From: jprocter <Jim Procter>
Date: Wed, 27 Aug 2008 14:20:59 +0000 (+0000)
Subject: applied copyright 2008
X-Git-Tag: Release_2_4_0~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=49685e6426d5ac136dce4907196751680c667670;p=jalview.git

applied copyright 2008
---

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 73ed7a7..d0c7da8 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index fc8478d..9bcf5c7 100755
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index e22b94e..e88c34a 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index 8e95c1b..8a67036 100755
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -1,80 +1,80 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package MCview;
-
-import java.awt.*;
-
-public class Bond
-{
-  float[] start;
-  float[] end;
-  Color startCol = Color.lightGray;
-  Color endCol = Color.lightGray;
-  public Atom at1;
-  public Atom at2;
-
-  public Bond(float[] start, float[] end, Atom at1, Atom 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 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);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 MCview;
+
+import java.awt.*;
+
+public class Bond
+{
+  float[] start;
+  float[] end;
+  Color startCol = Color.lightGray;
+  Color endCol = Color.lightGray;
+  public Atom at1;
+  public Atom at2;
+
+  public Bond(float[] start, float[] end, Atom at1, Atom 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 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 9eba886..64424ee 100755
--- a/src/MCview/MCMatrix.java
+++ b/src/MCview/MCMatrix.java
@@ -1,171 +1,171 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package 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 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]);
-    }
-
-    vect[0] = temp[0];
-    vect[1] = temp[1];
-    vect[2] = temp[2];
-
-    return vect;
-  }
-
-  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 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;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 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 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]);
+    }
+
+    vect[0] = temp[0];
+    vect[1] = temp[1];
+    vect[2] = temp[2];
+
+    return vect;
+  }
+
+  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 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/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 79871e8..0d807e3 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 30712f2..8dea416 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index e586707..bbb5724 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index e5ad565..83c346e 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java
index e99c746..e951737 100755
--- a/src/MCview/Residue.java
+++ b/src/MCview/Residue.java
@@ -1,49 +1,49 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package 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;
-  }
-
-  public Atom findAtom(String name)
-  {
-    for (int i = 0; i < atoms.size(); i++)
-    {
-      if ( ( (Atom) atoms.elementAt(i)).name.equals(name))
-      {
-        return (Atom) atoms.elementAt(i);
-      }
-    }
-
-    return null;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 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;
+  }
+
+  public Atom findAtom(String name)
+  {
+    for (int i = 0; i < atoms.size(); i++)
+    {
+      if ( ( (Atom) atoms.elementAt(i)).name.equals(name))
+      {
+        return (Atom) atoms.elementAt(i);
+      }
+    }
+
+    return null;
+  }
+}
diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index f7f2c39..59f0bfc 100755
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,75 +1,75 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package MCview;
-
-import java.util.*;
-
-public class Zsort
-{
-  public void Zsort(Vector bonds)
-  {
-    sort(bonds, 0, bonds.size() - 1);
-  }
-
-  public 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);
-    }
-  }
-
-  private int partition(Vector bonds, int p, int r)
-  {
-    float x = ( (Bond) bonds.elementAt(p)).start[2];
-    int i = p - 1;
-    int j = r + 1;
-    Bond tmp;
-    while (true)
-    {
-      do
-      {
-        j--;
-      }
-      while ( (j >= 0) && ( ( (Bond) bonds.elementAt(j)).start[2] > x));
-
-      do
-      {
-        i++;
-      }
-      while ( (i < bonds.size()) &&
-             ( ( (Bond) bonds.elementAt(i)).start[2] < x));
-
-      if (i < j)
-      {
-        tmp = (Bond) bonds.elementAt(i);
-        bonds.setElementAt(bonds.elementAt(j), i);
