue;
-      }
-
-      id = str.nextToken();
-      String seqsym = str.nextToken();
-      StringTokenizer symbols = new StringTokenizer(seqsym, ",");
-      // decide if we have more than just alphanumeric symbols
-      int numSymbols = symbols.countTokens();
-
-      if (numSymbols==0) {
-        continue;
-      }
-
-      if (seqsym.length() != (2 * numSymbols))
-      {
-        // Set of scalars for some property
-        if (Scores.containsKey(id))
-        {
-          int i = 1;
-          while (Scores.containsKey(id + "_" + i))
-          {
-            i++;
-          }
-          id = id + "_" + i;
-        }
-        Vector scores = new Vector();
-        // Typecheck from first entry
-        int i = 0;
-        String ascore="dead";
-        try
-        {
-          // store elements as floats...
-          while (symbols.hasMoreTokens()) {
-            ascore = symbols.nextToken();
-            Float score = new Float(ascore);
-            scores.addElement( (Object) score);
-          }
-          Scores.put(id, scores);
-        }
-        catch (Exception e)
-        {
-          // or just keep them as strings
-          i = scores.size();
-          for (int j = 0; j < i; j++)
-          {
-            scores.set(j,
-                       (Object) ( (Float) scores.get(j)).toString());
-          }
-          scores.addElement((Object) ascore);
-          while (symbols.hasMoreTokens()) {
-            {
-              ascore = symbols.nextToken();
-              scores.addElement( (Object) ascore);
-            }
-          }
-          Scores.put(id, scores);
-        }
-      }
-      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++)
-        {
-          conf.set(i, (Object) symbols.nextToken());
-        }
-      }
-      else
-        {
-          // Sequence or a prediction string (rendered as sequence)
-
-          StringBuffer newseq = new StringBuffer();
-
-          for (int i = 0; i < numSymbols; i++) {
-            newseq.append(symbols.nextToken());
-          }
-
-          if (id.indexOf(";") > -1) {
-            seq_entries.addElement(newseq);
-            int i=1;
-            String name = id.substring(id.indexOf(";")+1);
-            while (ids.lastIndexOf(name)>-1) {
-              name = id.substring(id.indexOf(";")+1)+"_"+1;
-            }
-            ids.addElement(name);
-
-            noSeqs++;
-          }
-          else
-          {
-            if (id.equals("JNETPRED")) {
-              id = "Predicted Secondary Structure";
-            }
-            seq_entries.addElement( newseq.toString() );
-            ids.addElement(id);
-            Symscores.put((Object) id, (Object) new Integer(ids.size()-1));
-          }
-      }
-    }
-
-
-    if (noSeqs < 1)
-    {
-      throw new IOException(
-      "JpredFile Parser: No sequence in the prediction!");
+      s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
     }
-    maxLength = seq_entries.elementAt(0).toString().length();
-    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()))
-      {
-        throw new IOException(
-      "JPredConcise: Not a valid protein sequence - ("
-      + ids.elementAt(i).toString() + ")");
-      }
+    String out = BLCFile.print(s);
 
-      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 = seqs.size();
-      }
-
-      seqs.addElement(newSeq);
-
-    }
+    AlignFrame af = new AlignFrame(null, s);
+    af.resize(700, 500);
+    af.show();
+    System.out.println(out);
   }
-
-  /**
-   * print
-   *
-   * @return String
-     */
-
-    public String print()
-    {
-      return "Not Supported";
-    }
-
-    public static void main(String[] args)
-    {
-      try
-      {
-        JPredFile blc = new JPredFile(args[0], "File");
-        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)
-      {
-        System.err.println("Exception " + e);
-        e.printStackTrace();
-      }
-    }
+  catch (java.io.IOException e)
+  {
+    System.out.println("Exception " + e);
   }
+ }
 
-  /*
-   StringBuffer out = new StringBuffer();
-
-   out.append("START PRED\n");
-   for (int i = 0; i < s[0].sequence.length(); i++)
-   {
-    out.append(s[0].sequence.substring(i, i + 1) + " ");
-    out.append(s[1].sequence.substring(i, i + 1) + " ");
-    out.append(s[1].score[0].elementAt(i) + " ");
-    out.append(s[1].score[1].elementAt(i) + " ");
-    out.append(s[1].score[2].elementAt(i) + " ");
-    out.append(s[1].score[3].elementAt(i) + " ");
-
-    out.append("\n");
-   }
-   out.append("END PRED\n");
-   return out.toString();
-   }
-
-      public static void main(String[] args)
-   {
-    try
-    {
-      BLCFile blc = new BLCFile(args[0], "File");
-      DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
-      for (int i = 0; i < blc.seqs.size(); i++)
-      {
-        s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
-      }
-      String out = BLCFile.print(s);
-
-      AlignFrame af = new AlignFrame(null, s);
-      af.resize(700, 500);
-      af.show();
-      System.out.println(out);
-    }
-    catch (java.io.IOException e)
-    {
-      System.out.println("Exception " + e);
-    }
-   }
-
-   }
-   */
+ }
+ */
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 5a29ba7..d44275a 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -16,20 +16,21 @@
 * 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
 // Author: ddanimal
 // http://forum.java.sun.com/thread.jspa?forumID=57&threadID=327712
-*///////////////////////////////////////////////////////////////////
+*/
 
+//////////////////////////////////////////////////////////////////
 package jalview.io;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import java.io.*;
+
 import java.util.*;
 
 import javax.swing.*;
@@ -38,341 +39,367 @@ import javax.swing.plaf.basic.*;
 import javax.swing.plaf.metal.*;
 import javax.swing.table.*;
 
-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;
-    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;
+
+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;
+
+        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;
+            }
+        }
+
+        if (chosen != null) {
+            setFileFilter(chosen);
+        }
+
+        initColumns();
     }
-    if(chosen!=null)
-      setFileFilter(chosen);
-    initColumns();
-  }
-
-  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";
-
-    return format;
-  }
-  public JalviewFileChooser(String dir)
-  {
-    super(dir);
-    initColumns();
-  }
-
-  public int showSaveDialog(Component parent) throws HeadlessException {
-      setDialogType(SAVE_DIALOG);
-      int ret = showDialog(parent, null);
-
-      if(getFileFilter() instanceof JalviewFileFilter)
-      {
-        JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
-        if (!jvf.accept(getSelectedFile()))
-        {
-          String withExtension = getSelectedFile() + "." + jvf.getAcceptableExtension();
-          setSelectedFile(new File(withExtension));
+
+    public JalviewFileChooser(String dir) {
+        super(dir);
+        initColumns();
+    }
+
+    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";
         }
-      }
-
-      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;
-  }
-
-
-  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)
-      };
+
+        return format;
     }
-  }
-
-  /**************************************************************************
-   * 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 final static class UI extends MetalFileChooserUI
-   {
-     private DirectoryModel model;
-
-     /**************************************************************************
-      * Must be overridden to extend
-      * @param e
-      *************************************************************************/
-     public UI(JFileChooser e)
-     {
-       super(e);
-     }
-
-     /**************************************************************************
-      * Overridden to create our own model
-      *************************************************************************/
-     protected final void createModel()
-     {
-       model = new DirectoryModel(getFileChooser());
-     }
-
-     /**************************************************************************
-      * Overridden to get our own model
-      * @return
-      *************************************************************************/
-     public final BasicDirectoryModel getModel() {       return model;     }
-
-     /**************************************************************************
-      * 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);
-           }
-         });
-       }
-       return panel;
-     }
-
-     /**************************************************************************
-      * 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;
-     }
-   }
-
-  /***************************************************************************
-   * 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);
-     }
-
-
-     /**************************************************************************
-      * 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;
-       switch (col)
-       {
-         case COLUMN_FILEDATE:
-           less = a.lastModified() > b.lastModified();
-           break;
-         case COLUMN_FILESIZE:
-           less = a.length() > b.length();
-           break;
-         default:
-           less = a.getName().compareToIgnoreCase(b.getName()) > 0;
-         break;
-       }
-       if (ascending) return less = !less;
-       return less;
-     }
-
-     /**************************************************************************
-      * 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 = " (^)";
-       if (ascending)
-         indicator = " (v)";
-
-       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] );
-       }
-
-       final TableColumn tc = tcm.getColumn( col ); // the column to change
-       tc.setHeaderValue( COLUMNS[col] + indicator );
-
-       th.repaint();
-
-       //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;
-       }
-     }
-  }
-}
 
+    public int showSaveDialog(Component parent) throws HeadlessException {
+        setDialogType(SAVE_DIALOG);
+
+        int ret = showDialog(parent, null);
+
+        if (getFileFilter() instanceof JalviewFileFilter) {
+            JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
+
+            if (!jvf.accept(getSelectedFile())) {
+                String withExtension = getSelectedFile() + "." +
+                    jvf.getAcceptableExtension();
+                setSelectedFile(new File(withExtension));
+            }
+        }
+
+        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;
+    }
+
+    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)
+                };
+        }
+    }
+
+    /**************************************************************************
+     * 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 final static class UI extends MetalFileChooserUI {
+        private DirectoryModel model;
+
+        /**************************************************************************
+         * Must be overridden to extend
+         * @param e
+         *************************************************************************/
+        public UI(JFileChooser e) {
+            super(e);
+        }
+
+        /**************************************************************************
+         * Overridden to create our own model
+         *************************************************************************/
+        protected final void createModel() {
+            model = new DirectoryModel(getFileChooser());
+        }
+
+        /**************************************************************************
+         * Overridden to get our own model
+         * @return
+         *************************************************************************/
+        public final BasicDirectoryModel getModel() {
+            return model;
+        }
+
+        /**************************************************************************
+         * 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);
+                            }
+                        }
+                    });
+            }
+
+            return panel;
+        }
+
+        /**************************************************************************
+         * 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;
+        }
+    }
+
+    /***************************************************************************
+     * 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);
+        }
+
+        /**************************************************************************
+         * 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;
+
+            switch (col) {
+            case COLUMN_FILEDATE:
+                less = a.lastModified() > b.lastModified();
+
+                break;
+
+            case COLUMN_FILESIZE:
+                less = a.length() > b.length();
+
+                break;
+
+            default:
+                less = a.getName().compareToIgnoreCase(b.getName()) > 0;
+
+                break;
+            }
+
+            if (ascending) {
+                return less = !less;
+            }
+
+            return less;
+        }
+
+        /**************************************************************************
+         * 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 = " (^)";
+
+            if (ascending) {
+                indicator = " (v)";
+            }
+
+            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]);
+            }
+
+            final TableColumn tc = tcm.getColumn(col); // the column to change
+            tc.setHeaderValue(COLUMNS[col] + indicator);
+
+            th.repaint();
+
+            //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;
+            }
+        }
+    }
+}
diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index d6c6d4b..e2692e2 100755
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -16,123 +16,139 @@
 * 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 javax.swing.filechooser.*;
 import java.io.File;
+
 import java.util.*;
 
-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();
+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;
 
-      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 extension, String description) {
+        setDescription(description);
+    }
 
-       StringTokenizer st = new StringTokenizer(extension, ",");
-       while(st.hasMoreElements())
-       {
-         addExtension(st.nextToken().trim());
-       }
-       setDescription(description);
-      }
+    public JalviewFileFilter(String[] filts) {
+        this(filts, null);
+    }
 
-      public JalviewFileFilter(String[] filts) {
-          this(filts, null);
-      }
+    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()
-      {
+        if (description != null) {
+            setDescription(description);
+        }
+    }
+
+    public String getAcceptableExtension() {
         return filters.keys().nextElement().toString();
-      }
-
-      public JalviewFileFilter(String[] filts, String description) {
-          for (int i = 0; i < filts.length; i++) {
-              // add filters one by one
-              addExtension(filts[i]);
-          }
-           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("")) {
+    }
+
+    // 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;
+                } else {
+                    if (filters.get(getExtension(f)) != null) {
+                        return true;
+                    }
+                }
+            }
+
+            if ((extension != null) && (filters.get(getExtension(f)) != null)) {
+                return true;
+            }
+        }
+
+        return false;
+    }
+
+    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);
+        }
+
+        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());
                     }
-                 }
-              }
-              if(extension != null && filters.get(getExtension(f)) != null) {
-                  return true;
-              }
-          }
-          return false;
-      }
-
-       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);
-          }
-          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();
-                      }
-                  }
-                  fullDescription += ")";
-              } else {
-                  fullDescription = description;
-              }
-          }
-          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;
-      }
-  }
+                }
+
+                fullDescription += ")";
+            } else {
+                fullDescription = description;
+            }
+        }
+
+        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 4df6576..f4c7f23 100755
--- a/src/jalview/io/JalviewFileView.java
+++ b/src/jalview/io/JalviewFileView.java
@@ -16,83 +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.io;
 
-import javax.swing.filechooser.FileView;
-import javax.swing.*;
 import java.io.*;
+
 import java.util.*;
 
-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");
-  }
-  public String getTypeDescription(File f)
-  {
-    String extension = getExtension(f);
-    String type = null;
-
-    if (extension != null)
-    {
-      if (alignSuffix.containsKey(extension))
-      {
-        type = alignSuffix.get(extension).toString();
-      }
+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");
     }
-    return type;
-  }
-
-  public Icon getIcon(File f)
-  {
-    String extension = getExtension(f);
-    Icon icon = null;
-
-    if (extension != null)
-    {
-      if (alignSuffix.containsKey(extension))
-      {
-        icon = createImageIcon("/images/file.png");
-      }
+
+    public String getTypeDescription(File f) {
+        String extension = getExtension(f);
+        String type = null;
+
+        if (extension != null) {
+            if (alignSuffix.containsKey(extension)) {
+                type = alignSuffix.get(extension).toString();
+            }
+        }
+
+        return type;
     }
-    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();
-      }
-      return ext;
-  }
-
-  /** 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;
-      }
-  }
 
-}
+    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;
+    }
+
+    /*
+     * 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();
+        }
 
+        return ext;
+    }
+
+    /** 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;
+        }
+    }
+}
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 104b9d7..2a6e10f 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -16,258 +16,286 @@
 * 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.*;
 
+
 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()
-  {}
+    public MSFfile() {
+    }
 
-  public MSFfile(String inStr) {
-    super(inStr);
-  }
+    public MSFfile(String inStr) {
+        super(inStr);
+    }
 
-  public MSFfile(String inFile, String type) throws IOException {
-    super(inFile,type);
-  }
+    public MSFfile(String inFile, String type) throws IOException {
+        super(inFile, type);
+    }
 
-  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 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());
+                        }
+                    }
+                }
+            }
+        } catch (IOException e) {
+            System.err.println("Exception parsing MSFFile " + e);
+            e.printStackTrace();
+        }
 
-  public void parse() {
-    int       i       = 0;
-    boolean   seqFlag = false;
-    String    key     = new String();
-    Vector    headers = new Vector();
-    Hashtable seqhash = new Hashtable();
-    String    line;
+        this.noSeqs = headers.size();
 
-    try {
-    while ((line = nextLine()) != null) {
+        //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();
 
-      StringTokenizer str = new StringTokenizer(line);
+                int start = 1;
+                int end = seq.length();
 
-      while (str.hasMoreTokens()) {
+                if (maxLength < head.length()) {
+                    maxLength = head.length();
+                }
 
-        String inStr = str.nextToken();
+                if (head.indexOf("/") > 0) {
+                    StringTokenizer st = new StringTokenizer(head, "/");
 
-        //If line has header information add to the headers vector
-        if (inStr.indexOf("Name:") != -1) {
-          key = str.nextToken();
-          headers.addElement(key);
-        }
+                    if (st.countTokens() == 2) {
+                        head = st.nextToken();
 
-        //if line has // set SeqFlag to 1 so we know sequences are coming
-        if (inStr.indexOf("//") != -1) {
-          seqFlag = true;
-        }
+                        String tmp = st.nextToken();
+                        st = new StringTokenizer(tmp, "-");
 
-        //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());
-          }
-        }
-      }
-    }
-    } catch (IOException e) {
-      System.err.println("Exception parsing MSFFile " + e);
-      e.printStackTrace();
-    }
-
-    this.noSeqs = headers.size();
+                        if (st.countTokens() == 2) {
+                            start = Integer.valueOf(st.nextToken()).intValue();
+                            end = Integer.valueOf(st.nextToken()).intValue();
+                        }
+                    }
+                }
 
-    //Add sequences to the hash
-    for (i = 0; i < headers.size(); i++ ) {
+                // Replace ~ with a sensible gap character
+                seq = gapre.replaceAll(seq);
 
-      if ( seqhash.get(headers.elementAt(i)) != null) {
-        String head =  headers.elementAt(i).toString();
-        String seq  =  seqhash.get(head).toString();
+                Sequence newSeq = new Sequence(head, seq, start, end);
 
-        int start = 1;
-        int end = seq.length();
+                seqs.addElement(newSeq);
+            } else {
+                System.err.println("MSFFile Parser: Can't find sequence for " +
+                    headers.elementAt(i));
+            }
+        }
+    }
 
-        if (maxLength <  head.length() ) {
-          maxLength =  head.length();
+    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();
+            }
         }
 
-        if (head.indexOf("/") > 0 ) {
+        return check % 10000;
+    }
+
+    public static String print(SequenceI[] s) {
+        return print(s, false);
+    }
+
+    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.
 
-          StringTokenizer st = new StringTokenizer(head,"/");
+        int max = 0;
+        int maxid = 0;
+        int i = 0;
+        String big = "";
 
-          if (st.countTokens() == 2) {
+        while ((i < s.length) && (s[i] != null)) {
+            String sq;
+            big += (sq = s[i].getSequence());
 
-            head = 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();
+            if (sq.length() > max) {
+                max = sq.length();
             }
-          }
-        }
-        // Replace ~ with a sensible gap character
-        seq = gapre.replaceAll(seq);
-        Sequence newSeq = new Sequence(head,seq,start,end);
 
-        seqs.addElement(newSeq);
+            i++;
+        }
 
-      } else {
-        System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i));
-      }
-    }
+        Format maxLenpad = new Format("%" + (new String("" + max)).length() +
+                "d");
+        Format maxChkpad = new Format("%" + (new String("1" + max)).length() +
+                "d");
+        i = 0;
+
+        long bigcheck = checkSum(big);
+        long maxNB = 0;
+        out.append("   MSF: " + s[0].getSequence().length() + "   Type: " +
+            (is_NA ? "N" : "P") + "    Check:  " + bigcheck + "   ..\n\n\n");
+
+        String[] nameBlock = new String[s.length];
+        String[] idBlock = new String[s.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());
+            nameBlock[i] = new String("  Name: " + name + " ");
+            idBlock[i] = new String("Len: " +
+                    maxLenpad.form(s[i].getSequence().length()) + "  Check:" +
+                    maxChkpad.form(check) + "  Weight: 1.00\n");
+
+            if (name.length() > maxid) {
+                maxid = name.length();
+            }
 
-  }
+            if (nameBlock[i].length() > maxNB) {
+                maxNB = nameBlock[i].length();
+            }
 
-  public static int checkSum(String seq) {
-    //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
-    int check = 0;
+            i++;
+        }
 
-    String index =  "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
-    index += "--------------------------------------------------------------------------------------------------------------------------------";
+        if (maxid < 10) {
+            maxid = 10;
+        }
 
-    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;
-          }
+        if (maxNB < 15) {
+            maxNB = 15;
         }
-      } catch (Exception e) {
-        System.err.println("Exception during MSF Checksum calculation");
-        e.printStackTrace();
-      }
-    }
-    return check % 10000;
-  }
-
-  public static String print(SequenceI[] s) {
-    return print(s, false);
-  }
-  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.
-
-    int max = 0;
-    int maxid = 0;
-    int i = 0;
-    String big = "";
-
-    while (i < s.length && s[i] != null) {
-      String sq;
-      big += (sq=s[i].getSequence());
-      if (sq.length() > max) {
-        max = sq.length();
-      }
-      i++;
-    }
-    Format maxLenpad = new Format("%"+(new String(""+max)).length()+"d");
-    Format maxChkpad = new Format("%"+(new String("1"+max)).length()+"d");
-    i = 0;
-    long bigcheck = checkSum(big);
-    long maxNB=0;
-    out.append("   MSF: " + s[0].getSequence().length() + "   Type: "+(is_NA?"N":"P")+"    Check:  " + bigcheck + "   ..\n\n\n");
-    String nameBlock[] = new String[s.length];
-    String idBlock[] = new String[s.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());
-      nameBlock[i]=new String("  Name: "+name+" ");
-      idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getSequence().length()) + "  Check:" + maxChkpad.form(check) + "  Weight: 1.00\n");
-
-      if (name.length() > maxid) {
-        maxid = name.length();
-      }
-      if (nameBlock[i].length()>maxNB) {
-        maxNB=nameBlock[i].length();
-      }
-
-      i++;
-    }
-    if (maxid < 10) {
-      maxid = 10;
-    }
-    if (maxNB<15) {
-      maxNB=15;
-    }
-    Format nbFormat = new Format("%-"+maxNB+"s");
-    for (i=0;i<s.length && s[i]!=null;i++) {
-      out.append(nbFormat.form(nameBlock[i])+idBlock[i]);
-    }
-    maxid++;
-    out.append( "\n\n//\n\n");
 
-    int len = 50;
+        Format nbFormat = new Format("%-" + maxNB + "s");
 
-    int nochunks =  max / len + 1;
-    if (max%len == 0) {
-      nochunks--;
-    }
-    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(re2gap.replaceAll(s[j].getSequence().substring(start,end)));
-            if (k < 4) {
-              // out.append(" ");
-            } else {
-              out.append("\n");
-            }
-          } else {
-            if (start < s[j].getSequence().length()) {
-              out.append(re2gap.replaceAll(s[j].getSequence().substring(start)));
-              out.append("\n");
-            } else {
-              if (k == 0) {
-                out.append("\n");
-              }
-            }
-          }
+        for (i = 0; (i < s.length) && (s[i] != null); i++) {
+            out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);
         }
-        j++;
-      }
-      out.append("\n");
 
-    }
-    return out.toString();
-  }
-  public String print() {
-    return print(getSeqsAsArray());
-  }
-}
+        maxid++;
+        out.append("\n\n//\n\n");
 
+        int len = 50;
 
+        int nochunks = (max / len) + 1;
 
+        if ((max % len) == 0) {
+            nochunks--;
+        }
 
+        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(re2gap.replaceAll(s[j].getSequence()
+                                                         .substring(start, end)));
+
+                        if (k < 4) {
+                            // out.append(" ");
+                        } else {
+                            out.append("\n");
+                        }
+                    } else {
+                        if (start < s[j].getSequence().length()) {
+                            out.append(re2gap.replaceAll(
+                                    s[j].getSequence().substring(start)));
+                            out.append("\n");
+                        } else {
+                            if (k == 0) {
+                                out.append("\n");
+                            }
+                        }
+                    }
+                }
+
+                j++;
+            }
 
+            out.append("\n");
+        }
 
+        return out.toString();
+    }
 
+    public String print() {
+        return print(getSeqsAsArray());
+    }
+}
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index a372ed3..a6f1580 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -15,522 +15,516 @@
 * 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
-*/
-
-// NewickFile.java
-// Tree I/O
-// http://evolution.genetics.washington.edu/phylip/newick_doc.html
-
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-import jalview.datamodel.*;
-
-public class NewickFile extends FileParse
-{
-  SequenceNode root;
-
-  private boolean HasBootstrap = false;
-  private boolean HasDistances = false;
-  private boolean RootHasDistance = false;
-
-  private String ErrorStringrange(String Error, String Er, int r, int p, String s) {
-    return ((Error==null) ? "" : Error)
-        + Er +
-        " at position "+p+" ( "
-        + s.substring((p-r)<0 ? 0 : (p-r),
-                      (p+r)>s.length() ? s.length() : (p+r))
-        + " )\n";
-  }
-
-  // @tree annotations
-  // These are set automatically by the reader
-  public boolean HasBootstrap() {
-    return HasBootstrap;
-  }
-
-  public boolean HasDistances() {
-    return HasDistances;
-  }
-  public NewickFile(String inStr) throws IOException
-  {
-    super(inStr, "Paste");
-  }
-
-  public NewickFile(String inFile, String type)
-      throws IOException
-  {
-
-    super(inFile, type);
-  }
-  // File IO Flags
-  boolean ReplaceUnderscores = false;
-
-  public void parse() throws IOException
-  {
-    String nf;
-
-    { // fill nf with complete tree file
-      StringBuffer file = new StringBuffer();
-      while ( (nf = nextLine()) != null)
-      {
-        file.append(nf);
-      }
-      nf = file.toString();
-    }
-
-    root = new SequenceNode();
-    SequenceNode realroot = null;
-    SequenceNode c = root;
-
-    int d = -1;
-    int cp = 0;
-    int flen = nf.length();
-
-    String Error = null;
-    String nodename = null;
-
-    float DefDistance = (float) 0.00001; // @param Default distance for a node - very very small
-    int DefBootstrap = 0; // @param Default bootstrap for a node
-
-    float distance=DefDistance;
-    int bootstrap=DefBootstrap;
-
-    boolean ascending = false; // flag indicating that we are leaving the current node
-
-    com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex("[(\\['),;]");
-
-    while (majorsyms.searchFrom(nf, cp) && Error==null) {
-      int fcp = majorsyms.matchedFrom();
-      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))
-          {
-            // Skip the comment field
-            cp = 1 + comment.matchedFrom();
-          }
-          else
-          {
-            Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp, nf);
-          }
-          ;
-          break;
-
-        case '(':
-
-          // ascending should not be set
-          // New Internal node
-          if (ascending)
-          {
-            Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
-            continue;
-          }
-          ;
-          d++;
-          if (c.right() == null)
-          {
-            c.setRight(new SequenceNode(null, c, null, DefDistance, DefBootstrap, false));
-            c = (SequenceNode) c.right();
-          }
-          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);
-              tmpn.SetChildren(c.left(), c.right());
-              c.setRight(tmpn);
-            }
-            c.setLeft(new SequenceNode(null, c, null, DefDistance, DefBootstrap, false));
-            c = (SequenceNode) c.left();
-          }
-          if (realroot==null) {
-            realroot = c;
-          }
-          nodename = null;
-          distance = DefDistance;
-          bootstrap = DefBootstrap;
-          cp = fcp + 1;
-          break;
-
-          // Deal with quoted fields
-        case '\'':
-          com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
-              "([^']|'')+'");
-          if (qnodename.searchFrom(nf, fcp))
-          {
-            int nl = qnodename.stringMatched().length();
-            nodename = new String(qnodename.stringMatched().substring(0, nl - 1));
-            cp = fcp + nl + 1;
-          }
-          else
-          {
-            Error = ErrorStringrange(Error, "Unterminated quotes for nodename",
-                                     7, fcp, nf);
-          }
-          break;
-
-        case ';':
-          if (d != -1)
-          {
-            Error = ErrorStringrange(Error,
-                                     "Wayward semicolon (depth=" + d + ")", 7,
-                                     fcp, nf);
-          }
-          // cp advanced at the end of default
-
-        default:
-
-          // Parse simpler field strings
-          String fstring = nf.substring(cp, fcp);
-          com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
-              "\\b([^' :;\\](),]+)");
-          com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
-              "\\S+([0-9+]+)\\S*:");
-          com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
-              ":([-0-9.+]+)");
-          if (uqnodename.search(fstring)
-              && (uqnodename.matchedFrom(1) == 0
-                  || fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':')) // JBPNote HACK!
-
-          {
-            if (nodename == null)
-            {
-              if (ReplaceUnderscores) {
-                nodename = uqnodename.stringMatched(1).replace('_', ' ');
-              } else {
-                nodename = uqnodename.stringMatched(1);
-              }
-            }
-            else
-            {
-              Error = ErrorStringrange(Error,
-                                       "File has broken algorithm - overwritten nodename",
-                                       10, fcp,
-                                       nf);
-            }
-          }
-          if (nbootstrap.search(fstring)
-              &&
-              nbootstrap.matchedFrom(1)
-              > uqnodename.matchedFrom(1) + uqnodename.stringMatched().length())
-          {
-            try
-            {
-              bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
-              HasBootstrap = true;
-            }
-            catch (Exception e)
-            {
-              Error = ErrorStringrange(Error, "Can't parse bootstrap value", 4,
-                                       cp + nbootstrap.matchedFrom(), nf);
-            }
-          }
-          boolean nodehasdistance=false;
-          if (ndist.search(fstring))
-          {
-            try
-            {
-              distance = (new Float(ndist.stringMatched(1))).floatValue();
-              HasDistances = true;
-              nodehasdistance = true;
-            }
-            catch (Exception e)
-            {
-              Error = ErrorStringrange(Error, "Can't parse node distance value",
-                                       7, cp + ndist.matchedFrom(), nf);
-            }
-          }
-
-          if (ascending)
-          {
-            // Write node info here
-            c.setName(nodename);
-            c.dist = (HasDistances) ? distance : 0;
-            c.setBootstrap((HasBootstrap) ? bootstrap : 0);
-            if (c==realroot) {
-              RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!
-            }
-          }
-          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)
-            {
-              c.setRight(newnode);
-            }
-            else
-            {
-              if (c.left() == null)
-              {
-                c.setLeft(newnode);
-              }
-              else
-              {
-                // Insert a dummy node for polytomy
-                SequenceNode newdummy = new SequenceNode(null, c, null, 0, 0, true);
-                newdummy.SetChildren(c.left(), newnode);
-                c.setLeft(newdummy);
-              }
-            }
-          }
-          if (ascending)
-          {
-            // move back up the tree from preceding closure
-            c = c.AscendTree();
-            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) == ')') {
-            d--;
-            ascending = true;
-          } else {
-            if (nf.charAt(fcp) == ',') {
-              if (ascending) {
-               ascending = false;
-             } else {
-               // Just advance focus, if we need to
-               if (c.left()!=null && (!c.left().isLeaf())) {
-                 c = (SequenceNode) c.left();
-               }
-             }
-            } // else : We do nothing if ';' is encountered.
-          }
-          // Reset new node properties to obvious fakes
-          nodename = null;
-          distance = DefDistance;
-          bootstrap = DefBootstrap;
-
-          cp=fcp+1;
-      }
-    }
-
-    if (Error!=null) {
-      throw(new IOException("NewickFile: "+Error+"\n"));
-    }
-
-    root = (SequenceNode) root.right().detach(); // remove the imaginary root.
-    if (!RootHasDistance) {
-      root.dist = 0;
-    }
-
-  }
-
-  public NewickFile(SequenceNode newtree) {
-    root = newtree;
-  }
-
-  public NewickFile(SequenceNode newtree, boolean bootstrap) {
-    HasBootstrap = bootstrap;
-    root=newtree;
-  }
-  public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances) {
-    root = newtree;
-    HasBootstrap = bootstrap;
-    HasDistances = distances;
-  }
-
-  public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances, boolean rootdistance) {
-      root = newtree;
-      HasBootstrap = bootstrap;
-      HasDistances = distances;
-      RootHasDistance = rootdistance;
-    }
-
-  public SequenceNode getTree() {
-    return root;
-  }
-
-  public String print() {
-    synchronized (this) {
-      StringBuffer tf = new StringBuffer();
-      print(tf, root);
-      return (tf.append(";").toString());
-    }
-  }
-
-  public String print(boolean withbootstraps) {
-    synchronized(this) {
-      boolean boots = this.HasBootstrap;
-      this.HasBootstrap = withbootstraps;
-      String rv = print();
-      this.HasBootstrap = boots;
-      return rv;
-    }
-  }
-
-  public String print(boolean withbootstraps, boolean withdists) {
-    synchronized(this) {
-      boolean dists = this.HasDistances;
-      this.HasDistances = withdists;
-      String rv = print(withbootstraps);
-      this.HasDistances = dists;
-      return rv;
-    }
-  }
-  boolean printRootInfo = false;
-
-
-  public String print(boolean withbootstraps, boolean withdists, boolean printRootInfo) {
-    synchronized(this) {
-      boolean rootinfo = printRootInfo;
-      this.printRootInfo = printRootInfo;
-      String rv = print(withbootstraps, withdists);
-      this.printRootInfo = rootinfo;
-      return rv;
-    }
-  }
-  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='\'';
-  char getQuoteChar() {
-    return QuoteChar;
-  }
-
-  char setQuoteChar(char c) {
-    char old = QuoteChar;
-    QuoteChar = c;
-    return old;
-  }
-
-  private String nodeName(String name) {
-    if (NodeSafeName[0].search(name)) {
-      return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
-    } else {
-      return NodeSafeName[2].replaceAll(name);
-    }
-  }
-  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) {
-
-      return (printRootInfo)
-          ? (( (root.getName() == null) ? ""
-               : nodeName(root.getName()))
-             + ( (HasBootstrap)
-                 ? ( (root.getBootstrap() > -1)
-                     ? " " + root.getBootstrap()
-                     : "")
-                 : "")
-             + ( (RootHasDistance)
-                 ? ":" + root.dist : ""))
-          : "";
-    }
-
-// Non recursive call deals with root node properties
-  public void print(StringBuffer tf, SequenceNode root) {
-    if (root!=null) {
-      if (root.isLeaf() && printRootInfo) {
-        tf.append(printRootField(root));
-      } else {
-        if (root.isDummy()) {
-          _print(tf, (SequenceNode) root.right());
-          _print(tf, (SequenceNode) root.left());
-        } else {
-          tf.append("(");
-          _print(tf, (SequenceNode) root.right());
-          if (root.left() != null) {
-            tf.append(",");
-          }
-          _print(tf, (SequenceNode) root.left());
-          tf.append(")" + printRootField(root));
-        }
-      }
-    }
-  }
-
-  // Recursive call for non-root nodes
-  public void _print(StringBuffer tf, SequenceNode c) {
-    if (c!=null) {
-      if (c.isLeaf()) {
-        tf.append(printNodeField(c));
-      } else {
-        if (c.isDummy()) {
-          _print(tf, (SequenceNode) c.right());
-          _print(tf, (SequenceNode) c.left());
-        } else {
-          tf.append("(");
-          _print(tf, (SequenceNode) c.right());
-          if (c.left() != null) {
-            tf.append(",");
-          }
-          _print(tf, (SequenceNode) c.left());
-          tf.append(")" + printNodeField(c));
-        }
-      }
-    }
-  }
-
-// Test
-  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) {
-      newickfile.append(l);
-    }
-    treefile.close();
-    System.out.println("Read file :\n");
-    NewickFile trf = new NewickFile(args[0], "File");
-    trf.parse();
-    System.out.println("Original file :\n");
-    com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
-    System.out.println(nonl.replaceAll(newickfile.toString())+"\n");
-
-    System.out.println("Parsed file.\n");
-    System.out.println("Default output type for original input.\n");
-    System.out.println(trf.print());
-    System.out.println("Without bootstraps.\n");
-    System.out.println(trf.print(false));
-    System.out.println("Without distances.\n");
-    System.out.println(trf.print(true,false));
-    System.out.println("Without bootstraps but with distanecs.\n");
-    System.out.println(trf.print(false, true));
-    System.out.println("Without bootstraps or distanecs.\n");
-    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)
-  {
-    System.err.println("Exception\n" + e);
-    e.printStackTrace();
-  }
-}
-
-}
+*/
+
+// NewickFile.java
+// Tree I/O
+// http://evolution.genetics.washington.edu/phylip/newick_doc.html
+package jalview.io;
+
+import jalview.datamodel.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+public class NewickFile extends FileParse {
+    SequenceNode root;
+    private boolean HasBootstrap = false;
+    private boolean HasDistances = false;
+    private boolean RootHasDistance = false;
+
+    // File IO Flags
+    boolean ReplaceUnderscores = false;
+    boolean printRootInfo = false;
+    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 {
+        super(inStr, "Paste");
+    }
+
+    public NewickFile(String inFile, String type) throws IOException {
+        super(inFile, type);
+    }
+
+    public NewickFile(SequenceNode newtree) {
+        root = newtree;
+    }
+
+    public NewickFile(SequenceNode newtree, boolean bootstrap) {
+        HasBootstrap = bootstrap;
+        root = newtree;
+    }
+
+    public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances) {
+        root = newtree;
+        HasBootstrap = bootstrap;
+        HasDistances = distances;
+    }
+
+    public NewickFile(SequenceNode newtree, boolean bootstrap,
+        boolean distances, boolean rootdistance) {
+        root = newtree;
+        HasBootstrap = bootstrap;
+        HasDistances = distances;
+        RootHasDistance = rootdistance;
+    }
+
+    private String ErrorStringrange(String Error, String Er, int r, int p,
+        String s) {
+        return ((Error == null) ? "" : Error) + Er + " at position " + p +
+        " ( " +
+        s.substring(((p - r) < 0) ? 0 : (p - r),
+            ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
+    }
+
+    // @tree annotations
+    // These are set automatically by the reader
+    public boolean HasBootstrap() {
+        return HasBootstrap;
+    }
+
+    public boolean HasDistances() {
+        return HasDistances;
+    }
+
+    public void parse() throws IOException {
+        String nf;
+
+        { // fill nf with complete tree file
+
+            StringBuffer file = new StringBuffer();
+
+            while ((nf = nextLine()) != null) {
+                file.append(nf);
+            }
+
+            nf = file.toString();
+        }
+
+        root = new SequenceNode();
+
+        SequenceNode realroot = null;
+        SequenceNode c = root;
+
+        int d = -1;
+        int cp = 0;
+        int flen = nf.length();
+
+        String Error = null;
+        String nodename = null;
+
+        float DefDistance = (float) 0.00001; // @param Default distance for a node - very very small
+        int DefBootstrap = 0; // @param Default bootstrap for a node
+
+        float distance = DefDistance;
+        int bootstrap = DefBootstrap;
+
+        boolean ascending = false; // flag indicating that we are leaving the current node
+
+        com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
+                "[(\\['),;]");
+
+        while (majorsyms.searchFrom(nf, cp) && (Error == null)) {
+            int fcp = majorsyms.matchedFrom();
+
+            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)) {
+                    // Skip the comment field
+                    cp = 1 + comment.matchedFrom();
+                } else {
+                    Error = ErrorStringrange(Error, "Unterminated comment", 3,
+                            fcp, nf);
+                }
+
+                ;
+
+                break;
+
+            case '(':
+
+                // ascending should not be set
+                // New Internal node
+                if (ascending) {
+                    Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
+
+                    continue;
+                }
+
+                ;
+                d++;
+
+                if (c.right() == null) {
+                    c.setRight(new SequenceNode(null, c, null, DefDistance,
+                            DefBootstrap, false));
+                    c = (SequenceNode) c.right();
+                } 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);
+                        tmpn.SetChildren(c.left(), c.right());
+                        c.setRight(tmpn);
+                    }
+
+                    c.setLeft(new SequenceNode(null, c, null, DefDistance,
+                            DefBootstrap, false));
+                    c = (SequenceNode) c.left();
+                }
+
+                if (realroot == null) {
+                    realroot = c;
+                }
+
+                nodename = null;
+                distance = DefDistance;
+                bootstrap = DefBootstrap;
+                cp = fcp + 1;
+
+                break;
+
+            // Deal with quoted fields
+            case '\'':
+
+                com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
+                        "([^']|'')+'");
+
+                if (qnodename.searchFrom(nf, fcp)) {
+                    int nl = qnodename.stringMatched().length();
+                    nodename = new String(qnodename.stringMatched().substring(0,
+                                nl - 1));
+                    cp = fcp + nl + 1;
+                } else {
+                    Error = ErrorStringrange(Error,
+                            "Unterminated quotes for nodename", 7, fcp, nf);
+                }
+
+                break;
+
+            case ';':
+
+                if (d != -1) {
+                    Error = ErrorStringrange(Error,
+                            "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
+                }
+
+            // cp advanced at the end of default
+            default:
+
+                // Parse simpler field strings
+                String fstring = nf.substring(cp, fcp);
+                com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
+                        "\\b([^' :;\\](),]+)");
+                com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
+                        "\\S+([0-9+]+)\\S*:");
+                com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
+                        ":([-0-9.+]+)");
+
+                if (uqnodename.search(fstring) &&
+                        ((uqnodename.matchedFrom(1) == 0) ||
+                        (fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!
+                 {
+                    if (nodename == null) {
+                        if (ReplaceUnderscores) {
+                            nodename = uqnodename.stringMatched(1).replace('_',
+                                    ' ');
+                        } else {
+                            nodename = uqnodename.stringMatched(1);
+                        }
+                    } else {
+                        Error = ErrorStringrange(Error,
+                                "File has broken algorithm - overwritten nodename",
+                                10, fcp, nf);
+                    }
+                }
+
+                if (nbootstrap.search(fstring) &&
+                        (nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +
+                        uqnodename.stringMatched().length()))) {
+                    try {
+                        bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
+                        HasBootstrap = true;
+                    } catch (Exception e) {
+                        Error = ErrorStringrange(Error,
+                                "Can't parse bootstrap value", 4,
+                                cp + nbootstrap.matchedFrom(), nf);
+                    }
+                }
+
+                boolean nodehasdistance = false;
+
+                if (ndist.search(fstring)) {
+                    try {
+                        distance = (new Float(ndist.stringMatched(1))).floatValue();
+                        HasDistances = true;
+                        nodehasdistance = true;
+                    } catch (Exception e) {
+                        Error = ErrorStringrange(Error,
+                                "Can't parse node distance value", 7,
+                                cp + ndist.matchedFrom(), nf);
+                    }
+                }
+
+                if (ascending) {
+                    // Write node info here
+                    c.setName(nodename);
+                    c.dist = (HasDistances) ? distance : 0;
+                    c.setBootstrap((HasBootstrap) ? bootstrap : 0);
+
+                    if (c == realroot) {
+                        RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!
+                    }
+                } 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) {
+                        c.setRight(newnode);
+                    } else {
+                        if (c.left() == null) {
+                            c.setLeft(newnode);
+                        } else {
+                            // Insert a dummy node for polytomy
+                            SequenceNode newdummy = new SequenceNode(null, c,
+                                    null, 0, 0, true);
+                            newdummy.SetChildren(c.left(), newnode);
+                            c.setLeft(newdummy);
+                        }
+                    }
+                }
+
+                if (ascending) {
+                    // move back up the tree from preceding closure
+                    c = c.AscendTree();
+
+                    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) == ')') {
+                    d--;
+                    ascending = true;
+                } else {
+                    if (nf.charAt(fcp) == ',') {
+                        if (ascending) {
+                            ascending = false;
+                        } else {
+                            // Just advance focus, if we need to
+                            if ((c.left() != null) && (!c.left().isLeaf())) {
+                                c = (SequenceNode) c.left();
+                            }
+                        }
+                    }
+                     // else : We do nothing if ';' is encountered.
+                }
+
+                // Reset new node properties to obvious fakes
+                nodename = null;
+                distance = DefDistance;
+                bootstrap = DefBootstrap;
+
+                cp = fcp + 1;
+            }
+        }
+
+        if (Error != null) {
+            throw (new IOException("NewickFile: " + Error + "\n"));
+        }
+
+        root = (SequenceNode) root.right().detach(); // remove the imaginary root.
+
+        if (!RootHasDistance) {
+            root.dist = 0;
+        }
+    }
+
+    public SequenceNode getTree() {
+        return root;
+    }
+
+    public String print() {
+        synchronized (this) {
+            StringBuffer tf = new StringBuffer();
+            print(tf, root);
+
+            return (tf.append(";").toString());
+        }
+    }
+
+    public String print(boolean withbootstraps) {
+        synchronized (this) {
+            boolean boots = this.HasBootstrap;
+            this.HasBootstrap = withbootstraps;
+
+            String rv = print();
+            this.HasBootstrap = boots;
+
+            return rv;
+        }
+    }
+
+    public String print(boolean withbootstraps, boolean withdists) {
+        synchronized (this) {
+            boolean dists = this.HasDistances;
+            this.HasDistances = withdists;
+
+            String rv = print(withbootstraps);
+            this.HasDistances = dists;
+
+            return rv;
+        }
+    }
+
+    public String print(boolean withbootstraps, boolean withdists,
+        boolean printRootInfo) {
+        synchronized (this) {
+            boolean rootinfo = printRootInfo;
+            this.printRootInfo = printRootInfo;
+
+            String rv = print(withbootstraps, withdists);
+            this.printRootInfo = rootinfo;
+
+            return rv;
+        }
+    }
+
+    char getQuoteChar() {
+        return QuoteChar;
+    }
+
+    char setQuoteChar(char c) {
+        char old = QuoteChar;
+        QuoteChar = c;
+
+        return old;
+    }
+
+    private String nodeName(String name) {
+        if (NodeSafeName[0].search(name)) {
+            return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
+        } else {
+            return NodeSafeName[2].replaceAll(name);
+        }
+    }
+
+    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) {
+        return (printRootInfo)
+        ? (((root.getName() == null) ? "" : nodeName(root.getName())) +
+        ((HasBootstrap)
+        ? ((root.getBootstrap() > -1) ? (" " + root.getBootstrap()) : "") : "") +
+        ((RootHasDistance) ? (":" + root.dist) : "")) : "";
+    }
+
+    // Non recursive call deals with root node properties
+    public void print(StringBuffer tf, SequenceNode root) {
+        if (root != null) {
+            if (root.isLeaf() && printRootInfo) {
+                tf.append(printRootField(root));
+            } else {
+                if (root.isDummy()) {
+                    _print(tf, (SequenceNode) root.right());
+                    _print(tf, (SequenceNode) root.left());
+                } else {
+                    tf.append("(");
+                    _print(tf, (SequenceNode) root.right());
+
+                    if (root.left() != null) {
+                        tf.append(",");
+                    }
+
+                    _print(tf, (SequenceNode) root.left());
+                    tf.append(")" + printRootField(root));
+                }
+            }
+        }
+    }
+
+    // Recursive call for non-root nodes
+    public void _print(StringBuffer tf, SequenceNode c) {
+        if (c != null) {
+            if (c.isLeaf()) {
+                tf.append(printNodeField(c));
+            } else {
+                if (c.isDummy()) {
+                    _print(tf, (SequenceNode) c.right());
+                    _print(tf, (SequenceNode) c.left());
+                } else {
+                    tf.append("(");
+                    _print(tf, (SequenceNode) c.right());
+
+                    if (c.left() != null) {
+                        tf.append(",");
+                    }
+
+                    _print(tf, (SequenceNode) c.left());
+                    tf.append(")" + printNodeField(c));
+                }
+            }
+        }
+    }
+
+    // Test
+    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) {
+                newickfile.append(l);
+            }
+
+            treefile.close();
+            System.out.println("Read file :\n");
+
+            NewickFile trf = new NewickFile(args[0], "File");
+            trf.parse();
+            System.out.println("Original file :\n");
+
+            com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
+            System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
+
+            System.out.println("Parsed file.\n");
+            System.out.println("Default output type for original input.\n");
+            System.out.println(trf.print());
+            System.out.println("Without bootstraps.\n");
+            System.out.println(trf.print(false));
+            System.out.println("Without distances.\n");
+            System.out.println(trf.print(true, false));
+            System.out.println("Without bootstraps but with distanecs.\n");
+            System.out.println(trf.print(false, true));
+            System.out.println("Without bootstraps or distanecs.\n");
+            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) {
+            System.err.println("Exception\n" + e);
+            e.printStackTrace();
+        }
+    }
+}
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 410628f..42334e3 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -16,120 +16,130 @@
 * 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.analysis.*;
 
+import jalview.datamodel.*;
+
 import java.io.*;
+
 import java.util.*;
 
+
 public class PIRFile extends AlignFile {
+    Vector words = new Vector(); //Stores the words in a line after splitting
+
+    public PIRFile() {
+    }
 
-  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, start, 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);
-      }
+    public PIRFile(String inStr) {
+        super(inStr);
+    }
 
+    public PIRFile(String inFile, String type) throws IOException {
+        super(inFile, type);
     }
-    catch(Exception ex){ex.printStackTrace();}
-  }
-
-  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");
+
+    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();
         }
-      }
-      i++;
     }
-    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);
-  }
-}
+    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");
+                }
+            }
+
+            i++;
+        }
+
+        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 d0ffbc9..b31a148 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -16,177 +16,182 @@
 * 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.*;
-
-public class PfamFile extends AlignFile {
-
-  Vector ids;
 
-  public PfamFile()
-  {}
+import java.util.*;
 
-  public PfamFile(String inStr) {
-    super(inStr);
-  }
 
-  public void initData() {
-    super.initData();
-    ids = new Vector();
-  }
+public class PfamFile extends AlignFile {
+    Vector ids;
 
-  public PfamFile(String inFile, String type) throws IOException {
-    super(inFile,type);
-  }
+    public PfamFile() {
+    }
 
-  public void parse() throws IOException{
-    int i = 0;
-    String line;
+    public PfamFile(String inStr) {
+        super(inStr);
+    }
 
+    public PfamFile(String inFile, String type) throws IOException {
+        super(inFile, type);
+    }
 
-    Hashtable seqhash = new Hashtable();
-    Vector    headers = new Vector();
+    public void initData() {
+        super.initData();
+        ids = new Vector();
+    }
 
+    public void parse() throws IOException {
+        int i = 0;
+        String line;
 
-      while ((line = nextLine()) != null)
-      {
+        Hashtable seqhash = new Hashtable();
+        Vector headers = new Vector();
 
-      if (line.indexOf(" ") != 0)
-      {
-        if (line.indexOf("#") != 0)
-        {
+        while ((line = nextLine()) != null) {
+            if (line.indexOf(" ") != 0) {
+                if (line.indexOf("#") != 0) {
+                    StringTokenizer str = new StringTokenizer(line, " ");
+                    String id = "";
 