-        bonds.setElementAt(tmp, j);
-      }
-      else
-      {
-        return j;
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 MCview;
+
+import java.util.*;
+
+public class Zsort
+{
+  public void Zsort(Vector bonds)
+  {
+    sort(bonds, 0, bonds.size() - 1);
+  }
+
+  public 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);
+    }
+  }
+
+  private int partition(Vector bonds, int p, int r)
+  {
+    float x = ( (Bond) bonds.elementAt(p)).start[2];
+    int i = p - 1;
+    int j = r + 1;
+    Bond tmp;
+    while (true)
+    {
+      do
+      {
+        j--;
+      }
+      while ( (j >= 0) && ( ( (Bond) bonds.elementAt(j)).start[2] > x));
+
+      do
+      {
+        i++;
+      }
+      while ( (i < bonds.size()) &&
+             ( ( (Bond) bonds.elementAt(i)).start[2] < x));
+
+      if (i < j)
+      {
+        tmp = (Bond) bonds.elementAt(i);
+        bonds.setElementAt(bonds.elementAt(j), i);
+        bonds.setElementAt(tmp, j);
+      }
+      else
+      {
+        return j;
+      }
+    }
+  }
+}
diff --git a/src/ext/vamsas/IRegistry.java b/src/ext/vamsas/IRegistry.java
index 9300f59..dbe55b5 100755
--- a/src/ext/vamsas/IRegistry.java
+++ b/src/ext/vamsas/IRegistry.java
@@ -1,10 +1,21 @@
-/**
- * IRegistry.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public interface IRegistry
diff --git a/src/ext/vamsas/IRegistryService.java b/src/ext/vamsas/IRegistryService.java
index 2590314..d68a1b4 100755
--- a/src/ext/vamsas/IRegistryService.java
+++ b/src/ext/vamsas/IRegistryService.java
@@ -1,10 +1,21 @@
-/**
- * IRegistryService.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public interface IRegistryService
diff --git a/src/ext/vamsas/IRegistryServiceLocator.java b/src/ext/vamsas/IRegistryServiceLocator.java
index 0d7c0da..cb477f3 100755
--- a/src/ext/vamsas/IRegistryServiceLocator.java
+++ b/src/ext/vamsas/IRegistryServiceLocator.java
@@ -1,10 +1,21 @@
-/**
- * IRegistryServiceLocator.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public class IRegistryServiceLocator
diff --git a/src/ext/vamsas/Jpred.java b/src/ext/vamsas/Jpred.java
index c3ab28b..674040c 100755
--- a/src/ext/vamsas/Jpred.java
+++ b/src/ext/vamsas/Jpred.java
@@ -1,10 +1,21 @@
-/**
- * Jpred.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public interface Jpred
diff --git a/src/ext/vamsas/JpredService.java b/src/ext/vamsas/JpredService.java
index 8917d77..c910a60 100755
--- a/src/ext/vamsas/JpredService.java
+++ b/src/ext/vamsas/JpredService.java
@@ -1,10 +1,21 @@
-/**
- * JpredService.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public interface JpredService
diff --git a/src/ext/vamsas/JpredServiceLocator.java b/src/ext/vamsas/JpredServiceLocator.java
index 433fa70..ae2511e 100755
--- a/src/ext/vamsas/JpredServiceLocator.java
+++ b/src/ext/vamsas/JpredServiceLocator.java
@@ -1,10 +1,21 @@
-/**
- * JpredServiceLocator.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public class JpredServiceLocator
diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java
index 4c8fc7f..235166d 100755
--- a/src/ext/vamsas/JpredSoapBindingStub.java
+++ b/src/ext/vamsas/JpredSoapBindingStub.java
@@ -1,10 +1,21 @@
-/**
- * JpredSoapBindingStub.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public class JpredSoapBindingStub
diff --git a/src/ext/vamsas/MuscleWS.java b/src/ext/vamsas/MuscleWS.java
index db1416e..e53770f 100755
--- a/src/ext/vamsas/MuscleWS.java
+++ b/src/ext/vamsas/MuscleWS.java
@@ -1,43 +1,54 @@
-/**
- * MuscleWS.java
- *
- * 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package 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;
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package 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 a4dc674..9531cda 100755
--- a/src/ext/vamsas/MuscleWSService.java
+++ b/src/ext/vamsas/MuscleWSService.java
@@ -1,38 +1,49 @@
-/**
- * MuscleWSService.java
- *
- * 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package 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;
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package 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 a269029..c822d92 100755
--- a/src/ext/vamsas/MuscleWSServiceLocator.java
+++ b/src/ext/vamsas/MuscleWSServiceLocator.java
@@ -1,208 +1,219 @@
-/**
- * MuscleWSServiceLocator.java
- *
- * 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package 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(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(javax.xml.namespace.QName portName,