-          StringTokenizer str = new StringTokenizer(line," ");
-          String id = "";
+                    if (str.hasMoreTokens()) {
+                        id = str.nextToken();
 
-          if (str.hasMoreTokens())
-          {
-            id = str.nextToken();
+                        StringBuffer tempseq;
 
-            StringBuffer tempseq;
+                        if (seqhash.containsKey(id)) {
+                            tempseq = (StringBuffer) seqhash.get(id);
+                        } else {
+                            tempseq = new StringBuffer();
+                            seqhash.put(id, 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 (!(headers.contains(id)))
-              headers.addElement(id);
+                        tempseq.append(str.nextToken());
+                    }
+                }
+            }
+        }
 
+        this.noSeqs = headers.size();
 
-            tempseq.append(str.nextToken());
-          }
+        if (noSeqs < 1) {
+            throw new IOException("No sequences found (PFAM input)");
         }
-      }
-    }
 
-    this.noSeqs = headers.size();
-    if(noSeqs<1)
-      throw new IOException("No sequences found (PFAM input)");
-
-    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;
+        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));
             }
-          } else
-            ids.addElement(headers.elementAt(i));
-
         }
-        else
-          ids.addElement(headers.elementAt(i));
+    }
 
+    public static String print(SequenceI[] s) {
+        StringBuffer out = new StringBuffer("");
 
-        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);
-        }
+        int max = 0;
+        int maxid = 0;
 
-        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));
+        int i = 0;
 
-    }
+        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();
+            }
 
-  public static String print(SequenceI[] s) {
-    StringBuffer out = new StringBuffer("");
+            if (tmp.length() > maxid) {
+                maxid = tmp.length();
+            }
 
-    int max = 0;
-    int maxid = 0;
+            i++;
+        }
 
-    int i = 0;
+        if (maxid < 15) {
+            maxid = 15;
+        }
 
-    while (i < s.length && s[i] != null) {
-      String tmp = s[i].getName() + "/" + s[i].getStart()+ "-" + s[i].getEnd();
+        int j = 0;
 
-      if (s[i].getSequence().length() > max) {
-        max = s[i].getSequence().length();
-      }
-      if (tmp.length() > maxid) {
-        maxid = tmp.length();
-      }
-      i++;
-    }
+        while ((j < s.length) && (s[j] != null)) {
+            out.append(new Format("%-" + maxid + "s").form(s[j].getName() +
+                    "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
 
-    if (maxid < 15) {
-      maxid = 15;
-    }
+            out.append(s[j].getSequence() + "\n");
+            j++;
+        }
 
-    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() ) + " ");
+        out.append("\n");
 
-      out.append(s[j].getSequence() + "\n");
-      j++;
+        return out.toString();
     }
-    out.append("\n");
-
-    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 f5f709e..9f879c0 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -15,10 +15,10 @@
 * 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;
-
+*/
+package jalview.io;
+
+
 /**
  * <p>Title: </p>
  *  PileUpfile
@@ -29,239 +29,248 @@ package jalview.io;
  *  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.*;
-
-
-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);
-        }
-
-        //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();
-  }
-
-  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();
-
-      if (maxLength <  head.length() ) {
-        maxLength =  head.length();
-      }
-
-      if (head.indexOf("/") > 0 ) {
-
-        StringTokenizer st = new StringTokenizer(head,"/");
-
-        if (st.countTokens() == 2) {
-
-          head = 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();
-          }
-        }
-      }
-
-      Sequence newSeq = new Sequence(head,seq,start,end);
-
-      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();
-    }
-  }
-  return check % 10000;
-}
-
-public static String print(SequenceI[] s) {
-  StringBuffer out = new StringBuffer("PileUp\n\n");
-
-  int max = 0;
-  int maxid = 0;
-
-  int i = 0;
-  String big = "";
-  while (i < s.length && s[i] != null) {
-    big += s[i].getSequence();
-    i++;
-  }
-  i = 0;
-  int bigcheck = checkSum(big);
-
-  out.append("   MSF: " + s[0].getSequence().length() + "   Type: P    Check:  " + bigcheck + "   ..\n\n\n");
-
-  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 (seq.length() > max) {
-      max = seq.length();
-    }
-    if (name.length() > maxid) {
-      maxid = name.length();
-    }
-    i++;
-  }
-
-  if (maxid < 10) {
-    maxid = 10;
-  }
-  maxid++;
-  out.append( "\n\n//\n\n");
-
-  int len = 50;
-
-  int nochunks =  max / len + 1;
-  if (max%len == 0) {
-    nochunks--;
-  }
-  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++;
-    }
-    out.append("\n");
-
-  }
-  return out.toString();
-}
-public String print() {
-  return print(getSeqsAsArray());
-}
-}
-
-
-
-
-
-
-
+ **/
+import jalview.datamodel.*;
+
+import jalview.util.*;
+
+import java.io.*;
+
+import java.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 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());
+                        }
+                    }
+                }
+            }
+        } 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();
+
+                if (maxLength < head.length()) {
+                    maxLength = head.length();
+                }
+
+                if (head.indexOf("/") > 0) {
+                    StringTokenizer st = new StringTokenizer(head, "/");
+
+                    if (st.countTokens() == 2) {
+                        head = 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();
+                        }
+                    }
+                }
+
+                Sequence newSeq = new Sequence(head, seq, start, end);
+
+                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();
+            }
+        }
+
+        return check % 10000;
+    }
+
+    public static String print(SequenceI[] s) {
+        StringBuffer out = new StringBuffer("PileUp\n\n");
+
+        int max = 0;
+        int maxid = 0;
+
+        int i = 0;
+        String big = "";
+
+        while ((i < s.length) && (s[i] != null)) {
+            big += s[i].getSequence();
+            i++;
+        }
+
+        i = 0;
+
+        int bigcheck = checkSum(big);
+
+        out.append("   MSF: " + s[0].getSequence().length() +
+            "   Type: P    Check:  " + bigcheck + "   ..\n\n\n");
+
+        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 (seq.length() > max) {
+                max = seq.length();
+            }
+
+            if (name.length() > maxid) {
+                maxid = name.length();
+            }
+
+            i++;
+        }
+
+        if (maxid < 10) {
+            maxid = 10;
+        }
+
+        maxid++;
+        out.append("\n\n//\n\n");
+
+        int len = 50;
+
+        int nochunks = (max / len) + 1;
+
+        if ((max % len) == 0) {
+            nochunks--;
+        }
+
+        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++;
+            }
+
+            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 b8300a0..c8c39dc 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -16,372 +16,404 @@
 * 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.io.*;
+
 import java.io.*;
+
 import java.util.*;
+
 import javax.swing.*;
-import jalview.io.*;
-import jalview.gui.*;
-import jalview.datamodel.*;
 
-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)
-  {
-    unknownSequences = new ArrayList();
-    this.align = align;
-    this.ap = ap;
-    Thread thread = new Thread(this);
-    thread.start();
-  }
-
-  public void run()
-{
-
-  String cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
-
-  RandomAccessFile out = null;
-
-  try{
-    if (cache == null)
-    {
-      jalview.bin.Cache.setProperty("UNIPROT_CACHE", System.getProperty("user.home")+"/uniprot.xml");
-      cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
-    }
 
+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) {
+        unknownSequences = new ArrayList();
+        this.align = align;
+        this.ap = ap;
 
-    File test = new File(cache);
-    if( !test.exists() )
-    {
-      out = new RandomAccessFile(cache, "rw");
-      out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
-      out.writeBytes("<UNIPROT_CACHE>\n");
-    }
-    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)
-          lastLine = out.getFilePointer();
-
-      }
-      out.seek(lastLine);
+        Thread thread = new Thread(this);
+        thread.start();
     }
 
-    int seqIndex = 0;
-    Vector sequences = align.getSequences();
+    public void run() {
+        String cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
 
-    while (seqIndex < sequences.size())
-    {
-      ArrayList ids = new ArrayList();
-      for (int i = 0; seqIndex < sequences.size() && i < 50; seqIndex++, i++)
-      {
-        SequenceI sequence = (SequenceI) sequences.get(seqIndex);
-        ids.add(sequence.getName());
-      }
+        RandomAccessFile out = null;
 
-      tryLocalCacheFirst(ids, align);
+        try {
+            if (cache == null) {
+                jalview.bin.Cache.setProperty("UNIPROT_CACHE",
+                    System.getProperty("user.home") + "/uniprot.xml");
+                cache = jalview.bin.Cache.getProperty("UNIPROT_CACHE");
+            }
 
-      if (ids.size() > 0)
-      {
-        StringBuffer remainingIds = new StringBuffer("uniprot:");
-        for (int i = 0; i < ids.size(); i++)
-          remainingIds.append(ids.get(i) + ";");
+            File test = new File(cache);
 
-         EBIFetchClient ebi = new EBIFetchClient();
-         String[] result = ebi.fetchData(remainingIds.toString(), "xml", null);
+            if (!test.exists()) {
+                out = new RandomAccessFile(cache, "rw");
+                out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+                out.writeBytes("<UNIPROT_CACHE>\n");
+            } else {
+                out = new RandomAccessFile(cache, "rw");
 
-        if(result!=null)
-          ReadUniprotFile(result, out, align);
-      }
+                // 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) {
+                        lastLine = out.getFilePointer();
+                    }
+                }
 
-    if (out != null)
-    {
-      out.writeBytes("</UNIPROT_CACHE>\n");
-      out.close();
-    }
-  }catch(Exception ex){ex.printStackTrace();}
+                out.seek(lastLine);
+            }
 
-  ap.repaint();
-  findMissingIds(align);
-  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"
-                   +"Save your alignment to maintain the updated id.\n\n"+sbuffer.toString());
-    Desktop.addInternalFrame(output, "Sequence names updated ", 600,300);
+            int seqIndex = 0;
+            Vector sequences = align.getSequences();
 
-  }
+            while (seqIndex < sequences.size()) {
+                ArrayList ids = new ArrayList();
 
-  if(unknownSequences.size()>0)
-  {
-    //ignore for now!!!!!!!!!!
-  //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
-  }
+                for (int i = 0; (seqIndex < sequences.size()) && (i < 50);
+                        seqIndex++, i++) {
+                    SequenceI sequence = (SequenceI) sequences.get(seqIndex);
+                    ids.add(sequence.getName());
+                }
 
-}
+                tryLocalCacheFirst(ids, align);
+
+                if (ids.size() > 0) {
+                    StringBuffer remainingIds = new StringBuffer("uniprot:");
 
-void ReadUniprotFile(String [] result, RandomAccessFile out, AlignmentI align)
-{
-  SequenceI sequence = null;
-  Vector features = null;
-  String type, description, status, start, end, pdb = null;
-
-
-  for (int r = 0; r < result.length; r++)
-  {
-    if(sequence==null && result[r].indexOf("<name>")>-1)
-    {
-      long filePointer = 0;
-
-      if(out!=null)
-      try{
-        filePointer=out.getFilePointer();
-        out.writeBytes("<entry>\n");
-      }catch(Exception ex){}
-
-      String seqName = parseElement( result[r], "<name>" , out);
-      sequence = align.findName( seqName ) ;
-      if(sequence==null)
-      {
-        sequence = align.findName( seqName.substring(0, seqName.indexOf('_')));
-        if(sequence!=null)
-        {
-          sbuffer.append("changing "+sequence.getName()+" to "+seqName+"\n");
-          sequence.setName(seqName);
+                    for (int i = 0; i < ids.size(); i++)
+                        remainingIds.append(ids.get(i) + ";");
+
+                    EBIFetchClient ebi = new EBIFetchClient();
+                    String[] result = ebi.fetchData(remainingIds.toString(),
+                            "xml", null);
+
+                    if (result != null) {
+                        ReadUniprotFile(result, out, align);
+                    }
+                }
+            }
+
+            if (out != null) {
+                out.writeBytes("</UNIPROT_CACHE>\n");
+                out.close();
+            }
+        } catch (Exception ex) {
+            ex.printStackTrace();
         }
-      }
-      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   { out.setLength(filePointer);  }  catch (Exception ex) {}
-        // now skip to next entry
-        while( result[r].indexOf("</entry>")==-1)
-          r++;
-      }
-
-      features = new Vector();
-      type=""; start="0"; end="0"; description=""; status=""; pdb="";
 
+        ap.repaint();
+        findMissingIds(align);
+
+        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" +
+                "Save your alignment to maintain the updated id.\n\n" +
+                sbuffer.toString());
+            Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
+        }
+
+        if (unknownSequences.size() > 0) {
+            //ignore for now!!!!!!!!!!
+            //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
+        }
     }
 
-    if(sequence==null)
-      continue;
-
-     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)
-     {
-       type = parseValue( result[r], "type=" , out);
-       description = parseValue( result[r], "description=" , null );
-       status = parseValue ( result[r], "status=", null);
-
-       while( result[r].indexOf("position")==-1)
-       {
-           r++;  //<location>
-       }
-      // r++;
-       if(result[r].indexOf("begin")>-1)
-       {
-         start = parseValue( result[r], "position=" , out);
-         end = parseValue( result[++r], "position=" , out);
-       }
-       else
-       {
-         start = parseValue( result[r], "position=" , out);
-         end = parseValue(   result[r], "position=" , null);
-       }
-       int sstart = Integer.parseInt(start);
-       int eend = Integer.parseInt(end);
-       if(out!=null)
-         try{ out.writeBytes("</feature>\n"); }catch(Exception ex){}
-
-         SequenceFeature sf = new SequenceFeature(type,
-             sstart,
-             eend,
-             description,
-             status);
-         features.add(sf);
-     }
-
-     if(result[r].indexOf("<sequence")>-1)
-     {
-       StringBuffer seqString = new StringBuffer();
-
-       if(out!=null)
-         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
-
-       while(result[++r].indexOf("</sequence>")==-1)
-       {
-         seqString.append(result[r]);
-         if(out!=null)
-         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
-       }
-
-       if(out!=null)
-         try  {  out.writeBytes(result[r]+"\n"); }   catch (Exception ex){}
-
-       StringBuffer nonGapped = new StringBuffer();
-       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)
-       {
-         unknownSequences.add(sequence.getName());
-         features = null;
-         sbuffer.append(sequence.getName()+ " SEQUENCE NOT %100 MATCH \n");
-         continue;
-       }
-
-       int absEnd =   absStart + nonGapped.toString().length();
-       absStart+=1;
-
-       if(absStart!=sequence.getStart() || absEnd!=sequence.getEnd())
-         sbuffer.append("Updated: "+sequence.getName()+" "+
-                           sequence.getStart()+"/"+sequence.getEnd()+"  to  "+ absStart+"/"+absEnd+"\n");
-
-
-       sequence.setStart(absStart);
-       sequence.setEnd(absEnd);
-
-     }
-
-     if(result[r].indexOf("</entry>")>-1)
-     {
-       if(features!=null)
-         sequence.setSequenceFeatures( features );
-       features = null;
-       sequence = null;
-       if(out!=null)
-         try{  out.writeBytes("</entry>\n"); }catch(Exception ex){}
-
-     }
-  }
-}
+    void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align) {
+        SequenceI sequence = null;
+        Vector features = null;
+        String type;
+        String description;
+        String status;
+        String start;
+        String end;
+        String pdb = null;
+
+        for (int r = 0; r < result.length; r++) {
+            if ((sequence == null) && (result[r].indexOf("<name>") > -1)) {
+                long filePointer = 0;
+
+                if (out != null) {
+                    try {
+                        filePointer = out.getFilePointer();
+                        out.writeBytes("<entry>\n");
+                    } catch (Exception ex) {
+                    }
+                }
+
+                String seqName = parseElement(result[r], "<name>", out);
+                sequence = align.findName(seqName);
+
+                if (sequence == null) {
+                    sequence = align.findName(seqName.substring(0,
+                                seqName.indexOf('_')));
+
+                    if (sequence != null) {
+                        sbuffer.append("changing " + sequence.getName() +
+                            " to " + seqName + "\n");
+                        sequence.setName(seqName);
+                    }
+                }
+
+                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 {
+                        out.setLength(filePointer);
+                    } catch (Exception ex) {
+                    }
+
+                    // now skip to next entry
+                    while (result[r].indexOf("</entry>") == -1)
+                        r++;
+                }
+
+                features = new Vector();
+                type = "";
+                start = "0";
+                end = "0";
+                description = "";
+                status = "";
+                pdb = "";
+            }
+
+            if (sequence == null) {
+                continue;
+            }
+
+            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) {
+                type = parseValue(result[r], "type=", out);
+                description = parseValue(result[r], "description=", null);
+                status = parseValue(result[r], "status=", null);
+
+                while (result[r].indexOf("position") == -1) {
+                    r++; //<location>
+                }
+
+                // r++;
+                if (result[r].indexOf("begin") > -1) {
+                    start = parseValue(result[r], "position=", out);
+                    end = parseValue(result[++r], "position=", out);
+                } else {
+                    start = parseValue(result[r], "position=", out);
+                    end = parseValue(result[r], "position=", null);
+                }
+
+                int sstart = Integer.parseInt(start);
+                int eend = Integer.parseInt(end);
+
+                if (out != null) {
+                    try {
+                        out.writeBytes("</feature>\n");
+                    } catch (Exception ex) {
+                    }
+                }
+
+                SequenceFeature sf = new SequenceFeature(type, sstart, eend,
+                        description, status);
+                features.add(sf);
+            }
+
+            if (result[r].indexOf("<sequence") > -1) {
+                StringBuffer seqString = new StringBuffer();
+
+                if (out != null) {
+                    try {
+                        out.writeBytes(result[r] + "\n");
+                    } catch (Exception ex) {
+                    }
+                }
+
+                while (result[++r].indexOf("</sequence>") == -1) {
+                    seqString.append(result[r]);
+
+                    if (out != null) {
+                        try {
+                            out.writeBytes(result[r] + "\n");
+                        } catch (Exception ex) {
+                        }
+                    }
+                }
+
+                if (out != null) {
+                    try {
+                        out.writeBytes(result[r] + "\n");
+                    } catch (Exception ex) {
+                    }
+                }
+
+                StringBuffer nonGapped = new StringBuffer();
+
+                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) {
+                    unknownSequences.add(sequence.getName());
+                    features = null;
+                    sbuffer.append(sequence.getName() +
+                        " SEQUENCE NOT %100 MATCH \n");
+
+                    continue;
+                }
+
+                int absEnd = absStart + nonGapped.toString().length();
+                absStart += 1;
+
+                if ((absStart != sequence.getStart()) ||
+                        (absEnd != sequence.getEnd())) {
+                    sbuffer.append("Updated: " + sequence.getName() + " " +
+                        sequence.getStart() + "/" + sequence.getEnd() +
+                        "  to  " + absStart + "/" + absEnd + "\n");
+                }
+
+                sequence.setStart(absStart);
+                sequence.setEnd(absEnd);
+            }
+
+            if (result[r].indexOf("</entry>") > -1) {
+                if (features != null) {
+                    sequence.setSequenceFeatures(features);
+                }
+
+                features = null;
+                sequence = null;
+
+                if (out != null) {
+                    try {
+                        out.writeBytes("</entry>\n");
+                    } catch (Exception ex) {
+                    }
+                }
+            }
+        }
+    }
 
-void findMissingIds(AlignmentI align)
-{
-  String data;
-  ArrayList cachedIds = new ArrayList();
-
-  try
-  {
-    BufferedReader in = new BufferedReader(
-        new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
-
-    while ( (data = in.readLine()) != null)
-    {
-      if (data.indexOf("name") > -1)
-      {
-        String name = parseElement(data, "<name>", null);
-        cachedIds.add(name);
-      }
+    void findMissingIds(AlignmentI align) {
+        String data;
+        ArrayList cachedIds = new ArrayList();
+
+        try {
+            BufferedReader in = new BufferedReader(new FileReader(
+                        jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
+
+            while ((data = in.readLine()) != null) {
+                if (data.indexOf("name") > -1) {
+                    String name = parseElement(data, "<name>", null);
+                    cachedIds.add(name);
+                }
+            }
+        } catch (Exception ex) {
+            ex.printStackTrace();
+        }
+
+        for (int i = 0; i < align.getHeight(); i++)
+            if (!cachedIds.contains(align.getSequenceAt(i).getName())) {
+                unknownSequences.add(align.getSequenceAt(i).getName());
+            }
     }
-  }
-  catch (Exception ex)
-  {   ex.printStackTrace();  }
 
-  for(int i=0; i<align.getHeight(); i++)
-    if( !cachedIds.contains( align.getSequenceAt(i).getName() ) )
-      unknownSequences.add( align.getSequenceAt(i).getName() );
+    void tryLocalCacheFirst(ArrayList ids, AlignmentI align) {
+        ArrayList cacheData = new ArrayList();
 
+        try {
+            BufferedReader in = new BufferedReader(new FileReader(
+                        jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
 
-}
+            // read through cache file, if the cache has sequences we're looking for
+            // add the lines to a new String array, Readthis new array and
+            // make sure we remove the ids from the list to retrieve from EBI
+            String data;
 
-void tryLocalCacheFirst(ArrayList ids, AlignmentI align)
-{
-  ArrayList cacheData = new ArrayList();
-  try{
-    BufferedReader in = new BufferedReader(
-          new FileReader(jalview.bin.Cache.getProperty("UNIPROT_CACHE")));
-
-    // read through cache file, if the cache has sequences we're looking for
-    // add the lines to a new String array, Readthis new array and
-    // 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)
-      {
-        String name = parseElement( data, "<name>" , null) ;
-        if(ids.contains( name ) )
-        {
-          cacheData.add("<entry>");
-          cacheData.add(data);
-          while( data.indexOf("</entry>")==-1)
-          {
-            data = in.readLine();
-            cacheData.add(data);
-          }
-          cacheData.add(data);
-
-          ids.remove( name );
-        }
-      }
-    }
-  }
-  catch(Exception ex){ex.printStackTrace();}
+            while ((data = in.readLine()) != null) {
+                if (data.indexOf("name") > -1) {
+                    String name = parseElement(data, "<name>", null);
 
-  String [] localData = new String[cacheData.size()];
-  cacheData.toArray( localData );
-  if(localData!=null && localData.length>0)
-    ReadUniprotFile(localData, null, align);
-}
+                    if (ids.contains(name)) {
+                        cacheData.add("<entry>");
+                        cacheData.add(data);
 
+                        while (data.indexOf("</entry>") == -1) {
+                            data = in.readLine();
+                            cacheData.add(data);
+                        }
 
-String parseValue(String line, String tag, RandomAccessFile out)
-{
-  if(out!=null)
-    try{  out.writeBytes(line+"\n"); }catch(Exception ex){}
+                        cacheData.add(data);
 
+                        ids.remove(name);
+                    }
+                }
+            }
+        } catch (Exception ex) {
+            ex.printStackTrace();
+        }
 
-  int index = line.indexOf(tag)+tag.length()+1;
-  if(index==tag.length())
-    return "";
+        String[] localData = new String[cacheData.size()];
+        cacheData.toArray(localData);
 
-  return line.substring( index, line.indexOf("\"", index+1) );
-}
+        if ((localData != null) && (localData.length > 0)) {
+            ReadUniprotFile(localData, null, align);
+        }
+    }
+
+    String parseValue(String line, String tag, RandomAccessFile out) {
+        if (out != null) {
+            try {
+                out.writeBytes(line + "\n");
+            } catch (Exception ex) {
+            }
+        }
 
+        int index = line.indexOf(tag) + tag.length() + 1;
 
-String parseElement(String line, String tag, RandomAccessFile out)
-{
-  if (out != null)
-    try
-    {
-      out.writeBytes(line + "\n");
+        if (index == tag.length()) {
+            return "";
+        }
+
+        return line.substring(index, line.indexOf("\"", index + 1));
     }
-    catch (Exception ex)
-    {}
 
-  int index = line.indexOf(tag) + tag.length();
-  return line.substring(index, line.indexOf("</"));
+    String parseElement(String line, String tag, RandomAccessFile out) {
+        if (out != null) {
+            try {
+                out.writeBytes(line + "\n");
+            } catch (Exception ex) {
+            }
+        }
 
-  }
+        int index = line.indexOf(tag) + tag.length();
+
+        return line.substring(index, line.indexOf("</"));
+    }
 }
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index fd82c9e..29a0900 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -16,192 +16,190 @@
 * 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 org.apache.axis.client.*;
-import javax.xml.namespace.QName;
-import java.util.*;
 import jalview.datamodel.*;
+
 import jalview.gui.*;
-import javax.swing.*;
-import java.util.*;
+
+import org.apache.axis.client.*;
+
 import java.awt.*;
 
-public class WSWUBlastClient
-{
-  CutAndPasteTransfer output = new CutAndPasteTransfer();
-  int jobsRunning = 0;
-
-  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++)
-    {
-     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)))
-          nonGapped.append(sequence.getCharAt(n));
-      }
-
-     BlastThread thread = new BlastThread(ids.get(i).toString(),  nonGapped.toString());
-     thread.start();
-     jobsRunning ++;
-     }
-     ImageTwirler thread = new ImageTwirler();
-     thread.start();
-  }
-
-  class ImageTwirler extends Thread
-  {
-    ImageIcon [] imageIcon;
-    int imageIndex = 0;
-    public ImageTwirler()
-    {
-      imageIcon = new ImageIcon[9];
-      for(int i=0; i<9; i++)
-      {
-        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
-        if (url != null)
-          imageIcon[i] = new ImageIcon(url);
-      }
-    }
+import java.util.*;
 
-    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.");
+import javax.swing.*;
 
-        }catch(Exception ex){}
+import javax.xml.namespace.QName;
 
-      }
-    }
-  }
 
+public class WSWUBlastClient {
+    CutAndPasteTransfer output = new CutAndPasteTransfer();
+    int jobsRunning = 0;
 
+    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++) {
+            SequenceI sequence = al.findName(ids.get(i).toString());
+            StringBuffer nonGapped = new StringBuffer();
 
-  class BlastThread extends Thread
-  {
-    String sequence;
-    String seqid;
-    String jobid;
-    boolean jobComplete = false;
+            for (int n = 0; n < sequence.getSequence().length(); n++) {
+                if (!jalview.util.Comparison.isGap(sequence.getCharAt(n))) {
+                    nonGapped.append(sequence.getCharAt(n));
+                }
+            }
+
+            BlastThread thread = new BlastThread(ids.get(i).toString(),
+                    nonGapped.toString());
+            thread.start();
+            jobsRunning++;
+        }
 
-    BlastThread(String id, String sequence)
-    {
-      this.sequence = sequence;
-      seqid = id;
+        ImageTwirler thread = new ImageTwirler();
+        thread.start();
     }
 
-    public void run()
-    {
-      StartJob();
-
-      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[]
-                                               {jobid, "xml"});
-          if(result.indexOf("JOB PENDING")==-1 && result.indexOf("JOB RUNNING")==-1)
-          {
-                parseResult(seqid, result);
-                jobComplete = true;
-                jobsRunning --;
-          }
-          Thread.sleep(5000);
-          // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug
+    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()) {
+            data = st.nextToken();
+
+            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) {
+                    data = st.nextToken();
+
+                    if (data.indexOf("<identity>") > -1) {
+                        int value = Integer.parseInt(data.substring(data.indexOf(
+                                        "<identity>") + 10,
+                                    data.indexOf("</identity>")));
+
+                        if (value >= maxFound) {
+                            maxFound = value;
+                            buffer.append(" " + id2 + " " + value + "%; ");
+                        }
+                    }
+                }
+            }
         }
-        catch (Exception ex)
-        {}
-      }
-    }
 
-    void StartJob()
-    {
-      HashMap params = new HashMap();
-      params.put("database", "uniprot");
-      params.put("sensitivity", "low");
-      params.put("sort", "totalscore");
-      params.put("matrix", "pam10");
-      params.put("program", "blastp");
-      params.put("alignments", "5");
-      params.put("outformat", "xml");
-      params.put("searchtype", "1");
-      byte[] seqbytes = sequence.getBytes();
-
-      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[]
-                                             {params, seqbytes});
-        jobid = result;
-        System.out.println("http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '"+jobid+"'");
-
-      }
-      catch (Exception exp)
-      {
-        System.err.println("WSWUBlastClient error:\n" + exp.toString());
-        exp.printStackTrace();
-      }
+        output.setText(output.getText() + buffer.toString());
     }
-  }
-
-    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() )
-      {
-        data = st.nextToken();
-
-        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)
-          {
-            data = st.nextToken();
-            if(data.indexOf("<identity>")>-1)
-            {
-              int value = Integer.parseInt( data.substring(data.indexOf("<identity>")+10, data.indexOf("</identity>")));
-              if(value>=maxFound)
-              {
-                maxFound = value;
-                buffer.append(" "+ id2 + " " + value+"%; ");
-              }
+
+    class ImageTwirler extends Thread {
+        ImageIcon[] imageIcon;
+        int imageIndex = 0;
+
+        public ImageTwirler() {
+            imageIcon = new ImageIcon[9];
+
+            for (int i = 0; i < 9; i++) {
+                java.net.URL url = getClass().getResource("/images/dna" +
+                        (i + 1) + ".gif");
+
+                if (url != null) {
+                    imageIcon[i] = new ImageIcon(url);
+                }
             }
-          }
+        }
 
+        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) {
+                }
+            }
         }
+    }
 
+    class BlastThread extends Thread {
+        String sequence;
+        String seqid;
+        String jobid;
+        boolean jobComplete = false;
 
-      }
+        BlastThread(String id, String sequence) {
+            this.sequence = sequence;
+            seqid = id;
+        }
 
-      output.setText(output.getText()+buffer.toString());
-    }
+        public void run() {
+            StartJob();
+
+            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[] {
+                                jobid, "xml"
+                            });
 
+                    if ((result.indexOf("JOB PENDING") == -1) &&
+                            (result.indexOf("JOB RUNNING") == -1)) {
+                        parseResult(seqid, result);
+                        jobComplete = true;
+                        jobsRunning--;
+                    }
+
+                    Thread.sleep(5000);
+
+                    // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug
+                } catch (Exception ex) {
+                }
+            }
+        }
+
+        void StartJob() {
+            HashMap params = new HashMap();
+            params.put("database", "uniprot");
+            params.put("sensitivity", "low");
+            params.put("sort", "totalscore");
+            params.put("matrix", "pam10");
+            params.put("program", "blastp");
+            params.put("alignments", "5");
+            params.put("outformat", "xml");
+            params.put("searchtype", "1");
+
+            byte[] seqbytes = sequence.getBytes();
+
+            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[] {
+                            params, seqbytes
+                        });
+                jobid = result;
+                System.out.println(
+                    "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +
+                    jobid + "'");
+            } 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 58c8029..a401b6e 100755
--- a/src/jalview/jbappletgui/GAlignFrame.java
+++ b/src/jalview/jbappletgui/GAlignFrame.java
@@ -16,1110 +16,816 @@
 * 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.jbappletgui;
 
-import java.awt.event.*;
 import java.awt.*;
-
-public class GAlignFrame extends Frame
-{
-  protected MenuBar alignFrameMenuBar = new MenuBar();
-  protected Menu fileMenu = new Menu();
-  protected MenuItem closeMenuItem = new MenuItem();
-  protected Menu editMenu = new Menu();
-  protected Menu viewMenu = new Menu();
-  protected Menu colourMenu = new Menu();
-  protected Menu calculateMenu = new Menu();
-  protected MenuItem selectAllSequenceMenuItem = new MenuItem();
-  protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
-  protected MenuItem invertSequenceMenuItem = new MenuItem();
-  protected MenuItem remove2LeftMenuItem = new MenuItem();
-  protected MenuItem remove2RightMenuItem = new MenuItem();
-  protected MenuItem removeGappedColumnMenuItem = new MenuItem();
-  protected MenuItem removeAllGapsMenuItem = new MenuItem();
-  protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
-  protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
-  protected MenuItem sortPairwiseMenuItem = new MenuItem();
-  protected MenuItem sortIDMenuItem = new MenuItem();
-  protected MenuItem sortGroupMenuItem = new MenuItem();
-  protected MenuItem removeRedundancyMenuItem = new MenuItem();
-  protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
-  protected MenuItem PCAMenuItem = new MenuItem();
-  protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
-  protected MenuItem neighbourTreeMenuItem = new MenuItem();
-  BorderLayout borderLayout1 = new BorderLayout();
-  public Label statusBar = new Label();
-  protected Menu outputTextboxMenu = new Menu();
-  protected MenuItem clustalColour = new MenuItem();
-  protected MenuItem zappoColour = new MenuItem();
-  protected MenuItem taylorColour = new MenuItem();
-  protected MenuItem hydrophobicityColour = new MenuItem();
-  protected MenuItem helixColour = new MenuItem();
-  protected MenuItem strandColour = new MenuItem();
-  protected MenuItem turnColour = new MenuItem();
-  protected MenuItem buriedColour = new MenuItem();
-  protected MenuItem userDefinedColour = new MenuItem();
-  protected MenuItem PIDColour = new MenuItem();
-  protected MenuItem BLOSUM62Colour = new MenuItem();
-  MenuItem njTreeBlosumMenuItem = new MenuItem();
-  MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
-  protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
-  protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
-  MenuItem overviewMenuItem = new MenuItem();
-  protected MenuItem undoMenuItem = new MenuItem();
-  protected MenuItem redoMenuItem = new MenuItem();
-  protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
-  MenuItem noColourmenuItem = new MenuItem();
-  protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
-  protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
-  MenuItem findMenuItem = new MenuItem();
-  Menu searchMenu = new Menu();
-  protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
-  protected MenuItem nucleotideColour = new MenuItem();
-  MenuItem deleteGroups = new MenuItem();
-  MenuItem delete = new MenuItem();
-  MenuItem copy = new MenuItem();
-  MenuItem cut = new MenuItem();
-  Menu Menu1 = new Menu();
-  MenuItem pasteNew = new MenuItem();
-  MenuItem pasteThis = new MenuItem();
-  protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
-  protected MenuItem font = new MenuItem();
-  protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();
-  protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
-  protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
-  protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
-  MenuItem modifyPID = new MenuItem();
-  MenuItem modifyConservation = new MenuItem();
-  protected Menu sortByTreeMenu = new Menu();
-  Menu sort = new Menu();
-  Menu calculate = new Menu();
-  MenuItem inputText = new MenuItem();
-  Menu helpMenu = new Menu();
-  MenuItem documentation = new MenuItem();
-  MenuItem about = new MenuItem();
-  public GAlignFrame()
-  {
-    try
-    {
-      jbInit();
-      setMenuBar(alignFrameMenuBar);
-
-      MenuItem item;
-      // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
-        item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
-        item.addActionListener(new java.awt.event.ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            saveAs_actionPerformed(e);
-          }
-        });
-
-        item = new MenuItem((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.setLabel("File");
-    closeMenuItem.setLabel("Close");
-    closeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        closeMenuItem_actionPerformed(e);
-      }
-    });
-    editMenu.setLabel("Edit");
-    viewMenu.setLabel("View");
-    colourMenu.setLabel("Colour");
-    calculateMenu.setLabel("Calculate");
-    selectAllSequenceMenuItem.setLabel("Select all");
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        selectAllSequenceMenuItem_actionPerformed(e);
-      }
-    });
-    deselectAllSequenceMenuItem.setLabel("Deselect All");
-    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deselectAllSequenceMenuItem_actionPerformed(e);
-      }
-    });
-    invertSequenceMenuItem.setLabel("Invert Selection");
-    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        invertSequenceMenuItem_actionPerformed(e);
-      }
-    });
-    remove2LeftMenuItem.setLabel("Remove Left");
-    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        remove2LeftMenuItem_actionPerformed(e);
-      }
-    });
-    remove2RightMenuItem.setLabel("Remove Right");
-    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        remove2RightMenuItem_actionPerformed(e);
-      }
-    });
-    removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeGappedColumnMenuItem_actionPerformed(e);
-      }
-    });
-    removeAllGapsMenuItem.setLabel("Remove All Gaps");
-    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeAllGapsMenuItem_actionPerformed(e);
-      }
-    });
-    viewBoxesMenuItem.setLabel("Boxes");
-    viewBoxesMenuItem.setState(true);
-    viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        viewBoxesMenuItem_actionPerformed(null);
-      }
-    });
-    viewTextMenuItem.setLabel("Text");
-    viewTextMenuItem.setState(true);
-    viewTextMenuItem.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        viewTextMenuItem_actionPerformed(null);
-      }
-    });
-    sortPairwiseMenuItem.setLabel("by Pairwise Identity");
-    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortPairwiseMenuItem_actionPerformed(e);
-      }
-    });
-    sortIDMenuItem.setLabel("by ID");
-    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortIDMenuItem_actionPerformed(e);
-      }
-    });
-    sortGroupMenuItem.setLabel("by Group");
-    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortGroupMenuItem_actionPerformed(e);
-      }
-    });
-    removeRedundancyMenuItem.setLabel("Remove Redundancy...");
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeRedundancyMenuItem_actionPerformed(e);
-      }
-    });
-    pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pairwiseAlignmentMenuItem_actionPerformed(e);
-      }
-    });
-    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...");
-    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        averageDistanceTreeMenuItem_actionPerformed(e);
-      }
-    });
-    neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");
-    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        neighbourTreeMenuItem_actionPerformed(e);
-      }
-    });
-    alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    statusBar.setBackground(Color.white);
-    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    statusBar.setText("Status bar");
-    outputTextboxMenu.setLabel("Output to Textbox");
-    clustalColour.setLabel("Clustalx");
-
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed(e);
-      }
-    });
-    zappoColour.setLabel("Zappo");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed(e);
-      }
-    });
-    taylorColour.setLabel("Taylor");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed(e);
-      }
-    });
-    hydrophobicityColour.setLabel("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed(e);
-      }
-    });
-    helixColour.setLabel("Helix Propensity");
-    helixColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed(e);
-      }
-    });
-    strandColour.setLabel("Strand Propensity");
-    strandColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed(e);
-      }
-    });
-    turnColour.setLabel("Turn Propensity");
-    turnColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed(e);
-      }
-    });
-    buriedColour.setLabel("Buried Index");
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed(e);
-      }
-    });
-    userDefinedColour.setLabel("User Defined...");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        userDefinedColour_actionPerformed(e);
-      }
-    });
-    PIDColour.setLabel("Percentage Identity");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        PIDColour_actionPerformed(e);
-      }
-    });
-    BLOSUM62Colour.setLabel("BLOSUM62 Score");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        BLOSUM62Colour_actionPerformed(e);
-      }
-    });
-    avDistanceTreeBlosumMenuItem.setLabel("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.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        njTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
-    annotationPanelMenuItem.setActionCommand("");
-    annotationPanelMenuItem.setState(true);
-    annotationPanelMenuItem.setLabel("Show Annotations");
-    annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        annotationPanelMenuItem_actionPerformed(null);
-      }
-    });
-    colourTextMenuItem.setLabel("Colour Text");
-    colourTextMenuItem.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        colourTextMenuItem_actionPerformed(null);
-      }
-    });
-    overviewMenuItem.setLabel("Overview Window...");
-    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        overviewMenuItem_actionPerformed(e);
-      }
-    });
-    undoMenuItem.setEnabled(false);
-    undoMenuItem.setLabel("Undo");
-    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        undoMenuItem_actionPerformed(e);
-      }
-    });
-    redoMenuItem.setEnabled(false);
-    redoMenuItem.setLabel("Redo");
-    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        redoMenuItem_actionPerformed(e);
-      }
-    });
-    conservationMenuItem.setLabel("by Conservation");
-    conservationMenuItem.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        conservationMenuItem_actionPerformed(null);
-      }
-    });
-    noColourmenuItem.setLabel("None");
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        noColourmenuItem_actionPerformed(e);
-      }
-    });
-    wrapMenuItem.setLabel("Wrap");
-    wrapMenuItem.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        wrapMenuItem_actionPerformed(null);
-      }
-    });
-    renderGapsMenuItem.setLabel("Show Gaps");
-    renderGapsMenuItem.setState(true);
-    renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener()
-    {
-
-      public void itemStateChanged(ItemEvent e)
-      {
-
-        renderGapsMenuItem_actionPerformed(null);
-      }
-    });
-    findMenuItem.setLabel("Find...");
-    findMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        findMenuItem_actionPerformed(e);
-      }
-    });
-    searchMenu.setLabel("Search");
-
-    abovePIDThreshold.setLabel("Above Identity Threshold");
-    abovePIDThreshold.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        abovePIDThreshold_actionPerformed(null);
-      }
-    });
-    nucleotideColour.setLabel("Nucleotide");
-    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideColour_actionPerformed(e);
-      }
-    });
-    deleteGroups.setLabel("Undefine Groups");
-    deleteGroups.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deleteGroups_actionPerformed(e);
-      }
-    });
-    copy.setLabel("Copy");
-    copy.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        copy_actionPerformed(e);
-      }
-    });
-    cut.setLabel("Cut");
-    cut.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cut_actionPerformed(e);
-      }
-    });
-    delete.setLabel("Delete");
-    delete.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        delete_actionPerformed(e);
-      }
-    });
-    Menu1.setLabel("Paste");
-    pasteNew.setLabel("To New Alignment");
-    pasteNew.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pasteNew_actionPerformed(e);
-      }
-    });
-    pasteThis.setLabel("Add To This Alignment");
-    pasteThis.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pasteThis_actionPerformed(e);
-      }
-    });
-    applyToAllGroups.setLabel("Apply Colour To All Groups");
-    applyToAllGroups.setState(true);
-    applyToAllGroups.addItemListener(new java.awt.event.ItemListener()
-   {
-     public void itemStateChanged(ItemEvent e)
-     {
-        applyToAllGroups_actionPerformed(null);
-      }
-    });
-    font.setLabel("Font...");
-    font.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        font_actionPerformed(e);
-      }
-    });
-    fullSeqId.setLabel("Show Full Sequence ID");
-    fullSeqId.setState(true);
-    fullSeqId.addItemListener(new java.awt.event.ItemListener()
-    {
-
-      public void itemStateChanged(ItemEvent e)
-      {
-        fullSeqId_actionPerformed(null);
-      }
-    });
-    scaleAbove.setLabel("Scale Above");
-    scaleAbove.setState(true);
-    scaleAbove.addItemListener(new java.awt.event.ItemListener()
-    {
-
-      public void itemStateChanged(ItemEvent e)
-      {
-
-        scaleAbove_actionPerformed(null);
-      }
-    });
-    scaleLeft.setEnabled(false);
-    scaleLeft.setState(true);
-    scaleLeft.setLabel("Scale Left");
-    scaleLeft.addItemListener(new java.awt.event.ItemListener()
-    {
-
-      public void itemStateChanged(ItemEvent e)
-      {
-
-        scaleLeft_actionPerformed(null);
-      }
-    });
-    scaleRight.setEnabled(false);
-    scaleRight.setState(true);
-    scaleRight.setLabel("Scale Right");
-    scaleRight.addItemListener(new java.awt.event.ItemListener()
-    {
-
-      public void itemStateChanged(ItemEvent e)
-      {
-
-        scaleRight_actionPerformed(null);
-      }
-    });
-    modifyPID.setLabel("Modify Identity Threshold...");
-    modifyPID.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyPID_actionPerformed(e);
-      }
-    });
-    modifyConservation.setLabel("Modify Conservation Threshold...");
-    modifyConservation.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyConservation_actionPerformed(e);
-      }
-    });
-    sortByTreeMenu.setLabel("By Tree Order");
-    sort.setLabel("Sort");
-    calculate.setLabel("Calculate Tree");
-    inputText.setLabel("Input from textbox");
-    inputText.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        inputText_actionPerformed(e);
-      }
-    });
-
-    helpMenu.setLabel("Help");
-    documentation.setLabel("Documentation");
-    documentation.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        documentation_actionPerformed(e);
-      }
-    });
-
-    about.setLabel("About...");
-    about.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        about_actionPerformed(e);
-      }
-    });
-
-    alignFrameMenuBar.add(fileMenu);
-    alignFrameMenuBar.add(editMenu);
-    alignFrameMenuBar.add(searchMenu);
-    alignFrameMenuBar.add(viewMenu);
-    alignFrameMenuBar.add(colourMenu);
-    alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(helpMenu);
-    fileMenu.add(inputText);
-    fileMenu.add(outputTextboxMenu);
-    fileMenu.addSeparator();
-    fileMenu.add(closeMenuItem);
-    editMenu.add(undoMenuItem);
-    editMenu.add(redoMenuItem);
-    editMenu.add(cut);
-    editMenu.add(copy);
-    editMenu.add(Menu1);
-    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);
-    searchMenu.add(findMenuItem);
-    viewMenu.add(font);
-    viewMenu.addSeparator();
-    viewMenu.add(wrapMenuItem);
-    viewMenu.add(scaleAbove);
-    viewMenu.add(scaleLeft);
-    viewMenu.add(scaleRight);
-    viewMenu.addSeparator();
-    viewMenu.add(fullSeqId);
-    viewMenu.add(viewBoxesMenuItem);
-    viewMenu.add(viewTextMenuItem);
-    viewMenu.add(colourTextMenuItem);
-    viewMenu.add(renderGapsMenuItem);
-    viewMenu.add(annotationPanelMenuItem);
-    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);
-    this.add(statusBar, BorderLayout.SOUTH);
-    Menu1.add(pasteNew);
-    Menu1.add(pasteThis);
-    sort.add(sortIDMenuItem);
-    sort.add(sortByTreeMenu);
-    sort.add(sortGroupMenuItem);
-    sort.add(sortPairwiseMenuItem);
-    calculate.add(averageDistanceTreeMenuItem);
-    calculate.add(neighbourTreeMenuItem);
-    calculate.add(avDistanceTreeBlosumMenuItem);
-    calculate.add(njTreeBlosumMenuItem);
-    helpMenu.add(documentation);
-    helpMenu.add(about);
-  }
-
-  protected void saveAs_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  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 averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-
-
-  protected void clustalColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void zappoColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void taylorColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void helixColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void strandColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void turnColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void buriedColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
+import java.awt.event.*;
 