-                                 java.lang.String address)
-      throws javax.xml.rpc.ServiceException
-  {
-    setEndpointAddress(portName.getLocalPart(), address);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package 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(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(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 de80f9e..49e49cf 100755
--- a/src/ext/vamsas/MuscleWSSoapBindingStub.java
+++ b/src/ext/vamsas/MuscleWSSoapBindingStub.java
@@ -1,470 +1,481 @@
-/**
- * MuscleWSSoapBindingStub.java
- *
- * 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package 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);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package 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/RegistryServiceSoapBindingStub.java b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
index 22bd8ed..830a0cb 100755
--- a/src/ext/vamsas/RegistryServiceSoapBindingStub.java
+++ b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
@@ -1,10 +1,21 @@
-/**
- * RegistryServiceSoapBindingStub.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public class RegistryServiceSoapBindingStub
diff --git a/src/ext/vamsas/SeqSearchI.java b/src/ext/vamsas/SeqSearchI.java
index 3c89161..4ac04b3 100644
--- a/src/ext/vamsas/SeqSearchI.java
+++ b/src/ext/vamsas/SeqSearchI.java
@@ -1,10 +1,21 @@
-/**
- * ScanPSService.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public interface SeqSearchI extends java.rmi.Remote {
diff --git a/src/ext/vamsas/SeqSearchServiceLocator.java b/src/ext/vamsas/SeqSearchServiceLocator.java
index 46b435b..90f6b81 100644
--- a/src/ext/vamsas/SeqSearchServiceLocator.java
+++ b/src/ext/vamsas/SeqSearchServiceLocator.java
@@ -1,10 +1,21 @@
-/**
- * ScanPSServiceServiceLocator.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public class SeqSearchServiceLocator extends org.apache.axis.client.Service implements ext.vamsas.SeqSearchServiceService {
diff --git a/src/ext/vamsas/SeqSearchServiceService.java b/src/ext/vamsas/SeqSearchServiceService.java
index 0dd4c14..867ab25 100644
--- a/src/ext/vamsas/SeqSearchServiceService.java
+++ b/src/ext/vamsas/SeqSearchServiceService.java
@@ -1,10 +1,21 @@
-/**
- * ScanPSServiceService.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public interface SeqSearchServiceService extends javax.xml.rpc.Service {
diff --git a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
index 614a85f..6a1a15e 100644
--- a/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
+++ b/src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
@@ -1,10 +1,21 @@
-/**
- * ScanPSServiceSoapBindingStub.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public class SeqSearchServiceSoapBindingStub extends org.apache.axis.client.Stub implements ext.vamsas.SeqSearchI {
@@ -18,7 +29,7 @@ public class SeqSearchServiceSoapBindingStub extends org.apache.axis.client.Stub
     static {
         _operations = new org.apache.axis.description.OperationDesc[5];
         _initOperationDesc1();
-    }
+    }
 
     private static void _initOperationDesc1(){
         org.apache.axis.description.OperationDesc oper;
diff --git a/src/ext/vamsas/ServiceHandle.java b/src/ext/vamsas/ServiceHandle.java
index 994ea5c..7d95b1a 100755
--- a/src/ext/vamsas/ServiceHandle.java
+++ b/src/ext/vamsas/ServiceHandle.java
@@ -1,10 +1,21 @@
-/**
- * ServiceHandle.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public class ServiceHandle
diff --git a/src/ext/vamsas/ServiceHandles.java b/src/ext/vamsas/ServiceHandles.java
index 1de1345..05a386f 100755
--- a/src/ext/vamsas/ServiceHandles.java
+++ b/src/ext/vamsas/ServiceHandles.java
@@ -1,10 +1,21 @@
-/**
- * ServiceHandles.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 ext.vamsas;
 
 public class ServiceHandles
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 03cdc15..a4418a4 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,156 +1,156 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.analysis;
-
-import java.util.*;
-
-import jalview.datamodel.*;
-
-/**
- * Takes in a vector or array of sequences and column start and column end
- * and returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
- * This class is used extensively in calculating alignment colourschemes
- * that depend on the amount of conservation in each alignment column.
- * @author $author$
- * @version $Revision$
- */
-public class AAFrequency
-{
-  //No need to store 1000s of strings which are not
-  //visible to the user.