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
+public class GAlignFrame extends Frame {
+    protected MenuBar alignFrameMenuBar = new MenuBar();
+    protected Menu fileMenu = new Menu();
+    protected MenuItem closeMenuItem = new MenuItem();
+    protected Menu editMenu = new Menu();
+    protected Menu viewMenu = new Menu();
+    protected Menu colourMenu = new Menu();
+    protected Menu calculateMenu = new Menu();
+    protected MenuItem selectAllSequenceMenuItem = new MenuItem();
+    protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
+    protected MenuItem invertSequenceMenuItem = new MenuItem();
+    protected MenuItem remove2LeftMenuItem = new MenuItem();
+    protected MenuItem remove2RightMenuItem = new MenuItem();
+    protected MenuItem removeGappedColumnMenuItem = new MenuItem();
+    protected MenuItem removeAllGapsMenuItem = new MenuItem();
+    protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+    protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+    protected MenuItem sortPairwiseMenuItem = new MenuItem();
+    protected MenuItem sortIDMenuItem = new MenuItem();
+    protected MenuItem sortGroupMenuItem = new MenuItem();
+    protected MenuItem removeRedundancyMenuItem = new MenuItem();
+    protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+    protected MenuItem PCAMenuItem = new MenuItem();
+    protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
+    protected MenuItem neighbourTreeMenuItem = new MenuItem();
+    BorderLayout borderLayout1 = new BorderLayout();
+    public Label statusBar = new Label();
+    protected Menu outputTextboxMenu = new Menu();
+    protected MenuItem clustalColour = new MenuItem();
+    protected MenuItem zappoColour = new MenuItem();
+    protected MenuItem taylorColour = new MenuItem();
+    protected MenuItem hydrophobicityColour = new MenuItem();
+    protected MenuItem helixColour = new MenuItem();
+    protected MenuItem strandColour = new MenuItem();
+    protected MenuItem turnColour = new MenuItem();
+    protected MenuItem buriedColour = new MenuItem();
+    protected MenuItem userDefinedColour = new MenuItem();
+    protected MenuItem PIDColour = new MenuItem();
+    protected MenuItem BLOSUM62Colour = new MenuItem();
+    MenuItem njTreeBlosumMenuItem = new MenuItem();
+    MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
+    protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
+    protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+    MenuItem overviewMenuItem = new MenuItem();
+    protected MenuItem undoMenuItem = new MenuItem();
+    protected MenuItem redoMenuItem = new MenuItem();
+    protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+    MenuItem noColourmenuItem = new MenuItem();
+    protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+    protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+    MenuItem findMenuItem = new MenuItem();
+    Menu searchMenu = new Menu();
+    protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+    protected MenuItem nucleotideColour = new MenuItem();
+    MenuItem deleteGroups = new MenuItem();
+    MenuItem delete = new MenuItem();
+    MenuItem copy = new MenuItem();
+    MenuItem cut = new MenuItem();
+    Menu Menu1 = new Menu();
+    MenuItem pasteNew = new MenuItem();
+    MenuItem pasteThis = new MenuItem();
+    protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+    protected MenuItem font = new MenuItem();
+    protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();
+    protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+    protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+    protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+    MenuItem modifyPID = new MenuItem();
+    MenuItem modifyConservation = new MenuItem();
+    protected Menu sortByTreeMenu = new Menu();
+    Menu sort = new Menu();
+    Menu calculate = new Menu();
+    MenuItem inputText = new MenuItem();
+    Menu helpMenu = new Menu();
+    MenuItem documentation = new MenuItem();
+    MenuItem about = new MenuItem();
+
+    public GAlignFrame() {
+        try {
+            jbInit();
+            setMenuBar(alignFrameMenuBar);
+
+            MenuItem item;
+
+            // dynamically fill save as menu with available formats
+            for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
+                item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(
+                            i));
+                item.addActionListener(new java.awt.event.ActionListener() {
+                        public void actionPerformed(ActionEvent e) {
+                            saveAs_actionPerformed(e);
+                        }
+                    });
+
+                item = new MenuItem((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.setLabel("File");
+        closeMenuItem.setLabel("Close");
+        closeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    closeMenuItem_actionPerformed(e);
+                }
+            });
+        editMenu.setLabel("Edit");
+        viewMenu.setLabel("View");
+        colourMenu.setLabel("Colour");
+        calculateMenu.setLabel("Calculate");
+        selectAllSequenceMenuItem.setLabel("Select all");
+        selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    selectAllSequenceMenuItem_actionPerformed(e);
+                }
+            });
+        deselectAllSequenceMenuItem.setLabel("Deselect All");
+        deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    deselectAllSequenceMenuItem_actionPerformed(e);
+                }
+            });
+        invertSequenceMenuItem.setLabel("Invert Selection");
+        invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    invertSequenceMenuItem_actionPerformed(e);
+                }
+            });
+        remove2LeftMenuItem.setLabel("Remove Left");
+        remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    remove2LeftMenuItem_actionPerformed(e);
+                }
+            });
+        remove2RightMenuItem.setLabel("Remove Right");
+        remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    remove2RightMenuItem_actionPerformed(e);
+                }
+            });
+        removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
+        removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    removeGappedColumnMenuItem_actionPerformed(e);
+                }
+            });
+        removeAllGapsMenuItem.setLabel("Remove All Gaps");
+        removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    removeAllGapsMenuItem_actionPerformed(e);
+                }
+            });
+        viewBoxesMenuItem.setLabel("Boxes");
+        viewBoxesMenuItem.setState(true);
+        viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    viewBoxesMenuItem_actionPerformed(null);
+                }
+            });
+        viewTextMenuItem.setLabel("Text");
+        viewTextMenuItem.setState(true);
+        viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    viewTextMenuItem_actionPerformed(null);
+                }
+            });
+        sortPairwiseMenuItem.setLabel("by Pairwise Identity");
+        sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    sortPairwiseMenuItem_actionPerformed(e);
+                }
+            });
+        sortIDMenuItem.setLabel("by ID");
+        sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    sortIDMenuItem_actionPerformed(e);
+                }
+            });
+        sortGroupMenuItem.setLabel("by Group");
+        sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    sortGroupMenuItem_actionPerformed(e);
+                }
+            });
+        removeRedundancyMenuItem.setLabel("Remove Redundancy...");
+        removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    removeRedundancyMenuItem_actionPerformed(e);
+                }
+            });
+        pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
+        pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    pairwiseAlignmentMenuItem_actionPerformed(e);
+                }
+            });
+        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...");
+        averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    averageDistanceTreeMenuItem_actionPerformed(e);
+                }
+            });
+        neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");
+        neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    neighbourTreeMenuItem_actionPerformed(e);
+                }
+            });
+        alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+        statusBar.setBackground(Color.white);
+        statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+        statusBar.setText("Status bar");
+        outputTextboxMenu.setLabel("Output to Textbox");
+        clustalColour.setLabel("Clustalx");
+
+        clustalColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    clustalColour_actionPerformed(e);
+                }
+            });
+        zappoColour.setLabel("Zappo");
+        zappoColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    zappoColour_actionPerformed(e);
+                }
+            });
+        taylorColour.setLabel("Taylor");
+        taylorColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    taylorColour_actionPerformed(e);
+                }
+            });
+        hydrophobicityColour.setLabel("Hydrophobicity");
+        hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    hydrophobicityColour_actionPerformed(e);
+                }
+            });
+        helixColour.setLabel("Helix Propensity");
+        helixColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    helixColour_actionPerformed(e);
+                }
+            });
+        strandColour.setLabel("Strand Propensity");
+        strandColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    strandColour_actionPerformed(e);
+                }
+            });
+        turnColour.setLabel("Turn Propensity");
+        turnColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    turnColour_actionPerformed(e);
+                }
+            });
+        buriedColour.setLabel("Buried Index");
+        buriedColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    buriedColour_actionPerformed(e);
+                }
+            });
+        userDefinedColour.setLabel("User Defined...");
+        userDefinedColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    userDefinedColour_actionPerformed(e);
+                }
+            });
+        PIDColour.setLabel("Percentage Identity");
+        PIDColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    PIDColour_actionPerformed(e);
+                }
+            });
+        BLOSUM62Colour.setLabel("BLOSUM62 Score");
+        BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    BLOSUM62Colour_actionPerformed(e);
+                }
+            });
+        avDistanceTreeBlosumMenuItem.setLabel(
+            "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.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    njTreeBlosumMenuItem_actionPerformed(e);
+                }
+            });
+        annotationPanelMenuItem.setActionCommand("");
+        annotationPanelMenuItem.setState(true);
+        annotationPanelMenuItem.setLabel("Show Annotations");
+        annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    annotationPanelMenuItem_actionPerformed(null);
+                }
+            });
+        colourTextMenuItem.setLabel("Colour Text");
+        colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    colourTextMenuItem_actionPerformed(null);
+                }
+            });
+        overviewMenuItem.setLabel("Overview Window...");
+        overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    overviewMenuItem_actionPerformed(e);
+                }
+            });
+        undoMenuItem.setEnabled(false);
+        undoMenuItem.setLabel("Undo");
+        undoMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    undoMenuItem_actionPerformed(e);
+                }
+            });
+        redoMenuItem.setEnabled(false);
+        redoMenuItem.setLabel("Redo");
+        redoMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    redoMenuItem_actionPerformed(e);
+                }
+            });
+        conservationMenuItem.setLabel("by Conservation");
+        conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    conservationMenuItem_actionPerformed(null);
+                }
+            });
+        noColourmenuItem.setLabel("None");
+        noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    noColourmenuItem_actionPerformed(e);
+                }
+            });
+        wrapMenuItem.setLabel("Wrap");
+        wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    wrapMenuItem_actionPerformed(null);
+                }
+            });
+        renderGapsMenuItem.setLabel("Show Gaps");
+        renderGapsMenuItem.setState(true);
+        renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    renderGapsMenuItem_actionPerformed(null);
+                }
+            });
+        findMenuItem.setLabel("Find...");
+        findMenuItem.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    findMenuItem_actionPerformed(e);
+                }
+            });
+        searchMenu.setLabel("Search");
+
+        abovePIDThreshold.setLabel("Above Identity Threshold");
+        abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    abovePIDThreshold_actionPerformed(null);
+                }
+            });
+        nucleotideColour.setLabel("Nucleotide");
+        nucleotideColour.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    nucleotideColour_actionPerformed(e);
+                }
+            });
+        deleteGroups.setLabel("Undefine Groups");
+        deleteGroups.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    deleteGroups_actionPerformed(e);
+                }
+            });
+        copy.setLabel("Copy");
+        copy.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    copy_actionPerformed(e);
+                }
+            });
+        cut.setLabel("Cut");
+        cut.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    cut_actionPerformed(e);
+                }
+            });
+        delete.setLabel("Delete");
+        delete.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    delete_actionPerformed(e);
+                }
+            });
+        Menu1.setLabel("Paste");
+        pasteNew.setLabel("To New Alignment");
+        pasteNew.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    pasteNew_actionPerformed(e);
+                }
+            });
+        pasteThis.setLabel("Add To This Alignment");
+        pasteThis.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    pasteThis_actionPerformed(e);
+                }
+            });
+        applyToAllGroups.setLabel("Apply Colour To All Groups");
+        applyToAllGroups.setState(true);
+        applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    applyToAllGroups_actionPerformed(null);
+                }
+            });
+        font.setLabel("Font...");
+        font.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    font_actionPerformed(e);
+                }
+            });
+        fullSeqId.setLabel("Show Full Sequence ID");
+        fullSeqId.setState(true);
+        fullSeqId.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    fullSeqId_actionPerformed(null);
+                }
+            });
+        scaleAbove.setLabel("Scale Above");
+        scaleAbove.setState(true);
+        scaleAbove.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    scaleAbove_actionPerformed(null);
+                }
+            });
+        scaleLeft.setEnabled(false);
+        scaleLeft.setState(true);
+        scaleLeft.setLabel("Scale Left");
+        scaleLeft.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    scaleLeft_actionPerformed(null);
+                }
+            });
+        scaleRight.setEnabled(false);
+        scaleRight.setState(true);
+        scaleRight.setLabel("Scale Right");
+        scaleRight.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    scaleRight_actionPerformed(null);
+                }
+            });
+        modifyPID.setLabel("Modify Identity Threshold...");
+        modifyPID.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    modifyPID_actionPerformed(e);
+                }
+            });
+        modifyConservation.setLabel("Modify Conservation Threshold...");
+        modifyConservation.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    modifyConservation_actionPerformed(e);
+                }
+            });
+        sortByTreeMenu.setLabel("By Tree Order");
+        sort.setLabel("Sort");
+        calculate.setLabel("Calculate Tree");
+        inputText.setLabel("Input from textbox");
+        inputText.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    inputText_actionPerformed(e);
+                }
+            });
+
+        helpMenu.setLabel("Help");
+        documentation.setLabel("Documentation");
+        documentation.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    documentation_actionPerformed(e);
+                }
+            });
+
+        about.setLabel("About...");
+        about.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    about_actionPerformed(e);
+                }
+            });
+
+        alignFrameMenuBar.add(fileMenu);
+        alignFrameMenuBar.add(editMenu);
+        alignFrameMenuBar.add(searchMenu);
+        alignFrameMenuBar.add(viewMenu);
+        alignFrameMenuBar.add(colourMenu);
+        alignFrameMenuBar.add(calculateMenu);
+        alignFrameMenuBar.add(helpMenu);
+        fileMenu.add(inputText);
+        fileMenu.add(outputTextboxMenu);
+        fileMenu.addSeparator();
+        fileMenu.add(closeMenuItem);
+        editMenu.add(undoMenuItem);
+        editMenu.add(redoMenuItem);
+        editMenu.add(cut);
+        editMenu.add(copy);
+        editMenu.add(Menu1);
+        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);
+        searchMenu.add(findMenuItem);
+        viewMenu.add(font);
+        viewMenu.addSeparator();
+        viewMenu.add(wrapMenuItem);
+        viewMenu.add(scaleAbove);
+        viewMenu.add(scaleLeft);
+        viewMenu.add(scaleRight);
+        viewMenu.addSeparator();
+        viewMenu.add(fullSeqId);
+        viewMenu.add(viewBoxesMenuItem);
+        viewMenu.add(viewTextMenuItem);
+        viewMenu.add(colourTextMenuItem);
+        viewMenu.add(renderGapsMenuItem);
+        viewMenu.add(annotationPanelMenuItem);
+        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);
+        this.add(statusBar, BorderLayout.SOUTH);
+        Menu1.add(pasteNew);
+        Menu1.add(pasteThis);
+        sort.add(sortIDMenuItem);
+        sort.add(sortByTreeMenu);
+        sort.add(sortGroupMenuItem);
+        sort.add(sortPairwiseMenuItem);
+        calculate.add(averageDistanceTreeMenuItem);
+        calculate.add(neighbourTreeMenuItem);
+        calculate.add(avDistanceTreeBlosumMenuItem);
+        calculate.add(njTreeBlosumMenuItem);
+        helpMenu.add(documentation);
+        helpMenu.add(about);
+    }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
-  {
+    protected void saveAs_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void outputText_actionPerformed(ActionEvent e) {
+    }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
+    protected void htmlMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void closeMenuItem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void redoMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void undoMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void printMenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void wrapMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void findMenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void viewTextMenuItem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void colourTextMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+    protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void overviewMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
-  {
+    protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void sortIDMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void nucleotideColour_actionPerformed(ActionEvent e)
-  {
+    protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void deleteGroups_actionPerformed(ActionEvent e)
-  {
+    protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void PCAMenuItem_actionPerformed(ActionEvent e) {
+    }
 
- protected void copy_actionPerformed(ActionEvent e)
-  {
+    protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void cut_actionPerformed(ActionEvent e)
-  {
+    protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void delete_actionPerformed(ActionEvent e)
-  {
+    protected void clustalColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void zappoColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void pasteNew_actionPerformed(ActionEvent e)
-  {
+    protected void taylorColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void hydrophobicityColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void pasteThis_actionPerformed(ActionEvent e)
-  {
+    protected void helixColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void strandColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
-  {
+    protected void turnColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void buriedColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void createPNG_actionPerformed(ActionEvent e)
-  {
+    protected void userDefinedColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void PIDColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void font_actionPerformed(ActionEvent e)
-  {
+    protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void noColourmenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
-  {
+    protected void conservationMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void printMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void epsFile_actionPerformed(ActionEvent e)
-  {
+    protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void findMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {
+    }
 
-  protected void jpred_actionPerformed(ActionEvent e)
-  {
+    protected void nucleotideColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void deleteGroups_actionPerformed(ActionEvent e) {
+    }
 
-  protected void scaleAbove_actionPerformed(ActionEvent e)
-  {
+    protected void copy_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void cut_actionPerformed(ActionEvent e) {
+    }
 
-  protected void scaleLeft_actionPerformed(ActionEvent e)
-  {
+    protected void delete_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void pasteNew_actionPerformed(ActionEvent e) {
+    }
 
-  protected void scaleRight_actionPerformed(ActionEvent e)
-  {
+    protected void pasteThis_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void applyToAllGroups_actionPerformed(ActionEvent e) {
+    }
 
-  protected void modifyPID_actionPerformed(ActionEvent e)
-  {
+    protected void createPNG_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void font_actionPerformed(ActionEvent e) {
+    }
 
-  protected void modifyConservation_actionPerformed(ActionEvent e)
-  {
+    protected void fullSeqId_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void epsFile_actionPerformed(ActionEvent e) {
+    }
 
-  protected void preferences_actionPerformed(ActionEvent e)
-  {
+    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void jpred_actionPerformed(ActionEvent e) {
+    }
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
+    protected void scaleAbove_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void scaleLeft_actionPerformed(ActionEvent e) {
+    }
 
-  protected void inputText_actionPerformed(ActionEvent e) {
+    protected void scaleRight_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void modifyPID_actionPerformed(ActionEvent e) {
+    }
 
-  protected void documentation_actionPerformed(ActionEvent e) {
+    protected void modifyConservation_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void preferences_actionPerformed(ActionEvent e) {
+    }
 
-  protected void about_actionPerformed(ActionEvent e) {
+    protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void inputText_actionPerformed(ActionEvent e) {
+    }
 
+    protected void documentation_actionPerformed(ActionEvent e) {
+    }
 
+    protected void about_actionPerformed(ActionEvent e) {
+    }
 }
-
diff --git a/src/jalview/jbappletgui/GAlignmentPanel.java b/src/jalview/jbappletgui/GAlignmentPanel.java
index 272e8df..683c9c1 100755
--- a/src/jalview/jbappletgui/GAlignmentPanel.java
+++ b/src/jalview/jbappletgui/GAlignmentPanel.java
@@ -16,85 +16,85 @@
 * 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.jbappletgui;
 
 import java.awt.*;
 
-public class GAlignmentPanel extends Panel
-{
-  protected Panel sequenceHolderPanel = new Panel();
-  protected Scrollbar vscroll = new Scrollbar();
-  protected  Scrollbar hscroll = new Scrollbar();
-  protected Panel seqPanelHolder = new Panel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout3 = new BorderLayout();
-  protected Panel scalePanelHolder = new Panel();
-  protected Panel idPanelHolder = new Panel();
-  BorderLayout borderLayout5 = new BorderLayout();
-  protected Panel idSpaceFillerPanel1 = new Panel();
-  public Panel annotationSpaceFillerHolder = new Panel();
-  BorderLayout borderLayout6 = new BorderLayout();
-  BorderLayout borderLayout7 = new BorderLayout();
-  Panel hscrollHolder = new Panel();
-  BorderLayout borderLayout10 = new BorderLayout();
-  protected Panel hscrollFillerPanel = new Panel();
-  BorderLayout borderLayout11 = new BorderLayout();
-  public Panel annotationScroller = new Panel();
-  BorderLayout borderLayout4 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
 
-  public GAlignmentPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
+public class GAlignmentPanel extends Panel {
+    protected Panel sequenceHolderPanel = new Panel();
+    protected Scrollbar vscroll = new Scrollbar();
+    protected Scrollbar hscroll = new Scrollbar();
+    protected Panel seqPanelHolder = new Panel();
+    BorderLayout borderLayout1 = new BorderLayout();
+    BorderLayout borderLayout3 = new BorderLayout();
+    protected Panel scalePanelHolder = new Panel();
+    protected Panel idPanelHolder = new Panel();
+    BorderLayout borderLayout5 = new BorderLayout();
+    protected Panel idSpaceFillerPanel1 = new Panel();
+    public Panel annotationSpaceFillerHolder = new Panel();
+    BorderLayout borderLayout6 = new BorderLayout();
+    BorderLayout borderLayout7 = new BorderLayout();
+    Panel hscrollHolder = new Panel();
+    BorderLayout borderLayout10 = new BorderLayout();
+    protected Panel hscrollFillerPanel = new Panel();
+    BorderLayout borderLayout11 = new BorderLayout();
+    public Panel annotationScroller = new Panel();
+    BorderLayout borderLayout4 = new BorderLayout();
+    BorderLayout borderLayout2 = new BorderLayout();
+
+    public GAlignmentPanel() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
     }
-  }
-  private void jbInit() throws Exception
-  {
-  //  idPanelHolder.setPreferredSize(new Dimension(70, 10));
-    this.setLayout(borderLayout7);
- //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
-    sequenceHolderPanel.setLayout(borderLayout3);
-    seqPanelHolder.setLayout(borderLayout1);
-    scalePanelHolder.setBackground(Color.white);
- // 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(Scrollbar.HORIZONTAL);
-    hscrollHolder.setLayout(borderLayout10);
-    hscrollFillerPanel.setBackground(Color.white);
-  //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
-    hscrollHolder.setBackground(Color.white);
- //    annotationScroller.setPreferredSize(new Dimension(10, 80));
-  //  this.setPreferredSize(new Dimension(220, 166));
-    seqPanelHolder.setBackground(Color.white);
-    idPanelHolder.setBackground(Color.white);
-    annotationScroller.setLayout(borderLayout2);
-    sequenceHolderPanel.add(scalePanelHolder,  BorderLayout.NORTH);
-    sequenceHolderPanel.add(seqPanelHolder,  BorderLayout.CENTER);
-    seqPanelHolder.add(vscroll, BorderLayout.EAST);
-    sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
-  //  Panel3.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);
-  }
 
+    private void jbInit() throws Exception {
+        //  idPanelHolder.setPreferredSize(new Dimension(70, 10));
+        this.setLayout(borderLayout7);
+
+        //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+        sequenceHolderPanel.setLayout(borderLayout3);
+        seqPanelHolder.setLayout(borderLayout1);
+        scalePanelHolder.setBackground(Color.white);
+
+        // 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(Scrollbar.HORIZONTAL);
+        hscrollHolder.setLayout(borderLayout10);
+        hscrollFillerPanel.setBackground(Color.white);
+
+        //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+        hscrollHolder.setBackground(Color.white);
+
+        //    annotationScroller.setPreferredSize(new Dimension(10, 80));
+        //  this.setPreferredSize(new Dimension(220, 166));
+        seqPanelHolder.setBackground(Color.white);
+        idPanelHolder.setBackground(Color.white);
+        annotationScroller.setLayout(borderLayout2);
+        sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
+        sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
+        seqPanelHolder.add(vscroll, BorderLayout.EAST);
+        sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
+
+        //  Panel3.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);
+    }
 }
diff --git a/src/jalview/jbappletgui/GCutAndPasteTransfer.java b/src/jalview/jbappletgui/GCutAndPasteTransfer.java
index 33fe5a6..df702fd 100755
--- a/src/jalview/jbappletgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbappletgui/GCutAndPasteTransfer.java
@@ -16,77 +16,63 @@
 * 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.jbappletgui;
 
 import java.awt.*;
 import java.awt.event.*;
 
 
-public class GCutAndPasteTransfer extends Panel
-{
-  protected TextArea textarea = new TextArea();
-  Button ok = new Button();
-  Button cancel = new Button();
-  protected Panel buttonPanel = new Panel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  public GCutAndPasteTransfer()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
-    }
-
-  }
-  private void jbInit() throws Exception
-  {
-    textarea.setFont(new java.awt.Font("Verdana", 0, 12));
-    textarea.setText("Paste your alignment file here");
-    textarea.addMouseListener(new java.awt.event.MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        textarea_mousePressed(e);
-      }
-    });
-    this.setLayout(borderLayout1);
-    ok.setLabel("OK");
-    ok.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setLabel("Cancel");
-    cancel.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
-        cancel_actionPerformed(e);
-      }
-    });
-    this.add(buttonPanel, BorderLayout.SOUTH);
-    buttonPanel.add(ok, null);
-    buttonPanel.add(cancel, null);
-    this.add(textarea, java.awt.BorderLayout.CENTER);
-  }
-
-
-
+public class GCutAndPasteTransfer extends Panel {
+    protected TextArea textarea = new TextArea();
+    Button ok = new Button();
+    Button cancel = new Button();
+    protected Panel buttonPanel = new Panel();
+    BorderLayout borderLayout1 = new BorderLayout();
 
-  void textarea_mousePressed(MouseEvent e)
-  {
-    if(textarea.getText().equals("Paste your alignment file here"))
-      textarea.setText("");
-  }
-
-  protected void ok_actionPerformed(ActionEvent e) {
+    public GCutAndPasteTransfer() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
 
-  }
+    private void jbInit() throws Exception {
+        textarea.setFont(new java.awt.Font("Verdana", 0, 12));
+        textarea.setText("Paste your alignment file here");
+        textarea.addMouseListener(new java.awt.event.MouseAdapter() {
+                public void mousePressed(MouseEvent e) {
+                    textarea_mousePressed(e);
+                }
+            });
+        this.setLayout(borderLayout1);
+        ok.setLabel("OK");
+        ok.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    ok_actionPerformed(e);
+                }
+            });
+        cancel.setLabel("Cancel");
+        cancel.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    cancel_actionPerformed(e);
+                }
+            });
+        this.add(buttonPanel, BorderLayout.SOUTH);
+        buttonPanel.add(ok, null);
+        buttonPanel.add(cancel, null);
+        this.add(textarea, java.awt.BorderLayout.CENTER);
+    }
 
-  protected void cancel_actionPerformed(ActionEvent e) {
+    void textarea_mousePressed(MouseEvent e) {
+        if (textarea.getText().equals("Paste your alignment file here")) {
+            textarea.setText("");
+        }
+    }
 
-  }
+    protected void ok_actionPerformed(ActionEvent e) {
+    }
 
+    protected void cancel_actionPerformed(ActionEvent e) {
+    }
 }
diff --git a/src/jalview/jbappletgui/GFinder.java b/src/jalview/jbappletgui/GFinder.java
index 283b28d..434c8ea 100755
--- a/src/jalview/jbappletgui/GFinder.java
+++ b/src/jalview/jbappletgui/GFinder.java
@@ -16,123 +16,96 @@
 * 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.jbappletgui;
 
 import java.awt.*;
 import java.awt.event.*;
 
 
-public class GFinder extends Panel
-{
-  Label jLabel1 = new Label();
-  protected TextField textfield = new TextField();
-  protected Button findAll = new Button();
-  protected Button findNext = new Button();
-  Panel jPanel1 = new Panel();
-  GridLayout gridLayout1 = new GridLayout();
-  protected Button createNewGroup = new Button();
-
-  public GFinder()
-  {
-    try
-    {
-      jbInit();
+public class GFinder extends Panel {
+    Label jLabel1 = new Label();
+    protected TextField textfield = new TextField();
+    protected Button findAll = new Button();
+    protected Button findNext = new Button();
+    Panel jPanel1 = new Panel();
+    GridLayout gridLayout1 = new GridLayout();
+    protected Button createNewGroup = new Button();
+
+    public GFinder() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
     }
-    catch(Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-  private void jbInit() throws Exception
-  {
-    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
-    jLabel1.setText("Find");
-    jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
-    this.setLayout(null);
-    textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    textfield.setText("");
-    textfield.setBounds(new Rectangle(40, 27, 133, 21));
-    textfield.addKeyListener(new java.awt.event.KeyAdapter()
-    {
-      public void keyTyped(KeyEvent e)
-      {
-        textfield_keyTyped(e);
-      }
-    });
-    textfield.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        textfield_actionPerformed(e);
-      }
-    });
-    findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    findAll.setLabel("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", Font.PLAIN, 10));
-    findNext.setLabel("Find Next");
-    findNext.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        findNext_actionPerformed(e);
-      }
-    });
-    jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
-    jPanel1.setLayout(gridLayout1);
-    gridLayout1.setHgap(0);
-    gridLayout1.setRows(3);
-    gridLayout1.setVgap(2);
-    createNewGroup.setEnabled(false);
-    createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    createNewGroup.setLabel("Create new group");
-    createNewGroup.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        createNewGroup_actionPerformed(e);
-      }
-    });
-    jPanel1.add(findNext, null);
-    jPanel1.add(findAll, null);
-    jPanel1.add(createNewGroup, null);
-    this.add(textfield, null);
-    this.add(jLabel1, null);
-    this.add(jPanel1, null);
-  }
-
-  protected void findNext_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void findAll_actionPerformed(ActionEvent e)
-  {
-
-  }
 
+    private void jbInit() throws Exception {
+        jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+        jLabel1.setText("Find");
+        jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
+        this.setLayout(null);
+        textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+        textfield.setText("");
+        textfield.setBounds(new Rectangle(40, 27, 133, 21));
+        textfield.addKeyListener(new java.awt.event.KeyAdapter() {
+                public void keyTyped(KeyEvent e) {
+                    textfield_keyTyped(e);
+                }
+            });
+        textfield.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    textfield_actionPerformed(e);
+                }
+            });
+        findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+        findAll.setLabel("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", Font.PLAIN, 10));
+        findNext.setLabel("Find Next");
+        findNext.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    findNext_actionPerformed(e);
+                }
+            });
+        jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
+        jPanel1.setLayout(gridLayout1);
+        gridLayout1.setHgap(0);
+        gridLayout1.setRows(3);
+        gridLayout1.setVgap(2);
+        createNewGroup.setEnabled(false);
+        createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+        createNewGroup.setLabel("Create new group");
+        createNewGroup.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    createNewGroup_actionPerformed(e);
+                }
+            });
+        jPanel1.add(findNext, null);
+        jPanel1.add(findAll, null);
+        jPanel1.add(createNewGroup, null);
+        this.add(textfield, null);
+        this.add(jLabel1, null);
+        this.add(jPanel1, null);
+    }
 
-  protected void textfield_actionPerformed(ActionEvent e)
-  {
-
-  }
+    protected void findNext_actionPerformed(ActionEvent e) {
+    }
 
-  void textfield_keyTyped(KeyEvent e)
-  {
-    findNext.setEnabled(true);
-  }
+    protected void findAll_actionPerformed(ActionEvent e) {
+    }
 
-  public void createNewGroup_actionPerformed(ActionEvent e)
-  {
+    protected void textfield_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    void textfield_keyTyped(KeyEvent e) {
+        findNext.setEnabled(true);
+    }
 
+    public void createNewGroup_actionPerformed(ActionEvent e) {
+    }
 }
diff --git a/src/jalview/jbappletgui/GFontChooser.java b/src/jalview/jbappletgui/GFontChooser.java
index 1c087c5..794dbbb 100755
--- a/src/jalview/jbappletgui/GFontChooser.java
+++ b/src/jalview/jbappletgui/GFontChooser.java
@@ -16,146 +16,118 @@
 * 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.jbappletgui;
 
 import java.awt.*;
 import java.awt.event.*;
 
 
-public class GFontChooser extends Panel
-{
-  Label label1 = new Label();
-  protected Choice fontSize = new Choice();
-  protected Choice fontStyle = new Choice();
-  Label label2 = new Label();
-  Label label3 = new Label();
-  protected Choice fontName = new Choice();
-  Button ok = new Button();
-  Button cancel = new Button();
-  Panel panel1 = new Panel();
-  Panel panel2 = new Panel();
-  Panel panel3 = new Panel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  BorderLayout borderLayout3 = new BorderLayout();
-  Panel panel4 = new Panel();
-  Panel panel5 = new Panel();
-  BorderLayout borderLayout4 = new BorderLayout();
-
-  public GFontChooser()
-  {
-    try
-    {
-      jbInit();
+public class GFontChooser extends Panel {
+    Label label1 = new Label();
+    protected Choice fontSize = new Choice();
+    protected Choice fontStyle = new Choice();
+    Label label2 = new Label();
+    Label label3 = new Label();
+    protected Choice fontName = new Choice();
+    Button ok = new Button();
+    Button cancel = new Button();
+    Panel panel1 = new Panel();
+    Panel panel2 = new Panel();
+    Panel panel3 = new Panel();
+    BorderLayout borderLayout1 = new BorderLayout();
+    BorderLayout borderLayout2 = new BorderLayout();
+    BorderLayout borderLayout3 = new BorderLayout();
+    Panel panel4 = new Panel();
+    Panel panel5 = new Panel();
+    BorderLayout borderLayout4 = new BorderLayout();
+
+    public GFontChooser() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
     }
-    catch(Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-  private void jbInit() throws Exception
-  {
-    label1.setFont(new java.awt.Font("Verdana", 0, 11));
-    label1.setAlignment(Label.RIGHT);
-    label1.setText("Font: ");
-    this.setLayout(borderLayout4);
-    fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontSize.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        fontSize_actionPerformed();
-      }
-    });
-    fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontStyle.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        fontStyle_actionPerformed();
-      }
-    });
-    label2.setAlignment(Label.RIGHT);
-    label2.setFont(new java.awt.Font("Verdana", 0, 11));
-     label2.setText("Size: ");
-      label3.setAlignment(Label.RIGHT);
-    label3.setFont(new java.awt.Font("Verdana", 0, 11));
-      label3.setText("Style: ");
-    fontName.setFont(new java.awt.Font("Verdana", 0, 11));
-     fontName.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        fontName_actionPerformed();
-      }
-    });
-    ok.setFont(new java.awt.Font("Verdana", 0, 11));
-    ok.setLabel("OK");
-    ok.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed();
-      }
-    });
-    cancel.setFont(new java.awt.Font("Verdana", 0, 11));
-    cancel.setLabel("Cancel");
-    cancel.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed();
-      }
-    });
-    this.setBackground(Color.white);
-    panel1.setLayout(borderLayout1);
-    panel2.setLayout(borderLayout3);
-     panel3.setLayout(borderLayout2);
-    panel5.setBackground(Color.white);
-    panel4.setBackground(Color.white);
-    panel1.setBackground(Color.white);
-    panel2.setBackground(Color.white);
-    panel3.setBackground(Color.white);
-    panel1.add(label1, BorderLayout.WEST);
-    panel1.add(fontName, BorderLayout.CENTER);
-    panel5.add(panel1, null);
-    panel5.add(panel3, null);
-    panel5.add(panel2, null);
-    panel2.add(label3,  BorderLayout.WEST);
-    panel2.add(fontStyle,  BorderLayout.CENTER);
-    panel3.add(label2, BorderLayout.WEST);
-    panel3.add(fontSize, BorderLayout.CENTER);
-    this.add(panel4,  BorderLayout.SOUTH);
-    panel4.add(ok, null);
-    panel4.add(cancel, null);
-    this.add(panel5, BorderLayout.CENTER);
-
-   }
-
-  protected void ok_actionPerformed()
-  {
-
-  }
-
-  protected void cancel_actionPerformed()
-  {
-
-  }
 
-  protected void fontName_actionPerformed()
-  {
-
-  }
+    private void jbInit() throws Exception {
+        label1.setFont(new java.awt.Font("Verdana", 0, 11));
+        label1.setAlignment(Label.RIGHT);
+        label1.setText("Font: ");
+        this.setLayout(borderLayout4);
+        fontSize.setFont(new java.awt.Font("Verdana", 0, 11));
+        fontSize.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    fontSize_actionPerformed();
+                }
+            });
+        fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
+        fontStyle.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    fontStyle_actionPerformed();
+                }
+            });
+        label2.setAlignment(Label.RIGHT);
+        label2.setFont(new java.awt.Font("Verdana", 0, 11));
+        label2.setText("Size: ");
+        label3.setAlignment(Label.RIGHT);
+        label3.setFont(new java.awt.Font("Verdana", 0, 11));
+        label3.setText("Style: ");
+        fontName.setFont(new java.awt.Font("Verdana", 0, 11));
+        fontName.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    fontName_actionPerformed();
+                }
+            });
+        ok.setFont(new java.awt.Font("Verdana", 0, 11));
+        ok.setLabel("OK");
+        ok.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    ok_actionPerformed();
+                }
+            });
+        cancel.setFont(new java.awt.Font("Verdana", 0, 11));
+        cancel.setLabel("Cancel");
+        cancel.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    cancel_actionPerformed();
+                }
+            });
+        this.setBackground(Color.white);
+        panel1.setLayout(borderLayout1);
+        panel2.setLayout(borderLayout3);
+        panel3.setLayout(borderLayout2);
+        panel5.setBackground(Color.white);
+        panel4.setBackground(Color.white);
+        panel1.setBackground(Color.white);
+        panel2.setBackground(Color.white);
+        panel3.setBackground(Color.white);
+        panel1.add(label1, BorderLayout.WEST);
+        panel1.add(fontName, BorderLayout.CENTER);
+        panel5.add(panel1, null);
+        panel5.add(panel3, null);
+        panel5.add(panel2, null);
+        panel2.add(label3, BorderLayout.WEST);
+        panel2.add(fontStyle, BorderLayout.CENTER);
+        panel3.add(label2, BorderLayout.WEST);
+        panel3.add(fontSize, BorderLayout.CENTER);
+        this.add(panel4, BorderLayout.SOUTH);
+        panel4.add(ok, null);
+        panel4.add(cancel, null);
+        this.add(panel5, BorderLayout.CENTER);
+    }
 
-  protected void fontSize_actionPerformed()
-  {
+    protected void ok_actionPerformed() {
+    }
 
-  }
+    protected void cancel_actionPerformed() {
+    }
 
-  protected void fontStyle_actionPerformed()
-  {
+    protected void fontName_actionPerformed() {
+    }
 
-  }
+    protected void fontSize_actionPerformed() {
+    }
 
+    protected void fontStyle_actionPerformed() {
+    }
 }
diff --git a/src/jalview/jbappletgui/GPCAPanel.java b/src/jalview/jbappletgui/GPCAPanel.java
index b13b563..f33521c 100755
--- a/src/jalview/jbappletgui/GPCAPanel.java
+++ b/src/jalview/jbappletgui/GPCAPanel.java
@@ -16,99 +16,80 @@
 * 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.jbappletgui;
 
 import java.awt.*;
 import java.awt.event.*;
 
-public class GPCAPanel extends Panel
-{
-  Panel jPanel2 = new Panel();
-  Label jLabel1 = new Label();
-  Label jLabel2 = new Label();
-  Label jLabel3 = new Label();
-  protected Choice xCombobox = new Choice();
-  protected Choice yCombobox = new Choice();
-  protected Choice zCombobox = new Choice();
-  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);
-    }
-  }
-  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);
-    zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    zCombobox.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        zCombobox_actionPerformed(null);
-      }
-    });
-    yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    yCombobox.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        yCombobox_actionPerformed(null);
-      }
-    });
-    xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
-    xCombobox.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        xCombobox_actionPerformed(null);
-      }
-    });
-    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 xCombobox_actionPerformed(ActionEvent e)
-  {
+public class GPCAPanel extends Panel {
+    Panel jPanel2 = new Panel();
+    Label jLabel1 = new Label();
+    Label jLabel2 = new Label();
+    Label jLabel3 = new Label();
+    protected Choice xCombobox = new Choice();
+    protected Choice yCombobox = new Choice();
+    protected Choice zCombobox = new Choice();
+    FlowLayout flowLayout1 = new FlowLayout();
+    BorderLayout borderLayout1 = new BorderLayout();
 
-  }
+    public GPCAPanel() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
 
-  protected void yCombobox_actionPerformed(ActionEvent e)
-  {
+        for (int i = 1; i < 8; i++) {
+            xCombobox.addItem("dim " + i);
+            yCombobox.addItem("dim " + i);
+            zCombobox.addItem("dim " + i);
+        }
+    }
 
-  }
+    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);
+        zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+        zCombobox.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    zCombobox_actionPerformed(null);
+                }
+            });
+        yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+        yCombobox.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    yCombobox_actionPerformed(null);
+                }
+            });
+        xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+        xCombobox.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    xCombobox_actionPerformed(null);
+                }
+            });
+        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/jbappletgui/GPairwiseAlignPanel.java b/src/jalview/jbappletgui/GPairwiseAlignPanel.java
index 54bb555..10bd01e 100755
--- a/src/jalview/jbappletgui/GPairwiseAlignPanel.java
+++ b/src/jalview/jbappletgui/GPairwiseAlignPanel.java
@@ -16,55 +16,44 @@
 * 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.jbappletgui;
 
 import java.awt.*;
 import java.awt.event.*;
 
 
-public class GPairwiseAlignPanel extends Panel
-{
-  protected ScrollPane scrollPane = new ScrollPane();
-  protected TextArea textarea = new TextArea();
-  protected Button viewInEditorButton = new Button();
-  Panel jPanel1 = new Panel();
-  BorderLayout borderLayout1 = new BorderLayout();
+public class GPairwiseAlignPanel extends Panel {
+    protected ScrollPane scrollPane = new ScrollPane();
+    protected TextArea textarea = new TextArea();
+    protected Button viewInEditorButton = new Button();
+    Panel jPanel1 = new Panel();
+    BorderLayout borderLayout1 = new BorderLayout();
 
-  public GPairwiseAlignPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
+    public GPairwiseAlignPanel() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
     }
-  }
-  private void jbInit() throws Exception
-  {
-    this.setLayout(borderLayout1);
-    textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
-    textarea.setText("");
-    viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
-    viewInEditorButton.setLabel("View in alignment editor");
-    viewInEditorButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        viewInEditorButton_actionPerformed(e);
-      }
-    });
-    this.add(scrollPane, BorderLayout.CENTER);
-    scrollPane.add(textarea);
-    this.add(jPanel1, BorderLayout.SOUTH);
-    jPanel1.add(viewInEditorButton, null);
-  }
-
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
 
-  }
+    private void jbInit() throws Exception {
+        this.setLayout(borderLayout1);
+        textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
+        textarea.setText("");
+        viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
+        viewInEditorButton.setLabel("View in alignment editor");
+        viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    viewInEditorButton_actionPerformed(e);
+                }
+            });
+        this.add(scrollPane, BorderLayout.CENTER);
+        scrollPane.add(textarea);
+        this.add(jPanel1, BorderLayout.SOUTH);
+        jPanel1.add(viewInEditorButton, null);
+    }
 
+    protected void viewInEditorButton_actionPerformed(ActionEvent e) {
+    }
 }
diff --git a/src/jalview/jbappletgui/GSliderPanel.java b/src/jalview/jbappletgui/GSliderPanel.java
index d8120b4..5e33300 100755
--- a/src/jalview/jbappletgui/GSliderPanel.java
+++ b/src/jalview/jbappletgui/GSliderPanel.java
@@ -16,121 +16,100 @@
 * 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.jbappletgui;
 
 import java.awt.*;
 import java.awt.event.*;
 
-public class GSliderPanel extends Panel
-{
-  // this is used for conservation colours, PID colours and redundancy threshold
-  protected Scrollbar slider = new Scrollbar();
-  protected TextField valueField = new TextField();
-  protected Label label = new Label();
-  Panel jPanel1 = new Panel();
-  Panel jPanel2 = new Panel();
-  protected Button applyButton = new Button();
-  protected Button undoButton = new Button();
-  FlowLayout flowLayout1 = new FlowLayout();
-  protected Checkbox allGroupsCheck = new Checkbox();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  FlowLayout flowLayout2 = new FlowLayout();
-
-  public GSliderPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-  private void jbInit() throws Exception
-  {
-    this.setLayout(borderLayout2);
-   // slider.setMajorTickSpacing(10);
-  //  slider.setMinorTickSpacing(1);
-  //  slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setFont(new java.awt.Font("Verdana", 0, 11));
-    slider.setOrientation(0);
-    valueField.setFont(new java.awt.Font("Verdana", 0, 11));
-    valueField.setText("      ");
-    valueField.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        valueField_actionPerformed(e);
-      }
-    });
-    label.setFont(new java.awt.Font("Verdana", 0, 11));
-    label.setText("set this label text");
-    jPanel1.setLayout(borderLayout1);
-    jPanel2.setLayout(flowLayout1);
-    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    applyButton.setLabel("Apply");
-    applyButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        applyButton_actionPerformed(e);
-      }
-    });
-    undoButton.setEnabled(false);
-    undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    undoButton.setLabel("Undo");
-    undoButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        undoButton_actionPerformed(e);
-      }
-    });
-    allGroupsCheck.setEnabled(false);
-    allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
-    allGroupsCheck.setLabel("Apply threshold to all groups");
-    allGroupsCheck.setName("Apply to all Groups");
-    allGroupsCheck.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        allGroupsCheck_actionPerformed();
-      }
-    });
-    this.setBackground(Color.white);
-    this.setForeground(Color.black);
-    jPanel2.add(label, null);
-    jPanel2.add(applyButton, null);
-    jPanel2.add(undoButton, null);
-    jPanel2.add(allGroupsCheck);
-    jPanel1.add(valueField, java.awt.BorderLayout.EAST);
-    jPanel1.add(slider, java.awt.BorderLayout.CENTER);
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-    this.add(jPanel2, java.awt.BorderLayout.CENTER);
-  }
-
-  protected void valueField_actionPerformed(ActionEvent e)
-  {
 
-  }
+public class GSliderPanel extends Panel {
+    // this is used for conservation colours, PID colours and redundancy threshold
+    protected Scrollbar slider = new Scrollbar();
+    protected TextField valueField = new TextField();
+    protected Label label = new Label();
+    Panel jPanel1 = new Panel();
+    Panel jPanel2 = new Panel();
+    protected Button applyButton = new Button();
+    protected Button undoButton = new Button();
+    FlowLayout flowLayout1 = new FlowLayout();
+    protected Checkbox allGroupsCheck = new Checkbox();
+    BorderLayout borderLayout1 = new BorderLayout();
+    BorderLayout borderLayout2 = new BorderLayout();
+    FlowLayout flowLayout2 = new FlowLayout();
 
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
+    public GSliderPanel() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
 
-  }
+    private void jbInit() throws Exception {
+        this.setLayout(borderLayout2);
 
-  protected void undoButton_actionPerformed(ActionEvent e)
-  {
+        // slider.setMajorTickSpacing(10);
+        //  slider.setMinorTickSpacing(1);
+        //  slider.setPaintTicks(true);
+        slider.setBackground(Color.white);
+        slider.setFont(new java.awt.Font("Verdana", 0, 11));
+        slider.setOrientation(0);
+        valueField.setFont(new java.awt.Font("Verdana", 0, 11));
+        valueField.setText("      ");
+        valueField.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    valueField_actionPerformed(e);
+                }
+            });
+        label.setFont(new java.awt.Font("Verdana", 0, 11));
+        label.setText("set this label text");
+        jPanel1.setLayout(borderLayout1);
+        jPanel2.setLayout(flowLayout1);
+        applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
+        applyButton.setLabel("Apply");
+        applyButton.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    applyButton_actionPerformed(e);
+                }
+            });
+        undoButton.setEnabled(false);
+        undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
+        undoButton.setLabel("Undo");
+        undoButton.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    undoButton_actionPerformed(e);
+                }
+            });
+        allGroupsCheck.setEnabled(false);
+        allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
+        allGroupsCheck.setLabel("Apply threshold to all groups");
+        allGroupsCheck.setName("Apply to all Groups");
+        allGroupsCheck.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    allGroupsCheck_actionPerformed();
+                }
+            });
+        this.setBackground(Color.white);
+        this.setForeground(Color.black);
+        jPanel2.add(label, null);
+        jPanel2.add(applyButton, null);
+        jPanel2.add(undoButton, null);
+        jPanel2.add(allGroupsCheck);
+        jPanel1.add(valueField, java.awt.BorderLayout.EAST);
+        jPanel1.add(slider, java.awt.BorderLayout.CENTER);
+        this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+        this.add(jPanel2, java.awt.BorderLayout.CENTER);
+    }
 
-  }
+    protected void valueField_actionPerformed(ActionEvent e) {
+    }
 
-  protected void allGroupsCheck_actionPerformed()
-  {
+    protected void applyButton_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void undoButton_actionPerformed(ActionEvent e) {
+    }
 
+    protected void allGroupsCheck_actionPerformed() {
+    }
 }
diff --git a/src/jalview/jbappletgui/GTreePanel.java b/src/jalview/jbappletgui/GTreePanel.java
index a663402..1810719 100755
--- a/src/jalview/jbappletgui/GTreePanel.java
+++ b/src/jalview/jbappletgui/GTreePanel.java
@@ -16,140 +16,106 @@
 * 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.jbappletgui;
 
 import java.awt.*;
 import java.awt.event.*;
 
-public class GTreePanel extends Frame
-{
-  BorderLayout borderLayout1 = new BorderLayout();
-  protected ScrollPane scrollPane = new ScrollPane();
-  MenuBar jMenuBar1 = new MenuBar();
-  Menu jMenu2 = new Menu();
-  protected MenuItem fontSize = new MenuItem();
-  protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
-  protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
-  protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
-  protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
-  Menu fileMenu = new Menu();
-  MenuItem newickOutput = new MenuItem();
 
-  public GTreePanel()
-  {
-    try
-    {
-      jbInit();
-      this.setMenuBar(jMenuBar1);
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
+public class GTreePanel extends Frame {
+    BorderLayout borderLayout1 = new BorderLayout();
+    protected ScrollPane scrollPane = new ScrollPane();
+    MenuBar jMenuBar1 = new MenuBar();
+    Menu jMenu2 = new Menu();
+    protected MenuItem fontSize = new MenuItem();
+    protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
+    protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
+    protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
+    protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
+    Menu fileMenu = new Menu();
+    MenuItem newickOutput = new MenuItem();
+
+    public GTreePanel() {
+        try {
+            jbInit();
+            this.setMenuBar(jMenuBar1);
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
     }
 
-  }
-  private void jbInit() throws Exception
-  {
-    setLayout(borderLayout1);
-    this.setBackground(Color.white);
-    this.setFont(new java.awt.Font("Verdana", 0, 12));
-    jMenu2.setLabel("View");
-    fontSize.setLabel("Font Size - 12");
-    fontSize.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontSize_actionPerformed(e);
-      }
-    });
-    bootstrapMenu.setLabel("Show Bootstrap Values");
-    bootstrapMenu.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        bootstrapMenu_actionPerformed(null);
-      }
-    });
-    distanceMenu.setLabel("Show Distances");
-    distanceMenu.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        distanceMenu_actionPerformed(null);
-      }
-    });
-    placeholdersMenu.setLabel("Mark Unassociated Leaves");
-    placeholdersMenu.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        placeholdersMenu_actionPerformed(null);
-      }
-    });
-    fitToWindow.setState(true);
-    fitToWindow.setLabel("Fit To Window");
-    fitToWindow.addItemListener(new java.awt.event.ItemListener()
-    {
-      public void itemStateChanged(ItemEvent e)
-      {
-        fitToWindow_actionPerformed(null);
-      }
-    });
-    fileMenu.setLabel("File");
-    newickOutput.setLabel("Newick Format");
-    newickOutput.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        newickOutput_actionPerformed(actionEvent);
-      }
-    });
-    add(scrollPane, BorderLayout.CENTER);
-    jMenuBar1.add(fileMenu);
-    jMenuBar1.add(jMenu2);
-    jMenu2.add(fitToWindow);
-    jMenu2.add(fontSize);
-    jMenu2.add(distanceMenu);
-    jMenu2.add(bootstrapMenu);
-    jMenu2.add(placeholdersMenu);
-    fileMenu.add(newickOutput);
-  }
-
-
-  protected void printMenu_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void distanceMenu_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-
-  }
+    private void jbInit() throws Exception {
+        setLayout(borderLayout1);
+        this.setBackground(Color.white);
+        this.setFont(new java.awt.Font("Verdana", 0, 12));
+        jMenu2.setLabel("View");
+        fontSize.setLabel("Font Size - 12");
+        fontSize.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    fontSize_actionPerformed(e);
+                }
+            });
+        bootstrapMenu.setLabel("Show Bootstrap Values");
+        bootstrapMenu.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    bootstrapMenu_actionPerformed(null);
+                }
+            });
+        distanceMenu.setLabel("Show Distances");
+        distanceMenu.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    distanceMenu_actionPerformed(null);
+                }
+            });
+        placeholdersMenu.setLabel("Mark Unassociated Leaves");
+        placeholdersMenu.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    placeholdersMenu_actionPerformed(null);
+                }
+            });
+        fitToWindow.setState(true);
+        fitToWindow.setLabel("Fit To Window");
+        fitToWindow.addItemListener(new java.awt.event.ItemListener() {
+                public void itemStateChanged(ItemEvent e) {
+                    fitToWindow_actionPerformed(null);
+                }
+            });
+        fileMenu.setLabel("File");
+        newickOutput.setLabel("Newick Format");
+        newickOutput.addActionListener(new ActionListener() {
+                public void actionPerformed(ActionEvent actionEvent) {
+                    newickOutput_actionPerformed(actionEvent);
+                }
+            });
+        add(scrollPane, BorderLayout.CENTER);
+        jMenuBar1.add(fileMenu);
+        jMenuBar1.add(jMenu2);
+        jMenu2.add(fitToWindow);
+        jMenu2.add(fontSize);
+        jMenu2.add(distanceMenu);
+        jMenu2.add(bootstrapMenu);
+        jMenu2.add(placeholdersMenu);
+        fileMenu.add(newickOutput);
+    }
 
-  protected void placeholdersMenu_actionPerformed(ActionEvent e)
-  {
+    protected void printMenu_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void fontSize_actionPerformed(ActionEvent e) {
+    }
 
-  protected void fitToWindow_actionPerformed(ActionEvent e)
-  {
+    protected void distanceMenu_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void bootstrapMenu_actionPerformed(ActionEvent e) {
+    }
 
-  public void newickOutput_actionPerformed(ActionEvent actionEvent)
-  {
+    protected void placeholdersMenu_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void fitToWindow_actionPerformed(ActionEvent e) {
+    }
 
+    public void newickOutput_actionPerformed(ActionEvent actionEvent) {
+    }
 }
diff --git a/src/jalview/jbappletgui/GUserDefinedColours.java b/src/jalview/jbappletgui/GUserDefinedColours.java
index 0acc0b1..bc57798 100755
--- a/src/jalview/jbappletgui/GUserDefinedColours.java
+++ b/src/jalview/jbappletgui/GUserDefinedColours.java
@@ -16,205 +16,174 @@
 * 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.jbappletgui;
 
 import java.awt.*;
 import java.awt.event.*;
 
 
-public class GUserDefinedColours extends Panel
-{
-  protected Panel buttonPanel = new Panel();
-  protected GridLayout gridLayout = new GridLayout();
-  Panel jPanel2 = new Panel();
-  protected Button okButton = new Button();
-  protected Button applyButton = new Button();
-  protected Button cancelButton = new Button();
-  protected Scrollbar rScroller = new Scrollbar();
-  Label label1 = new Label();
-  Panel panel2 = new Panel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  protected TextField rText = new TextField();
-  Panel panel3 = new Panel();
-  Label label4 = new Label();
-  protected Scrollbar gScroller = new Scrollbar();
-  protected TextField gText = new TextField();
-  BorderLayout borderLayout2 = new BorderLayout();
-  Panel panel4 = new Panel();
-  Label label5 = new Label();
-  protected Scrollbar bScroller = new Scrollbar();
-  protected TextField bText = new TextField();
-  BorderLayout borderLayout3 = new BorderLayout();
-  protected Panel target = new Panel();
-
-  public GUserDefinedColours()
-  {
-    try
-    {
-      jbInit();
+public class GUserDefinedColours extends Panel {
+    protected Panel buttonPanel = new Panel();
+    protected GridLayout gridLayout = new GridLayout();
+    Panel jPanel2 = new Panel();
+    protected Button okButton = new Button();
+    protected Button applyButton = new Button();
+    protected Button cancelButton = new Button();
+    protected Scrollbar rScroller = new Scrollbar();
+    Label label1 = new Label();
+    Panel panel2 = new Panel();
+    BorderLayout borderLayout1 = new BorderLayout();
+    protected TextField rText = new TextField();
+    Panel panel3 = new Panel();
+    Label label4 = new Label();
+    protected Scrollbar gScroller = new Scrollbar();
+    protected TextField gText = new TextField();
+    BorderLayout borderLayout2 = new BorderLayout();
+    Panel panel4 = new Panel();
+    Label label5 = new Label();
+    protected Scrollbar bScroller = new Scrollbar();
+    protected TextField bText = new TextField();
+    BorderLayout borderLayout3 = new BorderLayout();
+    protected Panel target = new Panel();
+
+    public GUserDefinedColours() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
     }
-    catch(Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-  private void jbInit() throws Exception
-  {
-    this.setLayout(null);
-    buttonPanel.setLayout(gridLayout);
-    gridLayout.setColumns(6);
-    gridLayout.setRows(4);
-    okButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    okButton.setLabel("OK");
-    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.setLabel("Apply");
-    applyButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        applyButton_actionPerformed(e);
-      }
-    });
-    cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    cancelButton.setLabel("Cancel");
-    cancelButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancelButton_actionPerformed(e);
-      }
-    });
-    this.setBackground(new Color(212, 208, 223));
-    jPanel2.setBounds(new Rectangle(0, 265, 400, 35));
-    buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));
-    rScroller.setMaximum(255);
-    rScroller.setMinimum(0);
-    rScroller.setOrientation(0);
-    rScroller.setUnitIncrement(1);
-    rScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {
-      public void adjustmentValueChanged(AdjustmentEvent e) {
-        rScroller_adjustmentValueChanged(e);
-      }
-    });
-    label1.setText("R");
-    panel2.setBounds(new Rectangle(20, 29, 180, 19));
-    panel2.setLayout(borderLayout1);
-    rText.setText("    0");
-    rText.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
-        rText_actionPerformed(e);
-      }
-    });
-    panel3.setLayout(borderLayout2);
-    label4.setText("G");
-    gScroller.setMaximum(255);
-    gScroller.setMinimum(0);
-    gScroller.setOrientation(0);
-    gScroller.setUnitIncrement(1);
-    gScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {
-      public void adjustmentValueChanged(AdjustmentEvent e) {
-        gScroller_adjustmentValueChanged(e);
-      }
-    });
-    gText.setText("    0");
-    gText.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
-        gText_actionPerformed(e);
-      }
-    });
-    panel3.setBounds(new Rectangle(19, 54, 181, 20));
-    panel4.setLayout(borderLayout3);
-    label5.setText("B");
-    bScroller.setMaximum(255);
-    bScroller.setMinimum(0);
-    bScroller.setOrientation(0);
-    bScroller.setUnitIncrement(1);
-    bScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {
-      public void adjustmentValueChanged(AdjustmentEvent e) {
-        bScroller_adjustmentValueChanged(e);
-      }
-    });
-    bText.setSelectionStart(6);
-    bText.setText("    0");
-    bText.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
-        bText_actionPerformed(e);
-      }
-    });
-    panel4.setBounds(new Rectangle(19, 87, 180, 20));
-    target.setBackground(Color.black);
-    target.setBounds(new Rectangle(229, 26, 134, 79));
-    this.add(jPanel2, null);
-    jPanel2.add(okButton, null);
-    jPanel2.add(applyButton, null);
-    jPanel2.add(cancelButton, null);
-    this.add(buttonPanel, null);
-    panel2.add(label1, BorderLayout.WEST);
-    panel2.add(rScroller, BorderLayout.CENTER);
-    panel2.add(rText, BorderLayout.EAST);
-    this.add(target, null);
-    this.add(panel4, null);
-    panel3.add(label4, BorderLayout.WEST);
-    panel3.add(gScroller, BorderLayout.CENTER);
-    panel3.add(gText, BorderLayout.EAST);
-    this.add(panel2, null);
-    panel4.add(label5, BorderLayout.WEST);
-    panel4.add(bScroller, BorderLayout.CENTER);
-    panel4.add(bText, BorderLayout.EAST);
-    this.add(panel3, null);
-  }
-
-
-  protected void okButton_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-
-  protected void cancelButton_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void rScroller_adjustmentValueChanged(AdjustmentEvent e) {
-
-  }
 
-  protected void gScroller_adjustmentValueChanged(AdjustmentEvent e) {
-
-  }
-
-  protected void bScroller_adjustmentValueChanged(AdjustmentEvent e) {
-
-  }
-
-  protected void rText_actionPerformed(ActionEvent e) {
+    private void jbInit() throws Exception {
+        this.setLayout(null);
+        buttonPanel.setLayout(gridLayout);
+        gridLayout.setColumns(6);
+        gridLayout.setRows(4);
+        okButton.setFont(new java.awt.Font("Verdana", 0, 11));
+        okButton.setLabel("OK");
+        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.setLabel("Apply");
+        applyButton.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    applyButton_actionPerformed(e);
+                }
+            });
+        cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
+        cancelButton.setLabel("Cancel");
+        cancelButton.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    cancelButton_actionPerformed(e);
+                }
+            });
+        this.setBackground(new Color(212, 208, 223));
+        jPanel2.setBounds(new Rectangle(0, 265, 400, 35));
+        buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));
+        rScroller.setMaximum(255);
+        rScroller.setMinimum(0);
+        rScroller.setOrientation(0);
+        rScroller.setUnitIncrement(1);
+        rScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {
+                public void adjustmentValueChanged(AdjustmentEvent e) {
+                    rScroller_adjustmentValueChanged(e);
+                }
+            });
+        label1.setText("R");
+        panel2.setBounds(new Rectangle(20, 29, 180, 19));
+        panel2.setLayout(borderLayout1);
+        rText.setText("    0");
+        rText.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    rText_actionPerformed(e);
+                }
+            });
+        panel3.setLayout(borderLayout2);
+        label4.setText("G");
+        gScroller.setMaximum(255);
+        gScroller.setMinimum(0);
+        gScroller.setOrientation(0);
+        gScroller.setUnitIncrement(1);
+        gScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {
+                public void adjustmentValueChanged(AdjustmentEvent e) {
+                    gScroller_adjustmentValueChanged(e);
+                }
+            });
+        gText.setText("    0");
+        gText.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    gText_actionPerformed(e);
+                }
+            });
+        panel3.setBounds(new Rectangle(19, 54, 181, 20));
+        panel4.setLayout(borderLayout3);
+        label5.setText("B");
+        bScroller.setMaximum(255);
+        bScroller.setMinimum(0);
+        bScroller.setOrientation(0);
+        bScroller.setUnitIncrement(1);
+        bScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {
+                public void adjustmentValueChanged(AdjustmentEvent e) {
+                    bScroller_adjustmentValueChanged(e);
+                }
+            });
+        bText.setSelectionStart(6);
+        bText.setText("    0");
+        bText.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    bText_actionPerformed(e);
+                }
+            });
+        panel4.setBounds(new Rectangle(19, 87, 180, 20));
+        target.setBackground(Color.black);
+        target.setBounds(new Rectangle(229, 26, 134, 79));
+        this.add(jPanel2, null);
+        jPanel2.add(okButton, null);
+        jPanel2.add(applyButton, null);
+        jPanel2.add(cancelButton, null);
+        this.add(buttonPanel, null);
+        panel2.add(label1, BorderLayout.WEST);
+        panel2.add(rScroller, BorderLayout.CENTER);
+        panel2.add(rText, BorderLayout.EAST);
+        this.add(target, null);
+        this.add(panel4, null);
+        panel3.add(label4, BorderLayout.WEST);
+        panel3.add(gScroller, BorderLayout.CENTER);
+        panel3.add(gText, BorderLayout.EAST);
+        this.add(panel2, null);
+        panel4.add(label5, BorderLayout.WEST);
+        panel4.add(bScroller, BorderLayout.CENTER);
+        panel4.add(bText, BorderLayout.EAST);
+        this.add(panel3, null);
+    }
 
-  }
+    protected void okButton_actionPerformed(ActionEvent e) {
+    }
 
-  protected void gText_actionPerformed(ActionEvent e) {
+    protected void applyButton_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void cancelButton_actionPerformed(ActionEvent e) {
+    }
 
-  protected void bText_actionPerformed(ActionEvent e) {
+    protected void rScroller_adjustmentValueChanged(AdjustmentEvent e) {
+    }
 
-  }
+    protected void gScroller_adjustmentValueChanged(AdjustmentEvent e) {
+    }
 
+    protected void bScroller_adjustmentValueChanged(AdjustmentEvent e) {
+    }
 
+    protected void rText_actionPerformed(ActionEvent e) {
+    }
 
+    protected void gText_actionPerformed(ActionEvent e) {
+    }
 
+    protected void bText_actionPerformed(ActionEvent e) {
+    }
 }
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 00b4bc9..81325d5 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -16,1266 +16,1014 @@
 * 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 javax.swing.*;
-import java.awt.event.*;
-import java.awt.*;
-
 import jalview.gui.Preferences;
-import jalview.schemes.ColourSchemeProperty;
-import javax.swing.event.AncestorListener;
-import javax.swing.event.AncestorEvent;
-
-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();
-  protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
-  protected 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();
-  protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
-  JMenuItem htmlMenuItem = new JMenuItem();
-  JMenuItem overviewMenuItem = new JMenuItem();
-  protected JMenuItem undoMenuItem = new JMenuItem();
-  protected JMenuItem redoMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
-  JMenuItem printMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
-  JMenuItem findMenuItem = new JMenuItem();
-  JMenu searchMenu = new JMenu();
-  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  protected 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();
-  protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
-  JMenuItem createPNG = new JMenuItem();
-  protected JMenuItem font = new JMenuItem();
-  protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
-  JMenuItem epsFile = new JMenuItem();
-  JMenuItem LoadtreeMenuItem = new JMenuItem();
-  JMenuItem jpred = new JMenuItem();
-  protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
-  protected 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);
-      }
-    });
-    jpred.setText("JPred...");
-    jpred.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(jpred);
-    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 averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-
-
-  protected void clustalColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void zappoColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void taylorColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void helixColour_actionPerformed(ActionEvent e)
-  {
 
-  }
-
-  protected void strandColour_actionPerformed(ActionEvent e)
-  {
-
-  }
+import jalview.schemes.ColourSchemeProperty;
 
-  protected void turnColour_actionPerformed(ActionEvent e)
-  {
+import java.awt.*;
+import java.awt.event.*;
 
-  }
+import javax.swing.*;
+import javax.swing.event.AncestorEvent;
+import javax.swing.event.AncestorListener;
 
-  protected void buriedColour_actionPerformed(ActionEvent e)
-  {
 
-  }
+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();
+    protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+    protected 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();
+    protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+    protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+    JMenuItem htmlMenuItem = new JMenuItem();
+    JMenuItem overviewMenuItem = new JMenuItem();
+    protected JMenuItem undoMenuItem = new JMenuItem();
+    protected JMenuItem redoMenuItem = new JMenuItem();
+    protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+    JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+    protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+    JMenuItem printMenuItem = new JMenuItem();
+    protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+    JMenuItem findMenuItem = new JMenuItem();
+    JMenu searchMenu = new JMenu();
+    protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+    protected 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();
+    protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+    JMenuItem createPNG = new JMenuItem();
+    protected JMenuItem font = new JMenuItem();
+    protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+    JMenuItem epsFile = new JMenuItem();
+    JMenuItem LoadtreeMenuItem = new JMenuItem();
+    JMenuItem jpred = new JMenuItem();
+    protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+    protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+    protected 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;
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
+            // 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();
+        }
+    }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
-  {
+    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);
+                }
+            });
+        jpred.setText("JPred...");
+        jpred.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(jpred);
+        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 BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
+    protected void htmlMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void closeMenuItem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void redoMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void undoMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void printMenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void wrapMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void findMenuItem_actionPerformed(ActionEvent e)
-  {
+    protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void viewTextMenuItem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void colourTextMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+    protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void overviewMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
-  {
+    protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void sortIDMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void nucleotideColour_actionPerformed(ActionEvent e)
-  {
+    protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void deleteGroups_actionPerformed(ActionEvent e)
-  {
+    protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void PCAMenuItem_actionPerformed(ActionEvent e) {
+    }
 
- protected void copy_actionPerformed(ActionEvent e)
-  {
+    protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void cut_actionPerformed(ActionEvent e)
-  {
+    protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void delete_actionPerformed(ActionEvent e)
-  {
+    protected void clustalColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void zappoColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void pasteNew_actionPerformed(ActionEvent e)
-  {
+    protected void taylorColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void hydrophobicityColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void pasteThis_actionPerformed(ActionEvent e)
-  {
+    protected void helixColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void strandColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
-  {
+    protected void turnColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void buriedColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void createPNG_actionPerformed(ActionEvent e)
-  {
+    protected void userDefinedColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void PIDColour_actionPerformed(ActionEvent e) {
+    }
 
-  protected void font_actionPerformed(ActionEvent e)
-  {
+    protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void noColourmenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
-  {
+    protected void conservationMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void printMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void epsFile_actionPerformed(ActionEvent e)
-  {
+    protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void findMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {
+    }
 
-  protected void jpred_actionPerformed(ActionEvent e)
-  {
+    protected void nucleotideColour_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void deleteGroups_actionPerformed(ActionEvent e) {
+    }
 
-  protected void scaleAbove_actionPerformed(ActionEvent e)
-  {
+    protected void copy_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void cut_actionPerformed(ActionEvent e) {
+    }
 
-  protected void scaleLeft_actionPerformed(ActionEvent e)
-  {
+    protected void delete_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void pasteNew_actionPerformed(ActionEvent e) {
+    }
 
-  protected void scaleRight_actionPerformed(ActionEvent e)
-  {
+    protected void pasteThis_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void applyToAllGroups_actionPerformed(ActionEvent e) {
+    }
 
-  protected void modifyPID_actionPerformed(ActionEvent e)
-  {
+    protected void createPNG_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void font_actionPerformed(ActionEvent e) {
+    }
 
-  protected void modifyConservation_actionPerformed(ActionEvent e)
-  {
+    protected void fullSeqId_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void epsFile_actionPerformed(ActionEvent e) {
+    }
 
-  protected void preferences_actionPerformed(ActionEvent e)
-  {
+    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void jpred_actionPerformed(ActionEvent e) {
+    }
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
+    protected void scaleAbove_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void scaleLeft_actionPerformed(ActionEvent e) {
+    }
 
-  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
-  {
+    protected void scaleRight_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void modifyPID_actionPerformed(ActionEvent e) {
+    }
 
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
-  {
+    protected void modifyConservation_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void preferences_actionPerformed(ActionEvent e) {
+    }
 
-  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
-  {
+    protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) {
+    }
 
-  protected void ClustalRealign_actionPerformed(ActionEvent e)
-  {
+    protected void saveAlignmentMenu_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void padGapsMenuitem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void ClustalRealign_actionPerformed(ActionEvent e) {
+    }
 }
diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index fc6fc1e..fc8b8dd 100755
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -15,93 +15,88 @@
 * 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.*;
-
-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();
-    }
-  }
-  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);
-  //  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);
-  }
-
-
-}
+*/
+package jalview.jbgui;
+
+import java.awt.*;
+
+import javax.swing.*;
+import javax.swing.border.*;
+
+
+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();
+        }
+    }
+
+    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);
+
+        //  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);
+    }
+}
diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index 7b0c621..8b2582c 100755
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -16,145 +16,114 @@
 * 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 javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
-import java.beans.VetoableChangeListener;
+
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyVetoException;
+import java.beans.VetoableChangeListener;
 
-public class GCutAndPasteTransfer extends JInternalFrame
-{
-  protected JTextArea textarea = new JTextArea();
-  protected JScrollPane scrollPane = new JScrollPane();
-  BorderLayout borderLayout1 = new BorderLayout();
-  JMenuBar editMenubar = new JMenuBar();
-  JMenu editMenu = new JMenu();
-  JMenuItem copyItem = new JMenuItem();
-  JMenuItem pasteMenu = new JMenuItem();
-  BorderLayout borderLayout2 = new BorderLayout();
-  protected JPanel inputButtonPanel = new JPanel();
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  public GCutAndPasteTransfer()
-  {
-    try
-    {
-      setJMenuBar(editMenubar);
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
-    }
-
-  }
-  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_actionPerformed(e);
-      }
-    });
-    cancel.setText("Cancel");
-    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_vetoableChange(evt);
-        }
-        catch (java.beans.PropertyVetoException exception0)
-        {
-          exception0.printStackTrace();
-        }
-
-      }
-    });
-    editMenubar.add(editMenu);
-    textarea.setFont(new java.awt.Font("Verdana", 0, 12));
-    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_actionPerformed(e);
-      }
-    });
-    copyItem.setText("Copy");
-    copyItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        copyItem_actionPerformed(e);
-      }
-    });
-    this.getContentPane().setLayout(borderLayout2);
-    scrollPane.setBorder(null);
-    scrollPane.getViewport().add(textarea, null);
-    editMenu.add(copyItem);
-    editMenu.add(pasteMenu);
-    this.getContentPane().add(scrollPane, java.awt.BorderLayout.CENTER);
-    inputButtonPanel.add(ok);
-    inputButtonPanel.add(cancel);
-
-  }
-
-  void textarea_mousePressed(MouseEvent e)
-  {
-    if(textarea.getText().equals("Paste your alignment file here"))
-      textarea.setText("");
-  }
-
-  public void copyItem_actionPerformed(ActionEvent e)
-  {
-
-  }
+import javax.swing.*;
 
-  public void pasteMenu_actionPerformed(ActionEvent e)
-  {
 
-  }
+public class GCutAndPasteTransfer extends JInternalFrame {
+    protected JTextArea textarea = new JTextArea();
+    protected JScrollPane scrollPane = new JScrollPane();
+    BorderLayout borderLayout1 = new BorderLayout();
+    JMenuBar editMenubar = new JMenuBar();
+    JMenu editMenu = new JMenu();
+    JMenuItem copyItem = new JMenuItem();
+    JMenuItem pasteMenu = new JMenuItem();
+    BorderLayout borderLayout2 = new BorderLayout();
+    protected JPanel inputButtonPanel = new JPanel();
+    JButton ok = new JButton();
+    JButton cancel = new JButton();
+
+    public GCutAndPasteTransfer() {
+        try {
+            setJMenuBar(editMenubar);
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
 
-  public void ok_actionPerformed(ActionEvent e)
-  {
+    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_actionPerformed(e);
+                }
+            });
+        cancel.setText("Cancel");
+        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_vetoableChange(evt);
+                    } catch (java.beans.PropertyVetoException exception0) {
+                        exception0.printStackTrace();
+                    }
+                }
+            });
+        editMenubar.add(editMenu);
+        textarea.setFont(new java.awt.Font("Verdana", 0, 12));
+        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_actionPerformed(e);
+                }
+            });
+        copyItem.setText("Copy");
+        copyItem.addActionListener(new ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    copyItem_actionPerformed(e);
+                }
+            });
+        this.getContentPane().setLayout(borderLayout2);
+        scrollPane.setBorder(null);
+        scrollPane.getViewport().add(textarea, null);
+        editMenu.add(copyItem);
+        editMenu.add(pasteMenu);
+        this.getContentPane().add(scrollPane, java.awt.BorderLayout.CENTER);
+        inputButtonPanel.add(ok);
+        inputButtonPanel.add(cancel);
+    }
 
-  }
+    void textarea_mousePressed(MouseEvent e) {
+        if (textarea.getText().equals("Paste your alignment file here")) {
+            textarea.setText("");
+        }
+    }
 
-  public void cancel_actionPerformed(ActionEvent e)
-  {
+    public void copyItem_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    public void pasteMenu_actionPerformed(ActionEvent e) {
+    }
 
-  public void textarea_vetoableChange(PropertyChangeEvent evt)
-      throws PropertyVetoException
-  {
+    public void ok_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    public void cancel_actionPerformed(ActionEvent e) {
+    }
 
+    public void textarea_vetoableChange(PropertyChangeEvent evt)
+        throws PropertyVetoException {
+    }
 }
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 1dc49b7..06340c3 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -16,194 +16,159 @@
 * 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 javax.swing.*;
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+public class GDesktop extends JFrame {
+    protected static JMenu windowMenu = new JMenu();
+    JMenuBar DesktopMenubar = new JMenuBar();
+    JMenu FileMenu = new JMenu();
+    JMenu HelpMenu = new JMenu();
+    JMenuItem inputLocalFileMenuItem = new JMenuItem();
+    JMenuItem inputURLMenuItem = new JMenuItem();
+    JMenuItem inputTextboxMenuItem = new JMenuItem();
+    JMenuItem quit = new JMenuItem();
+    JMenuItem aboutMenuItem = new JMenuItem();
+    JMenuItem documentationMenuItem = new JMenuItem();
+    FlowLayout flowLayout1 = new FlowLayout();
+    JMenu toolsMenu = new JMenu();
+    JMenuItem preferences = new JMenuItem();
+    JMenuItem saveState = new JMenuItem();
+    JMenuItem loadState = new JMenuItem();
+    JMenu jMenu1 = new JMenu();
+
+    public GDesktop() {
+        try {
+            jbInit();
+            this.setJMenuBar(DesktopMenubar);
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    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_actionPerformed(e);
+                }
+            });
+        inputURLMenuItem.setMnemonic('U');
+        inputURLMenuItem.setText("from URL");
+        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_actionPerformed(e);
+                }
+            });
+        quit.setMnemonic('Q');
+        quit.setText("Quit");
+        quit.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    quit_actionPerformed(e);
+                }
+            });
+        aboutMenuItem.setText("About");
+        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_actionPerformed(e);
+                }
+            });
+        this.getContentPane().setLayout(flowLayout1);
+        windowMenu.setText("Window");
+        preferences.setText("Preferences...");
+        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_actionPerformed(e);
+                }
+            });
+        loadState.setMnemonic('L');
+        loadState.setText("Load Project");
+        loadState.addActionListener(new ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    loadState_actionPerformed(e);
+                }
+            });
+        jMenu1.setMnemonic('I');
+        jMenu1.setText("Input Alignment");
+        DesktopMenubar.add(FileMenu);
+        DesktopMenubar.add(toolsMenu);
+        DesktopMenubar.add(HelpMenu);
+        DesktopMenubar.add(windowMenu);
+        FileMenu.addSeparator();
+        FileMenu.add(jMenu1);
+        FileMenu.addSeparator();
+        FileMenu.add(saveState);
+        FileMenu.add(loadState);
+        FileMenu.addSeparator();
+        FileMenu.add(quit);
+        HelpMenu.add(aboutMenuItem);
+        HelpMenu.add(documentationMenuItem);
+        toolsMenu.add(preferences);
+        jMenu1.add(inputLocalFileMenuItem);
+        jMenu1.add(inputURLMenuItem);
+        jMenu1.add(inputTextboxMenuItem);
+    }
+
+    protected void inputLocalFileMenuItem_actionPerformed(ActionEvent e) {
+    }
+
+    protected void inputURLMenuItem_actionPerformed(ActionEvent e) {
+    }
+
+    protected void inputTextboxMenuItem_actionPerformed(ActionEvent e) {
+    }
+
+    protected void quit_actionPerformed(ActionEvent e) {
+    }
+
+    protected void aboutMenuItem_actionPerformed(ActionEvent e) {
+    }
 
+    protected void documentationMenuItem_actionPerformed(ActionEvent e) {
+    }
+
+    public void SaveState_actionPerformed(ActionEvent e) {
+    }
 
-public class GDesktop extends JFrame
-{
-  JMenuBar DesktopMenubar = new JMenuBar();
-  JMenu FileMenu = new JMenu();
-  JMenu HelpMenu = new JMenu();
-  JMenuItem inputLocalFileMenuItem = new JMenuItem();
-  JMenuItem inputURLMenuItem = new JMenuItem();
-  JMenuItem inputTextboxMenuItem = new JMenuItem();
-  JMenuItem quit = new JMenuItem();
-  JMenuItem aboutMenuItem = new JMenuItem();
-  JMenuItem documentationMenuItem = new JMenuItem();
-  FlowLayout flowLayout1 = new FlowLayout();
-  protected static JMenu windowMenu = new JMenu();
-  JMenu toolsMenu = new JMenu();
-  JMenuItem preferences = new JMenuItem();
-  JMenuItem saveState = new JMenuItem();
-  JMenuItem loadState = new JMenuItem();
-  JMenu jMenu1 = new JMenu();
-  public GDesktop()
-  {
-    try
-    {
-      jbInit();
-      this.setJMenuBar(DesktopMenubar);
+    protected void preferences_actionPerformed(ActionEvent e) {
     }
-    catch(Exception e)
-    {
-      e.printStackTrace();
+
+    public void saveState_actionPerformed(ActionEvent e) {
     }
 
-  }
-  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_actionPerformed(e);
-      }
-    });
-    inputURLMenuItem.setMnemonic('U');
-    inputURLMenuItem.setText("from URL");
-    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_actionPerformed(e);
-      }
-    });
-    quit.setMnemonic('Q');
-    quit.setText("Quit");
-    quit.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        quit_actionPerformed(e);
-      }
-    });
-    aboutMenuItem.setText("About");
-    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_actionPerformed(e);
-      }
-    });
-    this.getContentPane().setLayout(flowLayout1);
-    windowMenu.setText("Window");
-    preferences.setText("Preferences...");
-    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_actionPerformed(e);
-      }
-    });
-    loadState.setMnemonic('L');
-    loadState.setText("Load Project");
-    loadState.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        loadState_actionPerformed(e);
-      }
-    });
-    jMenu1.setMnemonic('I');
-    jMenu1.setText("Input Alignment");
-    DesktopMenubar.add(FileMenu);
-    DesktopMenubar.add(toolsMenu);
-    DesktopMenubar.add(HelpMenu);
-    DesktopMenubar.add(windowMenu);
-    FileMenu.addSeparator();
-    FileMenu.add(jMenu1);
-    FileMenu.addSeparator();
-    FileMenu.add(saveState);
-    FileMenu.add(loadState);
-    FileMenu.addSeparator();
-    FileMenu.add(quit);
-    HelpMenu.add(aboutMenuItem);
-    HelpMenu.add(documentationMenuItem);
-    toolsMenu.add(preferences);
-    jMenu1.add(inputLocalFileMenuItem);
-    jMenu1.add(inputURLMenuItem);
-    jMenu1.add(inputTextboxMenuItem);
-
-  }
-
-  protected void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
-  { }
-
-  protected void inputURLMenuItem_actionPerformed(ActionEvent e)
-  {  }
-
-  protected void inputTextboxMenuItem_actionPerformed(ActionEvent e)
-  { }
-
-  protected void quit_actionPerformed(ActionEvent e)
-  {  }
-
-  protected void aboutMenuItem_actionPerformed(ActionEvent e)
-  { }
-
-  protected void documentationMenuItem_actionPerformed(ActionEvent e)
-  {  }
-
-  public void SaveState_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void preferences_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void saveState_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void loadState_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void loadJalviewAlign_actionPerformed(ActionEvent e)
-  {
-
-  }
+    public void loadState_actionPerformed(ActionEvent e) {
+    }
+
+    public void loadJalviewAlign_actionPerformed(ActionEvent e) {
+    }
 }
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index b7cd2e8..5aa9db1 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -16,126 +16,100 @@
 * 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 javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
 
+import javax.swing.*;
 
-public class GFinder extends JPanel
-{
-  JLabel jLabel1 = new JLabel();
-  protected JTextField textfield = new JTextField();
-  protected JButton findAll = new JButton();
-  protected JButton findNext = new JButton();
-  JPanel jPanel1 = new JPanel();
-  GridLayout gridLayout1 = new GridLayout();
-  protected JButton createNewGroup = new JButton();
 
-  public GFinder()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
+public class GFinder extends JPanel {
+    JLabel jLabel1 = new JLabel();
+    protected JTextField textfield = new JTextField();
+    protected JButton findAll = new JButton();
+    protected JButton findNext = new JButton();
+    JPanel jPanel1 = new JPanel();
+    GridLayout gridLayout1 = new GridLayout();
+    protected JButton createNewGroup = new JButton();
+
+    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");
-    jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
-    this.setLayout(null);
-    textfield.setFont(new java.awt.Font("Verdana", 0, 12));
-    textfield.setText("");
-    textfield.setBounds(new Rectangle(40, 27, 133, 21));
-    textfield.addKeyListener(new java.awt.event.KeyAdapter()
-    {
-      public void keyTyped(KeyEvent e)
-      {
-        textfield_keyTyped(e);
-      }
-    });
-    textfield.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        textfield_actionPerformed(e);
-      }
-    });
-    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);
-      }
-    });
-    jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
-    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);
-      }
-    });
-    jPanel1.add(findNext, null);
-    jPanel1.add(findAll, null);
-    jPanel1.add(createNewGroup, null);
-    this.add(textfield, null);
-    this.add(jLabel1, null);
-    this.add(jPanel1, null);
-  }
-
-  protected void findNext_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void findAll_actionPerformed(ActionEvent e)
-  {
-
-  }
 
+    private void jbInit() throws Exception {
+        jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+        jLabel1.setText("Find");
+        jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
+        this.setLayout(null);
+        textfield.setFont(new java.awt.Font("Verdana", 0, 12));
+        textfield.setText("");
+        textfield.setBounds(new Rectangle(40, 27, 133, 21));
+        textfield.addKeyListener(new java.awt.event.KeyAdapter() {
+                public void keyTyped(KeyEvent e) {
+                    textfield_keyTyped(e);
+                }
+            });
+        textfield.addActionListener(new java.awt.event.ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    textfield_actionPerformed(e);
+                }
+            });
+        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);
+                }
+            });
+        jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
+        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);
+                }
+            });
+        jPanel1.add(findNext, null);
+        jPanel1.add(findAll, null);
+        jPanel1.add(createNewGroup, null);
+        this.add(textfield, null);
+        this.add(jLabel1, null);
+        this.add(jPanel1, null);
+    }
 
-  protected void textfield_actionPerformed(ActionEvent e)
-  {
-
-  }
+    protected void findNext_actionPerformed(ActionEvent e) {
+    }
 
-  void textfield_keyTyped(KeyEvent e)
-  {
-    findNext.setEnabled(true);
-  }
+    protected void findAll_actionPerformed(ActionEvent e) {
+    }
 
-  public void createNewGroup_actionPerformed(ActionEvent e)
-  {
+    protected void textfield_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    void textfield_keyTyped(KeyEvent e) {
+        findNext.setEnabled(true);
+    }
 
+    public void createNewGroup_actionPerformed(ActionEvent e) {
+    }
 }
diff --git a/src/jalview/jbgui/GFontChooser.java b/src/jalview/jbgui/GFontChooser.java
index 5966af5..4ca3b42 100755
--- a/src/jalview/jbgui/GFontChooser.java
+++ b/src/jalview/jbgui/GFontChooser.java
@@ -16,167 +16,138 @@
 * 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 javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
 
+import javax.swing.*;
 
-public class GFontChooser extends JPanel
-{
-  JLabel jLabel1 = new JLabel();
-  protected JComboBox fontSize = new JComboBox();
-  protected JComboBox fontStyle = new JComboBox();
-  JLabel jLabel2 = new JLabel();
-  JLabel jLabel3 = new JLabel();
-  protected JComboBox fontName = new JComboBox();
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JPanel jPanel1 = new JPanel();
-  JPanel jPanel2 = new JPanel();
-  JPanel jPanel3 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  BorderLayout borderLayout3 = new BorderLayout();
-  FlowLayout flowLayout1 = new FlowLayout();
-  JButton defaultButton = new JButton();
 
-  public GFontChooser()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
+public class GFontChooser extends JPanel {
+    JLabel jLabel1 = new JLabel();
+    protected JComboBox fontSize = new JComboBox();
+    protected JComboBox fontStyle = new JComboBox();
+    JLabel jLabel2 = new JLabel();
+    JLabel jLabel3 = new JLabel();
+    protected JComboBox fontName = new JComboBox();
+    JButton ok = new JButton();
+    JButton cancel = new JButton();
+    JPanel jPanel1 = new JPanel();
+    JPanel jPanel2 = new JPanel();
+    JPanel jPanel3 = new JPanel();
+    BorderLayout borderLayout1 = new BorderLayout();
+    BorderLayout borderLayout2 = new BorderLayout();
+    BorderLayout borderLayout3 = new BorderLayout();
+    FlowLayout flowLayout1 = new FlowLayout();
+    JButton defaultButton = new JButton();
+
+    public GFontChooser() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
     }
-  }
-  private void jbInit() throws Exception
-  {
-    jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));
-    jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel1.setText("Font: ");
-    jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
-    this.setLayout(flowLayout1);
-    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_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_actionPerformed(e);
-      }
-    });
-    jLabel2.setFont(new java.awt.Font("Verdana", 0, 11));
-    jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel2.setText("Size: ");
-    jLabel2.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
-    jLabel3.setFont(new java.awt.Font("Verdana", 0, 11));
-    jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel3.setText("Style: ");
-    jLabel3.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
-    fontName.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontName.setMaximumSize(new Dimension(32767, 32767));
-    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_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_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_actionPerformed(e);
-      }
-    });
-    this.setBackground(Color.white);
-    jPanel1.setOpaque(false);
-    jPanel1.setLayout(borderLayout1);
-    jPanel2.setOpaque(false);
-    jPanel2.setLayout(borderLayout3);
-    jPanel3.setOpaque(false);
-    jPanel3.setLayout(borderLayout2);
-    flowLayout1.setAlignment(FlowLayout.CENTER);
-    flowLayout1.setVgap(5);
-    defaultButton.setText("Set as Default");
-    defaultButton.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        defaultButton_actionPerformed(e);
-      }
-    });
-    this.add(jPanel1, null);
-    jPanel1.add(jLabel1, BorderLayout.WEST);
-    jPanel1.add(fontName, BorderLayout.CENTER);
-    this.add(jPanel3, null);
-    this.add(jPanel2, null);
-    jPanel2.add(jLabel3,  BorderLayout.WEST);
-    jPanel2.add(fontStyle,  BorderLayout.CENTER);
-    jPanel3.add(jLabel2, BorderLayout.WEST);
-    jPanel3.add(fontSize, BorderLayout.CENTER);
-    this.add(ok, null);
-    this.add(cancel, null);
-    this.add(defaultButton);
-  }
-
-  protected void ok_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-
-  }
 
-  protected void fontName_actionPerformed(ActionEvent e)
-  {
-
-  }
+    private void jbInit() throws Exception {
+        jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));
+        jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
+        jLabel1.setText("Font: ");
+        jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+        this.setLayout(flowLayout1);
+        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_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_actionPerformed(e);
+                }
+            });
+        jLabel2.setFont(new java.awt.Font("Verdana", 0, 11));
+        jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
+        jLabel2.setText("Size: ");
+        jLabel2.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+        jLabel3.setFont(new java.awt.Font("Verdana", 0, 11));
+        jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);
+        jLabel3.setText("Style: ");
+        jLabel3.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+        fontName.setFont(new java.awt.Font("Verdana", 0, 11));
+        fontName.setMaximumSize(new Dimension(32767, 32767));
+        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_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_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_actionPerformed(e);
+                }
+            });
+        this.setBackground(Color.white);
+        jPanel1.setOpaque(false);
+        jPanel1.setLayout(borderLayout1);
+        jPanel2.setOpaque(false);
+        jPanel2.setLayout(borderLayout3);
+        jPanel3.setOpaque(false);
+        jPanel3.setLayout(borderLayout2);
+        flowLayout1.setAlignment(FlowLayout.CENTER);
+        flowLayout1.setVgap(5);
+        defaultButton.setText("Set as Default");
+        defaultButton.addActionListener(new ActionListener() {
+                public void actionPerformed(ActionEvent e) {
+                    defaultButton_actionPerformed(e);
+                }
+            });
+        this.add(jPanel1, null);
+        jPanel1.add(jLabel1, BorderLayout.WEST);
+        jPanel1.add(fontName, BorderLayout.CENTER);
+        this.add(jPanel3, null);
+        this.add(jPanel2, null);
+        jPanel2.add(jLabel3, BorderLayout.WEST);
+        jPanel2.add(fontStyle, BorderLayout.CENTER);
+        jPanel3.add(jLabel2, BorderLayout.WEST);
+        jPanel3.add(fontSize, BorderLayout.CENTER);
+        this.add(ok, null);
+        this.add(cancel, null);
+        this.add(defaultButton);
+    }
 
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
+    protected void ok_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void cancel_actionPerformed(ActionEvent e) {
+    }
 
-  protected void fontStyle_actionPerformed(ActionEvent e)
-  {
+    protected void fontName_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void fontSize_actionPerformed(ActionEvent e) {
+    }
 
-  public void defaultButton_actionPerformed(ActionEvent e)
-  {
+    protected void fontStyle_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    public void defaultButton_actionPerformed(ActionEvent e) {
+    }
 }
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 84e84c4..41d188e 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -15,102 +15,84 @@
 * 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 java.awt.event.*;
-
-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);
-    }
-  }
-  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 xCombobox_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void yCombobox_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void zCombobox_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-}
+*/
+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 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);
+        }
+    }
+
+    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 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 e8167cf..96a1a40 100755
--- a/src/jalview/jbgui/GPairwiseAlignPanel.java
+++ b/src/jalview/jbgui/GPairwiseAlignPanel.java
@@ -15,58 +15,48 @@
 * 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 javax.swing.*;
-import java.awt.*;
-import java.awt.event.*;
-
-
-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
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-  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_actionPerformed(e);
-      }
-    });
-    this.add(scrollPane, BorderLayout.CENTER);
-    scrollPane.getViewport().add(textarea, null);
-    this.add(jPanel1, BorderLayout.SOUTH);
-    jPanel1.add(viewInEditorButton, null);
-  }
-
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-}
+*/
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+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 {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    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_actionPerformed(e);
+                }
+            });
+        this.add(scrollPane, BorderLayout.CENTER);
+        scrollPane.getViewport().add(textarea, null);
+        this.add(jPanel1, BorderLayout.SOUTH);
+        jPanel1.add(viewInEditorButton, null);
+    }
+
+    protected void viewInEditorButton_actionPerformed(ActionEvent e) {
+    }
+}
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 1ead51c..2ab6edd 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -16,221 +16,193 @@
 * 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 javax.swing.*;
 import java.awt.*;
-import java.awt.event.ActionListener;
 import java.awt.event.ActionEvent;
-import javax.swing.border.TitledBorder;
+import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 
-public class GPreferences
-    extends JPanel
-{
-  public GPreferences()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(borderLayout1);
-    ok.setText("OK");
-    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_actionPerformed(e);
-      }
-    });
-    visual.setLayout(null);
-    quality.setEnabled(false);
-    quality.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    quality.setHorizontalAlignment(SwingConstants.RIGHT);
-    quality.setHorizontalTextPosition(SwingConstants.LEFT);
-    quality.setSelected(true);
-    quality.setText("Quality");
-    quality.setBounds(new Rectangle(248, 53, 81, 23));
-    jPanel2.setBorder(titledBorder1);
-    jPanel2.setBounds(new Rectangle(9, 20, 442, 241));
-    jPanel2.setLayout(null);
-    fullID.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    fullID.setHorizontalAlignment(SwingConstants.RIGHT);
-    fullID.setHorizontalTextPosition(SwingConstants.LEFT);
-    fullID.setText("Full Sequence ID");
-    fullID.setBounds(new Rectangle(9, 78, 129, 23));
-    fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
-    fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
-    fullScreen.setText("Maximise Window");
-    fullScreen.setBounds(new Rectangle(5, 29, 132, 23));
-    conservation.setEnabled(false);
-    conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    conservation.setHorizontalAlignment(SwingConstants.RIGHT);
-    conservation.setHorizontalTextPosition(SwingConstants.LEFT);
-    conservation.setSelected(true);
-    conservation.setText("Conservation");
-    conservation.setBounds(new Rectangle(137, 53, 113, 23));
-    identity.setEnabled(false);
-    identity.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    identity.setHorizontalAlignment(SwingConstants.RIGHT);
-    identity.setHorizontalTextPosition(SwingConstants.LEFT);
-    identity.setSelected(true);
-    identity.setText("Consensus");
-    identity.setBounds(new Rectangle(326, 53, 99, 23));
-    annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    annotations.setHorizontalAlignment(SwingConstants.RIGHT);
-    annotations.setHorizontalTextPosition(SwingConstants.LEFT);
-    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_actionPerformed(e);
-      }
-    });
-    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel1.setText("Gap Symbol");
-    jLabel1.setBounds(new Rectangle(41, 142, 76, 15));
-    colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    colour.setBounds(new Rectangle(121, 168, 154, 21));
-    jLabel2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel2.setText("Colour");
-    jLabel2.setBounds(new Rectangle(60, 172, 58, 15));
-    jLabel3.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel3.setText("Font");
-    jLabel3.setBounds(new Rectangle(83, 114, 34, 15));
-    fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    fontSizeCB.setBounds(new Rectangle(304, 109, 49, 21));
-    fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    fontStyleCB.setBounds(new Rectangle(353, 109, 80, 21));
-    fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    fontNameCB.setBounds(new Rectangle(121, 109, 183, 21));
-    gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    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)
-      {
-        jCheckBox1_actionPerformed(e);
-      }
-    });
-    startupCheckbox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
-    startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
-    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)
-      {
-        startupFileTextfield_mouseClicked();
-      }
-    });
-
-    jPanel2.add(annotations);
-    jPanel2.add(conservation);
-    jPanel2.add(quality);
-    jPanel2.add(fullID);
-    jPanel2.add(gapSymbolCB);
-    jPanel2.add(jLabel1);
-    jPanel2.add(fontNameCB);
-    jPanel2.add(jLabel2);
-    jPanel2.add(jLabel3);
-    jPanel2.add(colour);
-    jPanel2.add(fontSizeCB);
-    jPanel2.add(fontStyleCB);
-    jPanel2.add(identity);
-    jPanel2.add(fullScreen);
-    jPanel2.add(startupCheckbox);
-    jPanel2.add(startupFileTextfield);
-    jPanel1.add(ok);
-    jPanel1.add(cancel);
-    this.add(visaulTab, java.awt.BorderLayout.CENTER);
-    visaulTab.add(visual, "visual");
-    visual.add(jPanel2);
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-    DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
-    dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
-    gapSymbolCB.setRenderer(dlcr);
-
-  }
-
-  JTabbedPane visaulTab = new JTabbedPane();
-  JPanel visual = new JPanel();
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JPanel jPanel1 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  protected JCheckBox quality = new JCheckBox();
-  JPanel jPanel2 = new JPanel();
-  TitledBorder titledBorder1 = new TitledBorder("Open new alignment");
-  protected JCheckBox fullID = new JCheckBox();
-  protected JCheckBox fullScreen = new JCheckBox();
-  protected JCheckBox conservation = new JCheckBox();
-  protected JCheckBox identity = new JCheckBox();
-  protected JCheckBox annotations = new JCheckBox();
-  JLabel jLabel1 = new JLabel();
-  protected JComboBox colour = new JComboBox();
-  JLabel jLabel2 = new JLabel();
-  JLabel jLabel3 = new JLabel();
-  protected JComboBox fontSizeCB = new JComboBox();
-  protected JComboBox fontStyleCB = new JComboBox();
-  protected JComboBox fontNameCB = new JComboBox();
-  protected JComboBox gapSymbolCB = new JComboBox();
-  protected JCheckBox startupCheckbox = new JCheckBox();
-  protected JTextField startupFileTextfield = new JTextField();
-  public void ok_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-
-  }
+import javax.swing.*;
+import javax.swing.border.TitledBorder;
 
-  public void annotations_actionPerformed(ActionEvent e)
-  {
 
-  }
+public class GPreferences extends JPanel {
+    JTabbedPane visaulTab = new JTabbedPane();
+    JPanel visual = new JPanel();
+    JButton ok = new JButton();
+    JButton cancel = new JButton();
+    JPanel jPanel1 = new JPanel();
+    BorderLayout borderLayout1 = new BorderLayout();
+    protected JCheckBox quality = new JCheckBox();
+    JPanel jPanel2 = new JPanel();
+    TitledBorder titledBorder1 = new TitledBorder("Open new alignment");
+    protected JCheckBox fullID = new JCheckBox();
+    protected JCheckBox fullScreen = new JCheckBox();
+    protected JCheckBox conservation = new JCheckBox();
+    protected JCheckBox identity = new JCheckBox();
+    protected JCheckBox annotations = new JCheckBox();
+    JLabel jLabel1 = new JLabel();
+    protected JComboBox colour = new JComboBox();
+    JLabel jLabel2 = new JLabel();
+    JLabel jLabel3 = new JLabel();
+    protected JComboBox fontSizeCB = new JComboBox();
+    protected JComboBox fontStyleCB = new JComboBox();
+    protected JComboBox fontNameCB = new JComboBox();
+    protected JComboBox gapSymbolCB = new JComboBox();
+    protected JCheckBox startupCheckbox = new JCheckBox();
+    protected JTextField startupFileTextfield = new JTextField();
+
+    public GPreferences() {
+        try {
+            jbInit();
+        } catch (Exception ex) {
+            ex.printStackTrace();
+        }
+    }
 