-  public static final String MAXCOUNT = "C";
-  public static final String MAXRESIDUE = "R";
-  public static final String PID_GAPS = "G";
-  public static final String PID_NOGAPS = "N";
-
-  public static final Hashtable[] calculate(Vector sequences, int start,
-                                            int end)
-  {
-    SequenceI[] seqs = new SequenceI[sequences.size()];
-    int width = 0;
-    for (int i = 0; i < sequences.size(); i++)
-    {
-      seqs[i] = (SequenceI) sequences.elementAt(i);
-      if (seqs[i].getLength() > width)
-      {
-        width = seqs[i].getLength();
-      }
-    }
-
-    Hashtable[] reply = new Hashtable[width];
-
-    if (end >= width)
-    {
-      end = width;
-    }
-
-    calculate(seqs, start, end, reply);
-
-    return reply;
-  }
-
-  public static final void calculate(SequenceI[] sequences,
-                                     int start, int end,
-                                     Hashtable[] result)
-  {
-    Hashtable residueHash;
-    int maxCount, nongap, i, j, v, jSize = sequences.length;
-    String maxResidue;
-    char c;
-    float percentage;
-
-    int[] values = new int[255];
-
-    char[] seq;
-
-    for (i = start; i < end; i++)
-    {
-      residueHash = new Hashtable();
-      maxCount = 0;
-      maxResidue = "";
-      nongap = 0;
-      values = new int[255];
-
-      for (j = 0; j < jSize; j++)
-      {
-        seq = sequences[j].getSequence();
-        if (seq.length > i)
-        {
-          c = seq[i];
-
-          if (c == '.' || c == ' ')
-          {
-            c = '-';
-          }
-
-          if (c == '-')
-          {
-            values['-']++;
-            continue;
-          }
-          else if ('a' <= c && c <= 'z')
-          {
-            c -= 32; //('a' - 'A');
-          }
-
-          nongap++;
-          values[c]++;
-
-        }
-        else
-        {
-          values['-']++;
-        }
-      }
-
-      for (v = 'A'; v < 'Z'; v++)
-      {
-        if (values[v] < 2 || values[v] < maxCount)
-        {
-          continue;
-        }
-
-        if (values[v] > maxCount)
-        {
-          maxResidue = String.valueOf( (char) v);
-        }
-        else if (values[v] == maxCount)
-        {
-          maxResidue += String.valueOf( (char) v);
-        }
-        maxCount = values[v];
-      }
-
-      if (maxResidue.length() == 0)
-      {
-        maxResidue = "-";
-      }
-
-      residueHash.put(MAXCOUNT, new Integer(maxCount));
-      residueHash.put(MAXRESIDUE, maxResidue);
-
-      percentage = ( (float) maxCount * 100) / (float) jSize;
-      residueHash.put(PID_GAPS, new Float(percentage));
-
-      percentage = ( (float) maxCount * 100) / (float) nongap;
-      residueHash.put(PID_NOGAPS, new Float(percentage));
-      result[i] = residueHash;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.analysis;
+
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * Takes in a vector or array of sequences and column start and column end
+ * and returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
+ * This class is used extensively in calculating alignment colourschemes
+ * that depend on the amount of conservation in each alignment column.
+ * @author $author$
+ * @version $Revision$
+ */
+public class AAFrequency
+{
+  //No need to store 1000s of strings which are not
+  //visible to the user.