-  public void jCheckBox1_actionPerformed(ActionEvent e)
-  {
+    private void jbInit() throws Exception {
+        this.setLayout(borderLayout1);
+        ok.setText("OK");
+        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_actionPerformed(e);
+                }
+            });
+        visual.setLayout(null);
+        quality.setEnabled(false);
+        quality.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        quality.setHorizontalAlignment(SwingConstants.RIGHT);
+        quality.setHorizontalTextPosition(SwingConstants.LEFT);
+        quality.setSelected(true);
+        quality.setText("Quality");
+        quality.setBounds(new Rectangle(248, 53, 81, 23));
+        jPanel2.setBorder(titledBorder1);
+        jPanel2.setBounds(new Rectangle(9, 20, 442, 241));
+        jPanel2.setLayout(null);
+        fullID.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        fullID.setHorizontalAlignment(SwingConstants.RIGHT);
+        fullID.setHorizontalTextPosition(SwingConstants.LEFT);
+        fullID.setText("Full Sequence ID");
+        fullID.setBounds(new Rectangle(9, 78, 129, 23));
+        fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+        fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+        fullScreen.setText("Maximise Window");
+        fullScreen.setBounds(new Rectangle(5, 29, 132, 23));
+        conservation.setEnabled(false);
+        conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        conservation.setHorizontalAlignment(SwingConstants.RIGHT);
+        conservation.setHorizontalTextPosition(SwingConstants.LEFT);
+        conservation.setSelected(true);
+        conservation.setText("Conservation");
+        conservation.setBounds(new Rectangle(137, 53, 113, 23));
+        identity.setEnabled(false);
+        identity.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        identity.setHorizontalAlignment(SwingConstants.RIGHT);
+        identity.setHorizontalTextPosition(SwingConstants.LEFT);
+        identity.setSelected(true);
+        identity.setText("Consensus");
+        identity.setBounds(new Rectangle(326, 53, 99, 23));
+        annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        annotations.setHorizontalAlignment(SwingConstants.RIGHT);
+        annotations.setHorizontalTextPosition(SwingConstants.LEFT);
+        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_actionPerformed(e);
+                }
+            });
+        jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
+        jLabel1.setText("Gap Symbol");
+        jLabel1.setBounds(new Rectangle(41, 142, 76, 15));
+        colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        colour.setBounds(new Rectangle(121, 168, 154, 21));
+        jLabel2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        jLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
+        jLabel2.setText("Colour");
+        jLabel2.setBounds(new Rectangle(60, 172, 58, 15));
+        jLabel3.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        jLabel3.setHorizontalAlignment(SwingConstants.RIGHT);
+        jLabel3.setText("Font");
+        jLabel3.setBounds(new Rectangle(83, 114, 34, 15));
+        fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        fontSizeCB.setBounds(new Rectangle(304, 109, 49, 21));
+        fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        fontStyleCB.setBounds(new Rectangle(353, 109, 80, 21));
+        fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        fontNameCB.setBounds(new Rectangle(121, 109, 183, 21));
+        gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        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) {
+                    jCheckBox1_actionPerformed(e);
+                }
+            });
+        startupCheckbox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+        startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
+        startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
+        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) {
+                    startupFileTextfield_mouseClicked();
+                }
+            });
+
+        jPanel2.add(annotations);
+        jPanel2.add(conservation);
+        jPanel2.add(quality);
+        jPanel2.add(fullID);
+        jPanel2.add(gapSymbolCB);
+        jPanel2.add(jLabel1);
+        jPanel2.add(fontNameCB);
+        jPanel2.add(jLabel2);
+        jPanel2.add(jLabel3);
+        jPanel2.add(colour);
+        jPanel2.add(fontSizeCB);
+        jPanel2.add(fontStyleCB);
+        jPanel2.add(identity);
+        jPanel2.add(fullScreen);
+        jPanel2.add(startupCheckbox);
+        jPanel2.add(startupFileTextfield);
+        jPanel1.add(ok);
+        jPanel1.add(cancel);
+        this.add(visaulTab, java.awt.BorderLayout.CENTER);
+        visaulTab.add(visual, "visual");
+        visual.add(jPanel2);
+        this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+
+        DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+        dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+        gapSymbolCB.setRenderer(dlcr);
+    }
 
-  }
+    public void ok_actionPerformed(ActionEvent e) {
+    }
 
+    public void cancel_actionPerformed(ActionEvent e) {
+    }
 
-  public void startupFileTextfield_mouseClicked()
-  {
+    public void annotations_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    public void jCheckBox1_actionPerformed(ActionEvent e) {
+    }
 
+    public void startupFileTextfield_mouseClicked() {
+    }
 }
diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java
index 17fdb34..341263f 100755
--- a/src/jalview/jbgui/GSliderPanel.java
+++ b/src/jalview/jbgui/GSliderPanel.java
@@ -15,132 +15,111 @@
 * 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 java.awt.event.*;
-
-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();
-  protected JLabel label = new JLabel();
-  JPanel jPanel1 = new JPanel();
-  GridLayout gridLayout1 = new GridLayout();
-  JPanel jPanel2 = new JPanel();
-  protected JButton applyButton = new JButton();
-  protected JButton undoButton = new JButton();
-  FlowLayout flowLayout1 = new FlowLayout();
-  protected JCheckBox allGroupsCheck = new JCheckBox();
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  public GSliderPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-  private void jbInit() throws Exception
-  {
-    this.setLayout(gridLayout1);
-    slider.setMajorTickSpacing(10);
-    slider.setMinorTickSpacing(1);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setFont(new java.awt.Font("Verdana", 0, 11));
-    slider.setDoubleBuffered(true);
-    valueField.setFont(new java.awt.Font("Verdana", 0, 11));
-    valueField.setMinimumSize(new Dimension(6, 14));
-    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_actionPerformed(e);
-      }
-    });
-    label.setFont(new java.awt.Font("Verdana", 0, 11));
-    label.setOpaque(false);
-    label.setHorizontalAlignment(SwingConstants.CENTER);
-    label.setText("set this label text");
-    jPanel1.setLayout(borderLayout1);
-    gridLayout1.setRows(2);
-    jPanel2.setLayout(flowLayout1);
-    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_actionPerformed(e);
-      }
-    });
-    undoButton.setEnabled(false);
-    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_actionPerformed(e);
-      }
-    });
-    allGroupsCheck.setEnabled(false);
-    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_actionPerformed(e);
-      }
-    });
-    this.setBackground(Color.white);
-    this.setPreferredSize(new Dimension(415, 84));
-    jPanel2.setOpaque(false);
-    jPanel1.setOpaque(false);
-    this.add(jPanel2, null);
-    jPanel2.add(label, null);
-    jPanel2.add(applyButton, null);
-    jPanel2.add(undoButton, null);this.add(jPanel1, null);
-    jPanel1.add(slider,  BorderLayout.WEST);
-    jPanel1.add(valueField,  BorderLayout.CENTER);
-    jPanel1.add(allGroupsCheck, BorderLayout.EAST);
-
-  }
-
-  protected void valueField_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void undoButton_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void allGroupsCheck_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-}
+*/
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+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();
+    protected JLabel label = new JLabel();
+    JPanel jPanel1 = new JPanel();
+    GridLayout gridLayout1 = new GridLayout();
+    JPanel jPanel2 = new JPanel();
+    protected JButton applyButton = new JButton();
+    protected JButton undoButton = new JButton();
+    FlowLayout flowLayout1 = new FlowLayout();
+    protected JCheckBox allGroupsCheck = new JCheckBox();
+    BorderLayout borderLayout1 = new BorderLayout();
+
+    public GSliderPanel() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    private void jbInit() throws Exception {
+        this.setLayout(gridLayout1);
+        slider.setMajorTickSpacing(10);
+        slider.setMinorTickSpacing(1);
+        slider.setPaintTicks(true);
+        slider.setBackground(Color.white);
+        slider.setFont(new java.awt.Font("Verdana", 0, 11));
+        slider.setDoubleBuffered(true);
+        valueField.setFont(new java.awt.Font("Verdana", 0, 11));
+        valueField.setMinimumSize(new Dimension(6, 14));
+        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_actionPerformed(e);
+                }
+            });
+        label.setFont(new java.awt.Font("Verdana", 0, 11));
+        label.setOpaque(false);
+        label.setHorizontalAlignment(SwingConstants.CENTER);
+        label.setText("set this label text");
+        jPanel1.setLayout(borderLayout1);
+        gridLayout1.setRows(2);
+        jPanel2.setLayout(flowLayout1);
+        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_actionPerformed(e);
+                }
+            });
+        undoButton.setEnabled(false);
+        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_actionPerformed(e);
+                }
+            });
+        allGroupsCheck.setEnabled(false);
+        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_actionPerformed(e);
+                }
+            });
+        this.setBackground(Color.white);
+        this.setPreferredSize(new Dimension(415, 84));
+        jPanel2.setOpaque(false);
+        jPanel1.setOpaque(false);
+        this.add(jPanel2, null);
+        jPanel2.add(label, null);
+        jPanel2.add(applyButton, null);
+        jPanel2.add(undoButton, null);
+        this.add(jPanel1, null);
+        jPanel1.add(slider, BorderLayout.WEST);
+        jPanel1.add(valueField, BorderLayout.CENTER);
+        jPanel1.add(allGroupsCheck, BorderLayout.EAST);
+    }
+
+    protected void valueField_actionPerformed(ActionEvent e) {
+    }
+
+    protected void applyButton_actionPerformed(ActionEvent e) {
+    }
+
+    protected void undoButton_actionPerformed(ActionEvent e) {
+    }
+
+    protected void allGroupsCheck_actionPerformed(ActionEvent e) {
+    }
+}
diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index 93bb850..5b8c6fa 100755
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -16,202 +16,155 @@
 * 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 java.awt.event.*;
 
-public class GTreePanel extends JInternalFrame
-{
-  BorderLayout borderLayout1 = new BorderLayout();
-  protected JScrollPane scrollPane = new JScrollPane();
-  JMenuBar jMenuBar1 = new JMenuBar();
-  JMenu jMenu1 = new JMenu();
-  JMenuItem saveAsNewick = new JMenuItem();
-  JMenuItem printMenu = new JMenuItem();
-  JMenu jMenu2 = new JMenu();
-  protected JMenuItem fontSize = new JMenuItem();
-  protected JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
-  protected 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);
+import javax.swing.*;
+
+
+public class GTreePanel extends JInternalFrame {
+    BorderLayout borderLayout1 = new BorderLayout();
+    protected JScrollPane scrollPane = new JScrollPane();
+    JMenuBar jMenuBar1 = new JMenuBar();
+    JMenu jMenu1 = new JMenu();
+    JMenuItem saveAsNewick = new JMenuItem();
+    JMenuItem printMenu = new JMenuItem();
+    JMenu jMenu2 = new JMenu();
+    protected JMenuItem fontSize = new JMenuItem();
+    protected JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
+    protected JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
+    protected JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
+    protected 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);
+    }
+
+    protected void printMenu_actionPerformed(ActionEvent e) {
+    }
+
+    protected void fontSize_actionPerformed(ActionEvent e) {
+    }
+
+    protected void distanceMenu_actionPerformed(ActionEvent e) {
+    }
+
+    protected void bootstrapMenu_actionPerformed(ActionEvent e) {
+    }
+
+    protected void fitToWindow_actionPerformed(ActionEvent e) {
+    }
+
+    protected void pngTree_actionPerformed(ActionEvent e) {
+    }
+
+    protected void epsTree_actionPerformed(ActionEvent e) {
     }
-    catch(Exception e)
-    {
-      e.printStackTrace();
+
+    protected void saveAsNewick_actionPerformed(ActionEvent e) {
     }
 
-  }
-  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);
-  }
-
-
-  protected void printMenu_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void distanceMenu_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void fitToWindow_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void pngTree_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void epsTree_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void saveAsNewick_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void placeholdersMenu_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void textbox_actionPerformed(ActionEvent e)
-  {
-
-  }
+    protected 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 4d62593..3cd9f51 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -16,125 +16,99 @@
 * 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 javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
 
+import javax.swing.*;
 
-public class GUserDefinedColours extends JPanel
-{
-  protected JColorChooser colorChooser = new JColorChooser();
-  protected JPanel buttonPanel = new JPanel();
-  protected GridLayout gridLayout = new GridLayout();
-  JPanel jPanel2 = new JPanel();
-  protected JButton okButton = new JButton();
-  protected JButton applyButton = new JButton();
-  protected JButton loadbutton = new JButton();
-  protected JButton savebutton = new JButton();
-  protected JButton cancelButton = new JButton();
-  FlowLayout flowLayout1 = new FlowLayout();
 
-  public GUserDefinedColours()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
+public class GUserDefinedColours extends JPanel {
+    protected JColorChooser colorChooser = new JColorChooser();
+    protected JPanel buttonPanel = new JPanel();
+    protected GridLayout gridLayout = new GridLayout();
+    JPanel jPanel2 = new JPanel();
+    protected JButton okButton = new JButton();
+    protected JButton applyButton = new JButton();
+    protected JButton loadbutton = new JButton();
+    protected JButton savebutton = new JButton();
+    protected JButton cancelButton = new JButton();
+    FlowLayout flowLayout1 = new FlowLayout();
+
+    public GUserDefinedColours() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
     }
-  }
-  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_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_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_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_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_actionPerformed(e);
-      }
-    });
-    this.setBackground(new Color(212, 208, 223));
-    jPanel2.setOpaque(false);
-    colorChooser.setOpaque(false);
-    this.add(colorChooser, null);
-    this.add(buttonPanel, null);
-     this.add(jPanel2, null);
-    jPanel2.add(okButton, null);
-    jPanel2.add(applyButton, null);
-    jPanel2.add(loadbutton, null);
-    jPanel2.add(savebutton, null);
-    jPanel2.add(cancelButton, null);
-  }
-
-
-  protected void okButton_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
 
-  }
-
-  protected void loadbutton_actionPerformed(ActionEvent e)
-  {
+    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_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_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_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_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_actionPerformed(e);
+                }
+            });
+        this.setBackground(new Color(212, 208, 223));
+        jPanel2.setOpaque(false);
+        colorChooser.setOpaque(false);
+        this.add(colorChooser, null);
+        this.add(buttonPanel, null);
+        this.add(jPanel2, null);
+        jPanel2.add(okButton, null);
+        jPanel2.add(applyButton, null);
+        jPanel2.add(loadbutton, null);
+        jPanel2.add(savebutton, null);
+        jPanel2.add(cancelButton, null);
+    }
 
-  }
+    protected void okButton_actionPerformed(ActionEvent e) {
+    }
 
-  protected void savebutton_actionPerformed(ActionEvent e)
-  {
+    protected void applyButton_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void loadbutton_actionPerformed(ActionEvent e) {
+    }
 
-  protected void cancelButton_actionPerformed(ActionEvent e)
-  {
+    protected void savebutton_actionPerformed(ActionEvent e) {
+    }
 
-  }
+    protected void cancelButton_actionPerformed(ActionEvent e) {
+    }
 }
diff --git a/src/jalview/jbgui/GWebserviceInfo.java b/src/jalview/jbgui/GWebserviceInfo.java
index 4d3aab6..54eab04 100755
--- a/src/jalview/jbgui/GWebserviceInfo.java
+++ b/src/jalview/jbgui/GWebserviceInfo.java
@@ -15,86 +15,80 @@
 * 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 java.awt.event.*;
-
-public class GWebserviceInfo extends JPanel
-{
-  protected JTextArea infoText = new JTextArea();
-  JScrollPane jScrollPane1 = new JScrollPane();
-  JScrollPane jScrollPane2 = new JScrollPane();
-  protected JTextArea progressText = new JTextArea();
-  JPanel jPanel1 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  protected JPanel titlePanel = new JPanel();
-  BorderLayout borderLayout3 = new BorderLayout();
-  JPanel jPanel2 = new JPanel();
-  protected JButton cancel = new JButton();
-  GridBagLayout gridBagLayout1 = new GridBagLayout();
-
-  public GWebserviceInfo()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-  private void jbInit() throws Exception
-  {
-    infoText.setFont(new java.awt.Font("Verdana", 0, 10));
-    infoText.setBorder(null);
-    infoText.setEditable(false);
-    infoText.setText("");
-    infoText.setLineWrap(true);
-    infoText.setWrapStyleWord(true);
-    this.setLayout(borderLayout1);
-    progressText.setFont(new java.awt.Font("Verdana", 0, 10));
-    progressText.setBorder(null);
-    progressText.setEditable(false);
-    progressText.setText("");
-    progressText.setLineWrap(true);
-    progressText.setWrapStyleWord(true);
-    jPanel1.setLayout(borderLayout2);
-    titlePanel.setBackground(Color.white);
-    titlePanel.setPreferredSize(new Dimension(0, 60));
-    titlePanel.setLayout(borderLayout3);
-    jScrollPane2.setBorder(null);
-    jScrollPane1.setBorder(null);
-    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_actionPerformed(e);
-      }
-    });
-    jPanel2.setLayout(gridBagLayout1);
-    jPanel2.setOpaque(false);
-    this.add(jScrollPane2, BorderLayout.CENTER);
-    this.add(jPanel1, BorderLayout.NORTH);
-    jPanel1.add(jScrollPane1, BorderLayout.CENTER);
-    jScrollPane1.getViewport().add(infoText, null);
-    jScrollPane2.getViewport().add(progressText, null);
-    jPanel1.add(titlePanel, BorderLayout.NORTH);
-    titlePanel.add(jPanel2, BorderLayout.EAST);
-    jPanel2.add(cancel,    new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0
-            ,GridBagConstraints.SOUTH, GridBagConstraints.NONE, new Insets(24, 5, 21, 5), 0, 0));
-  }
-
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-
-  }
-}
+*/
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+public class GWebserviceInfo extends JPanel {
+    protected JTextArea infoText = new JTextArea();
+    JScrollPane jScrollPane1 = new JScrollPane();
+    JScrollPane jScrollPane2 = new JScrollPane();
+    protected JTextArea progressText = new JTextArea();
+    JPanel jPanel1 = new JPanel();
+    BorderLayout borderLayout1 = new BorderLayout();
+    BorderLayout borderLayout2 = new BorderLayout();
+    protected JPanel titlePanel = new JPanel();
+    BorderLayout borderLayout3 = new BorderLayout();
+    JPanel jPanel2 = new JPanel();
+    protected JButton cancel = new JButton();
+    GridBagLayout gridBagLayout1 = new GridBagLayout();
+
+    public GWebserviceInfo() {
+        try {
+            jbInit();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    private void jbInit() throws Exception {
+        infoText.setFont(new java.awt.Font("Verdana", 0, 10));
+        infoText.setBorder(null);
+        infoText.setEditable(false);
+        infoText.setText("");
+        infoText.setLineWrap(true);
+        infoText.setWrapStyleWord(true);
+        this.setLayout(borderLayout1);
+        progressText.setFont(new java.awt.Font("Verdana", 0, 10));
+        progressText.setBorder(null);
+        progressText.setEditable(false);
+        progressText.setText("");
+        progressText.setLineWrap(true);
+        progressText.setWrapStyleWord(true);
+        jPanel1.setLayout(borderLayout2);
+        titlePanel.setBackground(Color.white);
+        titlePanel.setPreferredSize(new Dimension(0, 60));
+        titlePanel.setLayout(borderLayout3);
+        jScrollPane2.setBorder(null);
+        jScrollPane1.setBorder(null);
+        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_actionPerformed(e);
+                }
+            });
+        jPanel2.setLayout(gridBagLayout1);
+        jPanel2.setOpaque(false);
+        this.add(jScrollPane2, BorderLayout.CENTER);
+        this.add(jPanel1, BorderLayout.NORTH);
+        jPanel1.add(jScrollPane1, BorderLayout.CENTER);
+        jScrollPane1.getViewport().add(infoText, null);
+        jScrollPane2.getViewport().add(progressText, null);
+        jPanel1.add(titlePanel, BorderLayout.NORTH);
+        titlePanel.add(jPanel2, BorderLayout.EAST);
+        jPanel2.add(cancel,
+            new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
+                GridBagConstraints.SOUTH, GridBagConstraints.NONE,
+                new Insets(24, 5, 21, 5), 0, 0));
+    }
+
+    protected void cancel_actionPerformed(ActionEvent e) {
+    }
+}
diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 3b93d6d..30c534b 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -16,576 +16,623 @@
 * 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.math;
 
 import jalview.util.*;
 
 import java.io.*;
 
-public class Matrix {
-
-  /**
-   * SMJSPUBLIC
-   */
-  public double[][] value;
-  public int rows;
-  public int cols;
-  public double[] d;  // Diagonal
-  public double[] e;  // off diagonal
-
-  public Matrix(double[][] value, int rows, int cols) {
-    this.rows = rows;
-    this.cols = cols;
-    this.value = value;
-  }
-
-  public Matrix transpose() {
-    double[][] out = new double[cols][rows];
-
-    for (int i = 0; i < cols; i++) {
-      for (int j = 0; j < rows ; j++) {
-        out[i][j] = value[j][i];
-      }
-    }
-    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++) {
-        Format.print(ps,"%8.2f",value[i][j]);
-      }
-      ps.println();
+public class Matrix {
+    /**
+     * SMJSPUBLIC
+     */
+    public double[][] value;
+    public int rows;
+    public int cols;
+    public double[] d; // Diagonal
+    public double[] e; // off diagonal
+
+    public Matrix(double[][] value, int rows, int cols) {
+        this.rows = rows;
+        this.cols = cols;
+        this.value = value;
     }
-  }
 
+    public Matrix transpose() {
+        double[][] out = new double[cols][rows];
 
-  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++ ) {
-        tmp[i][j] = 0.0;
-
-        for (int k = 0; k < in.cols; k++) {
-          tmp[i][j] += in.value[i][k]*this.value[k][j];
+        for (int i = 0; i < cols; i++) {
+            for (int j = 0; j < rows; j++) {
+                out[i][j] = value[j][i];
+            }
         }
 
-      }
+        return new Matrix(out, cols, rows);
     }
 
-    return new Matrix(tmp,in.rows,this.cols);
-  }
+    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]);
+            }
 
-  public double[] vectorPostMultiply(double[] in) {
-    double[] out = new double[in.length];
-    for (int i = 0; i < in.length; i++) {
-      out[i] = 0.0;
-      for (int k=0; k < in.length; k++) {
-        out[i] += value[i][k] * in[k];
-      }
+            ps.println();
+        }
     }
-    return out;
-  }
-  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++ ) {
+    public Matrix preMultiply(Matrix in) {
+        double[][] tmp = new double[in.rows][this.cols];
 
-        out[i][j] = 0.0;
+        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 < rows; k++) {
-          out[i][j] = out[i][j] + value[i][k]*in.value[k][j];
+                for (int k = 0; k < in.cols; k++) {
+                    tmp[i][j] += (in.value[i][k] * this.value[k][j]);
+                }
+            }
         }
 
-      }
+        return new Matrix(tmp, in.rows, this.cols);
     }
-    return new Matrix(out,this.cols,in.rows);
-  }
 
-  public Matrix copy() {
-    double[][] newmat = new double[rows][cols];
+    public double[] vectorPostMultiply(double[] in) {
+        double[] out = new double[in.length];
 
-    for (int i = 0; i < rows; i++) {
-      for (int j = 0; j < cols; j++) {
-        newmat[i][j] = value[i][j];
-      }
-    }
-    return new Matrix(newmat,rows,cols);
-  }
-
-  public void tred() {
-    int n = rows;
-    int l;
-    int k;
-    int j;
-    int i;
-
-    double scale;
-    double hh;
-    double h;
-    double g;
-    double f;
-
-    this.d = new double[rows];
-    this.e = new double[rows];
-
-    for (i=n; i >= 2;i--) {
-      l=i-1;
-      h = 0.0;
-      scale = 0.0;
-
-      if (l > 1) {
-        for (k=1;k<=l;k++) {
-          scale += Math.abs(value[i-1][k-1]);
-        }
-        if (scale == 0.0) {
-          e[i-1] = value[i-1][l-1];
-        } 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) {
-            g = -1.0*Math.sqrt(h);
-          } else {
-            g = Math.sqrt(h);
-          }
-          e[i-1] = scale*g;
-          h -= f*g;
-          value[i-1][l-1] = f-g;
-          f=0.0;
-          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++) {
-              g += value[j-1][k-1]*value[i-1][k-1];
-            }
-            for (k=j+1; k<=l;k++) {
-              g+= value[k-1][j-1]*value[i-1][k-1];
-            }
-            e[j-1] = g/h;
-            f+=e[j-1]*value[i-1][j-1];
-          }
-          hh=f/(h+h);
-          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++) {
-              value[j-1][k-1] -= (f*e[k-1]+g*value[i-1][k-1]);
-            }
-          }
-        }
-      } else {
-        e[i-1] = value[i-1][l-1];
-      }
-      d[i-1] = h;
-    }
-    d[0] = 0.0;
-    e[0] = 0.0;
-    for (i=1;i<=n;i++) {
-      l=i-1;
-      if (d[i-1] != 0.0) {
-        for (j=1;j<=l;j++) {
-          g=0.0;
-          for (k=1;k<=l;k++) {
-            g+= value[i-1][k-1]*value[k-1][j-1];
-          }
-          for (k=1;k<=l;k++) {
-            value[k-1][j-1] -= g*value[k-1][i-1];
-          }
-        }
-      }
-      d[i-1] = value[i-1][i-1];
-      value[i-1][i-1] = 1.0;
-      for (j=1;j<=l;j++) {
-        value[j-1][i-1] = 0.0;
-        value[i-1][j-1] = 0.0;
-      }
-    }
-  }
-
-  public void tqli() {
-    int n = rows;
-
-    int m;
-    int l;
-    int iter;
-    int i;
-    int k;
-    double s;
-    double r;
-    double p;
-    ;
-    double g;
-    double f;
-    double dd;
-    double c;
-    double b;
-
-    for (i=2;i<=n;i++) {
-      e[i-2] = e[i-1];
-    }
-    e[n-1] = 0.0;
-    for (l=1;l<=n;l++) {
-      iter=0;
-      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)
-            break;
-        }
-        if (m != l) {
-          iter++;
-          if (iter == 30) {
-            System.err.print("Too many iterations in tqli");
-            System.exit(0); // JBPNote - should this really be here ???
-          } else {
-            //	    System.out.println("Iteration " + iter);
-          }
-          g=(d[l]-d[l-1])/(2.0*e[l-1]);
-          r = Math.sqrt((g*g) + 1.0);
-          g=d[m-1]-d[l-1]+e[l-1]/(g + sign(r,g));
-          c = 1.0;
-          s = c;
-          p=0.0;
-          for (i=m-1;i>=l;i--) {
-            f = s*e[i-1];
-            b = c*e[i-1];
-            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 {
-              s=f/g;
-              r = Math.sqrt((s*s)+1.0);
-              e[i] = g*r;
-              c = 1.0/r;
-              s *= c;
-            }
-            g=d[i] -p;
-            r=(d[i-1]-g)*s + 2.0*c*b;
-            p=s*r;
-            d[i] = g + p;
-            g = c * r - b;
-            for (k=1; k <= n; k++) {
-              f=value[k-1][i];
-              value[k-1][i] = s*value[k-1][i-1] + c*f;
-              value[k-1][i-1] = c*value[k-1][i-1] - s*f;
-            }
-          }
-          d[l-1] = d[l-1] - p;
-          e[l-1] = g;
-          e[m-1] = 0.0;
-        }
-      } while ( m != l);
-    }
-  }
-  public void tred2() {
-    int n = rows;
-    int l;
-    int k;
-    int j;
-    int i;
-
-    double scale;
-    double hh;
-    double h;
-    double g;
-    double f;
-
-    this.d = new double[rows];
-    this.e = new double[rows];
-
-    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++) {
-          scale += Math.abs(value[i][k]);
-        }
-        if (scale == 0.0) {
-          e[i] = value[i][l];
-        } 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) {
-            g = -1.0*Math.sqrt(h);
-          } else {
-            g = Math.sqrt(h);
-          }
-          e[i] = scale*g;
-          h -= f*g;
-          value[i][l] = f-g;
-          f=0.0;
-          for (j=0; j < l; j++) {
-            value[j][i] = value[i][j]/h;
-            g=0.0;
-            for (k= 0; k < j; k++) {
-              g += value[j][k]*value[i][k];
-            }
-            for (k=j; k<l;k++) {
-              g+= value[k][j]*value[i][k];
-            }
-            e[j] = g/h;
-            f+=e[j]*value[i][j];
-          }
-          hh=f/(h+h);
-          for (j=0;j<l;j++) {
-            f=value[i][j];
-            g = e[j] - hh*f;
-            e[j] = g;
-            for (k=0;k<j;k++) {
-              value[j][k] -= (f*e[k]+g*value[i][k]);
-            }
-          }
-        }
-      } else {
-        e[i] = value[i][l];
-      }
-      d[i] = h;
-    }
-    d[0] = 0.0;
-    e[0] = 0.0;
-    for (i=0;i<n;i++) {
-      l=i-1;
-      if (d[i] != 0.0) {
-        for (j=0;j<l;j++) {
-          g=0.0;
-          for (k=0;k<l;k++) {
-            g+= value[i][k]*value[k][j];
-          }
-          for (k=0;k<l;k++) {
-            value[k][j] -= g*value[k][i];
-          }
-        }
-      }
-      d[i] = value[i][i];
-      value[i][i] = 1.0;
-      for (j=0;j<l;j++) {
-        value[j][i] = 0.0;
-        value[i][j] = 0.0;
-      }
-    }
-  }
-
-  public void tqli2() {
-    int n = rows;
-
-    int m;
-    int l;
-    int iter;
-    int i;
-    int k;
-    double s;
-    double r;
-    double p;
-    ;
-    double g;
-    double f;
-    double dd;
-    double c;
-    double b;
-
-    for (i=2;i<=n;i++) {
-      e[i-2] = e[i-1];
-    }
-    e[n-1] = 0.0;
-    for (l=1;l<=n;l++) {
-      iter=0;
-      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)
-            break;
-        }
-        if (m != l) {
-          iter++;
-          if (iter == 30) {
-            System.err.print("Too many iterations in tqli");
-            System.exit(0); // JBPNote - same as above - not a graceful exit!
-          } else {
-            //	    System.out.println("Iteration " + iter);
-          }
-          g=(d[l]-d[l-1])/(2.0*e[l-1]);
-          r = Math.sqrt((g*g) + 1.0);
-          g=d[m-1]-d[l-1]+e[l-1]/(g + sign(r,g));
-          c = 1.0;
-          s = c;
-          p=0.0;
-          for (i=m-1;i>=l;i--) {
-            f = s*e[i-1];
-            b = c*e[i-1];
-            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 {
-              s=f/g;
-              r = Math.sqrt((s*s)+1.0);
-              e[i] = g*r;
-              c = 1.0/r;
-              s *= c;
-            }
-            g=d[i] -p;
-            r=(d[i-1]-g)*s + 2.0*c*b;
-            p=s*r;
-            d[i] = g + p;
-            g = c * r - b;
-            for (k=1; k <= n; k++) {
-              f=value[k-1][i];
-              value[k-1][i] = s*value[k-1][i-1] + c*f;
-              value[k-1][i-1] = c*value[k-1][i-1] - s*f;
+        for (int i = 0; i < in.length; i++) {
+            out[i] = 0.0;
+
+            for (int k = 0; k < in.length; k++) {
+                out[i] += (value[i][k] * in[k]);
             }
-          }
-          d[l-1] = d[l-1] - p;
-          e[l-1] = g;
-          e[m-1] = 0.0;
         }
-      } while ( m != l);
-    }
-  }
 
-  public double sign(double a, double b) {
-    if (b < 0) {
-      return -Math.abs(a);
-    } else {
-      return Math.abs(a);
+        return out;
     }
-  }
 
-  public double[] getColumn(int n) {
-    double[] out  = new double[rows];
-    for (int i=0;i<rows;i++) {
-      out[i] = value[i][n];
-    }
-    return out;
-  }
+    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++) {
+                out[i][j] = 0.0;
 
-  public void printD(PrintStream ps) {
+                for (int k = 0; k < rows; k++) {
+                    out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
+                }
+            }
+        }
 
-    for (int j = 0; j < rows;j++) {
-      Format.print(ps,"%15.4e",d[j]);
+        return new Matrix(out, this.cols, in.rows);
     }
-  }
-  public void printE(PrintStream ps) {
 
-    for (int j = 0; j < rows;j++) {
-      Format.print(ps,"%15.4e",e[j]);
-    }
-  }
+    public Matrix copy() {
+        double[][] newmat = new double[rows][cols];
 
-  public static void main(String[] args) {
-    int n = Integer.parseInt(args[0]);
-    double[][] in = new double[n][n];
+        for (int i = 0; i < rows; i++) {
+            for (int j = 0; j < cols; j++) {
+                newmat[i][j] = value[i][j];
+            }
+        }
 
-    for (int i = 0;i < n;i++) {
-      for (int j = 0; j < n; j++) {
-        in[i][j] = (double)Math.random();
-      }
+        return new Matrix(newmat, rows, cols);
     }
 
-    Matrix origmat = new Matrix(in,n,n);
-    //    System.out.println(" --- Original matrix ---- ");
-    ///    origmat.print(System.out);
-    //System.out.println();
-
-    //System.out.println(" --- transpose matrix ---- ");
-    Matrix trans = origmat.transpose();
-    //trans.print(System.out);
-    //System.out.println();
-
-    //System.out.println(" --- OrigT * Orig ---- ");
-
-    Matrix symm = trans.postMultiply(origmat);
-    //symm.print(System.out);
-    //System.out.println();
-
-    // Copy the symmetric matrix for later
-    Matrix origsymm = symm.copy();
+    public void tred() {
+        int n = rows;
+        int l;
+        int k;
+        int j;
+        int i;
+
+        double scale;
+        double hh;
+        double h;
+        double g;
+        double f;
+
+        this.d = new double[rows];
+        this.e = new double[rows];
+
+        for (i = n; i >= 2; i--) {
+            l = i - 1;
+            h = 0.0;
+            scale = 0.0;
+
+            if (l > 1) {
+                for (k = 1; k <= l; k++) {
+                    scale += Math.abs(value[i - 1][k - 1]);
+                }
+
+                if (scale == 0.0) {
+                    e[i - 1] = value[i - 1][l - 1];
+                } 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) {
+                        g = -1.0 * Math.sqrt(h);
+                    } else {
+                        g = Math.sqrt(h);
+                    }
+
+                    e[i - 1] = scale * g;
+                    h -= (f * g);
+                    value[i - 1][l - 1] = f - g;
+                    f = 0.0;
+
+                    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++) {
+                            g += (value[j - 1][k - 1] * value[i - 1][k - 1]);
+                        }
+
+                        for (k = j + 1; k <= l; k++) {
+                            g += (value[k - 1][j - 1] * value[i - 1][k - 1]);
+                        }
+
+                        e[j - 1] = g / h;
+                        f += (e[j - 1] * value[i - 1][j - 1]);
+                    }
+
+                    hh = f / (h + h);
+
+                    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++) {
+                            value[j - 1][k - 1] -= ((f * e[k - 1]) +
+                            (g * value[i - 1][k - 1]));
+                        }
+                    }
+                }
+            } else {
+                e[i - 1] = value[i - 1][l - 1];
+            }
 
+            d[i - 1] = h;
+        }
 
-    // This produces the tridiagonal transformation matrix
-    long tstart = System.currentTimeMillis();
-    symm.tred();
-    long tend = System.currentTimeMillis();
-    //System.out.println("Time take for tred = " + (tend-tstart) + "ms");
-    //System.out.println(" ---Tridiag transform matrix ---");
-    //symm.print(System.out);
-    //System.out.println();
+        d[0] = 0.0;
+        e[0] = 0.0;
 
-    //System.out.println(" --- D vector ---");
-    //symm.printD(System.out);
-    //System.out.println();
-    //System.out.println(" --- E vector ---");
-    //symm.printE(System.out);
-    //System.out.println();
+        for (i = 1; i <= n; i++) {
+            l = i - 1;
 
+            if (d[i - 1] != 0.0) {
+                for (j = 1; j <= l; j++) {
+                    g = 0.0;
 
-    // Now produce the diagonalization matrix
-    tstart = System.currentTimeMillis();
-    symm.tqli();
-    tend = System.currentTimeMillis();
-    //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
+                    for (k = 1; k <= l; k++) {
+                        g += (value[i - 1][k - 1] * value[k - 1][j - 1]);
+                    }
 
-    //System.out.println(" --- New diagonalization matrix ---");
-    //symm.print(System.out);
-    //System.out.println();
+                    for (k = 1; k <= l; k++) {
+                        value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);
+                    }
+                }
+            }
 
-    //System.out.println(" --- D vector ---");
-    //symm.printD(System.out);
-    //System.out.println();
-    //System.out.println(" --- E vector ---");
-    //symm.printE(System.out);
-    //System.out.println();
+            d[i - 1] = value[i - 1][i - 1];
+            value[i - 1][i - 1] = 1.0;
 
-    //System.out.println(" --- First eigenvector --- ");
-    //double[] eigenv = symm.getColumn(0);
-    //for (int i=0; i < eigenv.length;i++) {
-    //  Format.print(System.out,"%15.4f",eigenv[i]);
-    // }
-    //System.out.println();
+            for (j = 1; j <= l; j++) {
+                value[j - 1][i - 1] = 0.0;
+                value[i - 1][j - 1] = 0.0;
+            }
+        }
+    }
 
-    //double[] neigenv = origsymm.vectorPostMultiply(eigenv);
+    public void tqli() {
+        int n = rows;
+
+        int m;
+        int l;
+        int iter;
+        int i;
+        int k;
+        double s;
+        double r;
+        double p;
+        ;
+
+        double g;
+        double f;
+        double dd;
+        double c;
+        double b;
+
+        for (i = 2; i <= n; i++) {
+            e[i - 2] = e[i - 1];
+        }
 
-    //for (int i=0; i < neigenv.length;i++) {
-    //  Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]);
-    //}
+        e[n - 1] = 0.0;
+
+        for (l = 1; l <= n; l++) {
+            iter = 0;
+
+            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) {
+                        break;
+                    }
+                }
+
+                if (m != l) {
+                    iter++;
+
+                    if (iter == 30) {
+                        System.err.print("Too many iterations in tqli");
+                        System.exit(0); // JBPNote - should this really be here ???
+                    } else {
+                        //	    System.out.println("Iteration " + iter);
+                    }
+
+                    g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
+                    r = Math.sqrt((g * g) + 1.0);
+                    g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g)));
+                    c = 1.0;
+                    s = c;
+                    p = 0.0;
+
+                    for (i = m - 1; i >= l; i--) {
+                        f = s * e[i - 1];
+                        b = c * e[i - 1];
+
+                        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 {
+                            s = f / g;
+                            r = Math.sqrt((s * s) + 1.0);
+                            e[i] = g * r;
+                            c = 1.0 / r;
+                            s *= c;
+                        }
+
+                        g = d[i] - p;
+                        r = ((d[i - 1] - g) * s) + (2.0 * c * b);
+                        p = s * r;
+                        d[i] = g + p;
+                        g = (c * r) - b;
+
+                        for (k = 1; k <= n; k++) {
+                            f = value[k - 1][i];
+                            value[k - 1][i] = (s * value[k - 1][i - 1]) +
+                                (c * f);
+                            value[k - 1][i - 1] = (c * value[k - 1][i - 1]) -
+                                (s * f);
+                        }
+                    }
+
+                    d[l - 1] = d[l - 1] - p;
+                    e[l - 1] = g;
+                    e[m - 1] = 0.0;
+                }
+            } while (m != l);
+        }
+    }
 
-    //System.out.println();
-  }
+    public void tred2() {
+        int n = rows;
+        int l;
+        int k;
+        int j;
+        int i;
+
+        double scale;
+        double hh;
+        double h;
+        double g;
+        double f;
+
+        this.d = new double[rows];
+        this.e = new double[rows];
+
+        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++) {
+                    scale += Math.abs(value[i][k]);
+                }
+
+                if (scale == 0.0) {
+                    e[i] = value[i][l];
+                } 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) {
+                        g = -1.0 * Math.sqrt(h);
+                    } else {
+                        g = Math.sqrt(h);
+                    }
+
+                    e[i] = scale * g;
+                    h -= (f * g);
+                    value[i][l] = f - g;
+                    f = 0.0;
+
+                    for (j = 0; j < l; j++) {
+                        value[j][i] = value[i][j] / h;
+                        g = 0.0;
+
+                        for (k = 0; k < j; k++) {
+                            g += (value[j][k] * value[i][k]);
+                        }
+
+                        for (k = j; k < l; k++) {
+                            g += (value[k][j] * value[i][k]);
+                        }
+
+                        e[j] = g / h;
+                        f += (e[j] * value[i][j]);
+                    }
+
+                    hh = f / (h + h);
+
+                    for (j = 0; j < l; j++) {
+                        f = value[i][j];
+                        g = e[j] - (hh * f);
+                        e[j] = g;
+
+                        for (k = 0; k < j; k++) {
+                            value[j][k] -= ((f * e[k]) + (g * value[i][k]));
+                        }
+                    }
+                }
+            } else {
+                e[i] = value[i][l];
+            }
 
-}
+            d[i] = h;
+        }
 
+        d[0] = 0.0;
+        e[0] = 0.0;
 
+        for (i = 0; i < n; i++) {
+            l = i - 1;
 
+            if (d[i] != 0.0) {
+                for (j = 0; j < l; j++) {
+                    g = 0.0;
 
+                    for (k = 0; k < l; k++) {
+                        g += (value[i][k] * value[k][j]);
+                    }
 
+                    for (k = 0; k < l; k++) {
+                        value[k][j] -= (g * value[k][i]);
+                    }
+                }
+            }
 
+            d[i] = value[i][i];
+            value[i][i] = 1.0;
 
+            for (j = 0; j < l; j++) {
+                value[j][i] = 0.0;
+                value[i][j] = 0.0;
+            }
+        }
+    }
 
+    public void tqli2() {
+        int n = rows;
+
+        int m;
+        int l;
+        int iter;
+        int i;
+        int k;
+        double s;
+        double r;
+        double p;
+        ;
+
+        double g;
+        double f;
+        double dd;
+        double c;
+        double b;
+
+        for (i = 2; i <= n; i++) {
+            e[i - 2] = e[i - 1];
+        }
 
+        e[n - 1] = 0.0;
+
+        for (l = 1; l <= n; l++) {
+            iter = 0;
+
+            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) {
+                        break;
+                    }
+                }
+
+                if (m != l) {
+                    iter++;
+
+                    if (iter == 30) {
+                        System.err.print("Too many iterations in tqli");
+                        System.exit(0); // JBPNote - same as above - not a graceful exit!
+                    } else {
+                        //	    System.out.println("Iteration " + iter);
+                    }
+
+                    g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
+                    r = Math.sqrt((g * g) + 1.0);
+                    g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g)));
+                    c = 1.0;
+                    s = c;
+                    p = 0.0;
+
+                    for (i = m - 1; i >= l; i--) {
+                        f = s * e[i - 1];
+                        b = c * e[i - 1];
+
+                        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 {
+                            s = f / g;
+                            r = Math.sqrt((s * s) + 1.0);
+                            e[i] = g * r;
+                            c = 1.0 / r;
+                            s *= c;
+                        }
+
+                        g = d[i] - p;
+                        r = ((d[i - 1] - g) * s) + (2.0 * c * b);
+                        p = s * r;
+                        d[i] = g + p;
+                        g = (c * r) - b;
+
+                        for (k = 1; k <= n; k++) {
+                            f = value[k - 1][i];
+                            value[k - 1][i] = (s * value[k - 1][i - 1]) +
+                                (c * f);
+                            value[k - 1][i - 1] = (c * value[k - 1][i - 1]) -
+                                (s * f);
+                        }
+                    }
+
+                    d[l - 1] = d[l - 1] - p;
+                    e[l - 1] = g;
+                    e[m - 1] = 0.0;
+                }
+            } while (m != l);
+        }
+    }
 
+    public double sign(double a, double b) {
+        if (b < 0) {
+            return -Math.abs(a);
+        } else {
+            return Math.abs(a);
+        }
+    }
 
+    public double[] getColumn(int n) {
+        double[] out = new double[rows];
 
+        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++) {
+            Format.print(ps, "%15.4e", d[j]);
+        }
+    }
 
+    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) {
+        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++) {
+                in[i][j] = (double) Math.random();
+            }
+        }
 
+        Matrix origmat = new Matrix(in, n, n);
+
+        //    System.out.println(" --- Original matrix ---- ");
+        ///    origmat.print(System.out);
+        //System.out.println();
+        //System.out.println(" --- transpose matrix ---- ");
+        Matrix trans = origmat.transpose();
+
+        //trans.print(System.out);
+        //System.out.println();
+        //System.out.println(" --- OrigT * Orig ---- ");
+        Matrix symm = trans.postMultiply(origmat);
+
+        //symm.print(System.out);
+        //System.out.println();
+        // Copy the symmetric matrix for later
+        Matrix origsymm = symm.copy();
+
+        // This produces the tridiagonal transformation matrix
+        long tstart = System.currentTimeMillis();
+        symm.tred();
+
+        long tend = System.currentTimeMillis();
+
+        //System.out.println("Time take for tred = " + (tend-tstart) + "ms");
+        //System.out.println(" ---Tridiag transform matrix ---");
+        //symm.print(System.out);
+        //System.out.println();
+        //System.out.println(" --- D vector ---");
+        //symm.printD(System.out);
+        //System.out.println();
+        //System.out.println(" --- E vector ---");
+        //symm.printE(System.out);
+        //System.out.println();
+        // Now produce the diagonalization matrix
+        tstart = System.currentTimeMillis();
+        symm.tqli();
+        tend = System.currentTimeMillis();
+
+        //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
+        //System.out.println(" --- New diagonalization matrix ---");
+        //symm.print(System.out);
+        //System.out.println();
+        //System.out.println(" --- D vector ---");
+        //symm.printD(System.out);
+        //System.out.println();
+        //System.out.println(" --- E vector ---");
+        //symm.printE(System.out);
+        //System.out.println();
+        //System.out.println(" --- First eigenvector --- ");
+        //double[] eigenv = symm.getColumn(0);
+        //for (int i=0; i < eigenv.length;i++) {
+        //  Format.print(System.out,"%15.4f",eigenv[i]);
+        // }
+        //System.out.println();
+        //double[] neigenv = origsymm.vectorPostMultiply(eigenv);
+        //for (int i=0; i < neigenv.length;i++) {
+        //  Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]);
+        //}
+        //System.out.println();
+    }
+}
diff --git a/src/jalview/math/RotatableMatrix.java b/src/jalview/math/RotatableMatrix.java
index d9f4bd5..c0ec1c9 100755
--- a/src/jalview/math/RotatableMatrix.java
+++ b/src/jalview/math/RotatableMatrix.java
@@ -16,374 +16,241 @@
 * 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.math;
 
-
-
 public class RotatableMatrix {
+    float[][] matrix;
+    float[] temp;
+    float[][] rot;
 
-  float matrix[][];
-
-  float[] temp;
-
-  float[][] rot;
-
-
-
-  public RotatableMatrix(int rows, int cols) {
-
-    matrix = new float[rows][cols];
-
-    temp = new float[3];
-
-    rot = new float[3][3];
-
-  }
-
-
-
-  public void addElement(int i, int j, float value) {
-
-    matrix[i][j] = value;
-
-  }
-
-
-
-  public void print() {
-
-    System.out.println(matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);
-
-    System.out.println(matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);
-
-    System.out.println(matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);
-
-  }
-
-
-
-  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') {
-
-
+    public RotatableMatrix(int rows, int cols) {
+        matrix = new float[rows][cols];
 
-      rot[0][0] = (float)costheta;
-
-      rot[0][1] = (float)-sintheta;
-
-      rot[0][2] = (float)0.0;
-
-
-
-      rot[1][0] = (float)sintheta;
-
-      rot[1][1] = (float)costheta;
-
-      rot[1][2] = (float)0.0;
-
-
-
-      rot[2][0] = (float)0.0;
-
-      rot[2][1] = (float)0.0;
-
-      rot[2][2] = (float)1.0;
-
-
-
-      preMultiply(rot);
+        temp = new float[3];
 
+        rot = new float[3][3];
     }
 
-    if (axis == 'x') {
-
-      rot[0][0] = (float)1.0;
-
-      rot[0][1] = (float)0.0;
-
-      rot[0][2] = (float)0.0;
-
-
-
-      rot[1][0] = (float)0.0;
-
-      rot[1][1] = (float)costheta;
-
-      rot[1][2] = (float)sintheta;
-
-
-
-      rot[2][0] = (float)0.0;
-
-      rot[2][1] = (float)-sintheta;
-
-      rot[2][2] = (float)costheta;
-
-
-
-      preMultiply(rot);
-
-
-
+    public void addElement(int i, int j, float value) {
+        matrix[i][j] = value;
     }
 
-    if (axis == 'y') {
-
-      rot[0][0] = (float)costheta;
-
-      rot[0][1] = (float)0.0;
-
-      rot[0][2] = (float)-sintheta;
-
-
-
-      rot[1][0] = (float)0.0;
-
-      rot[1][1] = (float)1.0;
-
-      rot[1][2] = (float)0.0;
-
-
-
-      rot[2][0] = (float)sintheta;
-
-      rot[2][1] = (float)0.0;
-
-      rot[2][2] = (float)costheta;
-
-
-
-      preMultiply(rot);
-
+    public void print() {
+        System.out.println(matrix[0][0] + " " + matrix[0][1] + " " +
+            matrix[0][2]);
 
+        System.out.println(matrix[1][0] + " " + matrix[1][1] + " " +
+            matrix[1][2]);
 
+        System.out.println(matrix[2][0] + " " + matrix[2][1] + " " +
+            matrix[2][2]);
     }
 
+    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);
 
-  }
-
-
-
-  public float[] vectorMultiply(float[] vect) {
+        if (axis == 'z') {
+            rot[0][0] = (float) costheta;
 
-    temp[0] = vect[0];
+            rot[0][1] = (float) -sintheta;
 
-    temp[1] = vect[1];
+            rot[0][2] = (float) 0.0;
 