+  public static final String MAXCOUNT = "C";
+  public static final String MAXRESIDUE = "R";
+  public static final String PID_GAPS = "G";
+  public static final String PID_NOGAPS = "N";
+
+  public static final Hashtable[] calculate(Vector sequences, int start,
+                                            int end)
+  {
+    SequenceI[] seqs = new SequenceI[sequences.size()];
+    int width = 0;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      seqs[i] = (SequenceI) sequences.elementAt(i);
+      if (seqs[i].getLength() > width)
+      {
+        width = seqs[i].getLength();
+      }
+    }
+
+    Hashtable[] reply = new Hashtable[width];
+
+    if (end >= width)
+    {
+      end = width;
+    }
+
+    calculate(seqs, start, end, reply);
+
+    return reply;
+  }
+
+  public static final void calculate(SequenceI[] sequences,
+                                     int start, int end,
+                                     Hashtable[] result)
+  {
+    Hashtable residueHash;
+    int maxCount, nongap, i, j, v, jSize = sequences.length;
+    String maxResidue;
+    char c;
+    float percentage;
+
+    int[] values = new int[255];
+
+    char[] seq;
+
+    for (i = start; i < end; i++)
+    {
+      residueHash = new Hashtable();
+      maxCount = 0;
+      maxResidue = "";
+      nongap = 0;
+      values = new int[255];
+
+      for (j = 0; j < jSize; j++)
+      {
+        seq = sequences[j].getSequence();
+        if (seq.length > i)
+        {
+          c = seq[i];
+
+          if (c == '.' || c == ' ')
+          {
+            c = '-';
+          }
+
+          if (c == '-')
+          {
+            values['-']++;
+            continue;
+          }
+          else if ('a' <= c && c <= 'z')
+          {
+            c -= 32; //('a' - 'A');
+          }
+
+          nongap++;
+          values[c]++;
+
+        }
+        else
+        {
+          values['-']++;
+        }
+      }
+
+      for (v = 'A'; v < 'Z'; v++)
+      {
+        if (values[v] < 2 || values[v] < maxCount)
+        {
+          continue;
+        }
+
+        if (values[v] > maxCount)
+        {
+          maxResidue = String.valueOf( (char) v);
+        }
+        else if (values[v] == maxCount)
+        {
+          maxResidue += String.valueOf( (char) v);
+        }
+        maxCount = values[v];
+      }
+
+      if (maxResidue.length() == 0)
+      {
+        maxResidue = "-";
+      }
+
+      residueHash.put(MAXCOUNT, new Integer(maxCount));
+      residueHash.put(MAXRESIDUE, maxResidue);
+
+      percentage = ( (float) maxCount * 100) / (float) jSize;
+      residueHash.put(PID_GAPS, new Float(percentage));
+
+      percentage = ( (float) maxCount * 100) / (float) nongap;
+      residueHash.put(PID_NOGAPS, new Float(percentage));
+      result[i] = residueHash;
+    }
+  }
+}
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 0de8167..1f1c6fa 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index a3493f7..ed29101 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index c216471..f276a55 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 159d96a..2da8773 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
 import java.util.Enumeration;
@@ -562,4 +580,4 @@ public class CrossRef
    * System.out.println("Prod "+p+": "+prod[p].getDisplayId(true)); } }
    *  } }
    */
-}
\ No newline at end of file
+}
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index c6bcfda..74166c8 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
 import java.util.Enumeration;
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 5280467..8bda592 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
 import java.util.*;
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 3569be1..dd2dbbf 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index c11610a..0cc2e76 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -1,239 +1,239 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.analysis;
-
-import java.io.*;
-
-import jalview.datamodel.*;
-import jalview.math.*;
-
-/**
- * Performs Principal Component Analysis on given sequences
- *
- * @author $author$
- * @version $Revision$
- */
-public class PCA
-    implements Runnable
-{
-  Matrix m;
-  Matrix symm;
-  Matrix m2;
-  double[] eigenvalue;
-  Matrix eigenvector;
-  StringBuffer details = new StringBuffer();
-
-  /**
-   * Creates a new PCA object.
-   *
-   * @param s Set of sequences to perform PCA on
-   */
-  public PCA(String[] s)
-  {
-
-    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);
-
-  }
-
-  /**
-   * Returns the matrix used in PCA calculation
-   *
-   * @return java.math.Matrix object
-   */
-
-  public Matrix getM()
-  {
-    return m;
-  }
-
-  /**
-   * Returns Eigenvalue
-   *
-   * @param i Index of diagonal within matrix
-   *
-   * @return Returns value of diagonal from matrix
-   */
-  public double getEigenvalue(int i)
-  {
-    return eigenvector.d[i];
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param l DOCUMENT ME!
-   * @param n DOCUMENT ME!
-   * @param mm DOCUMENT ME!
-   * @param factor DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public float[][] getComponents(int l, int n, int mm, float factor)
-  {
-    float[][] out = new float[m.rows][3];
-
-    for (int i = 0; i < m.rows; i++)
-    {
-      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;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public double[] component(int n)
-  {
-    // n = index of eigenvector
-    double[] out = new double[m.rows];
-
-    for (int i = 0; i < m.rows; i++)
-    {
-      out[i] = component(i, n);
-    }
-
-    return out;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param row DOCUMENT ME!