-    temp[2] = vect[2];
+            rot[1][0] = (float) sintheta;
 
+            rot[1][1] = (float) costheta;
 
+            rot[1][2] = (float) 0.0;
 
-    for (int i = 0; i < 3; i++) {
+            rot[2][0] = (float) 0.0;
 
-      temp[i] = matrix[i][0]*vect[0] + matrix[i][1]*vect[1] + matrix[i][2]*vect[2];
+            rot[2][1] = (float) 0.0;
 
-    }
-
-
-
-    vect[0] = temp[0];
-
-    vect[1] = temp[1];
-
-    vect[2] = temp[2];
-
-
-
-    return vect;
+            rot[2][2] = (float) 1.0;
 
-  }
+            preMultiply(rot);
+        }
 
+        if (axis == 'x') {
+            rot[0][0] = (float) 1.0;
 
+            rot[0][1] = (float) 0.0;
 
-  public void preMultiply(float mat[][]) {
+            rot[0][2] = (float) 0.0;
 
-    float tmp[][]  = new float[3][3];
+            rot[1][0] = (float) 0.0;
 
+            rot[1][1] = (float) costheta;
 
+            rot[1][2] = (float) sintheta;
 
-    for (int i = 0; i < 3 ; i++) {
+            rot[2][0] = (float) 0.0;
 
-      for (int j = 0; j < 3; j++ ) {
+            rot[2][1] = (float) -sintheta;
 
-        tmp[i][j] = mat[i][0]*matrix[0][j] +
+            rot[2][2] = (float) costheta;
 
-                    mat[i][1]*matrix[1][j] +
+            preMultiply(rot);
+        }
 
-                    mat[i][2]*matrix[2][j];
+        if (axis == 'y') {
+            rot[0][0] = (float) costheta;
 
-      }
+            rot[0][1] = (float) 0.0;
 
-    }
+            rot[0][2] = (float) -sintheta;
 
+            rot[1][0] = (float) 0.0;
 
+            rot[1][1] = (float) 1.0;
 
-    for (int i = 0; i < 3 ; i++) {
+            rot[1][2] = (float) 0.0;
 
-      for (int j = 0; j < 3; j++ ) {
+            rot[2][0] = (float) sintheta;
 
-        matrix[i][j] = tmp[i][j];
+            rot[2][1] = (float) 0.0;
 
-      }
+            rot[2][2] = (float) costheta;
 
+            preMultiply(rot);
+        }
     }
 
-  }
-
-
-
-  public void postMultiply(float mat[][]) {
-
-    float tmp[][]  = new float[3][3];
+    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]);
+        }
 
-      for (int j = 0; j < 3; j++ ) {
+        vect[0] = temp[0];
 
-        tmp[i][j] = matrix[i][0]*mat[0][j] +
+        vect[1] = temp[1];
 
-                    matrix[i][1]*mat[1][j] +
-
-                    matrix[i][2]*mat[2][j];
-
-      }
+        vect[2] = temp[2];
 
+        return vect;
     }
 
-
-
-    for (int i = 0; i < 3 ; i++) {
-
-      for (int j = 0; j < 3; j++ ) {
-
-        matrix[i][j] = tmp[i][j];
-
-      }
-
+    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++) {
+                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++) {
+                matrix[i][j] = tmp[i][j];
+            }
+        }
     }
 
-  }
-
-
-
-  public static void main(String[] args) {
-
-
-
-    RotatableMatrix m = new  RotatableMatrix(3,3);
-
-    m.addElement(0,0,1);
-
-    m.addElement(0,1,0);
-
-    m.addElement(0,2,0);
-
-    m.addElement(1,0,0);
-
-    m.addElement(1,1,2);
-
-    m.addElement(1,2,0);
-
-    m.addElement(2,0,0);
-
-    m.addElement(2,1,0);
-
-    m.addElement(2,2,1);
-
-
-
-    m.print();
-
-
-
-    RotatableMatrix n = new  RotatableMatrix(3,3);
-
-    n.addElement(0,0,2);
-
-    n.addElement(0,1,1);
-
-    n.addElement(0,2,1);
-
-    n.addElement(1,0,2);
-
-    n.addElement(1,1,1);
+    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++) {
+                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++) {
+                matrix[i][j] = tmp[i][j];
+            }
+        }
+    }
 
-    n.addElement(1,2,1);
+    public static void main(String[] args) {
+        RotatableMatrix m = new RotatableMatrix(3, 3);
 
-    n.addElement(2,0,2);
+        m.addElement(0, 0, 1);
 
-    n.addElement(2,1,1);
+        m.addElement(0, 1, 0);
 
-    n.addElement(2,2,1);
+        m.addElement(0, 2, 0);
 
+        m.addElement(1, 0, 0);
 
+        m.addElement(1, 1, 2);
 
-    n.print();
+        m.addElement(1, 2, 0);
 
+        m.addElement(2, 0, 0);
 
+        m.addElement(2, 1, 0);
 
-    //m.postMultiply(n.matrix);
+        m.addElement(2, 2, 1);
 
-    //m.print();
+        m.print();
 
-    //     m.rotate(45,'z',new RotatableMatrix(3,3));
+        RotatableMatrix n = new RotatableMatrix(3, 3);
 
+        n.addElement(0, 0, 2);
 
+        n.addElement(0, 1, 1);
 
-    float vect[] = new float[3];
+        n.addElement(0, 2, 1);
 
-    vect[0] = 2;
+        n.addElement(1, 0, 2);
 
-    vect[1] = 4;
+        n.addElement(1, 1, 1);
 
-    vect[2] = 6;
+        n.addElement(1, 2, 1);
 
+        n.addElement(2, 0, 2);
 
+        n.addElement(2, 1, 1);
 
-    vect = m.vectorMultiply(vect);
+        n.addElement(2, 2, 1);
 
-    System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
+        n.print();
 
+        //m.postMultiply(n.matrix);
+        //m.print();
+        //     m.rotate(45,'z',new RotatableMatrix(3,3));
+        float[] vect = new float[3];
 
+        vect[0] = 2;
 
-  }
+        vect[1] = 4;
 
-  public void setIdentity() {
+        vect[2] = 6;
 
-    matrix[0][0] = (float)1.0;
+        vect = m.vectorMultiply(vect);
 
-    matrix[1][1] = (float)1.0;
+        System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
+    }
 
-    matrix[2][2] = (float)1.0;
+    public void setIdentity() {
+        matrix[0][0] = (float) 1.0;
 
-    matrix[0][1] = (float)0.0;
+        matrix[1][1] = (float) 1.0;
 
-    matrix[0][2] = (float)0.0;
+        matrix[2][2] = (float) 1.0;
 
-    matrix[1][0] = (float)0.0;
+        matrix[0][1] = (float) 0.0;
 
-    matrix[1][2] = (float) 0.0;
+        matrix[0][2] = (float) 0.0;
 
-    matrix[2][0] = (float)0.0;
+        matrix[1][0] = (float) 0.0;
 
-    matrix[2][1] = (float)0.0;
+        matrix[1][2] = (float) 0.0;
 
-  }
+        matrix[2][0] = (float) 0.0;
 
+        matrix[2][1] = (float) 0.0;
+    }
 }
-
-
-
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 40243f2..9c720ee 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -16,53 +16,48 @@
 * 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.util.*;
 import java.awt.*;
 
-public class Blosum62ColourScheme extends ResidueColourScheme
-{
-
-  public Blosum62ColourScheme()
-  {
-    super();
-  }
-
-  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 {
+import java.util.*;
 
-        int c = 0,
-            max_aa=0,
-            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;
-      }
+public class Blosum62ColourScheme extends ResidueColourScheme {
+    public Blosum62ColourScheme() {
+        super();
     }
-    else
-        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);
+
+                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 8b0305d..186b98a 100755
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -16,18 +16,18 @@
 * 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 BuriedColourScheme extends ScoreColourScheme {
 
-  public BuriedColourScheme() {
-    super(ResidueProperties.buried,ResidueProperties.buriedmin,ResidueProperties.buriedmax);
-  }
+public class BuriedColourScheme extends ScoreColourScheme {
+    public BuriedColourScheme() {
+        super(ResidueProperties.buried, ResidueProperties.buriedmin,
+            ResidueProperties.buriedmax);
+    }
 
-  public Color makeColour(float c) {
-    return new Color(0,(float)(1.0-c),c);
-  }
+    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 bbca4de..17398fc 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -16,267 +16,259 @@
 * 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.*;
 
-public class ClustalxColourScheme extends ResidueColourScheme
-{
-  Hashtable[] cons;
-  int[][] cons2;
-  ConsensusColour[] colours;
-  ConsensusColour[] ResidueColour;
-  int size;
-    Consensus[] conses = new Consensus[32];
+import java.util.*;
+
+
+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));
-
+        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));
     }
-  Vector colourTable = new Vector();
-
-  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++)
-      for (int i=0; i < maxWidth;i++)
-        cons2[i][j] = 0;
-
-      int res,i, 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();
-          cons2[i][res]++;
-        }
-        j++;
-      }
-
-    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;
-
-
-     int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();
-
-     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 == 4)
-    {
-      if (conses[27].isConserved(cons2, j, size))
-        c = (Color) colhash.get("PINK");
+
+    public ClustalxColourScheme(Vector seqs, int maxWidth) {
+        resetClustalX(seqs, maxWidth);
     }
 
+    public void resetClustalX(Vector seqs, int maxWidth) {
+        cons2 = new int[maxWidth][24];
 
-     return c;
+        int start = 0;
 
-   }
-}
+        // Initialize the array
+        for (int j = 0; j < 24; j++)
+            for (int i = 0; i < maxWidth; i++)
+                cons2[i][j] = 0;
 
-class ConsensusColour {
+        int res;
+        int i;
+        int j = 0;
+        String seq;
 
-  Consensus[] conses;
-  Color c;
+        while (j < seqs.size()) {
+            seq = ((SequenceI) seqs.elementAt(j)).getSequence();
 
-  public ConsensusColour(Color c,Consensus[] conses) {
-    this.conses = conses;
-    //    this.list = list;
-    this.c = c;
-  }
-}
+            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();
+                }
 
+                cons2[i][res]++;
+            }
 
+            j++;
+        }
+
+        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;
+        }
 
+        int i = ((Integer) ResidueProperties.aaHash.get(s)).intValue();
 
+        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 == 4) {
+            if (conses[27].isConserved(cons2, j, size)) {
+                c = (Color) colhash.get("PINK");
+            }
+        }
 
+        return c;
+    }
+}
 
 
+class ConsensusColour {
+    Consensus[] conses;
+    Color c;
 
+    public ConsensusColour(Color c, Consensus[] conses) {
+        this.conses = conses;
 
+        //    this.list = list;
+        this.c = c;
+    }
+}
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 250cae5..2e28695 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -16,15 +16,17 @@
 * 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.*;
 
-public interface ColourSchemeI
-{
-  public Color   findColour(String aa);
-  public Color   findColour(String s,int j);
-  public void    setConsensus(Vector v);
+
+public interface ColourSchemeI {
+    public Color findColour(String aa);
+
+    public Color findColour(String s, int j);
+
+    public void setConsensus(Vector v);
 }
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index a981549..6e7a711 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -16,133 +16,223 @@
 * 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 ColourSchemeProperty
-{
-  public static final int CLUSTAL = 0;
-  public static final int BLOSUM = 1;
-  public static final int PID = 2;
-  public static final int ZAPPO = 3;
-  public static final int HYDROPHOBIC=4;
-  public static final int HELIX=5;
-  public static final int STRAND=6;
-  public static final int TURN = 7;
-  public static final int BURIED = 8;
-  public static final int NUCLEOTIDE = 9;
-  public static final int USER_DEFINED = 10;
-  public static final int NONE = 11;
-
-  public static int getColourIndexFromName(String name)
-  {
-    int ret=11;
-    if(name.equalsIgnoreCase("Clustal"))
-      ret = CLUSTAL;
-    else if(name.equalsIgnoreCase("Blosum62"))
-      ret = BLOSUM;
-    else if(name.equalsIgnoreCase("% Identity"))
-      ret = PID;
-    else if(name.equalsIgnoreCase("Zappo"))
-      ret = ZAPPO;
-    else if(name.equalsIgnoreCase("Hydrophobic"))
-      ret = HYDROPHOBIC;
-    else if(name.equalsIgnoreCase("Helix Propensity"))
-      ret = HELIX;
-    else if(name.equalsIgnoreCase("Strand Propensity"))
-      ret = STRAND;
-    else if(name.equalsIgnoreCase("Turn Propensity"))
-      ret = TURN;
-    else if(name.equalsIgnoreCase("Buried Index"))
-      ret = BURIED;
-    else if(name.equalsIgnoreCase("Nucleotide"))
-      ret = NUCLEOTIDE;
-    else if(name.equalsIgnoreCase("User Defined"))
-      ret =  USER_DEFINED;
-
-    return ret;
-  }
-
-  public static String getColourName(ColourSchemeI cs)
-  {
-    if(cs instanceof ConservationColourScheme)
-     cs = ((ConservationColourScheme)cs).cs;
-
-
-    int index = 11;
-    if(cs instanceof ClustalxColourScheme)
-      index = CLUSTAL;
-    else if(cs instanceof  Blosum62ColourScheme)
-      index = BLOSUM;
-    else if(cs instanceof  PIDColourScheme)
-      index = PID;
-    else if(cs instanceof  ZappoColourScheme)
-      index = ZAPPO;
-    else if(cs instanceof  HydrophobicColourScheme)
-      index = HYDROPHOBIC;
-    else if(cs instanceof  HelixColourScheme)
-      index = HELIX;
-    else if(cs instanceof  StrandColourScheme)
-      index = STRAND;
-    else if(cs instanceof  TurnColourScheme)
-      index = TURN;
-    else if(cs instanceof  BuriedColourScheme)
-      index = BURIED;
-    else if(cs instanceof  NucleotideColourScheme)
-      index = NUCLEOTIDE;
-    else if(cs instanceof  UserColourScheme)
-      index = USER_DEFINED;
-
-    return getColourName(index);
-  }
-
-  public static String getColourName(int index)
-  {
-    String ret=null;
-    switch(index)
-    {
-      case CLUSTAL: ret = "Clustal";    break;
-      case BLOSUM:  ret = "Blosum62";   break;
-      case PID:     ret = "% Identity"; break;
-      case ZAPPO:   ret = "Zappo";      break;
-      case HYDROPHOBIC: ret="Hydrophobic";break;
-      case HELIX:   ret="Helix Propensity";break;
-      case STRAND:  ret="Strand Propensity";break;
-      case TURN:    ret="Turn Propensity";break;
-      case BURIED:  ret="Buried Index";break;
-      case NUCLEOTIDE:ret="Nucleotide"; break;
-      case USER_DEFINED:ret="User Defined";break;
-      default: ret = "None"; break;
+public class ColourSchemeProperty {
+    public static final int CLUSTAL = 0;
+    public static final int BLOSUM = 1;
+    public static final int PID = 2;
+    public static final int ZAPPO = 3;
+    public static final int HYDROPHOBIC = 4;
+    public static final int HELIX = 5;
+    public static final int STRAND = 6;
+    public static final int TURN = 7;
+    public static final int BURIED = 8;
+    public static final int NUCLEOTIDE = 9;
+    public static final int USER_DEFINED = 10;
+    public static final int NONE = 11;
+
+    public static int getColourIndexFromName(String name) {
+        int ret = 11;
+
+        if (name.equalsIgnoreCase("Clustal")) {
+            ret = CLUSTAL;
+        } else if (name.equalsIgnoreCase("Blosum62")) {
+            ret = BLOSUM;
+        } else if (name.equalsIgnoreCase("% Identity")) {
+            ret = PID;
+        } else if (name.equalsIgnoreCase("Zappo")) {
+            ret = ZAPPO;
+        } else if (name.equalsIgnoreCase("Hydrophobic")) {
+            ret = HYDROPHOBIC;
+        } else if (name.equalsIgnoreCase("Helix Propensity")) {
+            ret = HELIX;
+        } else if (name.equalsIgnoreCase("Strand Propensity")) {
+            ret = STRAND;
+        } else if (name.equalsIgnoreCase("Turn Propensity")) {
+            ret = TURN;
+        } else if (name.equalsIgnoreCase("Buried Index")) {
+            ret = BURIED;
+        } else if (name.equalsIgnoreCase("Nucleotide")) {
+            ret = NUCLEOTIDE;
+        } else if (name.equalsIgnoreCase("User Defined")) {
+            ret = USER_DEFINED;
+        }
+
+        return ret;
+    }
+
+    public static String getColourName(ColourSchemeI cs) {
+        if (cs instanceof ConservationColourScheme) {
+            cs = ((ConservationColourScheme) cs).cs;
+        }
+
+        int index = 11;
+
+        if (cs instanceof ClustalxColourScheme) {
+            index = CLUSTAL;
+        } else if (cs instanceof Blosum62ColourScheme) {
+            index = BLOSUM;
+        } else if (cs instanceof PIDColourScheme) {
+            index = PID;
+        } else if (cs instanceof ZappoColourScheme) {
+            index = ZAPPO;
+        } else if (cs instanceof HydrophobicColourScheme) {
+            index = HYDROPHOBIC;
+        } else if (cs instanceof HelixColourScheme) {
+            index = HELIX;
+        } else if (cs instanceof StrandColourScheme) {
+            index = STRAND;
+        } else if (cs instanceof TurnColourScheme) {
+            index = TURN;
+        } else if (cs instanceof BuriedColourScheme) {
+            index = BURIED;
+        } else if (cs instanceof NucleotideColourScheme) {
+            index = NUCLEOTIDE;
+        } else if (cs instanceof UserColourScheme) {
+            index = USER_DEFINED;
+        }
+
+        return getColourName(index);
+    }
+
+    public static String getColourName(int index) {
+        String ret = null;
+
+        switch (index) {
+        case CLUSTAL:
+            ret = "Clustal";
+
+            break;
+
+        case BLOSUM:
+            ret = "Blosum62";
+
+            break;
+
+        case PID:
+            ret = "% Identity";
+
+            break;
+
+        case ZAPPO:
+            ret = "Zappo";
+
+            break;
+
+        case HYDROPHOBIC:
+            ret = "Hydrophobic";
+
+            break;
+
+        case HELIX:
+            ret = "Helix Propensity";
+
+            break;
+
+        case STRAND:
+            ret = "Strand Propensity";
+
+            break;
+
+        case TURN:
+            ret = "Turn Propensity";
+
+            break;
+
+        case BURIED:
+            ret = "Buried Index";
+
+            break;
+
+        case NUCLEOTIDE:
+            ret = "Nucleotide";
+
+            break;
+
+        case USER_DEFINED:
+            ret = "User Defined";
+
+            break;
+
+        default:
+            ret = "None";
+
+            break;
+        }
+
+        return ret;
     }
-    return ret;
-  }
-
-  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
-  {
-    return getColour(al, getColourIndexFromName(name));
-  }
-
-  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)
-  {
-    ColourSchemeI cs = null;
-    switch(index)
-    {
-      case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;
-      case BLOSUM: cs = new Blosum62ColourScheme(); break;
-      case PID: cs = new PIDColourScheme();  break;
-      case ZAPPO: cs = new ZappoColourScheme(); break;
-      case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;
-      case HELIX: cs = new HelixColourScheme(); break;
-      case STRAND: cs = new StrandColourScheme(); break;
-      case TURN: cs = new TurnColourScheme(); break;
-      case BURIED: cs = new BuriedColourScheme(); break;
-      case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
-      case USER_DEFINED: cs = new UserColourScheme(null);
-        break;
-
-      default: break;
+
+    public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
+        String name) {
+        return getColour(al, getColourIndexFromName(name));
     }
 
-    return cs;
-  }
+    public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
+        int index) {
+        ColourSchemeI cs = null;
+
+        switch (index) {
+        case CLUSTAL:
+            cs = new ClustalxColourScheme(al.getSequences(), al.getWidth());
+
+            break;
+
+        case BLOSUM:
+            cs = new Blosum62ColourScheme();
+
+            break;
+
+        case PID:
+            cs = new PIDColourScheme();
+
+            break;
+
+        case ZAPPO:
+            cs = new ZappoColourScheme();
+
+            break;
+
+        case HYDROPHOBIC:
+            cs = new HydrophobicColourScheme();
+
+            break;
+
+        case HELIX:
+            cs = new HelixColourScheme();
+
+            break;
+
+        case STRAND:
+            cs = new StrandColourScheme();
+
+            break;
+
+        case TURN:
+            cs = new TurnColourScheme();
+
+            break;
+
+        case BURIED:
+            cs = new BuriedColourScheme();
+
+            break;
+
+        case NUCLEOTIDE:
+            cs = new NucleotideColourScheme();
+
+            break;
+
+        case USER_DEFINED:
+            cs = new UserColourScheme(null);
+
+            break;
+
+        default:
+            break;
+        }
+
+        return cs;
+    }
 }
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 27c5906..8ca0223 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -16,62 +16,57 @@
 * 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;
 
-  int[] mask;
-  double threshold;
-   String maskstr;
-
-  public Consensus(String mask, double threshold) {
-    // this.id = id;
-    //    this.mask = mask;
+    public Consensus(String mask, double threshold) {
+        // this.id = id;
+        //    this.mask = mask;
         this.maskstr = mask;
-    setMask(mask);
-    this.threshold = threshold;
-  }
+        setMask(mask);
+        this.threshold = threshold;
+    }
 
-  public void setMask(String s) {
-    this.mask = setNums(s);
-    //   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++)
-      tot += cons2[col][mask[i]];
+        //   for (int i=0; i < mask.length; i++) {
+        //  System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+        // }
+    }
 
-    if ( (double) tot > threshold * size / 100)
-      return true;
+    public boolean isConserved(int[][] cons2, int col, int size) {
+        int tot = 0;
 
-    return false;
-  }
+        for (int i = 0; i < mask.length; i++)
+            tot += cons2[col][mask[i]];
 
-  int[] setNums(String s)
-  {
-    int [] out = new int[s.length()];
-    int i = 0;
-    while (i < s.length())
-    {
-      out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
-      i++;
+        if ((double) tot > ((threshold * size) / 100)) {
+            return true;
+        }
 
+        return false;
     }
 
-    return out;
-  }
+    int[] setNums(String s) {
+        int[] out = new int[s.length()];
+        int i = 0;
 
+        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 8c3f694..bbc0edd 100755
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -16,73 +16,87 @@
 * 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 jalview.analysis.*;
+
+import java.awt.*;
+
 import java.util.Vector;
 
+
 public class ConservationColourScheme extends ResidueColourScheme {
-  public Conservation conserve;
-  public ColourSchemeI cs;
-  public int inc = 30;
-
-  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
-  {
-    super();
-    conserve = cons;
-    cs = oldcs;
-  }
-
-  public void setConsensus(Vector consensus)
-  {
-    this.consensus = consensus;
-    if(cs!=null)
-      cs.setConsensus(consensus);
-  }
-
-   public Color findColour(String s, int i)
-   {
-     Color c = Color.white;
-     if (cs == null)
-       return c;
-
-     char ch = conserve.getConsSequence().getSequence().charAt(i);
-     if (ch == '*' || ch == '+')
-     {
-       c = cs.findColour(s, i);
-     }
-     else
-     {
-       int tmp = 10;
-       int t = 0;
-       if (!jalview.util.Comparison.isGap(ch))
-         t = Integer.parseInt(ch + "");
-
-       c = cs.findColour(s, i);
-
-       while (tmp >= t)
-       {
-         c = lighter(c, inc);
-         tmp--;
-       }
-
-     }
-
-   return c;
-   }
-
-
-  public Color lighter(Color c, int inc) {
-    int red = c.getRed();
-    int blue = c.getBlue();
-    int green = c.getGreen();
-
-    if (red < 255-inc) { red = red +inc;} else {red = 255;}
-    if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}
-    if (green < 255-inc) { green = green +inc;} else {green = 255;}
-
-    return new Color(red,green,blue);
-  }
+    public Conservation conserve;
+    public ColourSchemeI cs;
+    public int inc = 30;
+
+    public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs) {
+        super();
+        conserve = cons;
+        cs = oldcs;
+    }
+
+    public void setConsensus(Vector consensus) {
+        this.consensus = consensus;
+
+        if (cs != null) {
+            cs.setConsensus(consensus);
+        }
+    }
+
+    public Color findColour(String s, int i) {
+        Color c = Color.white;
+
+        if (cs == null) {
+            return c;
+        }
+
+        char ch = conserve.getConsSequence().getSequence().charAt(i);
+
+        if ((ch == '*') || (ch == '+')) {
+            c = cs.findColour(s, i);
+        } else {
+            int tmp = 10;
+            int t = 0;
+
+            if (!jalview.util.Comparison.isGap(ch)) {
+                t = Integer.parseInt(ch + "");
+            }
+
+            c = cs.findColour(s, i);
+
+            while (tmp >= t) {
+                c = lighter(c, inc);
+                tmp--;
+            }
+        }
+
+        return c;
+    }
+
+    public Color lighter(Color c, int inc) {
+        int red = c.getRed();
+        int blue = c.getBlue();
+        int green = c.getGreen();
+
+        if (red < (255 - inc)) {
+            red = red + inc;
+        } else {
+            red = 255;
+        }
+
+        if (blue < (255 - inc)) {
+            blue = blue + inc;
+        } else {
+            blue = 255;
+        }
+
+        if (green < (255 - inc)) {
+            green = green + inc;
+        } else {
+            green = 255;
+        }
 
+        return new Color(red, green, blue);
+    }
 }
diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index 35e1a26..a25f014 100755
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -16,19 +16,18 @@
 * 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 e1eef48..eeb43a3 100755
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -16,18 +16,18 @@
 * 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 HydrophobicColourScheme extends ScoreColourScheme {
 
-  public HydrophobicColourScheme() {
-    super(ResidueProperties.hyd,ResidueProperties.hydmin,ResidueProperties.hydmax);
-  }
+public class HydrophobicColourScheme extends ScoreColourScheme {
+    public HydrophobicColourScheme() {
+        super(ResidueProperties.hyd, ResidueProperties.hydmin,
+            ResidueProperties.hydmax);
+    }
 
-  public Color makeColour(float c) {
-    return new Color(c,(float)0.0,(float)1.0-c);
-  }
+    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 0f2101e..0cca608 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -16,39 +16,30 @@
 * 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 NucleotideColourScheme extends ResidueColourScheme
-{
-  public NucleotideColourScheme() {
-  super(ResidueProperties.nucleotide,0);
-  }
-
-
-  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
-      {
-        return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
-      }
-      catch (Exception ex)
-      {
-        return Color.white;
-      }
-    else
-      return Color.white;
-
-  }
 
+public class NucleotideColourScheme extends ResidueColourScheme {
+    public NucleotideColourScheme() {
+        super(ResidueProperties.nucleotide, 0);
+    }
+
+    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 {
+                return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+            } catch (Exception ex) {
+                return Color.white;
+            }
+        } else {
+            return Color.white;
+        }
+    }
 }
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 34c47ed..2535154 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -16,52 +16,52 @@
 * 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.*;
+
+
 public class PIDColourScheme extends ResidueColourScheme {
     public Color[] pidColours;
     public float[] thresholds;
-
     SequenceGroup group;
 
     public PIDColourScheme() {
-	this.pidColours = ResidueProperties.pidColours;
-	this.thresholds = ResidueProperties.pidThresholds;
+        this.pidColours = ResidueProperties.pidColours;
+        this.thresholds = ResidueProperties.pidThresholds;
     }
 
+    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);
 
-  public Color findColour(String s, int j) {
+        double sc = 0;
 
-    if( threshold!=0 && !aboveThreshold(s,j))
-      return Color.white;
+        if ((Integer.parseInt(hash.get("maxCount").toString()) != -1) &&
+                hash.contains(s)) {
+            sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
+                    "size")).intValue();
 
-    Color     c    = Color.white;
-      Hashtable hash =  (Hashtable)consensus.elementAt(j);
+            // 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];
 
-      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() ;
-        // 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 e90e6cc..a688593 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -16,66 +16,64 @@
 * 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.util.*;
 import java.awt.*;
 
-public class ResidueColourScheme implements ColourSchemeI{
-    Color    [] colors;
-    int       threshold = 0;
-    public Vector   consensus;
+import java.util.*;
+
+
+public class ResidueColourScheme implements ColourSchemeI {
+    Color[] colors;
+    int threshold = 0;
+    public Vector consensus;
 
     public ResidueColourScheme(Color[] colors, int threshold) {
-        this.colors    = colors;
-	this.threshold = threshold;
+        this.colors = colors;
+        this.threshold = threshold;
     }
 
-    public ResidueColourScheme()
-    {   }
+    public ResidueColourScheme() {
+    }
 
-    public void setConsensus(Vector consensus)
-    {
-      this.consensus = consensus;
+    public void setConsensus(Vector consensus) {
+        this.consensus = consensus;
     }
 
-    public Color findColour(String aa)
-    {
-      return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
+    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))
-          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
-       else
-          return Color.white;
-
+        if ((threshold == 0) || aboveThreshold(s, j)) {
+            return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];
+        } else {
+            return Color.white;
+        }
     }
 
     public int getThreshold() {
-	return threshold;
+        return threshold;
     }
 
     public void setThreshold(int ct) {
-	threshold = ct;
+        threshold = ct;
     }
 
-    public boolean aboveThreshold(String s, int j)
-    {
-	Hashtable hash = (Hashtable)consensus.elementAt(j);
-
-        if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))
-        {
-               ////  resCount////////////////////                  ///////////////seq count////////////
-          double sc = ( (Integer) hash.get(s)).intValue()  * 100.0 / ( (Integer) hash.get("size")).intValue();
+    public boolean aboveThreshold(String s, int j) {
+        Hashtable hash = (Hashtable) consensus.elementAt(j);
 
-          if (sc >= threshold)
-            return true;
+        if ((((Integer) hash.get("maxCount")).intValue() != -1) &&
+                hash.contains(s)) {
+            ////  resCount////////////////////                  ///////////////seq count////////////
+            double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
+                    "size")).intValue();
 
+            if (sc >= threshold) {
+                return true;
+            }
         }
 
-	return false;
+        return false;
     }
 }
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 002917b..552a463 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -16,1020 +16,1116 @@
 * 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);
+    }
+
+    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));
+    }
 
-  //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 double getHydmax() {
-    return hydmax;
-  }
-  public static double getHydmin() {
-    return hydmin;
-  }
-  public static double[] getHyd() {
-    return hyd;
-  }
-  //public static final double hydmax = 1.38;
-  //public static final double hydmin = -2.53;
-
-  static final int[][] BLOSUM62 = {
-    //A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X  -
-    { 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 = {
-    //  C  T  A  G  -
-    { 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 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);
+    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));
     }
-    return pog ;
-  }
-
-  public static Color[] pidColours = {
-    midBlue,
-    new Color(153,153,255),
-    //    Color.lightGray,
-    new Color(204,204,255),
-  };
-  public static float[] pidThresholds = {
-    80,
-    60,
-    40,
-  } ;
-  private ResidueProperties() {}
-
-  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 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;
-      }
+
+    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;
     }
-    return null;
-  }
-  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);
-  }
-  public static Hashtable getChainColours() {
-    return chainColours;
-  }
 }
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index b6dc45b..12f252d 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -16,55 +16,53 @@
 * 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 ScoreColourScheme extends ResidueColourScheme {
-  public double min;
-  public double max;
-  public double[] scores;
-
-  public ScoreColourScheme( double[] scores,
-			   double min,
-			   double max) {
 
-    super();
+public class ScoreColourScheme extends ResidueColourScheme {
+    public double min;
+    public double max;
+    public double[] scores;
 
-    this.scores = scores;
-    this.min = min;
-    this.max = max;
-  }
+    public ScoreColourScheme(double[] scores, double min, double max) {
+        super();
 
+        this.scores = scores;
+        this.min = min;
+        this.max = max;
+    }
 
-    public Color findColour(String s,int j)
-    {
+    public Color findColour(String s, int j) {
+        if (threshold > 0) {
+            if (!aboveThreshold(s, j)) {
+                return Color.white;
+            }
+        }
 
-      if (threshold > 0)
-      {
-         if (!aboveThreshold(s,j))
-             return Color.white;
-      }
+        float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -
+            (float) min) / (float) (max - min);
 
-	float red = (float)(scores[((Integer)ResidueProperties.aaHash.get(s)).intValue()]
-			    - (float)min)/(float)(max - min);
-	if (red > 1.0f)
-	    red = 1.0f;
+        if (red > 1.0f) {
+            red = 1.0f;
+        }
 
-	if (red < 0.0f)
-	    red = 0.0f;
+        if (red < 0.0f) {
+            red = 0.0f;
+        }
 
-    char c = s.charAt(0);
+        char c = s.charAt(0);
 
-    if(jalview.util.Comparison.isGap((c)))
-        return Color.white;
+        if (jalview.util.Comparison.isGap((c))) {
+            return Color.white;
+        }
 
-	// This isn';t great - pool of colours in here?
-	return makeColour(red);
+        // This isn';t great - pool of colours in here?
+        return makeColour(red);
     }
+
     public Color makeColour(float c) {
-	return new Color(c,(float)0.0,(float)1.0-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 466ae4f..717e6dc 100755
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -16,20 +16,18 @@
 * 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 StrandColourScheme extends ScoreColourScheme {
-
 
-  public StrandColourScheme() {
-    super(ResidueProperties.strand,ResidueProperties.strandmin,ResidueProperties.strandmax);
-  }
+public class StrandColourScheme extends ScoreColourScheme {
+    public StrandColourScheme() {
+        super(ResidueProperties.strand, ResidueProperties.strandmin,
+            ResidueProperties.strandmax);
+    }
 
-  public Color makeColour(float c) {
-    return new Color(c,c,(float)1.0-c);
-  }
+    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 490425e..10277e9 100755
--- a/src/jalview/schemes/TaylorColourScheme.java
+++ b/src/jalview/schemes/TaylorColourScheme.java
@@ -16,13 +16,10 @@
 * 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 TaylorColourScheme() {
+        super(ResidueProperties.taylor, 0);
+    }
 }
diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index 2964bae..e86c44c 100755
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -16,19 +16,18 @@
 * 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 TurnColourScheme extends ScoreColourScheme {
 
-  public TurnColourScheme() {
-    super(ResidueProperties.turn,ResidueProperties.turnmin,ResidueProperties.turnmax);
-  }
+public class TurnColourScheme extends ScoreColourScheme {
+    public TurnColourScheme() {
+        super(ResidueProperties.turn, ResidueProperties.turnmin,
+            ResidueProperties.turnmax);
+    }
 
-  public Color makeColour(float c) {
-    return new Color(c,1-c,1-c);
-  }
+    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 b4decde..38a1291 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -16,20 +16,17 @@
 * 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 Color[] getColours()
-  {
-    return colors;
-  }
+public class UserColourScheme extends ResidueColourScheme {
+    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 e042acb..2a439c0 100755
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -16,12 +16,10 @@
 * 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 ZappoColourScheme extends ResidueColourScheme {
-
-  public ZappoColourScheme() {
-    super(ResidueProperties.color,0);
-  }
+    public ZappoColourScheme() {
+        super(ResidueProperties.color, 0);
+    }
 }
diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index aef74d5..12d6f02 100755
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -15,17 +15,18 @@
 * 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;
-
+*/
+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
@@ -69,551 +70,698 @@ import java.lang.reflect.Method;
  *
  * @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.
-         */
-        private static boolean loadedWithoutErrors;
-
-        /** The com.apple.mrj.MRJFileUtils class */
-        private static Class mrjFileUtilsClass;
-
-        /** The com.apple.mrj.MRJOSType class */
-        private static Class mrjOSTypeClass;
-
-        /** The com.apple.MacOS.AEDesc class */
-        private static Class aeDescClass;
-
-        /** The &lt;init&gt;(int) method of com.apple.MacOS.AETarget */
-        private static Constructor aeTargetConstructor;
-
-        /** The &lt;init&gt;(int, int, int) method of com.apple.MacOS.AppleEvent */
-        private static Constructor appleEventConstructor;
-
-        /** The &lt;init&gt;(String) method of com.apple.MacOS.AEDesc */
-        private static Constructor aeDescConstructor;
-
-        /** The findFolder method of com.apple.mrj.MRJFileUtils */
-        private static Method findFolder;
-
-        /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
-        private static Method getFileCreator;
-
-        /** The getFileType method of com.apple.mrj.MRJFileUtils */
-        private static Method getFileType;
-
-        /** The openURL method of com.apple.mrj.MRJFileUtils */
-        private static Method openURL;
-
-        /** The makeOSType method of com.apple.MacOS.OSUtils */
-        private static Method makeOSType;
-
-        /** The putParameter method of com.apple.MacOS.AppleEvent */
-        private static Method putParameter;
-
-        /** The sendNoReply method of com.apple.MacOS.AppleEvent */
-        private static Method sendNoReply;
-
-        /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
-        private static Object kSystemFolderType;
-
-        /** The keyDirectObject AppleEvent parameter type */
-        private static Integer keyDirectObject;
-
-        /** The kAutoGenerateReturnID AppleEvent code */
-        private static Integer kAutoGenerateReturnID;
-
-        /** The kAnyTransactionID AppleEvent code */
-        private static Integer kAnyTransactionID;
-
-        /** The linkage object required for JDirect 3 on Mac OS X. */
-        private static Object linkage;
-
-        /** 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 MRJ 2.0 */
-        private static final int MRJ_2_0 = 0;
-
-        /** JVM constant for MRJ 2.1 or later */
-        private static final int MRJ_2_1 = 1;
-
-        /** 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 3.1 */
-        private static final int MRJ_3_1 = 4;
-
-        /** JVM constant for any Windows NT JVM */
-        private static final int WINDOWS_NT = 5;
-
-        /** JVM constant for any Windows 9x JVM */
-        private static final int WINDOWS_9x = 6;
-
-        /** JVM constant for any other platform */
-        private static final int OTHER = -1;
-
-        /**
-         * 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 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 name for the AppleEvent type corresponding to a GetURL event. */
-        private static final String GURL_EVENT = "GURL";
-
-        /**
-         * 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 second parameter for Runtime.exec() on Windows. */
-    private static final String SECOND_WINDOWS_PARAMETER = "start";
-
+ */
+public class BrowserLauncher {
     /**
-     * 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 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;
-
-        /**
-         * 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;
-                }
-
-                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();
-                                        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;
-                                }
-                                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();
-                                        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;
-                                }
-                                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;
-                                } catch (NoSuchMethodException nsme) {
-                                        errorMessage = nsme.getMessage();
-                                        return false;
-                                } catch (InvocationTargetException ite) {
-                                        errorMessage = ite.getMessage();
-                                        return false;
-                                } catch (InstantiationException ie) {
-                                        errorMessage = ie.getMessage();
-                                        return false;
-                                } catch (IllegalAccessException iae) {
-                                        errorMessage = iae.getMessage();
-                                        return false;
-                                }
-                                break;
-                        case MRJ_3_1:
-                                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 (NoSuchMethodException nsme) {
-                                        errorMessage = nsme.getMessage();
-                                        return false;
-                                }
-                                break;
-                        default:
-                            break;
-                }
-                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;
-                }
-                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;
-                                }
-                        case MRJ_2_1:
-                                File systemFolder;
-                                try {
-                                        systemFolder = (File) findFolder.invoke(null, new Object[] { kSystemFolderType });
-                                } catch (IllegalArgumentException iare) {
-                                        browser = null;
-                                        errorMessage = iare.getMessage();
-                                        return browser;
-                                } catch (IllegalAccessException iae) {
-                                        browser = null;
-                                        errorMessage = iae.getMessage();
-                                        return browser;
-                                } catch (InvocationTargetException ite) {
-                                        browser = null;
-                                        errorMessage = ite.getTargetException().getClass() + ": " + ite.getTargetException().getMessage();
-                                        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;
-                                        }
-                                }
-                                browser = null;
-                                break;
-                        case MRJ_3_0:
-                        case MRJ_3_1:
-                                browser = "";	// Return something non-null
-                                break;
-                        case WINDOWS_NT:
-                                browser = "cmd.exe";
-                                break;
-                        case WINDOWS_9x:
-                                browser = "command.com";
-                                break;
-                        case OTHER:
-                        default:
-                                browser = jalview.bin.Cache.applicationProperties.getProperty("jalview.browser");
-                                if (browser==null) {
-                                  // hope firefox exists :-/
-                                  browser = "firefox";
-                                }
-                                break;
-                }
-                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);
-                }
-                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;
-                        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 MRJ_3_1:
-                                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 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;
-                        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
-       // JBPNote log debug
-       //       System.out.println("Executing : "+browser+" "+url+"\n");
-       Runtime.getRuntime().exec(new String[] { (String) browser, url });
-                                        }
-                                } catch (InterruptedException ie) {
-                                        throw new IOException("InterruptedException while launching browser: " + ie.getMessage());
-                                }
-                                break;
-                        default:
-                                // This should never occur, but if it does, we'll try the simplest thing possible
-                                Runtime.getRuntime().exec(new String[] { (String) browser, url });
-                                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);
-        private native static int ICStop(int[] instance);
-        private native static int ICLaunchURL(int instance, byte[] hint, byte[] data, int len,
-                                                                                        int[] selectionStart, int[] selectionEnd);
-}
+ * 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.
+ */
+    private static boolean loadedWithoutErrors;
+
+    /** The com.apple.mrj.MRJFileUtils class */
+    private static Class mrjFileUtilsClass;
+
+    /** The com.apple.mrj.MRJOSType class */
+    private static Class mrjOSTypeClass;
+
+    /** The com.apple.MacOS.AEDesc class */
+    private static Class aeDescClass;
+
+    /** The &lt;init&gt;(int) method of com.apple.MacOS.AETarget */
+    private static Constructor aeTargetConstructor;
+
+    /** The &lt;init&gt;(int, int, int) method of com.apple.MacOS.AppleEvent */
+    private static Constructor appleEventConstructor;
+
+    /** The &lt;init&gt;(String) method of com.apple.MacOS.AEDesc */
+    private static Constructor aeDescConstructor;
+
+    /** The findFolder method of com.apple.mrj.MRJFileUtils */
+    private static Method findFolder;
+
+    /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
+    private static Method getFileCreator;
+
+    /** The getFileType method of com.apple.mrj.MRJFileUtils */
+    private static Method getFileType;
+
+    /** The openURL method of com.apple.mrj.MRJFileUtils */
+    private static Method openURL;
+
+    /** The makeOSType method of com.apple.MacOS.OSUtils */
+    private static Method makeOSType;
+
+    /** The putParameter method of com.apple.MacOS.AppleEvent */
+    private static Method putParameter;
+
+    /** The sendNoReply method of com.apple.MacOS.AppleEvent */
+    private static Method sendNoReply;
+
+    /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
+    private static Object kSystemFolderType;
+
+    /** The keyDirectObject AppleEvent parameter type */
+    private static Integer keyDirectObject;
+
+    /** The kAutoGenerateReturnID AppleEvent code */
+    private static Integer kAutoGenerateReturnID;
+
+    /** The kAnyTransactionID AppleEvent code */
+    private static Integer kAnyTransactionID;
+
+    /** The linkage object required for JDirect 3 on Mac OS X. */
+    private static Object linkage;
+
+    /** 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 MRJ 2.0 */
+    private static final int MRJ_2_0 = 0;
+
+    /** JVM constant for MRJ 2.1 or later */
+    private static final int MRJ_2_1 = 1;
+
+    /** 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 3.1 */
+    private static final int MRJ_3_1 = 4;
+
+    /** JVM constant for any Windows NT JVM */
+    private static final int WINDOWS_NT = 5;
+
+    /** JVM constant for any Windows 9x JVM */
+    private static final int WINDOWS_9x = 6;
+
+    /** JVM constant for any other platform */
+    private static final int OTHER = -1;
+
+    /**
+ * 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 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 name for the AppleEvent type corresponding to a GetURL event. */
+    private static final String GURL_EVENT = "GURL";
+
+    /**
+ * 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 second parameter for Runtime.exec() on Windows. */
+    private static final String SECOND_WINDOWS_PARAMETER = "start";
+
+    /**
+ * 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 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;
+
+    /**
+ * 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;
+        }
+
+        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();
+
+                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;
+            }
+
+            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();
+
+                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;
+            }
+
+            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;
+            } catch (NoSuchMethodException nsme) {
+                errorMessage = nsme.getMessage();
+
+                return false;
+            } catch (InvocationTargetException ite) {
+                errorMessage = ite.getMessage();
+
+                return false;
+            } catch (InstantiationException ie) {
+                errorMessage = ie.getMessage();
+
+                return false;
+            } catch (IllegalAccessException iae) {
+                errorMessage = iae.getMessage();
+
+                return false;
+            }
+
+            break;
+
+        case MRJ_3_1:
+
+            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 (NoSuchMethodException nsme) {
+                errorMessage = nsme.getMessage();
+
+                return false;
+            }
+
+            break;
+
+        default:
+            break;
+        }
+
+        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;
+        }
+
+        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;
+            }
+
+        case MRJ_2_1:
+
+            File systemFolder;
+
+            try {
+                systemFolder = (File) findFolder.invoke(null,
+                        new Object[] { kSystemFolderType });
+            } catch (IllegalArgumentException iare) {
+                browser = null;
+                errorMessage = iare.getMessage();
+
+                return browser;
+            } catch (IllegalAccessException iae) {
+                browser = null;
+                errorMessage = iae.getMessage();
+
+                return browser;
+            } catch (InvocationTargetException ite) {
+                browser = null;
+                errorMessage = ite.getTargetException().getClass() + ": " +
+                    ite.getTargetException().getMessage();
+
+                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;
+                }
+            }
+
+            browser = null;
+
+            break;
+
+        case MRJ_3_0:
+        case MRJ_3_1:
+            browser = ""; // Return something non-null
+
+            break;
+
+        case WINDOWS_NT:
+            browser = "cmd.exe";
+
+            break;
+
+        case WINDOWS_9x:
+            browser = "command.com";
+
+            break;
+
+        case OTHER:default:
+            browser = jalview.bin.Cache.applicationProperties.getProperty(
+                    "jalview.browser");
+
+            if (browser == null) {
+                // hope firefox exists :-/
+                browser = "firefox";
+            }
+
+            break;
+        }
+
+        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);
+        }
+
+        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;
+
+        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 MRJ_3_1:
+
+            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 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;
+
+        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;
+
+        default:
+
+            // This should never occur, but if it does, we'll try the simplest thing possible
+            Runtime.getRuntime().exec(new String[] { (String) browser, url });
+
+            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);
+
+    private native static int ICStop(int[] instance);
+
+    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 320855a..8041d80 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -16,166 +16,165 @@
 * 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 jalview.datamodel.*;
 
+
 public class Comparison {
+    public static String GapChars = " .-";
 
-  public static float compare(SequenceI ii, SequenceI jj)
-  {
-    return Comparison.compare(ii,jj,0,ii.getLength()-1);
-  }
-  /**
-   * this was supposed to be an ungapped pid calculation
-   * @param ii SequenceI
-   * @param jj SequenceI
-   * @param start int
-   * @param end int
-   * @return float
-   */
-  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)))
-     {
-       ilen--;
-     }
-
-     while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
-     {
-       jlen--;
-     }
-
-     int   count = 0;
-     int   match = 0;
-     float pid   = -1;
-
-     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))) {
-           match++;
-         }
-         count++;
-       }
-       pid = (float)match/(float)ilen * 100;
-     } else {
-       for (int j = 0; j < jlen; j++) {
-         if (si.substring(start + j,start + j+1).equals(sj.substring(start + j,start + j+1))) {
-           match++;
-         }
-         count++;
-       }
-       pid = (float)match/(float)jlen * 100;
-     }
-
-    return pid;
-  }
-
-  /**
-   * this is a gapped PID calculation
-   *
-   * @param s1 SequenceI
-   * @param s2 SequenceI
-   * @return float
-   */
-  public static float PID(SequenceI s1 , SequenceI s2)
-  {
-    int len;
-
-    if (s1.getSequence().length() > s2.getSequence().length())
-      len = s1.getSequence().length();
-    else
-      len = s2.getSequence().length();
-
-
-    int bad = 0;
-
-    for (int i = 0; i < len; i++)
-    {
-      char chr1;
-      char chr2;
-
-      if (i < s1.getSequence().length())
-        chr1 = s1.getSequence().charAt(i);
-      else
-        chr1 = '.';
-
-
-      if (i < s2.getSequence().length())
-        chr2 = s2.getSequence().charAt(i);
-      else
-        chr2 = '.';
-
-
-      if (!(jalview.util.Comparison.isGap( chr1 ))  &&  !(jalview.util.Comparison.isGap( chr2 )))
-      {
-        if (chr1!=chr2)
-          bad++;
-      }
+    public static float compare(SequenceI ii, SequenceI jj) {
+        return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
     }
 
-    return (float)100*(len-bad)/len;
-  }
-
-  // Another pid with region specification
-
-  public static float PID(SequenceI s1 , SequenceI s2, int start, int end)
-  {
-    int len;
-
-    if (s1.getSequence().length() > s2.getSequence().length())
-      len = s1.getSequence().length();
-    else
-      len = s2.getSequence().length();
-
-    if (end<len)
-      len=end;
-
-    if (len<start) {
-      start = len - 1; // we just use a single residue for the difference
+    /**
+     * this was supposed to be an ungapped pid calculation
+     * @param ii SequenceI
+     * @param jj SequenceI
+     * @param start int
+     * @param end int
+     * @return float
+     */
+    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))) {
+            ilen--;
+        }
+
+        while (jalview.util.Comparison.isGap(sj.charAt(start + jlen))) {
+            jlen--;
+        }
+
+        int count = 0;
+        int match = 0;
+        float pid = -1;
+
+        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))) {
+                    match++;
+                }
+
+                count++;
+            }
+
+            pid = (float) match / (float) ilen * 100;
+        } else {
+            for (int j = 0; j < jlen; j++) {
+                if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
+                                j, start + j + 1))) {
+                    match++;
+                }
+
+                count++;
+            }
+
+            pid = (float) match / (float) jlen * 100;
+        }
+
+        return pid;
     }
 