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  double component(int row, int n)
-  {
-    double out = 0.0;
-
-    for (int i = 0; i < symm.cols; i++)
-    {
-      out += (symm.value[row][i] * eigenvector.value[i][n]);
-    }
-
-    return out / eigenvector.d[n];
-  }
-
-  public String getDetails()
-  {
-    return details.toString();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void run()
-  {
-    Matrix mt = m.transpose();
-
-    details.append(" --- OrigT * Orig ---- \n");
-    eigenvector = mt.preMultiply(m2);
-
-    PrintStream ps = new PrintStream(System.out)
-    {
-      public void print(String x)
-      {
-        details.append(x);
-      }
-
-      public void println()
-      {
-        details.append("\n");
-      }
-    };
-
-    eigenvector.print(ps);
-
-    symm = eigenvector.copy();
-
-    eigenvector.tred();
-
-    details.append(" ---Tridiag transform matrix ---\n");
-    details.append(" --- D vector ---\n");
-    eigenvector.printD(ps);
-    ps.println();
-    details.append("--- E vector ---\n");
-    eigenvector.printE(ps);
-    ps.println();
-
-    // Now produce the diagonalization matrix
-    eigenvector.tqli();
-
-    details.append(" --- New diagonalization matrix ---\n");
-    details.append(" --- Eigenvalues ---\n");
-    eigenvector.printD(ps);
-    ps.println();
-    //  taps.println();
-    //  taps.println("Transformed sequences = ");
-    // Matrix trans =  m.preMultiply(eigenvector);
-    //  trans.print(System.out);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.analysis;
+
+import java.io.*;
+
+import jalview.datamodel.*;
+import jalview.math.*;
+
+/**
+ * Performs Principal Component Analysis on given sequences
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PCA
+    implements Runnable
+{
+  Matrix m;
+  Matrix symm;
+  Matrix m2;
+  double[] eigenvalue;
+  Matrix eigenvector;
+  StringBuffer details = new StringBuffer();
+
+  /**
+   * Creates a new PCA object.
+   *
+   * @param s Set of sequences to perform PCA on
+   */
+  public PCA(String[] s)
+  {
+
+    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);
+
+  }
+
+  /**
+   * Returns the matrix used in PCA calculation
+   *
+   * @return java.math.Matrix object
+   */
+
+  public Matrix getM()
+  {
+    return m;
+  }
+
+  /**
+   * Returns Eigenvalue
+   *
+   * @param i Index of diagonal within matrix
+   *
+   * @return Returns value of diagonal from matrix
+   */
+  public double getEigenvalue(int i)
+  {
+    return eigenvector.d[i];
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param l DOCUMENT ME!
+   * @param n DOCUMENT ME!
+   * @param mm DOCUMENT ME!
+   * @param factor DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float[][] getComponents(int l, int n, int mm, float factor)
+  {
+    float[][] out = new float[m.rows][3];
+
+    for (int i = 0; i < m.rows; i++)
+    {
+      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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public double[] component(int n)
+  {
+    // n = index of eigenvector
+    double[] out = new double[m.rows];
+
+    for (int i = 0; i < m.rows; i++)
+    {
+      out[i] = component(i, n);
+    }
+
+    return out;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param row DOCUMENT ME!
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  double component(int row, int n)
+  {
+    double out = 0.0;
+
+    for (int i = 0; i < symm.cols; i++)
+    {
+      out += (symm.value[row][i] * eigenvector.value[i][n]);
+    }
+
+    return out / eigenvector.d[n];
+  }
+
+  public String getDetails()
+  {
+    return details.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    Matrix mt = m.transpose();
+
+    details.append(" --- OrigT * Orig ---- \n");
+    eigenvector = mt.preMultiply(m2);
+
+    PrintStream ps = new PrintStream(System.out)
+    {
+      public void print(String x)
+      {
+        details.append(x);
+      }
+
+      public void println()
+      {
+        details.append("\n");
+      }
+    };
+
+    eigenvector.print(ps);
+
+    symm = eigenvector.copy();
+
+    eigenvector.tred();
+
+    details.append(" ---Tridiag transform matrix ---\n");
+    details.append(" --- D vector ---\n");
+    eigenvector.printD(ps);
+    ps.println();
+    details.append("--- E vector ---\n");
+    eigenvector.printE(ps);
+    ps.println();
+
+    // Now produce the diagonalization matrix
+    eigenvector.tqli();
+
+    details.append(" --- New diagonalization matrix ---\n");
+    details.append(" --- Eigenvalues ---\n");
+    eigenvector.printD(ps);
+    ps.println();
+    //  taps.println();
+    //  taps.println("Transformed sequences = ");
+    // Matrix trans =  m.preMultiply(eigenvector);
+    //  trans.print(System.out);
+  }
+}
diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 79c1325..4435ae1 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
 import com.stevesoft.pat.Regex;
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 0aa2bd5..c81f673 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 0744937..bb53814 100755
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -1,246 +1,246 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.analysis;
-
-import java.util.*;
-
-import jalview.datamodel.*;
-
-/**
- * <p>Title: </p>
- * SequenceIdMatcher
- * <p>Description: </p>
- * Routine which does approximate Sequence Id resolution by name using
- * string containment (on word boundaries) rather than equivalence. It also
- * attempts to resolve ties where no exact match is available by picking the
- * the id closest to the query.