-    int bad = 0;
-
-    for (int i = start; i < len; i++)
-    {
-      char chr1;
-      char chr2;
-
-      if (i < s1.getSequence().length())
-        chr1 = s1.getSequence().charAt(i);
-      else
-        chr1 = '.';
-
-
-      if (i < s2.getSequence().length())
-        chr2 = s2.getSequence().charAt(i);
-      else
-        chr2 = '.';
-
-
-      if (!(jalview.util.Comparison.isGap( chr1 ))  &&  !(jalview.util.Comparison.isGap( chr2 )))
-      {
-        if (chr1!=chr2)
-          bad++;
-      }
+    /**
+     * this is a gapped PID calculation
+     *
+     * @param s1 SequenceI
+     * @param s2 SequenceI
+     * @return float
+     */
+    public static float PID(SequenceI s1, SequenceI s2) {
+        int len;
+
+        if (s1.getSequence().length() > s2.getSequence().length()) {
+            len = s1.getSequence().length();
+        } else {
+            len = s2.getSequence().length();
+        }
+
+        int bad = 0;
+
+        for (int i = 0; i < len; i++) {
+            char chr1;
+            char chr2;
+
+            if (i < s1.getSequence().length()) {
+                chr1 = s1.getSequence().charAt(i);
+            } else {
+                chr1 = '.';
+            }
+
+            if (i < s2.getSequence().length()) {
+                chr2 = s2.getSequence().charAt(i);
+            } else {
+                chr2 = '.';
+            }
+
+            if (!(jalview.util.Comparison.isGap(chr1)) &&
+                    !(jalview.util.Comparison.isGap(chr2))) {
+                if (chr1 != chr2) {
+                    bad++;
+                }
+            }
+        }
+
+        return ((float) 100 * (len - bad)) / len;
     }
 
-    return (float)100*(len-bad)/len;
-  }
-
+    // Another pid with region specification
+    public static float PID(SequenceI s1, SequenceI s2, int start, int end) {
+        int len;
+
+        if (s1.getSequence().length() > s2.getSequence().length()) {
+            len = s1.getSequence().length();
+        } else {
+            len = s2.getSequence().length();
+        }
+
+        if (end < len) {
+            len = end;
+        }
+
+        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++) {
+            char chr1;
+            char chr2;
+
+            if (i < s1.getSequence().length()) {
+                chr1 = s1.getSequence().charAt(i);
+            } else {
+                chr1 = '.';
+            }
+
+            if (i < s2.getSequence().length()) {
+                chr2 = s2.getSequence().charAt(i);
+            } else {
+                chr2 = '.';
+            }
+
+            if (!(jalview.util.Comparison.isGap(chr1)) &&
+                    !(jalview.util.Comparison.isGap(chr2))) {
+                if (chr1 != chr2) {
+                    bad++;
+                }
+            }
+        }
+
+        return ((float) 100 * (len - bad)) / len;
+    }
 
-  public static String GapChars = " .-";
-  public static boolean isGap(char c)
-  {
-    return  (c != '.' && c != '-' && c != ' ') ? false : true;
-  }
+    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 798dc8f..4c47f65 100755
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -25,13 +25,126 @@
  * @version 1.03 25 Oct 1997
  * @author Cay Horstmann
  */
-
-
 package jalview.util;
 
 import java.io.*;
 
+
 public class Format {
+    private int width;
+    private int precision;
+    private String pre;
+    private String post;
+    private boolean leading_zeroes;
+    private boolean show_plus;
+    private boolean alternate;
+    private boolean show_space;
+    private boolean left_align;
+    private char fmt; // one of cdeEfgGiosxXos
+
+    public Format(String s) {
+        width = 0;
+        precision = -1;
+        pre = "";
+        post = "";
+        leading_zeroes = false;
+        show_plus = false;
+        alternate = false;
+        show_space = false;
+        left_align = false;
+        fmt = ' ';
+
+        int state = 0;
+        int length = s.length();
+        int parse_state = 0;
+
+        // 0 = prefix, 1 = flags, 2 = width, 3 = precision,
+        // 4 = format, 5 = end
+        int i = 0;
+
+        while (parse_state == 0) {
+            if (i >= length) {
+                parse_state = 5;
+            } else if (s.charAt(i) == '%') {
+                if (i < (length - 1)) {
+                    if (s.charAt(i + 1) == '%') {
+                        pre = pre + '%';
+                        i++;
+                    } else {
+                        parse_state = 1;
+                    }
+                } else {
+                    throw new java.lang.IllegalArgumentException();
+                }
+            } else {
+                pre = pre + s.charAt(i);
+            }
+
+            i++;
+        }
+
+        while (parse_state == 1) {
+            if (i >= length) {
+                parse_state = 5;
+            } else if (s.charAt(i) == ' ') {
+                show_space = true;
+            } else if (s.charAt(i) == '-') {
+                left_align = true;
+            } else if (s.charAt(i) == '+') {
+                show_plus = true;
+            } else if (s.charAt(i) == '0') {
+                leading_zeroes = true;
+            } else if (s.charAt(i) == '#') {
+                alternate = true;
+            } else {
+                parse_state = 2;
+                i--;
+            }
+
+            i++;
+        }
+
+        while (parse_state == 2) {
+            if (i >= length) {
+                parse_state = 5;
+            } else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9')) {
+                width = ((width * 10) + s.charAt(i)) - '0';
+                i++;
+            } else if (s.charAt(i) == '.') {
+                parse_state = 3;
+                precision = 0;
+                i++;
+            } else {
+                parse_state = 4;
+            }
+        }
+
+        while (parse_state == 3) {
+            if (i >= length) {
+                parse_state = 5;
+            } else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9')) {
+                precision = ((precision * 10) + s.charAt(i)) - '0';
+                i++;
+            } else {
+                parse_state = 4;
+            }
+        }
+
+        if (parse_state == 4) {
+            if (i >= length) {
+                parse_state = 5;
+            } else {
+                fmt = s.charAt(i);
+            }
+
+            i++;
+        }
+
+        if (i < length) {
+            post = s.substring(i, length);
+        }
+    }
+
     /**
      * Formats the number following printf conventions.
      * Main limitation: Can only handle one format parameter at a time
@@ -68,565 +181,525 @@ public class Format {
      * @exception IllegalArgumentException if bad format
      *
      */
+    public static String getHexString(java.awt.Color color) {
+        String r;
+        String g;
+        String b;
+        r = Integer.toHexString(color.getRed());
+
+        if (r.length() < 2) {
+            r = "0" + r;
+        }
 
-  public static String getHexString(java.awt.Color color)
-  {
-    String r, g, b;
-    r = Integer.toHexString(color.getRed());
-    if (r.length() < 2)
-      r = "0" + r;
-    g = Integer.toHexString(color.getGreen());
-    if (g.length() < 2)
-      g = "0" + g;
-    b = Integer.toHexString(color.getBlue());
-    if (b.length() < 2)
-      b = "0" + b;
-
-    return r+g+b;
-  }
-
-
-  public Format(String s) {
-    width = 0;
-    precision = -1;
-    pre = "";
-    post = "";
-    leading_zeroes = false;
-    show_plus = false;
-    alternate = false;
-    show_space = false;
-    left_align = false;
-    fmt = ' ';
-
-    int state = 0;
-    int length = s.length();
-    int parse_state = 0;
-    // 0 = prefix, 1 = flags, 2 = width, 3 = precision,
-    // 4 = format, 5 = end
-    int i = 0;
-
-    while (parse_state == 0) {
-      if (i >= length)
-        parse_state = 5;
-      else if (s.charAt(i) == '%') {
-        if (i < length - 1) {
-          if (s.charAt(i + 1) == '%') {
-            pre = pre + '%';
-            i++;
-          } else
-            parse_state = 1;
-        } else
-          throw new java.lang.IllegalArgumentException();
-      } else
-        pre = pre + s.charAt(i);
-      i++;
+        g = Integer.toHexString(color.getGreen());
+
+        if (g.length() < 2) {
+            g = "0" + g;
+        }
+
+        b = Integer.toHexString(color.getBlue());
+
+        if (b.length() < 2) {
+            b = "0" + b;
+        }
+
+        return r + g + b;
     }
-    while (parse_state == 1) {
-      if (i >= length)
-        parse_state = 5;
-      else if (s.charAt(i) == ' ')
-        show_space = true;
-      else if (s.charAt(i) == '-')
-        left_align = true;
-      else if (s.charAt(i) == '+')
-        show_plus = true;
-      else if (s.charAt(i) == '0')
-        leading_zeroes = true;
-      else if (s.charAt(i) == '#')
-        alternate = true;
-      else {
-        parse_state = 2;
-        i--;
-      }
-      i++;
+
+    /**
+    * prints a formatted number following printf conventions
+    * @param s a PrintStream
+    * @param fmt the format string
+    * @param x the double to print
+    */
+    public static void print(java.io.PrintStream s, String fmt, double x) {
+        s.print(new Format(fmt).form(x));
     }
-    while (parse_state == 2) {
-      if (i >= length)
-        parse_state = 5;
-      else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') {
-        width = width * 10 + s.charAt(i) - '0';
-        i++;
-      } else if (s.charAt(i) == '.') {
-        parse_state = 3;
-        precision = 0;
-        i++;
-      } else
-        parse_state = 4;
+
+    /**
+    * prints a formatted number following printf conventions
+    * @param s a PrintStream
+    * @param fmt the format string
+    * @param x the long to print
+    */
+    public static void print(java.io.PrintStream s, String fmt, long x) {
+        s.print(new Format(fmt).form(x));
     }
-    while (parse_state == 3) {
-      if (i >= length)
-        parse_state = 5;
-      else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') {
-        precision = precision * 10 + s.charAt(i) - '0';
-        i++;
-      } else
-        parse_state = 4;
+
+    /**
+    * prints a formatted number following printf conventions
+    * @param s a PrintStream
+    * @param fmt the format string
+    * @param x the character to
+    */
+    public static void print(java.io.PrintStream s, String fmt, char x) {
+        s.print(new Format(fmt).form(x));
     }
-    if (parse_state == 4) {
-      if (i >= length)
-        parse_state = 5;
-      else
-        fmt = s.charAt(i);
-      i++;
+
+    /**
+    * prints a formatted number following printf conventions
+    * @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) {
+        s.print(new Format(fmt).form(x));
     }
-    if (i < length)
-      post = s.substring(i, length);
-  }
-
-  /**
-  * prints a formatted number following printf conventions
-  * @param s a PrintStream
-  * @param fmt the format string
-  * @param x the double to print
-  */
-
-  public static void print(java.io.PrintStream s, String fmt, double x) {
-    s.print(new Format(fmt).form(x));
-  }
-
-  /**
-  * prints a formatted number following printf conventions
-  * @param s a PrintStream
-  * @param fmt the format string
-  * @param x the long to print
-  */
-  public static void print(java.io.PrintStream s, String fmt, long x) {
-    s.print(new Format(fmt).form(x));
-  }
-
-  /**
-  * prints a formatted number following printf conventions
-  * @param s a PrintStream
-  * @param fmt the format string
-  * @param x the character to
-  */
-
-  public static void print(java.io.PrintStream s, String fmt, char x) {
-    s.print(new Format(fmt).form(x));
-  }
-
-  /**
-  * prints a formatted number following printf conventions
-  * @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) {
-    s.print(new Format(fmt).form(x));
-  }
-
-  /**
-  * Converts a string of digits (decimal, octal or hex) to an integer
-  * @param s a string
-  * @return the numeric value of the prefix of s representing a base 10 integer
-  */
-
-  public static int atoi(String s) {
-    return (int)atol(s);
-  }
-
-  /**
-  * Converts a string of digits (decimal, octal or hex) to a long integer
-  * @param s a string
-  * @return the numeric value of the prefix of s representing a base 10 integer
-  */
-
-  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 + 1 < s.length() && (s.charAt(i + 1) == 'x' || s.charAt(i + 1) == 'X'))
-        return parseLong(s.substring(i + 2), 16);
-      else
-        return parseLong(s, 8);
-    } else
-      return parseLong(s, 10);
-  }
-
-  private static long parseLong(String s, int base) {
-    int i = 0;
-    int sign = 1;
-    long r = 0;
-
-    while (i < s.length() && Character.isWhitespace(s.charAt(i)))
-      i++;
-    if (i < s.length() && s.charAt(i) == '-') {
-      sign = -1;
-      i++;
-    } else if (i < s.length() && s.charAt(i) == '+') {
-      i++;
+
+    /**
+    * Converts a string of digits (decimal, octal or hex) to an integer
+    * @param s a string
+    * @return the numeric value of the prefix of s representing a base 10 integer
+    */
+    public static int atoi(String s) {
+        return (int) atol(s);
     }
-    while (i < s.length()) {
-      char ch = s.charAt(i);
-      if ('0' <= ch && ch < '0' + base)
-        r = r * base + ch - '0';
-      else if ('A' <= ch && ch < 'A' + base - 10)
-        r = r * base + ch - 'A' + 10 ;
-      else if ('a' <= ch && ch < 'a' + base - 10)
-        r = r * base + ch - 'a' + 10 ;
-      else
-        return r * sign;
-      i++;
+
+    /**
+    * Converts a string of digits (decimal, octal or hex) to a long integer
+    * @param s a string
+    * @return the numeric value of the prefix of s representing a base 10 integer
+    */
+    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 + 1) < s.length()) &&
+                    ((s.charAt(i + 1) == 'x') || (s.charAt(i + 1) == 'X'))) {
+                return parseLong(s.substring(i + 2), 16);
+            } else {
+                return parseLong(s, 8);
+            }
+        } else {
+            return parseLong(s, 10);
+        }
     }
-    return r * sign;
-  }
-
-  /**
-  * Converts a string of digits to an double
-  * @param s a string
-  */
-
-  public static double atof(String s) {
-    int i = 0;
-    int sign = 1;
-    double r = 0; // integer part
-    double f = 0; // fractional part
-    double p = 1; // exponent of fractional part
-    int state = 0; // 0 = int part, 1 = frac part
-
-    while (i < s.length() && Character.isWhitespace(s.charAt(i)))
-      i++;
-    if (i < s.length() && s.charAt(i) == '-') {
-      sign = -1;
-      i++;
-    } else if (i < s.length() && s.charAt(i) == '+') {
-      i++;
+
+    private static long parseLong(String s, int base) {
+        int i = 0;
+        int sign = 1;
+        long r = 0;
+
+        while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
+            i++;
+
+        if ((i < s.length()) && (s.charAt(i) == '-')) {
+            sign = -1;
+            i++;
+        } else if ((i < s.length()) && (s.charAt(i) == '+')) {
+            i++;
+        }
+
+        while (i < s.length()) {
+            char ch = s.charAt(i);
+
+            if (('0' <= ch) && (ch < ('0' + base))) {
+                r = ((r * base) + ch) - '0';
+            } else if (('A' <= ch) && (ch < (('A' + base) - 10))) {
+                r = ((r * base) + ch) - 'A' + 10;
+            } else if (('a' <= ch) && (ch < (('a' + base) - 10))) {
+                r = ((r * base) + ch) - 'a' + 10;
+            } else {
+                return r * sign;
+            }
+
+            i++;
+        }
+
+        return r * sign;
     }
-    while (i < s.length()) {
-      char ch = s.charAt(i);
-      if ('0' <= ch && ch <= '9') {
-        if (state == 0)
-          r = r * 10 + ch - '0';
-        else if (state == 1) {
-          p = p / 10;
-          r = r + p * (ch - '0');
-        }
-      } else if (ch == '.') {
-        if (state == 0)
-          state = 1;
-        else
-          return sign * r;
-      } else if (ch == 'e' || ch == 'E') {
-        long e = (int)parseLong(s.substring(i + 1), 10);
-        return sign * r * Math.pow(10, e);
-      } else
+
+    /**
+    * Converts a string of digits to an double
+    * @param s a string
+    */
+    public static double atof(String s) {
+        int i = 0;
+        int sign = 1;
+        double r = 0; // integer part
+        double f = 0; // fractional part
+        double p = 1; // exponent of fractional part
+        int state = 0; // 0 = int part, 1 = frac part
+
+        while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
+            i++;
+
+        if ((i < s.length()) && (s.charAt(i) == '-')) {
+            sign = -1;
+            i++;
+        } else if ((i < s.length()) && (s.charAt(i) == '+')) {
+            i++;
+        }
+
+        while (i < s.length()) {
+            char ch = s.charAt(i);
+
+            if (('0' <= ch) && (ch <= '9')) {
+                if (state == 0) {
+                    r = ((r * 10) + ch) - '0';
+                } else if (state == 1) {
+                    p = p / 10;
+                    r = r + (p * (ch - '0'));
+                }
+            } else if (ch == '.') {
+                if (state == 0) {
+                    state = 1;
+                } else {
+                    return sign * r;
+                }
+            } else if ((ch == 'e') || (ch == 'E')) {
+                long e = (int) parseLong(s.substring(i + 1), 10);
+
+                return sign * r * Math.pow(10, e);
+            } else {
+                return sign * r;
+            }
+
+            i++;
+        }
+
         return sign * r;
-      i++;
     }
-    return sign * r;
-  }
-
-  /**
-  * Formats a double into a string (like sprintf in C)
-  * @param x the number to format
-  * @return the formatted string
-  * @exception IllegalArgumentException if bad argument
-  */
-
-  public String form(double x) {
-    String r;
-    if (precision < 0)
-      precision = 6;
-    int s = 1;
-    if (x < 0) {
-      x = -x;
-      s = -1;
+
+    /**
+    * Formats a double into a string (like sprintf in C)
+    * @param x the number to format
+    * @return the formatted string
+    * @exception IllegalArgumentException if bad argument
+    */
+    public String form(double x) {
+        String r;
+
+        if (precision < 0) {
+            precision = 6;
+        }
+
+        int s = 1;
+
+        if (x < 0) {
+            x = -x;
+            s = -1;
+        }
+
+        if (fmt == 'f') {
+            r = fixed_format(x);
+        } else if ((fmt == 'e') || (fmt == 'E') || (fmt == 'g') ||
+                (fmt == 'G')) {
+            r = exp_format(x);
+        } else {
+            throw new java.lang.IllegalArgumentException();
+        }
+
+        return pad(sign(s, r));
     }
-    if (fmt == 'f')
-      r = fixed_format(x);
-    else if (fmt == 'e' || fmt == 'E' || fmt == 'g' || fmt == 'G')
-      r = exp_format(x);
-    else
-      throw new java.lang.IllegalArgumentException();
-
-    return pad(sign(s, r));
-  }
-
-  /**
-  * Formats a long integer into a string (like sprintf in C)
-  * @param x the number to format
-  * @return the formatted string
-  */
-
-  public String form(long x) {
-    String r;
-    int s = 0;
-    if (fmt == 'd' || fmt == 'i') {
-      if (x < 0) {
-        r = ("" + x).substring(1);
-        s = -1;
-      } else {
-        r = "" + x;
-        s = 1;
-      }
-    } else if (fmt == 'o')
-      r = convert(x, 3, 7, "01234567");
-    else if (fmt == 'x')
-      r = convert(x, 4, 15, "0123456789abcdef");
-    else if (fmt == 'X')
-      r = convert(x, 4, 15, "0123456789ABCDEF");
-    else
-      throw new java.lang.IllegalArgumentException();
-
-    return pad(sign(s, r));
-  }
-
-  /**
-  * Formats a character into a string (like sprintf in C)
-  * @param x the value to format
-  * @return the formatted string
-  */
-
-  public String form(char c) {
-    if (fmt != 'c')
-      throw new java.lang.IllegalArgumentException();
-
-    String r = "" + c;
-    return pad(r);
-  }
-
-  /**
-  * Formats a string into a larger string (like sprintf in C)
-  * @param x the value to format
-  * @return the formatted string
-  */
-
-  public String form(String s) {
-    if (fmt != 's')
-      throw new java.lang.IllegalArgumentException();
-    if (precision >= 0)
-      s = s.substring(0, precision);
-    return pad(s);
-  }
-
-
-  /**
-  * a test stub for the format class
-  */
-
-  public static void main(String[] a) {
-    double x = 1.23456789012;
-    double y = 123;
-    double z = 1.2345e30;
-    double w = 1.02;
-    double u = 1.234e-5;
-    int d = 0xCAFE;
-    Format.print(System.out, "x = |%f|\n", x);
-    Format.print(System.out, "u = |%20f|\n", u);
-    Format.print(System.out, "x = |% .5f|\n", x);
-    Format.print(System.out, "w = |%20.5f|\n", w);
-    Format.print(System.out, "x = |%020.5f|\n", x);
-    Format.print(System.out, "x = |%+20.5f|\n", x);
-    Format.print(System.out, "x = |%+020.5f|\n", x);
-    Format.print(System.out, "x = |% 020.5f|\n", x);
-    Format.print(System.out, "y = |%#+20.5f|\n", y);
-    Format.print(System.out, "y = |%-+20.5f|\n", y);
-    Format.print(System.out, "z = |%20.5f|\n", z);
-
-    Format.print(System.out, "x = |%e|\n", x);
-    Format.print(System.out, "u = |%20e|\n", u);
-    Format.print(System.out, "x = |% .5e|\n", x);
-    Format.print(System.out, "w = |%20.5e|\n", w);
-    Format.print(System.out, "x = |%020.5e|\n", x);
-    Format.print(System.out, "x = |%+20.5e|\n", x);
-    Format.print(System.out, "x = |%+020.5e|\n", x);
-    Format.print(System.out, "x = |% 020.5e|\n", x);
-    Format.print(System.out, "y = |%#+20.5e|\n", y);
-    Format.print(System.out, "y = |%-+20.5e|\n", y);
-
-    Format.print(System.out, "x = |%g|\n", x);
-    Format.print(System.out, "z = |%g|\n", z);
-    Format.print(System.out, "w = |%g|\n", w);
-    Format.print(System.out, "u = |%g|\n", u);
-    Format.print(System.out, "y = |%.2g|\n", y);
-    Format.print(System.out, "y = |%#.2g|\n", y);
-
-    Format.print(System.out, "d = |%d|\n", d);
-    Format.print(System.out, "d = |%20d|\n", d);
-    Format.print(System.out, "d = |%020d|\n", d);
-    Format.print(System.out, "d = |%+20d|\n", d);
-    Format.print(System.out, "d = |% 020d|\n", d);
-    Format.print(System.out, "d = |%-20d|\n", d);
-    Format.print(System.out, "d = |%20.8d|\n", d);
-    Format.print(System.out, "d = |%x|\n", d);
-    Format.print(System.out, "d = |%20X|\n", d);
-    Format.print(System.out, "d = |%#20x|\n", d);
-    Format.print(System.out, "d = |%020X|\n", d);
-    Format.print(System.out, "d = |%20.8x|\n", d);
-    Format.print(System.out, "d = |%o|\n", d);
-    Format.print(System.out, "d = |%020o|\n", d);
-    Format.print(System.out, "d = |%#20o|\n", d);
-    Format.print(System.out, "d = |%#020o|\n", d);
-    Format.print(System.out, "d = |%20.12o|\n", d);
-
-    Format.print(System.out, "s = |%-20s|\n", "Hello");
-    Format.print(System.out, "s = |%-20c|\n", '!');
-
-    // regression test to confirm fix of reported bugs
-
-    Format.print(System.out, "|%i|\n", Long.MIN_VALUE);
-
-    Format.print(System.out, "|%6.2e|\n", 0.0);
-    Format.print(System.out, "|%6.2g|\n", 0.0);
-
-    Format.print(System.out, "|%6.2f|\n", 9.99);
-    Format.print(System.out, "|%6.2f|\n", 9.999);
-
-    Format.print(System.out, "|%6.0f|\n", 9.999);
-  }
-
-  private static String repeat(char c, int n) {
-    if (n <= 0)
-      return "";
-    StringBuffer s = new StringBuffer(n);
-    for (int i = 0; i < n; i++)
-      s.append(c);
-    return s.toString();
-  }
-
-  private static String convert(long x, int n, int m, String d) {
-    if (x == 0)
-      return "0";
-    String r = "";
-    while (x != 0) {
-      r = d.charAt((int)(x & m)) + r;
-      x = x >>> n;
+
+    /**
+    * Formats a long integer into a string (like sprintf in C)
+    * @param x the number to format
+    * @return the formatted string
+    */
+    public String form(long x) {
+        String r;
+        int s = 0;
+
+        if ((fmt == 'd') || (fmt == 'i')) {
+            if (x < 0) {
+                r = ("" + x).substring(1);
+                s = -1;
+            } else {
+                r = "" + x;
+                s = 1;
+            }
+        } else if (fmt == 'o') {
+            r = convert(x, 3, 7, "01234567");
+        } else if (fmt == 'x') {
+            r = convert(x, 4, 15, "0123456789abcdef");
+        } else if (fmt == 'X') {
+            r = convert(x, 4, 15, "0123456789ABCDEF");
+        } else {
+            throw new java.lang.IllegalArgumentException();
+        }
+
+        return pad(sign(s, r));
     }
-    return r;
-  }
-
-  private String pad(String r) {
-    String p = repeat(' ', width - r.length());
-    if (left_align)
-      return pre + r + p + post;
-    else
-      return pre + p + r + post;
-  }
-
-  private String sign(int s, String r) {
-    String p = "";
-    if (s < 0)
-      p = "-";
-    else if (s > 0) {
-      if (show_plus)
-        p = "+";
-      else if (show_space)
-        p = " ";
-    } else {
-      if (fmt == 'o' && alternate && r.length() > 0 && r.charAt(0) != '0')
-        p = "0";
-      else if (fmt == 'x' && alternate)
-        p = "0x";
-      else if (fmt == 'X' && alternate)
-        p = "0X";
+
+    /**
+    * Formats a character into a string (like sprintf in C)
+    * @param x the value to format
+    * @return the formatted string
+    */
+    public String form(char c) {
+        if (fmt != 'c') {
+            throw new java.lang.IllegalArgumentException();
+        }
+
+        String r = "" + c;
+
+        return pad(r);
     }
-    int w = 0;
-    if (leading_zeroes)
-      w = width;
-    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) {
-    boolean removeTrailing
-    = (fmt == 'G' || fmt == 'g') && !alternate;
-    // remove trailing zeroes and decimal point
-
-    if (d > 0x7FFFFFFFFFFFFFFFL)
-      return exp_format(d);
-    if (precision == 0)
-      return (long)(d + 0.5) + (removeTrailing ? "" : ".");
-
-    long whole = (long)d;
-    double fr = d - whole; // fractional part
-    if (fr >= 1 || fr < 0)
-      return exp_format(d);
-
-    double factor = 1;
-    String leading_zeroes = "";
-    for (int i = 1; i <= precision && factor <= 0x7FFFFFFFFFFFFFFFL; i++) {
-      factor *= 10;
-      leading_zeroes = leading_zeroes + "0";
+
+    /**
+    * Formats a string into a larger string (like sprintf in C)
+    * @param x the value to format
+    * @return the formatted string
+    */
+    public String form(String s) {
+        if (fmt != 's') {
+            throw new java.lang.IllegalArgumentException();
+        }
+
+        if (precision >= 0) {
+            s = s.substring(0, precision);
+        }
+
+        return pad(s);
     }
-    long l = (long) (factor * fr + 0.5);
-    if (l >= factor) {
-      l = 0;
-      whole++;
-    } // CSH 10-25-97
-
-    String z = leading_zeroes + l;
-    z = "." + z.substring(z.length() - precision, z.length());
-
-    if (removeTrailing) {
-      int t = z.length() - 1;
-      while (t >= 0 && z.charAt(t) == '0')
-        t--;
-      if (t >= 0 && z.charAt(t) == '.')
-        t--;
-      z = z.substring(0, t + 1);
+
+    /**
+    * a test stub for the format class
+    */
+    public static void main(String[] a) {
+        double x = 1.23456789012;
+        double y = 123;
+        double z = 1.2345e30;
+        double w = 1.02;
+        double u = 1.234e-5;
+        int d = 0xCAFE;
+        Format.print(System.out, "x = |%f|\n", x);
+        Format.print(System.out, "u = |%20f|\n", u);
+        Format.print(System.out, "x = |% .5f|\n", x);
+        Format.print(System.out, "w = |%20.5f|\n", w);
+        Format.print(System.out, "x = |%020.5f|\n", x);
+        Format.print(System.out, "x = |%+20.5f|\n", x);
+        Format.print(System.out, "x = |%+020.5f|\n", x);
+        Format.print(System.out, "x = |% 020.5f|\n", x);
+        Format.print(System.out, "y = |%#+20.5f|\n", y);
+        Format.print(System.out, "y = |%-+20.5f|\n", y);
+        Format.print(System.out, "z = |%20.5f|\n", z);
+
+        Format.print(System.out, "x = |%e|\n", x);
+        Format.print(System.out, "u = |%20e|\n", u);
+        Format.print(System.out, "x = |% .5e|\n", x);
+        Format.print(System.out, "w = |%20.5e|\n", w);
+        Format.print(System.out, "x = |%020.5e|\n", x);
+        Format.print(System.out, "x = |%+20.5e|\n", x);
+        Format.print(System.out, "x = |%+020.5e|\n", x);
+        Format.print(System.out, "x = |% 020.5e|\n", x);
+        Format.print(System.out, "y = |%#+20.5e|\n", y);
+        Format.print(System.out, "y = |%-+20.5e|\n", y);
+
+        Format.print(System.out, "x = |%g|\n", x);
+        Format.print(System.out, "z = |%g|\n", z);
+        Format.print(System.out, "w = |%g|\n", w);
+        Format.print(System.out, "u = |%g|\n", u);
+        Format.print(System.out, "y = |%.2g|\n", y);
+        Format.print(System.out, "y = |%#.2g|\n", y);
+
+        Format.print(System.out, "d = |%d|\n", d);
+        Format.print(System.out, "d = |%20d|\n", d);
+        Format.print(System.out, "d = |%020d|\n", d);
+        Format.print(System.out, "d = |%+20d|\n", d);
+        Format.print(System.out, "d = |% 020d|\n", d);
+        Format.print(System.out, "d = |%-20d|\n", d);
+        Format.print(System.out, "d = |%20.8d|\n", d);
+        Format.print(System.out, "d = |%x|\n", d);
+        Format.print(System.out, "d = |%20X|\n", d);
+        Format.print(System.out, "d = |%#20x|\n", d);
+        Format.print(System.out, "d = |%020X|\n", d);
+        Format.print(System.out, "d = |%20.8x|\n", d);
+        Format.print(System.out, "d = |%o|\n", d);
+        Format.print(System.out, "d = |%020o|\n", d);
+        Format.print(System.out, "d = |%#20o|\n", d);
+        Format.print(System.out, "d = |%#020o|\n", d);
+        Format.print(System.out, "d = |%20.12o|\n", d);
+
+        Format.print(System.out, "s = |%-20s|\n", "Hello");
+        Format.print(System.out, "s = |%-20c|\n", '!');
+
+        // regression test to confirm fix of reported bugs
+        Format.print(System.out, "|%i|\n", Long.MIN_VALUE);
+
+        Format.print(System.out, "|%6.2e|\n", 0.0);
+        Format.print(System.out, "|%6.2g|\n", 0.0);
+
+        Format.print(System.out, "|%6.2f|\n", 9.99);
+        Format.print(System.out, "|%6.2f|\n", 9.999);
+
+        Format.print(System.out, "|%6.0f|\n", 9.999);
     }
 
-    return whole + z;
-  }
-
-  private String exp_format(double d) {
-    String f = "";
-    int e = 0;
-    double dd = d;
-    double factor = 1;
-    if (d != 0) {
-      while (dd > 10) {
-        e++;
-        factor /= 10;
-        dd = dd / 10;
-      }
-      while (dd < 1) {
-        e--;
-        factor *= 10;
-        dd = dd * 10;
-      }
+    private static String repeat(char c, int n) {
+        if (n <= 0) {
+            return "";
+        }
+
+        StringBuffer s = new StringBuffer(n);
+
+        for (int i = 0; i < n; i++)
+            s.append(c);
+
+        return s.toString();
     }
-    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')
-      f = f + "e";
-    else
-      f = f + "E";
-
-    String p = "000";
-    if (e >= 0) {
-      f = f + "+";
-      p = p + e;
-    } else {
-      f = f + "-";
-      p = p + (-e);
+
+    private static String convert(long x, int n, int m, String d) {
+        if (x == 0) {
+            return "0";
+        }
+
+        String r = "";
+
+        while (x != 0) {
+            r = d.charAt((int) (x & m)) + r;
+            x = x >>> n;
+        }
+
+        return r;
     }
 
-    return f + p.substring(p.length() - 3, p.length());
-  }
-
-  private int width;
-  private int precision;
-  private String pre;
-  private String post;
-  private boolean leading_zeroes;
-  private boolean show_plus;
-  private boolean alternate;
-  private boolean show_space;
-  private boolean left_align;
-  private char fmt; // one of cdeEfgGiosxXos
-}
+    private String pad(String r) {
+        String p = repeat(' ', width - r.length());
+
+        if (left_align) {
+            return pre + r + p + post;
+        } else {
+            return pre + p + r + post;
+        }
+    }
 
+    private String sign(int s, String r) {
+        String p = "";
+
+        if (s < 0) {
+            p = "-";
+        } else if (s > 0) {
+            if (show_plus) {
+                p = "+";
+            } else if (show_space) {
+                p = " ";
+            }
+        } else {
+            if ((fmt == 'o') && alternate && (r.length() > 0) &&
+                    (r.charAt(0) != '0')) {
+                p = "0";
+            } else if ((fmt == 'x') && alternate) {
+                p = "0x";
+            } else if ((fmt == 'X') && alternate) {
+                p = "0X";
+            }
+        }
+
+        int w = 0;
+
+        if (leading_zeroes) {
+            w = width;
+        } 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) {
+        boolean removeTrailing = ((fmt == 'G') || (fmt == 'g')) && !alternate;
 
+        // remove trailing zeroes and decimal point
+        if (d > 0x7FFFFFFFFFFFFFFFL) {
+            return exp_format(d);
+        }
+
+        if (precision == 0) {
+            return (long) (d + 0.5) + (removeTrailing ? "" : ".");
+        }
+
+        long whole = (long) d;
+        double fr = d - whole; // fractional part
+
+        if ((fr >= 1) || (fr < 0)) {
+            return exp_format(d);
+        }
+
+        double factor = 1;
+        String leading_zeroes = "";
+
+        for (int i = 1; (i <= precision) && (factor <= 0x7FFFFFFFFFFFFFFFL);
+                i++) {
+            factor *= 10;
+            leading_zeroes = leading_zeroes + "0";
+        }
+
+        long l = (long) ((factor * fr) + 0.5);
+
+        if (l >= factor) {
+            l = 0;
+            whole++;
+        }
+         // CSH 10-25-97
 
+        String z = leading_zeroes + l;
+        z = "." + z.substring(z.length() - precision, z.length());
 
+        if (removeTrailing) {
+            int t = z.length() - 1;
 
+            while ((t >= 0) && (z.charAt(t) == '0'))
+                t--;
+
+            if ((t >= 0) && (z.charAt(t) == '.')) {
+                t--;
+            }
+
+            z = z.substring(0, t + 1);
+        }
+
+        return whole + z;
+    }
+
+    private String exp_format(double d) {
+        String f = "";
+        int e = 0;
+        double dd = d;
+        double factor = 1;
+
+        if (d != 0) {
+            while (dd > 10) {
+                e++;
+                factor /= 10;
+                dd = dd / 10;
+            }
+
+            while (dd < 1) {
+                e--;
+                factor *= 10;
+                dd = dd * 10;
+            }
+        }
+
+        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')) {
+            f = f + "e";
+        } else {
+            f = f + "E";
+        }
+
+        String p = "000";
+
+        if (e >= 0) {
+            f = f + "+";
+            p = p + e;
+        } else {
+            f = f + "-";
+            p = p + (-e);
+        }
+
+        return f + p.substring(p.length() - 3, p.length());
+    }
+}
diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index 3624144..127b419 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -16,95 +16,90 @@
 * 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 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 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 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);
+        if (p < r) {
+            q = stringPartition(arr, p, r, s);
+            stringSort(arr, p, q, s);
+            stringSort(arr, q + 1, r, s);
+        }
     }
-  }
 
-  public static void sort(float[] 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 = partition(arr,p,r,s);
-      sort(arr,p,q,s);
-      sort(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);
+        }
     }
-  }
-
-  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 674743e..3711db0 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -16,438 +16,379 @@
 * 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 org.apache.axis.client.*;
-import javax.xml.namespace.QName;
-import java.util.*;
+import ext.vamsas.*;
+
+import jalview.analysis.AlignSeq;
+
 import jalview.datamodel.*;
+
 import jalview.gui.*;
-import javax.swing.*;
-import java.util.*;
+
+import org.apache.axis.client.*;
+
 import java.awt.*;
-import jalview.analysis.AlignSeq;
-import ext.vamsas.*;
 
-public class JPredClient
-    extends WSClient
-{
-  ext.vamsas.JPredWS server;
-  String altitle = "";
-  java.util.Hashtable SequenceInfo = null;
-  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;
-      }
-      return true;
+import java.util.*;
+
+import javax.swing.*;
+
+import javax.xml.namespace.QName;
+
+
+public class JPredClient extends WSClient {
+    ext.vamsas.JPredWS server;
+    String altitle = "";
+    java.util.Hashtable SequenceInfo = null;
+
+    public JPredClient(String title, SequenceI[] msf) {
+        wsInfo = setWebService();
+
+        SequenceI seq = msf[0];
+        altitle = "JNet prediction on " + seq.getName() +
+            " using alignment from " + title;
+
+        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);
+
+        if (!locateWebService()) {
+            return;
+        }
+
+        JPredThread jthread = new JPredThread(msf);
+        jthread.start();
     }
 
-    public JPredClient(String title, SequenceI[] msf)
-    {
-      wsInfo = setWebService();
-      SequenceI seq = msf[0];
-      altitle = "JNet prediction on " + seq.getName() +
-          " using alignment from " + title;
-
-      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);
-      if (!locateWebService())
-        return;
-
-      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;
+        }
+
+        JPredThread jthread = new JPredThread(seq);
+        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;
+    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";
 
-      SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+        WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
+                WebServiceReference);
 
-      if (!locateWebService())
-              return;
+        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;
+        }
 
-      JPredThread jthread = new JPredThread(seq);
-      jthread.start();
+        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()));
-      }
-
-      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));
-      }
-
-      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"));
-            }
+    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()));
+        }
 
-            if (result.isRunning())
-            {
-              wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-            }
-            else if (result.isQueued())
-            {
-              wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+        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));
+        }
+
+        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) {
+                    }
+                }
             }
 
-            if (result.isFinished())
-            {
-              parseResult();
-              jobComplete = true;
-              jobsRunning--;
+            if (!(result.isJobFailed() || result.isServerError())) {
+                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+            } else {
+                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
             }
-            else
-            {
-              wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
-              if (! (result.isJobFailed() || result.isServerError()))
-              {
-                try
-                {
-                  Thread.sleep(5000);
+        }
+
+        void StartJob() {
+            try {
+                if (msa != null) {
+                    jobId = server.predictOnMsa(msa);
+                } else {
+                    jobId = server.predict(sequence);
                 }
-                catch (InterruptedException ex1)
-                {
+
+                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");
                 }
-                //  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)
-            {
+            } catch (Exception e) {
+                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+                allowedServerExceptions = 0;
+                jobComplete = false;
+                wsInfo.appendProgressText("Failed to submit the prediction: " +
+                    e.toString() + "\nJust close the window\n");
+                System.err.println(
+                    "JPredWS Client: Failed to submit the prediction\n" +
+                    e.toString() + "\n");
+
+                // e.printStackTrace(); TODO: JBPNote DEBUG
             }
-          }
         }
 
-        if (! (result.isJobFailed() || result.isServerError()))
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+        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));
         }
-      }
-
-      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);
+
+        void parseResult() {
+            // OutputHeader = output.getText();
+            if (result.isFailed()) {
+                OutputHeader += "Job failed.\n";
             }
-            else
-            {
-              System.out.println(WsURL + " Job Id '" + jobId + "'");
+
+            if (result.getStatus() != null) {
+                OutputHeader += ("\n" + result.getStatus());
             }
-          }
-          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: " +
-                                    e.toString() + "\nJust close the window\n");
-          System.err.println(
-              "JPredWS Client: Failed to submit the prediction\n" +
-              e.toString() + "\n");
-          // e.printStackTrace(); TODO: JBPNote DEBUG
-        }
-      }
-
-      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));
-      }
-
-      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;
+            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
             }
-            else
-            {
-              throw (new Exception("Unknown format 'format' for file : \n" +
-                                   result.getAligfile()));
+
+            if (result.getAligfile() != null) {
+                OutputHeader += ("\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);
+            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();
                 }
-              }
-              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);
+
+                if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+                            al.getSequenceAt(FirstSeq), SequenceInfo)) {
+                    throw (new Exception(
+                        "Couldn't recover sequence properties for JNet Query sequence!"));
                 }
-              }
-              else
-              {
-                for (int j = 0; j < width; j++)
-                {
-                  annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j) +
-                      "", "", ' ', 0);
+
+                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"));
                 }
-              }
-
-              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);
+                // 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++;
+                }
 
-            addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-           "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
+                Hashtable scores = prediction.getScores();
 
-            addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
-                                "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
-           */
-          AlignFrame af = new AlignFrame(al);
+                /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
+                                      "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
 