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-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]);
-    }
-  }
-
-  /**
-   * returns the closest SequenceI in matches to SeqIdName and returns all the matches
-   * to the names hash.
-   * @param candName SeqIdName
-   * @param matches Vector of SequenceI objects
-   * @return SequenceI closest SequenceI to SeqIdName
-   */
-  private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
-  {
-    SequenceI match = null;
-    if (candName == null || matches == null || matches.size() == 0)
-    {
-      return null;
-    }
-    match = (SequenceI) matches.elementAt(0);
-    matches.removeElementAt(0);
-    names.put(new SeqIdName(match.getName()), match);
-    int matchlen = match.getName().length();
-    int namlen = candName.id.length();
-    while (matches.size() > 0)
-    {
-      // look through for a better one.
-      SequenceI cand = (SequenceI) matches.elementAt(0);
-      names.put(new SeqIdName(cand.getName()), cand);
-      int candlen = cand.getName().length();
-      // keep the one with an id 'closer' to the given seqnam string
-      if (Math.abs(matchlen - namlen) > Math.abs(candlen - namlen) &&
-          candlen > matchlen)
-      {
-        match = cand;
-        matchlen = candlen;
-      }
-    }
-    return match;
-  }
-
-  /**
-   * get SequenceI with closest SequenceI.getName() to seq.getName()
-   * @param seq SequenceI
-   * @return SequenceI
-   */
-  SequenceI findIdMatch(SequenceI seq)
-  {
-    SeqIdName nam = new SeqIdName(seq.getName());
-    return findIdMatch(nam);
-  }
-
-  SequenceI findIdMatch(String seqnam)
-  {
-    SeqIdName nam = new SeqIdName(seqnam);
-    return findIdMatch(nam);
-  }
-
-  /**
-   * findIdMatch
-   *
-   * Return pointers to sequences (or sequence object containers)
-   * which have same Id as a given set of different sequence objects
-   *
-   * @param seqs SequenceI[]
-   * @return SequenceI[]
-   */
-  SequenceI[] findIdMatch(SequenceI[] seqs)
-  {
-    SequenceI[] namedseqs = null;
-    int i = 0;
-    SeqIdName nam;
-
-    if (seqs.length > 0)
-    {
-      namedseqs = new SequenceI[seqs.length];
-      do
-      {
-        nam = new SeqIdName(seqs[i].getName());
-
-        if (names.containsKey(nam))
-        {
-          namedseqs[i] = findIdMatch(nam);
-        }
-        else
-        {
-          namedseqs[i] = null;
-        }
-      }
-      while (++i < seqs.length);
-    }
-
-    return namedseqs;
-  }
-
-  /**
-   * core findIdMatch search method
-   * @param nam SeqIdName
-   * @return SequenceI
-   */
-  private SequenceI findIdMatch(jalview.analysis.SequenceIdMatcher.SeqIdName
-                                nam)
-  {
-    Vector matches = new Vector();
-    while (names.containsKey(nam))
-    {
-      matches.addElement(names.remove(nam));
-    }
-    return pickbestMatch(nam, matches);
-  }
-
-  private class SeqIdName
-  {
-    String id;
-
-    SeqIdName(String s)
-    {
-      if (s != null)
-      {
-        id = new String(s);
-      }
-      else
-      {
-        id = "";
-      }
-    }
-
-    public int hashCode()
-    {
-      return ( (id.length() >= 4) ? id.substring(0, 4).hashCode() : id.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;
-    }
-
-    /**
-     * Characters that define the end of a unique sequence ID at
-     * the beginning of an arbitrary ID string
-     * JBPNote: This is a heuristic that will fail for arbritrarily extended sequence id's
-     * (like portions of an aligned set of repeats from one sequence)
-     */
-    private String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_";
-
-    /**
-     * matches if one ID properly contains another at a whitespace boundary.