-          Desktop.addInternalFrame(af,
-                                   altitle,
-                                   AlignFrame.NEW_WINDOW_WIDTH,
-                                   AlignFrame.NEW_WINDOW_HEIGHT);
-        }
-        catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
+                  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();
+            }
+        }
     }
-  }
+}
diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 32f5c43..b5e7938 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -15,339 +15,363 @@
 * 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 org.apache.axis.client.*;
-import javax.xml.namespace.QName;
-import java.util.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import javax.swing.*;
-import java.util.*;
-import java.awt.*;
-import jalview.analysis.AlignSeq;
-import ext.vamsas.*;
-import vamsas.objects.*;
-
-
-
-
-public class MsaWSClient
-    extends WSClient
-{
+*/
+package jalview.ws;
+
+import ext.vamsas.*;
+
+import jalview.analysis.AlignSeq;
+
+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.
-     */
-    ext.vamsas.MuscleWS server;
-    // JBPNote Nasty object-global state setting methods shouldn't be allowed
-  private boolean setWebService(String MsaWSName) {
-    if (MsaWServices.info.containsKey(MsaWSName)) {
-      WebServiceName = MsaWSName;
-      String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
-      WsURL = wsinfo[0];
-      WebServiceJobTitle = wsinfo[1];
-      WebServiceReference = wsinfo[2];
-      return true;
-    } else {
-      return false;
-    }
-  }
-
-  private boolean locateWebService() {
-      // TODO: MuscleWS transmuted to generic MsaWS client
-      MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
-      try {
-        this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
-        ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout
-      }
-      catch (Exception ex) {
-        wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
-                       +WsURL+"\n"+ex.getMessage());
-        wsInfo.setStatus(wsInfo.ERROR);
-        ex.printStackTrace();
-        return false;
-      }
-      loc.getEngine().setOption("axis","1");
-      return true;
-  }
-
-  public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa, boolean submitGaps, boolean preserveOrder)
-  {
-    if (setWebService(MsaWSName)==false) {
-      JOptionPane.showMessageDialog(Desktop.desktop, "The Multiple Sequence Alignment Service named "+MsaWSName+" is unknown",
-                                    "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
-      return;
-    }
-
-    wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle, WebServiceReference);
-
-    if (!locateWebService())
-      return;
-
-    wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")+" of "+altitle+"\nJob details\n");
-
-    MsaWSThread musclethread = new MsaWSThread(WebServiceName+" alignment of "+altitle, msa, submitGaps, preserveOrder);
-    wsInfo.setthisService(musclethread);
-    musclethread.start();
-  }
-
-
-  protected class MsaWSThread extends Thread implements WSClientI
-  {
-    String ServiceName = WebServiceName;
-
-    public boolean isCancellable()
-    {
-      return true;
-    }
-
-    String OutputHeader;
-    vamsas.objects.simple.MsaResult result = null;
-
-    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
-        SequenceSet();
-
-    Hashtable SeqNames = null;
-    boolean submitGaps = false,// default is to strip gaps from sequences
-        preserveOrder = true; // and always store and recover sequence order
-
-    String jobId;
-    String alTitle; // name which will be used to form new alignment window.
-    int allowedServerExceptions = 3; // thread dies if too many exceptions.
-    MsaWSThread(String title, SequenceI[] msa, boolean subgaps, boolean presorder)
-    {
-      alTitle = title;
-      submitGaps = subgaps;
-      preserveOrder = presorder;
-
-      OutputHeader = wsInfo.getProgressText();
-      SeqNames = new Hashtable();
-      vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
-          Sequence[msa.length];
-
-      for (int i = 0; i < msa.length; i++)
-      {
-        String newname = jalview.analysis.SeqsetUtils.unique_name(i);
-        // uniquify as we go
-        // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
-        SeqNames.put(newname, jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
-        seqarray[i] = new vamsas.objects.simple.Sequence();
-        seqarray[i].setId(newname);
-        seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()
-                           : AlignSeq.extractGaps(jalview.util.Comparison.GapChars, msa[i].getSequence()));
-      }
-
-      this.seqs = new vamsas.objects.simple.SequenceSet();
-      this.seqs.setSeqs(seqarray);
-    }
-
-    boolean jobComplete = false;
-
-    public void cancelJob() {
-      if (jobId!=null && !jobId.equals("") && !jobComplete) {
-        String cancelledMessage="";
-        try {
-          vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
-          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)
-          {
-            // VALID UNSTOPPABLE JOB
-            cancelledMessage +=
-                "Server cannot cancel this job. just close the window.\n";
-          }
-          if (cancelledJob.getJobId() != null)
-            cancelledMessage += "[" + cancelledJob.getJobId() + "]";
-          cancelledMessage +="\n";
-        } catch (Exception exc) {
-          cancelledMessage +="\nProblems cancelling the job : Exception received...\n"+exc+"\n";
-          exc.printStackTrace();
-        }
-        wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");
-      } 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()
-    {
-
-      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
-          {
-            if (result.getStatus() != null)
-              wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
-            if (! (result.isJobFailed() || result.isServerError()))
-            {
-              Thread.sleep(5000);
-              //  System.out.println("I'm alive "+seqid+" "+jobid);
-            }
-            else
-            {
-              break;
-            }
-          }
-        }
-        catch (Exception ex)
-        {
-          allowedServerExceptions--;
-          wsInfo.appendProgressText("\n" + ServiceName + " Server exception!\n" +
-                                    ex.getMessage());
-          System.err.println(ServiceName + " Server exception: " +
-                                    ex.getMessage());
-          //          ex.printStackTrace(); JBPNote Debug
-          try
-          {
-            if (allowedServerExceptions>0)
-              Thread.sleep(5000);
-          }
-          catch (InterruptedException ex1)
-          {
-          }
-
-        }
-      }
-      if (allowedServerExceptions == 0)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      }
-      else
-      {
-        if (! (result != null && (result.isJobFailed() || result.isServerError())))
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-        else
-        {
-          if (result.isFailed())
-            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-          if (result.isServerError())
-            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        }
-      }
-    }
-    void StartJob()
-    {
-      try
-      {
-        vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
-        if (jobsubmit!=null && jobsubmit.getStatus()==1) {
-          jobId=jobsubmit.getJobId();
-          System.out.println(WsURL+" Job Id '"+jobId+"'");
-        } 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)
-      {
-        // TODO: JBPNote catch timeout or other fault types explicitly
-        // For unexpected errors
-        System.err.println(WebServiceName + " Client: Failed to submit the sequences for alignment.\n"+WsURL+" : " +
-                           e.toString() + "\n");
-        this.allowedServerExceptions=0;
-        wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
-        wsInfo.appendProgressText("Server problems! "+e.toString()+"\nFailed to submit sequences for alignment. Just close the window\n");
-        // e.printStackTrace(); // TODO: JBPNote DEBUG
-      }
-    }
-
-    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 jalview.datamodel.Sequence[] getVamsasAlignment(vamsas.objects.simple.Alignment valign) {
-      vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
-      jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
-      for (int i=0, j=seqs.length; i<j;i++)
-        msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i].getSeq());
-      return msa;
-    }
-    void parseResult()
-    {
-      SequenceI[] seqs=null;
-      try {
-        // OutputHeader = output.getText();
-        if (result.isFailed()) {
-          OutputHeader +="Job failed.\n";
-        }
-        if (result.getStatus()!=null) {
-          OutputHeader += "\n"+result.getStatus();
-        }
-        if (result.getMsa()!=null) {
-          OutputHeader += "\nAlignment Object Method Notes\n";
-          String lines[] = result.getMsa().getMethod();
-          for (int line=0;line<lines.length; line++)
-            OutputHeader+=lines[line]+"\n";
-
-          // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
-          seqs = getVamsasAlignment(result.getMsa());
-        }
-
-        wsInfo.setProgressText(OutputHeader);
-        if (seqs!=null) {
-          AlignmentOrder msaorder = new AlignmentOrder(seqs);
-
-          if (preserveOrder) {
-            jalview.analysis.AlignmentSorter.recoverOrder(seqs);
-          }
-
-          jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
-
-          Alignment al = new Alignment(seqs);
-
-          // TODO: JBPNote Should also rename the query sequence sometime...
-          AlignFrame af = new AlignFrame(al);
-          af.addSortByOrderMenuItem(ServiceName+" Ordering", msaorder);
-
-          Desktop.addInternalFrame(af,
-                                   alTitle,
-                                   AlignFrame.NEW_WINDOW_WIDTH,
-                                   AlignFrame.NEW_WINDOW_HEIGHT);
-        }
-      }catch(Exception ex){ex.printStackTrace();}
-
-    }
-
-  }
-}
-
-
+ * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+ */
+    ext.vamsas.MuscleWS server;
+
+    public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa,
+        boolean submitGaps, boolean preserveOrder) {
+        if (setWebService(MsaWSName) == false) {
+            JOptionPane.showMessageDialog(Desktop.desktop,
+                "The Multiple Sequence Alignment Service named " + MsaWSName +
+                " is unknown", "Internal Jalview Error",
+                JOptionPane.WARNING_MESSAGE);
+
+            return;
+        }
+
+        wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle,
+                WebServiceReference);
+
+        if (!locateWebService()) {
+            return;
+        }
+
+        wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") +
+            " of " + altitle + "\nJob details\n");
+
+        MsaWSThread musclethread = new MsaWSThread(WebServiceName +
+                " alignment of " + altitle, msa, submitGaps, preserveOrder);
+        wsInfo.setthisService(musclethread);
+        musclethread.start();
+    }
+
+    // JBPNote Nasty object-global state setting methods shouldn't be allowed
+    private boolean setWebService(String MsaWSName) {
+        if (MsaWServices.info.containsKey(MsaWSName)) {
+            WebServiceName = MsaWSName;
+
+            String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
+            WsURL = wsinfo[0];
+            WebServiceJobTitle = wsinfo[1];
+            WebServiceReference = wsinfo[2];
+
+            return true;
+        } else {
+            return false;
+        }
+    }
+
+    private boolean locateWebService() {
+        // TODO: MuscleWS transmuted to generic MsaWS client
+        MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
+
+        try {
+            this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+            ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout
+        } catch (Exception ex) {
+            wsInfo.setProgressText("Serious! " + WebServiceName +
+                " Service location failed\nfor URL :" + WsURL + "\n" +
+                ex.getMessage());
+            wsInfo.setStatus(wsInfo.ERROR);
+            ex.printStackTrace();
+
+            return false;
+        }
+
+        loc.getEngine().setOption("axis", "1");
+
+        return true;
+    }
+
+    protected class MsaWSThread extends Thread implements WSClientI {
+        String ServiceName = WebServiceName;
+        String OutputHeader;
+        vamsas.objects.simple.MsaResult result = null;
+        vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
+        Hashtable SeqNames = null;
+        boolean submitGaps = false; // and always store and recover sequence order
+        boolean preserveOrder = true; // and always store and recover sequence order
+        String jobId;
+        String alTitle; // name which will be used to form new alignment window.
+        int allowedServerExceptions = 3; // thread dies if too many exceptions.
+        boolean jobComplete = false;
+
+        MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
+            boolean presorder) {
+            alTitle = title;
+            submitGaps = subgaps;
+            preserveOrder = presorder;
+
+            OutputHeader = wsInfo.getProgressText();
+            SeqNames = new Hashtable();
+
+            vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.Sequence[msa.length];
+
+            for (int i = 0; i < msa.length; i++) {
+                String newname = jalview.analysis.SeqsetUtils.unique_name(i);
+
+                // uniquify as we go
+                // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
+                SeqNames.put(newname,
+                    jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
+                seqarray[i] = new vamsas.objects.simple.Sequence();
+                seqarray[i].setId(newname);
+                seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()
+                                                : AlignSeq.extractGaps(
+                        jalview.util.Comparison.GapChars, msa[i].getSequence()));
+            }
+
+            this.seqs = new vamsas.objects.simple.SequenceSet();
+            this.seqs.setSeqs(seqarray);
+        }
+
+        public boolean isCancellable() {
+            return true;
+        }
+
+        public void cancelJob() {
+            if ((jobId != null) && !jobId.equals("") && !jobComplete) {
+                String cancelledMessage = "";
+
+                try {
+                    vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
+
+                    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) {
+                        // VALID UNSTOPPABLE JOB
+                        cancelledMessage += "Server cannot cancel this job. just close the window.\n";
+                    }
+
+                    if (cancelledJob.getJobId() != null) {
+                        cancelledMessage += ("[" + cancelledJob.getJobId() +
+                        "]");
+                    }
+
+                    cancelledMessage += "\n";
+                } catch (Exception exc) {
+                    cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" +
+                    exc + "\n");
+                    exc.printStackTrace();
+                }
+
+                wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");
+            } 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() {
+            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 {
+                        if (result.getStatus() != null) {
+                            wsInfo.setProgressText(OutputHeader + "\n" +
+                                result.getStatus());
+                        }
+
+                        if (!(result.isJobFailed() || result.isServerError())) {
+                            Thread.sleep(5000);
+
+                            //  System.out.println("I'm alive "+seqid+" "+jobid);
+                        } else {
+                            break;
+                        }
+                    }
+                } catch (Exception ex) {
+                    allowedServerExceptions--;
+                    wsInfo.appendProgressText("\n" + ServiceName +
+                        " Server exception!\n" + ex.getMessage());
+                    System.err.println(ServiceName + " Server exception: " +
+                        ex.getMessage());
+
+                    //          ex.printStackTrace(); JBPNote Debug
+                    try {
+                        if (allowedServerExceptions > 0) {
+                            Thread.sleep(5000);
+                        }
+                    } catch (InterruptedException ex1) {
+                    }
+                }
+            }
+
+            if (allowedServerExceptions == 0) {
+                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+            } else {
+                if (!((result != null) &&
+                        (result.isJobFailed() || result.isServerError()))) {
+                    wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+                } else {
+                    if (result.isFailed()) {
+                        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+                    }
+
+                    if (result.isServerError()) {
+                        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+                    }
+                }
+            }
+        }
+
+        void StartJob() {
+            try {
+                vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
+
+                if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) {
+                    jobId = jobsubmit.getJobId();
+                    System.out.println(WsURL + " Job Id '" + jobId + "'");
+                } 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) {
+                // TODO: JBPNote catch timeout or other fault types explicitly
+                // For unexpected errors
+                System.err.println(WebServiceName +
+                    " Client: Failed to submit the sequences for alignment.\n" +
+                    WsURL + " : " + e.toString() + "\n");
+                this.allowedServerExceptions = 0;
+                wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
+                wsInfo.appendProgressText("Server problems! " + e.toString() +
+                    "\nFailed to submit sequences for alignment. Just close the window\n");
+
+                // e.printStackTrace(); // TODO: JBPNote DEBUG
+            }
+        }
+
+        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 jalview.datamodel.Sequence[] getVamsasAlignment(
+            vamsas.objects.simple.Alignment valign) {
+            vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
+            jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
+
+            for (int i = 0, j = seqs.length; i < j; i++)
+                msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
+                        seqs[i].getSeq());
+
+            return msa;
+        }
+
+        void parseResult() {
+            SequenceI[] seqs = null;
+
+            try {
+                // OutputHeader = output.getText();
+                if (result.isFailed()) {
+                    OutputHeader += "Job failed.\n";
+                }
+
+                if (result.getStatus() != null) {
+                    OutputHeader += ("\n" + result.getStatus());
+                }
+
+                if (result.getMsa() != null) {
+                    OutputHeader += "\nAlignment Object Method Notes\n";
+
+                    String[] lines = result.getMsa().getMethod();
+
+                    for (int line = 0; line < lines.length; line++)
+                        OutputHeader += (lines[line] + "\n");
+
+                    // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
+                    seqs = getVamsasAlignment(result.getMsa());
+                }
+
+                wsInfo.setProgressText(OutputHeader);
+
+                if (seqs != null) {
+                    AlignmentOrder msaorder = new AlignmentOrder(seqs);
+
+                    if (preserveOrder) {
+                        jalview.analysis.AlignmentSorter.recoverOrder(seqs);
+                    }
+
+                    jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
+
+                    Alignment al = new Alignment(seqs);
+
+                    // TODO: JBPNote Should also rename the query sequence sometime...
+                    AlignFrame af = new AlignFrame(al);
+                    af.addSortByOrderMenuItem(ServiceName + " Ordering",
+                        msaorder);
+
+                    Desktop.addInternalFrame(af, alTitle,
+                        AlignFrame.NEW_WINDOW_WIDTH,
+                        AlignFrame.NEW_WINDOW_HEIGHT);
+                }
+            } catch (Exception ex) {
+                ex.printStackTrace();
+            }
+        }
+    }
+}
diff --git a/src/jalview/ws/MsaWServices.java b/src/jalview/ws/MsaWServices.java
index f881bd5..ac89f68 100755
--- a/src/jalview/ws/MsaWServices.java
+++ b/src/jalview/ws/MsaWServices.java
@@ -15,10 +15,12 @@
 * 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 java.util.Hashtable;
+*/
+package jalview.ws;
+
+import java.util.Hashtable;
+
+
 /**
  * <p>Title: MsaWServices </p>
  *
@@ -30,32 +32,31 @@ import java.util.Hashtable;
  *
  * @author not attributable
  * @version 1.0
- */
+ */
 /**
  * TODO: MsaWServices will be set from properties and be dynamically discovered.
- */
-public class MsaWServices {
-  public static Hashtable info;
-  static
-  {
-    info = new Hashtable();
-    info.put("ClustalWS",
-             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, submitted, June 1994."
-    });
-    info.put("MuscleWS",
-             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."
-    });
-  };
-}
+ */
+public class MsaWServices {
+    public static Hashtable info;
+
+    static {
+        info = new Hashtable();
+        info.put("ClustalWS",
+            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, submitted, June 1994."
+            });
+        info.put("MuscleWS",
+            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 1d03eab..506bd9b 100755
--- a/src/jalview/ws/WSClient.java
+++ b/src/jalview/ws/WSClient.java
@@ -15,28 +15,26 @@
 * 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 {
+    /**
 
-package jalview.ws;
-
-import jalview.gui.WebserviceInfo;
-
-public class WSClient
-{
-  public WSClient()
-  {
-  }
-  /**
-
-  * MsaWSClient
-  *
-  * @param msa SequenceI[]
-  */
-
- protected String WebServiceName;
- protected String WebServiceJobTitle;
- protected String WebServiceReference;
- protected String WsURL;
- protected WebserviceInfo wsInfo;
-  int jobsRunning = 0;
-}
+* 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 7bd4ab8..c2db8c1 100755
--- a/src/jalview/ws/WSClientI.java
+++ b/src/jalview/ws/WSClientI.java
@@ -15,12 +15,11 @@
 * 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();
-}
+*/
+package jalview.ws;
+
+public interface WSClientI {
+    boolean isCancellable();
+
+    void cancelJob();
+}
diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 177d373..574a1e9 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,138 +22,147 @@
 * 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 vamsas.objects.simple;
-
-public class Alignment  extends vamsas.objects.simple.Object  implements java.io.Serializable {
-    private java.lang.String gapchar;
-    private java.lang.String[] method;
-    private vamsas.objects.simple.SequenceSet seqs;
-
-    public Alignment() {
-    }
-
-    public Alignment(
-           java.lang.String gapchar,
-           java.lang.String[] method,
-           vamsas.objects.simple.SequenceSet seqs) {
-           this.gapchar = gapchar;
-           this.method = method;
-           this.seqs = seqs;
-    }
-
-
+*/
+package vamsas.objects.simple;
+
+public class Alignment extends vamsas.objects.simple.Object
+    implements java.io.Serializable {
+    private java.lang.String gapchar;
+    private java.lang.String[] method;
+    private vamsas.objects.simple.SequenceSet seqs;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public Alignment() {
+    }
+
+    public Alignment(java.lang.String gapchar, java.lang.String[] method,
+        vamsas.objects.simple.SequenceSet seqs) {
+        this.gapchar = gapchar;
+        this.method = method;
+        this.seqs = seqs;
+    }
+
     /**
-     * Gets the gapchar value for this Alignment.
-     *
-     * @return gapchar
-     */
-    public java.lang.String getGapchar() {
-        return gapchar;
-    }
-
-
+ * Gets the gapchar value for this Alignment.
+ *
+ * @return gapchar
+ */
+    public java.lang.String getGapchar() {
+        return gapchar;
+    }
+
     /**
-     * Sets the gapchar value for this Alignment.
-     *
-     * @param gapchar
-     */
-    public void setGapchar(java.lang.String gapchar) {
-        this.gapchar = gapchar;
-    }
-
-
+ * Sets the gapchar value for this Alignment.
+ *
+ * @param gapchar
+ */
+    public void setGapchar(java.lang.String gapchar) {
+        this.gapchar = gapchar;
+    }
+
     /**
-     * Gets the method value for this Alignment.
-     *
-     * @return method
-     */
-    public java.lang.String[] getMethod() {
-        return method;
-    }
-
-
+ * Gets the method value for this Alignment.
+ *
+ * @return method
+ */
+    public java.lang.String[] getMethod() {
+        return method;
+    }
+
     /**
-     * Sets the method value for this Alignment.
-     *
-     * @param method
-     */
-    public void setMethod(java.lang.String[] method) {
-        this.method = method;
-    }
-
-
+ * Sets the method value for this Alignment.
+ *
+ * @param method
+ */
+    public void setMethod(java.lang.String[] method) {
+        this.method = method;
+    }
+
     /**
-     * Gets the seqs value for this Alignment.
-     *
-     * @return seqs
-     */
-    public vamsas.objects.simple.SequenceSet getSeqs() {
-        return seqs;
-    }
-
-
+ * Gets the seqs value for this Alignment.
+ *
+ * @return seqs
+ */
+    public vamsas.objects.simple.SequenceSet getSeqs() {
+        return seqs;
+    }
+
     /**
-     * Sets the seqs value for this Alignment.
-     *
-     * @param seqs
-     */
-    public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
-        this.seqs = seqs;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Alignment)) return false;
-        Alignment other = (Alignment) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = super.equals(obj) &&
-            ((this.gapchar==null && other.getGapchar()==null) ||
-             (this.gapchar!=null &&
-              this.gapchar.equals(other.getGapchar()))) &&
-            ((this.method==null && other.getMethod()==null) ||
-             (this.method!=null &&
-              java.util.Arrays.equals(this.method, other.getMethod()))) &&
-            ((this.seqs==null && other.getSeqs()==null) ||
-             (this.seqs!=null &&
-              this.seqs.equals(other.getSeqs())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = super.hashCode();
-        if (getGapchar() != null) {
-            _hashCode += getGapchar().hashCode();
-        }
-        if (getMethod() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getMethod());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getMethod(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        if (getSeqs() != null) {
-            _hashCode += getSeqs().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+ * Sets the seqs value for this Alignment.
+ *
+ * @param seqs
+ */
+    public void setSeqs(vamsas.objects.simple.SequenceSet seqs) {
+        this.seqs = seqs;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Alignment)) {
+            return false;
+        }
+
+        Alignment other = (Alignment) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = super.equals(obj) &&
+            (((this.gapchar == null) && (other.getGapchar() == null)) ||
+            ((this.gapchar != null) && this.gapchar.equals(other.getGapchar()))) &&
+            (((this.method == null) && (other.getMethod() == null)) ||
+            ((this.method != null) &&
+            java.util.Arrays.equals(this.method, other.getMethod()))) &&
+            (((this.seqs == null) && (other.getSeqs() == null)) ||
+            ((this.seqs != null) && this.seqs.equals(other.getSeqs())));
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = super.hashCode();
+
+        if (getGapchar() != null) {
+            _hashCode += getGapchar().hashCode();
+        }
+
+        if (getMethod() != null) {
+            for (int i = 0; i < java.lang.reflect.Array.getLength(getMethod());
+                    i++) {
+                java.lang.Object obj = java.lang.reflect.Array.get(getMethod(),
+                        i);
+
+                if ((obj != null) && !obj.getClass().isArray()) {
+                    _hashCode += obj.hashCode();
+                }
+            }
+        }
+
+        if (getSeqs() != null) {
+            _hashCode += getSeqs().hashCode();
+        }
+
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+}
diff --git a/src/vamsas/objects/simple/Alignment_Helper.java b/src/vamsas/objects/simple/Alignment_Helper.java
index 57cd7ca..3f57064 100755
--- a/src/vamsas/objects/simple/Alignment_Helper.java
+++ b/src/vamsas/objects/simple/Alignment_Helper.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,63 +22,62 @@
 * 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 vamsas.objects.simple;
-
-public class Alignment_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Alignment.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("gapchar");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "gapchar"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("method");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "method"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("seqs");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
-        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+*/
+package vamsas.objects.simple;
+
+public class Alignment_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Alignment.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "Alignment"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("gapchar");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "gapchar"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("method");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "method"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("seqs");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "SequenceSet"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/vamsas/objects/simple/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java
index e4af81e..43a8c6e 100755
--- a/src/vamsas/objects/simple/MsaResult.java
+++ b/src/vamsas/objects/simple/MsaResult.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,72 +22,85 @@
 * 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 vamsas.objects.simple;
-
-public class MsaResult  extends vamsas.objects.simple.Result  implements java.io.Serializable {
-    private vamsas.objects.simple.Alignment msa;
-
-    public MsaResult() {
-    }
-
-    public MsaResult(
-           vamsas.objects.simple.Alignment msa) {
-           this.msa = msa;
-    }
-
-
+*/
+package vamsas.objects.simple;
+
+public class MsaResult extends vamsas.objects.simple.Result
+    implements java.io.Serializable {
+    private vamsas.objects.simple.Alignment msa;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public MsaResult() {
+    }
+
+    public MsaResult(vamsas.objects.simple.Alignment msa) {
+        this.msa = msa;
+    }
+
     /**
-     * Gets the msa value for this MsaResult.
-     *
-     * @return msa
-     */
-    public vamsas.objects.simple.Alignment getMsa() {
-        return msa;
-    }
-
-
+ * Gets the msa value for this MsaResult.
+ *
+ * @return msa
+ */
+    public vamsas.objects.simple.Alignment getMsa() {
+        return msa;
+    }
+
     /**
-     * Sets the msa value for this MsaResult.
-     *
-     * @param msa
-     */
-    public void setMsa(vamsas.objects.simple.Alignment msa) {
-        this.msa = msa;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof MsaResult)) return false;
-        MsaResult other = (MsaResult) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = super.equals(obj) &&
-            ((this.msa==null && other.getMsa()==null) ||
-             (this.msa!=null &&
-              this.msa.equals(other.getMsa())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = super.hashCode();
-        if (getMsa() != null) {
-            _hashCode += getMsa().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+ * Sets the msa value for this MsaResult.
+ *
+ * @param msa
+ */
+    public void setMsa(vamsas.objects.simple.Alignment msa) {
+        this.msa = msa;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof MsaResult)) {
+            return false;
+        }
+
+        MsaResult other = (MsaResult) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = super.equals(obj) &&
+            (((this.msa == null) && (other.getMsa() == null)) ||
+            ((this.msa != null) && this.msa.equals(other.getMsa())));
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = super.hashCode();
+
+        if (getMsa() != null) {
+            _hashCode += getMsa().hashCode();
+        }
+
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+}
diff --git a/src/vamsas/objects/simple/MsaResult_Helper.java b/src/vamsas/objects/simple/MsaResult_Helper.java
index ff8aefc..87db2d2 100755
--- a/src/vamsas/objects/simple/MsaResult_Helper.java
+++ b/src/vamsas/objects/simple/MsaResult_Helper.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,53 +22,50 @@
 * 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 vamsas.objects.simple;
-
-public class MsaResult_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(MsaResult.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "MsaResult"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("msa");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "msa"));
-        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Alignment"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+*/
+package vamsas.objects.simple;
+
+public class MsaResult_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(MsaResult.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "MsaResult"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("msa");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "msa"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "Alignment"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/vamsas/objects/simple/Object.java b/src/vamsas/objects/simple/Object.java
index ea22e9e..ae1b515 100755
--- a/src/vamsas/objects/simple/Object.java
+++ b/src/vamsas/objects/simple/Object.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,40 +22,54 @@
 * 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 vamsas.objects.simple;
-
-public abstract class Object  implements java.io.Serializable {
-
-    public Object() {
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Object)) return false;
-        Object other = (Object) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true;
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+*/
+package vamsas.objects.simple;
+
+public abstract class Object implements java.io.Serializable {
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public Object() {
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Object)) {
+            return false;
+        }
+
+        Object other = (Object) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = true;
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = 1;
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+}
diff --git a/src/vamsas/objects/simple/Object_Helper.java b/src/vamsas/objects/simple/Object_Helper.java
index e6012f4..f31c945 100755
--- a/src/vamsas/objects/simple/Object_Helper.java
+++ b/src/vamsas/objects/simple/Object_Helper.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,48 +22,43 @@
 * 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 vamsas.objects.simple;
-
-public class Object_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Object.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("http://simple.objects.vamsas", "Object"));
-    }
-
+*/
+package vamsas.objects.simple;
+
+public class Object_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Object.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "http://simple.objects.vamsas", "Object"));
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/vamsas/objects/simple/Result.java b/src/vamsas/objects/simple/Result.java
index 1444911..49756e2 100755
--- a/src/vamsas/objects/simple/Result.java
+++ b/src/vamsas/objects/simple/Result.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,322 +22,306 @@
 * 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 vamsas.objects.simple;
-
-public class Result  implements java.io.Serializable {
-    private boolean broken;
-    private boolean failed;
-    private boolean finished;
-    private boolean invalid;
-    private boolean jobFailed;
-    private boolean queued;
-    private boolean running;
-    private boolean serverError;
-    private int state;
-    private java.lang.String status;
-    private boolean suspended;
-
-    public Result() {
-    }
-
-    public Result(
-           boolean broken,
-           boolean failed,
-           boolean finished,
-           boolean invalid,
-           boolean jobFailed,
-           boolean queued,
-           boolean running,
-           boolean serverError,
-           int state,
-           java.lang.String status,
-           boolean suspended) {
-           this.broken = broken;
-           this.failed = failed;
-           this.finished = finished;
-           this.invalid = invalid;
-           this.jobFailed = jobFailed;
-           this.queued = queued;
-           this.running = running;
-           this.serverError = serverError;
-           this.state = state;
-           this.status = status;
-           this.suspended = suspended;
-    }
-
-
+*/
+package vamsas.objects.simple;
+
+public class Result implements java.io.Serializable {
+    private boolean broken;
+    private boolean failed;
+    private boolean finished;
+    private boolean invalid;
+    private boolean jobFailed;
+    private boolean queued;
+    private boolean running;
+    private boolean serverError;
+    private int state;
+    private java.lang.String status;
+    private boolean suspended;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public Result() {
+    }
+
+    public Result(boolean broken, boolean failed, boolean finished,
+        boolean invalid, boolean jobFailed, boolean queued, boolean running,
+        boolean serverError, int state, java.lang.String status,
+        boolean suspended) {
+        this.broken = broken;
+        this.failed = failed;
+        this.finished = finished;
+        this.invalid = invalid;
+        this.jobFailed = jobFailed;
+        this.queued = queued;
+        this.running = running;
+        this.serverError = serverError;
+        this.state = state;
+        this.status = status;
+        this.suspended = suspended;
+    }
+
     /**
-     * Gets the broken value for this Result.
-     *
-     * @return broken
-     */
-    public boolean isBroken() {
-        return broken;
-    }
-
-
+ * Gets the broken value for this Result.
+ *
+ * @return broken
+ */
+    public boolean isBroken() {
+        return broken;
+    }
+
     /**
-     * Sets the broken value for this Result.
-     *
-     * @param broken
-     */
-    public void setBroken(boolean broken) {
-        this.broken = broken;
-    }
-
-
+ * Sets the broken value for this Result.
+ *
+ * @param broken
+ */
+    public void setBroken(boolean broken) {
+        this.broken = broken;
+    }
+
     /**
-     * Gets the failed value for this Result.
-     *
-     * @return failed
-     */
-    public boolean isFailed() {
-        return failed;
-    }
-
-
+ * Gets the failed value for this Result.
+ *
+ * @return failed
+ */
+    public boolean isFailed() {
+        return failed;
+    }
+
     /**
-     * Sets the failed value for this Result.
-     *
-     * @param failed
-     */
-    public void setFailed(boolean failed) {
-        this.failed = failed;
-    }
-
-
+ * Sets the failed value for this Result.
+ *
+ * @param failed
+ */
+    public void setFailed(boolean failed) {
+        this.failed = failed;
+    }
+
     /**
-     * Gets the finished value for this Result.
-     *
-     * @return finished
-     */
-    public boolean isFinished() {
-        return finished;
-    }
-
-
+ * Gets the finished value for this Result.
+ *
+ * @return finished
+ */
+    public boolean isFinished() {
+        return finished;
+    }
+
     /**
-     * Sets the finished value for this Result.
-     *
-     * @param finished
-     */
-    public void setFinished(boolean finished) {
-        this.finished = finished;
-    }
-
-
+ * Sets the finished value for this Result.
+ *
+ * @param finished
+ */
+    public void setFinished(boolean finished) {
+        this.finished = finished;
+    }
+
     /**
-     * Gets the invalid value for this Result.
-     *
-     * @return invalid
-     */
-    public boolean isInvalid() {
-        return invalid;
-    }
-
-
+ * Gets the invalid value for this Result.
+ *
+ * @return invalid
+ */
+    public boolean isInvalid() {
+        return invalid;
+    }
+
     /**
-     * Sets the invalid value for this Result.
-     *
-     * @param invalid
-     */
-    public void setInvalid(boolean invalid) {
-        this.invalid = invalid;
-    }
-
-
+ * Sets the invalid value for this Result.
+ *
+ * @param invalid
+ */
+    public void setInvalid(boolean invalid) {
+        this.invalid = invalid;
+    }
+
     /**
-     * Gets the jobFailed value for this Result.
-     *
-     * @return jobFailed
-     */
-    public boolean isJobFailed() {
-        return jobFailed;
-    }
-
-
+ * Gets the jobFailed value for this Result.
+ *
+ * @return jobFailed
+ */
+    public boolean isJobFailed() {
+        return jobFailed;
+    }
+
     /**
-     * Sets the jobFailed value for this Result.
-     *
-     * @param jobFailed
-     */
-    public void setJobFailed(boolean jobFailed) {
-        this.jobFailed = jobFailed;
-    }
-
-
+ * Sets the jobFailed value for this Result.
+ *
+ * @param jobFailed
+ */
+    public void setJobFailed(boolean jobFailed) {
+        this.jobFailed = jobFailed;
+    }
+
     /**
-     * Gets the queued value for this Result.
-     *
-     * @return queued
-     */
-    public boolean isQueued() {
-        return queued;
-    }
-
-
+ * Gets the queued value for this Result.
+ *
+ * @return queued
+ */
+    public boolean isQueued() {
+        return queued;
+    }
+
     /**
-     * Sets the queued value for this Result.
-     *
-     * @param queued
-     */
-    public void setQueued(boolean queued) {
-        this.queued = queued;
-    }
-
-
+ * Sets the queued value for this Result.
+ *
+ * @param queued
+ */
+    public void setQueued(boolean queued) {
+        this.queued = queued;
+    }
+
     /**
-     * Gets the running value for this Result.
-     *
-     * @return running
-     */
-    public boolean isRunning() {
-        return running;
-    }
-
-
+ * Gets the running value for this Result.
+ *
+ * @return running
+ */
+    public boolean isRunning() {
+        return running;
+    }
+
     /**
-     * Sets the running value for this Result.
-     *
-     * @param running
-     */
-    public void setRunning(boolean running) {
-        this.running = running;
-    }
-
-
+ * Sets the running value for this Result.
+ *
+ * @param running
+ */
+    public void setRunning(boolean running) {
+        this.running = running;
+    }
+
     /**
-     * Gets the serverError value for this Result.
-     *
-     * @return serverError
-     */
-    public boolean isServerError() {
-        return serverError;
-    }
-
-
+ * Gets the serverError value for this Result.
+ *
+ * @return serverError
+ */
+    public boolean isServerError() {
+        return serverError;
+    }
+
     /**
-     * Sets the serverError value for this Result.
-     *
-     * @param serverError
-     */
-    public void setServerError(boolean serverError) {
-        this.serverError = serverError;
-    }
-
-
+ * Sets the serverError value for this Result.
+ *
+ * @param serverError
+ */
+    public void setServerError(boolean serverError) {
+        this.serverError = serverError;
+    }
+
     /**
-     * Gets the state value for this Result.
-     *
-     * @return state
-     */
-    public int getState() {
-        return state;
-    }
-
-
+ * Gets the state value for this Result.
+ *
+ * @return state
+ */
+    public int getState() {
+        return state;
+    }
+
     /**
-     * Sets the state value for this Result.
-     *
-     * @param state
-     */
-    public void setState(int state) {
-        this.state = state;
-    }
-
-
+ * Sets the state value for this Result.
+ *
+ * @param state
+ */
+    public void setState(int state) {
+        this.state = state;
+    }
+
     /**
-     * Gets the status value for this Result.
-     *
-     * @return status
-     */
-    public java.lang.String getStatus() {
-        return status;
-    }
-
-
+ * Gets the status value for this Result.
+ *
+ * @return status
+ */
+    public java.lang.String getStatus() {
+        return status;
+    }
+
     /**
-     * Sets the status value for this Result.
-     *
-     * @param status
-     */
-    public void setStatus(java.lang.String status) {
-        this.status = status;
-    }
-
-
+ * Sets the status value for this Result.
+ *
+ * @param status
+ */
+    public void setStatus(java.lang.String status) {
+        this.status = status;
+    }
+
     /**
-     * Gets the suspended value for this Result.
-     *
-     * @return suspended
-     */
-    public boolean isSuspended() {
-        return suspended;
-    }
-
-
+ * Gets the suspended value for this Result.
+ *
+ * @return suspended
+ */
+    public boolean isSuspended() {
+        return suspended;
+    }
+
     /**
-     * Sets the suspended value for this Result.
-     *
-     * @param suspended
-     */
-    public void setSuspended(boolean suspended) {
-        this.suspended = suspended;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Result)) return false;
-        Result other = (Result) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true &&
-            this.broken == other.isBroken() &&
-            this.failed == other.isFailed() &&
-            this.finished == other.isFinished() &&
-            this.invalid == other.isInvalid() &&
-            this.jobFailed == other.isJobFailed() &&
-            this.queued == other.isQueued() &&
-            this.running == other.isRunning() &&
-            this.serverError == other.isServerError() &&
-            this.state == other.getState() &&
-            ((this.status==null && other.getStatus()==null) ||
-             (this.status!=null &&
-              this.status.equals(other.getStatus()))) &&
-            this.suspended == other.isSuspended();
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        _hashCode += getState();
-        if (getStatus() != null) {
-            _hashCode += getStatus().hashCode();
-        }
-        _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+ * Sets the suspended value for this Result.
+ *
+ * @param suspended
+ */
+    public void setSuspended(boolean suspended) {
+        this.suspended = suspended;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Result)) {
+            return false;
+        }
+
+        Result other = (Result) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = true && (this.broken == other.isBroken()) &&
+            (this.failed == other.isFailed()) &&
+            (this.finished == other.isFinished()) &&
+            (this.invalid == other.isInvalid()) &&
+            (this.jobFailed == other.isJobFailed()) &&
+            (this.queued == other.isQueued()) &&
+            (this.running == other.isRunning()) &&
+            (this.serverError == other.isServerError()) &&
+            (this.state == other.getState()) &&
+            (((this.status == null) && (other.getStatus() == null)) ||
+            ((this.status != null) && this.status.equals(other.getStatus()))) &&
+            (this.suspended == other.isSuspended());
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = 1;
+        _hashCode += (isBroken() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isFinished() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isInvalid() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isJobFailed() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isQueued() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isRunning() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += (isServerError() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        _hashCode += getState();
+
+        if (getStatus() != null) {
+            _hashCode += getStatus().hashCode();
+        }
+
+        _hashCode += (isSuspended() ? Boolean.TRUE : Boolean.FALSE).hashCode();
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+}
diff --git a/src/vamsas/objects/simple/Result_Helper.java b/src/vamsas/objects/simple/Result_Helper.java
index f61a0c9..42584f5 100755
--- a/src/vamsas/objects/simple/Result_Helper.java
+++ b/src/vamsas/objects/simple/Result_Helper.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,103 +22,110 @@
 * 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 vamsas.objects.simple;
-
-public class Result_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Result.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Result"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("broken");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "broken"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("failed");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "failed"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("finished");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "finished"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("invalid");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "invalid"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("jobFailed");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "jobFailed"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("queued");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "queued"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("running");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "running"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("serverError");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "serverError"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("state");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "state"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("status");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("suspended");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "suspended"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "boolean"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+*/
+package vamsas.objects.simple;
+
+public class Result_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Result.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "Result"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("broken");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "broken"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("failed");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "failed"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("finished");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "finished"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("invalid");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "invalid"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("jobFailed");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "jobFailed"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("queued");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "queued"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("running");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "running"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("serverError");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "serverError"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("state");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "state"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "int"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("status");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("suspended");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "suspended"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "boolean"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/vamsas/objects/simple/Sequence.java b/src/vamsas/objects/simple/Sequence.java
index c8dd81e..ddf0177 100755
--- a/src/vamsas/objects/simple/Sequence.java
+++ b/src/vamsas/objects/simple/Sequence.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,101 +22,110 @@
 * 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 vamsas.objects.simple;
-
-public class Sequence  implements java.io.Serializable {
-    private java.lang.String id;
-    private java.lang.String seq;
-
-    public Sequence() {
-    }
-
-    public Sequence(
-           java.lang.String id,
-           java.lang.String seq) {
-           this.id = id;
-           this.seq = seq;
-    }
-
-
+*/
+package vamsas.objects.simple;
+
+public class Sequence implements java.io.Serializable {
+    private java.lang.String id;
+    private java.lang.String seq;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public Sequence() {
+    }
+
+    public Sequence(java.lang.String id, java.lang.String seq) {
+        this.id = id;
+        this.seq = seq;
+    }
+
     /**
-     * Gets the id value for this Sequence.
-     *
-     * @return id
-     */
-    public java.lang.String getId() {
-        return id;
-    }
-
-
+ * Gets the id value for this Sequence.
+ *
+ * @return id
+ */
+    public java.lang.String getId() {
+        return id;
+    }
+
     /**
-     * Sets the id value for this Sequence.
-     *
-     * @param id
-     */
-    public void setId(java.lang.String id) {
-        this.id = id;
-    }
-
-
+ * Sets the id value for this Sequence.
+ *
+ * @param id
+ */
+    public void setId(java.lang.String id) {
+        this.id = id;
+    }
+
     /**
-     * Gets the seq value for this Sequence.
-     *
-     * @return seq
-     */
-    public java.lang.String getSeq() {
-        return seq;
-    }
-
-
+ * Gets the seq value for this Sequence.
+ *
+ * @return seq
+ */
+    public java.lang.String getSeq() {
+        return seq;
+    }
+
     /**
-     * Sets the seq value for this Sequence.
-     *
-     * @param seq
-     */
-    public void setSeq(java.lang.String seq) {
-        this.seq = seq;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof Sequence)) return false;
-        Sequence other = (Sequence) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true &&
-            ((this.id==null && other.getId()==null) ||
-             (this.id!=null &&
-              this.id.equals(other.getId()))) &&
-            ((this.seq==null && other.getSeq()==null) ||
-             (this.seq!=null &&
-              this.seq.equals(other.getSeq())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getId() != null) {
-            _hashCode += getId().hashCode();
-        }
-        if (getSeq() != null) {
-            _hashCode += getSeq().hashCode();
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+ * Sets the seq value for this Sequence.
+ *
+ * @param seq
+ */
+    public void setSeq(java.lang.String seq) {
+        this.seq = seq;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof Sequence)) {
+            return false;
+        }
+
+        Sequence other = (Sequence) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = true &&
+            (((this.id == null) && (other.getId() == null)) ||
+            ((this.id != null) && this.id.equals(other.getId()))) &&
+            (((this.seq == null) && (other.getSeq() == null)) ||
+            ((this.seq != null) && this.seq.equals(other.getSeq())));
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = 1;
+
+        if (getId() != null) {
+            _hashCode += getId().hashCode();
+        }
+
+        if (getSeq() != null) {
+            _hashCode += getSeq().hashCode();
+        }
+
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+}
diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java
index f7fc39e..afecdb9 100755
--- a/src/vamsas/objects/simple/SequenceSet.java
+++ b/src/vamsas/objects/simple/SequenceSet.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,80 +22,92 @@
 * 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 vamsas.objects.simple;
-
-public class SequenceSet  implements java.io.Serializable {
-    private vamsas.objects.simple.Sequence[] seqs;
-
-    public SequenceSet() {
-    }
-
-    public SequenceSet(
-           vamsas.objects.simple.Sequence[] seqs) {
-           this.seqs = seqs;
-    }
-
-
+*/
+package vamsas.objects.simple;
+
+public class SequenceSet implements java.io.Serializable {
+    private vamsas.objects.simple.Sequence[] seqs;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public SequenceSet() {
+    }
+
+    public SequenceSet(vamsas.objects.simple.Sequence[] seqs) {
+        this.seqs = seqs;
+    }
+
     /**
-     * Gets the seqs value for this SequenceSet.
-     *
-     * @return seqs
-     */
-    public vamsas.objects.simple.Sequence[] getSeqs() {
-        return seqs;
-    }
-
-
+ * Gets the seqs value for this SequenceSet.
+ *
+ * @return seqs
+ */
+    public vamsas.objects.simple.Sequence[] getSeqs() {
+        return seqs;
+    }
+
     /**
-     * Sets the seqs value for this SequenceSet.
-     *
-     * @param seqs
-     */
-    public void setSeqs(vamsas.objects.simple.Sequence[] seqs) {
-        this.seqs = seqs;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof SequenceSet)) return false;
-        SequenceSet other = (SequenceSet) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true &&
-            ((this.seqs==null && other.getSeqs()==null) ||
-             (this.seqs!=null &&
-              java.util.Arrays.equals(this.seqs, other.getSeqs())));
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getSeqs() != null) {
-            for (int i=0;
-                 i<java.lang.reflect.Array.getLength(getSeqs());
-                 i++) {
-                java.lang.Object obj = java.lang.reflect.Array.get(getSeqs(), i);
-                if (obj != null &&
-                    !obj.getClass().isArray()) {
-                    _hashCode += obj.hashCode();
-                }
-            }
-        }
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+ * Sets the seqs value for this SequenceSet.
+ *
+ * @param seqs
+ */
+    public void setSeqs(vamsas.objects.simple.Sequence[] seqs) {
+        this.seqs = seqs;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof SequenceSet)) {
+            return false;
+        }
+
+        SequenceSet other = (SequenceSet) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = true &&
+            (((this.seqs == null) && (other.getSeqs() == null)) ||
+            ((this.seqs != null) &&
+            java.util.Arrays.equals(this.seqs, other.getSeqs())));
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = 1;
+
+        if (getSeqs() != null) {
+            for (int i = 0; i < java.lang.reflect.Array.getLength(getSeqs());
+                    i++) {
+                java.lang.Object obj = java.lang.reflect.Array.get(getSeqs(), i);
+
+                if ((obj != null) && !obj.getClass().isArray()) {
+                    _hashCode += obj.hashCode();
+                }
+            }
+        }
+
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+}
diff --git a/src/vamsas/objects/simple/SequenceSet_Helper.java b/src/vamsas/objects/simple/SequenceSet_Helper.java
index d5f04a0..ec56cb2 100755
--- a/src/vamsas/objects/simple/SequenceSet_Helper.java
+++ b/src/vamsas/objects/simple/SequenceSet_Helper.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,53 +22,50 @@
 * 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 vamsas.objects.simple;
-
-public class SequenceSet_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(SequenceSet.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "SequenceSet"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("seqs");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
-        elemField.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+*/
+package vamsas.objects.simple;
+
+public class SequenceSet_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(SequenceSet.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "SequenceSet"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("seqs");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "seqs"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "Sequence"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/vamsas/objects/simple/Sequence_Helper.java b/src/vamsas/objects/simple/Sequence_Helper.java
index c8118c4..b080dc5 100755
--- a/src/vamsas/objects/simple/Sequence_Helper.java
+++ b/src/vamsas/objects/simple/Sequence_Helper.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,58 +22,56 @@
 * 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 vamsas.objects.simple;
-
-public class Sequence_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(Sequence.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "Sequence"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("id");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "id"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("seq");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "seq"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+*/
+package vamsas.objects.simple;
+
+public class Sequence_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(Sequence.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "Sequence"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("id");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "id"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("seq");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "seq"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
diff --git a/src/vamsas/objects/simple/WsJobId.java b/src/vamsas/objects/simple/WsJobId.java
index 891201f..fb882db 100755
--- a/src/vamsas/objects/simple/WsJobId.java
+++ b/src/vamsas/objects/simple/WsJobId.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,97 +22,106 @@
 * 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 vamsas.objects.simple;
-
-public class WsJobId  implements java.io.Serializable {
-    private java.lang.String jobId;
-    private int status;
-
-    public WsJobId() {
-    }
-
-    public WsJobId(
-           java.lang.String jobId,
-           int status) {
-           this.jobId = jobId;
-           this.status = status;
-    }
-
-
+*/
+package vamsas.objects.simple;
+
+public class WsJobId implements java.io.Serializable {
+    private java.lang.String jobId;
+    private int status;
+    private java.lang.Object __equalsCalc = null;
+    private boolean __hashCodeCalc = false;
+
+    public WsJobId() {
+    }
+
+    public WsJobId(java.lang.String jobId, int status) {
+        this.jobId = jobId;
+        this.status = status;
+    }
+
     /**
-     * Gets the jobId value for this WsJobId.
-     *
-     * @return jobId
-     */
-    public java.lang.String getJobId() {
-        return jobId;
-    }
-
-
+ * Gets the jobId value for this WsJobId.
+ *
+ * @return jobId
+ */
+    public java.lang.String getJobId() {
+        return jobId;
+    }
+
     /**
-     * Sets the jobId value for this WsJobId.
-     *
-     * @param jobId
-     */
-    public void setJobId(java.lang.String jobId) {
-        this.jobId = jobId;
-    }
-
-
+ * Sets the jobId value for this WsJobId.
+ *
+ * @param jobId
+ */
+    public void setJobId(java.lang.String jobId) {
+        this.jobId = jobId;
+    }
+
     /**
-     * Gets the status value for this WsJobId.
-     *
-     * @return status
-     */
-    public int getStatus() {
-        return status;
-    }
-
-
+ * Gets the status value for this WsJobId.
+ *
+ * @return status
+ */
+    public int getStatus() {
+        return status;
+    }
+
     /**
-     * Sets the status value for this WsJobId.
-     *
-     * @param status
-     */
-    public void setStatus(int status) {
-        this.status = status;
-    }
-
-    private java.lang.Object __equalsCalc = null;
-    public synchronized boolean equals(java.lang.Object obj) {
-        if (!(obj instanceof WsJobId)) return false;
-        WsJobId other = (WsJobId) obj;
-        if (obj == null) return false;
-        if (this == obj) return true;
-        if (__equalsCalc != null) {
-            return (__equalsCalc == obj);
-        }
-        __equalsCalc = obj;
-        boolean _equals;
-        _equals = true &&
-            ((this.jobId==null && other.getJobId()==null) ||
-             (this.jobId!=null &&
-              this.jobId.equals(other.getJobId()))) &&
-            this.status == other.getStatus();
-        __equalsCalc = null;
-        return _equals;
-    }
-
-    private boolean __hashCodeCalc = false;
-    public synchronized int hashCode() {
-        if (__hashCodeCalc) {
-            return 0;
-        }
-        __hashCodeCalc = true;
-        int _hashCode = 1;
-        if (getJobId() != null) {
-            _hashCode += getJobId().hashCode();
-        }
-        _hashCode += getStatus();
-        __hashCodeCalc = false;
-        return _hashCode;
-    }
-
-}
+ * Sets the status value for this WsJobId.
+ *
+ * @param status
+ */
+    public void setStatus(int status) {
+        this.status = status;
+    }
+
+    public synchronized boolean equals(java.lang.Object obj) {
+        if (!(obj instanceof WsJobId)) {
+            return false;
+        }
+
+        WsJobId other = (WsJobId) obj;
+
+        if (obj == null) {
+            return false;
+        }
+
+        if (this == obj) {
+            return true;
+        }
+
+        if (__equalsCalc != null) {
+            return (__equalsCalc == obj);
+        }
+
+        __equalsCalc = obj;
+
+        boolean _equals;
+        _equals = true &&
+            (((this.jobId == null) && (other.getJobId() == null)) ||
+            ((this.jobId != null) && this.jobId.equals(other.getJobId()))) &&
+            (this.status == other.getStatus());
+        __equalsCalc = null;
+
+        return _equals;
+    }
+
+    public synchronized int hashCode() {
+        if (__hashCodeCalc) {
+            return 0;
+        }
+
+        __hashCodeCalc = true;
+
+        int _hashCode = 1;
+
+        if (getJobId() != null) {
+            _hashCode += getJobId().hashCode();
+        }
+
+        _hashCode += getStatus();
+        __hashCodeCalc = false;
+
+        return _hashCode;
+    }
+}
diff --git a/src/vamsas/objects/simple/WsJobId_Helper.java b/src/vamsas/objects/simple/WsJobId_Helper.java
index 042a32e..75418c4 100755
--- a/src/vamsas/objects/simple/WsJobId_Helper.java
+++ b/src/vamsas/objects/simple/WsJobId_Helper.java
@@ -3,8 +3,8 @@
  *
  * This file was auto-generated from WSDL
  * by the Apache Axis 1.2RC2 Nov 16, 2004 (12:19:44 EST) WSDL2Java emitter.
- */
-
+ */
+
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -22,58 +22,56 @@
 * 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 vamsas.objects.simple;
-
-public class WsJobId_Helper {
-    // Type metadata
-    private static org.apache.axis.description.TypeDesc typeDesc =
-        new org.apache.axis.description.TypeDesc(WsJobId.class, true);
-
-    static {
-        typeDesc.setXmlType(new javax.xml.namespace.QName("simple.objects.vamsas", "WsJobId"));
-        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("jobId");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "jobId"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://schemas.xmlsoap.org/soap/encoding/", "string"));
-        typeDesc.addFieldDesc(elemField);
-        elemField = new org.apache.axis.description.ElementDesc();
-        elemField.setFieldName("status");
-        elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
-        elemField.setXmlType(new javax.xml.namespace.QName("http://www.w3.org/2001/XMLSchema", "int"));
-        typeDesc.addFieldDesc(elemField);
-    }
-
+*/
+package vamsas.objects.simple;
+
+public class WsJobId_Helper {
+    // Type metadata
+    private static org.apache.axis.description.TypeDesc typeDesc = new org.apache.axis.description.TypeDesc(WsJobId.class,
+            true);
+
+    static {
+        typeDesc.setXmlType(new javax.xml.namespace.QName(
+                "simple.objects.vamsas", "WsJobId"));
+
+        org.apache.axis.description.ElementDesc elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("jobId");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "jobId"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://schemas.xmlsoap.org/soap/encoding/", "string"));
+        typeDesc.addFieldDesc(elemField);
+        elemField = new org.apache.axis.description.ElementDesc();
+        elemField.setFieldName("status");
+        elemField.setXmlName(new javax.xml.namespace.QName("", "status"));
+        elemField.setXmlType(new javax.xml.namespace.QName(
+                "http://www.w3.org/2001/XMLSchema", "int"));
+        typeDesc.addFieldDesc(elemField);
+    }
+
     /**
-     * Return type metadata object
-     */
-    public static org.apache.axis.description.TypeDesc getTypeDesc() {
-        return typeDesc;
-    }
-
+ * Return type metadata object
+ */
+    public static org.apache.axis.description.TypeDesc getTypeDesc() {
+        return typeDesc;
+    }
+
     /**
-     * Get Custom Serializer
-     */
-    public static org.apache.axis.encoding.Serializer getSerializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanSerializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
+ * Get Custom Serializer
+ */
+    public static org.apache.axis.encoding.Serializer getSerializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanSerializer(_javaType,
+            _xmlType, typeDesc);
+    }
+
     /**
-     * Get Custom Deserializer
-     */
-    public static org.apache.axis.encoding.Deserializer getDeserializer(
-           java.lang.String mechType,
-           java.lang.Class _javaType,
-           javax.xml.namespace.QName _xmlType) {
-        return
-          new  org.apache.axis.encoding.ser.BeanDeserializer(
-            _javaType, _xmlType, typeDesc);
-    }
-
-}
+ * Get Custom Deserializer
+ */
+    public static org.apache.axis.encoding.Deserializer getDeserializer(
+        java.lang.String mechType, java.lang.Class _javaType,
+        javax.xml.namespace.QName _xmlType) {
+        return new org.apache.axis.encoding.ser.BeanDeserializer(_javaType,
+            _xmlType, typeDesc);
+    }
+}
-- 
1.7.10.2