-     * TODO: (JBPNote) These are not efficient. should use char[] for speed
-     * todo: (JBPNote) Set separator characters appropriately
-     * @param s SeqIdName
-     * @return boolean
-     */
-    public boolean equals(SeqIdName s)
-    {
-      if (id.length() > s.id.length())
-      {
-        return id.startsWith(s.id) ?
-            (WORD_SEP.indexOf(id.charAt(s.id.length())) > -1)
-            : false;
-      }
-      else
-      {
-        return s.id.startsWith(id) ?
-            (s.id.equals(id) ? true :
-             (WORD_SEP.indexOf(s.id.charAt(id.length())) > -1))
-            : false;
-      }
-    }
-
-    public boolean equals(String s)
-    {
-      if (id.length() > s.length())
-      {
-        return id.startsWith(s) ?
-            (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
-            : false;
-      }
-      else
-      {
-        return s.startsWith(id) ?
-            (s.equals(id) ? true :
-             (WORD_SEP.indexOf(s.charAt(id.length())) > -1))
-            : false;
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.analysis;
+
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * <p>Title: </p>
+ * SequenceIdMatcher
+ * <p>Description: </p>
+ * Routine which does approximate Sequence Id resolution by name using
+ * string containment (on word boundaries) rather than equivalence. It also
+ * attempts to resolve ties where no exact match is available by picking the
+ * the id closest to the query.
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+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]);
+    }
+  }
+
+  /**
+   * returns the closest SequenceI in matches to SeqIdName and returns all the matches
+   * to the names hash.
+   * @param candName SeqIdName
+   * @param matches Vector of SequenceI objects
+   * @return SequenceI closest SequenceI to SeqIdName
+   */
+  private SequenceI pickbestMatch(SeqIdName candName, Vector matches)
+  {
+    SequenceI match = null;
+    if (candName == null || matches == null || matches.size() == 0)
+    {
+      return null;
+    }
+    match = (SequenceI) matches.elementAt(0);
+    matches.removeElementAt(0);
+    names.put(new SeqIdName(match.getName()), match);
+    int matchlen = match.getName().length();
+    int namlen = candName.id.length();
+    while (matches.size() > 0)
+    {
+      // look through for a better one.
+      SequenceI cand = (SequenceI) matches.elementAt(0);
+      names.put(new SeqIdName(cand.getName()), cand);
+      int candlen = cand.getName().length();
+      // keep the one with an id 'closer' to the given seqnam string
+      if (Math.abs(matchlen - namlen) > Math.abs(candlen - namlen) &&
+          candlen > matchlen)
+      {
+        match = cand;
+        matchlen = candlen;
+      }
+    }
+    return match;
+  }
+
+  /**
+   * get SequenceI with closest SequenceI.getName() to seq.getName()
+   * @param seq SequenceI
+   * @return SequenceI
+   */
+  SequenceI findIdMatch(SequenceI seq)
+  {
+    SeqIdName nam = new SeqIdName(seq.getName());
+    return findIdMatch(nam);
+  }
+
+  SequenceI findIdMatch(String seqnam)
+  {
+    SeqIdName nam = new SeqIdName(seqnam);
+    return findIdMatch(nam);
+  }
+
+  /**
+   * findIdMatch
+   *
+   * Return pointers to sequences (or sequence object containers)
+   * which have same Id as a given set of different sequence objects
+   *
+   * @param seqs SequenceI[]
+   * @return SequenceI[]
+   */
+  SequenceI[] findIdMatch(SequenceI[] seqs)
+  {
+    SequenceI[] namedseqs = null;
+    int i = 0;
+    SeqIdName nam;
+
+    if (seqs.length > 0)
+    {
+      namedseqs = new SequenceI[seqs.length];
+      do
+      {
+        nam = new SeqIdName(seqs[i].getName());
+
+        if (names.containsKey(nam))
+        {
+          namedseqs[i] = findIdMatch(nam);
+        }
+        else
+        {
+          namedseqs[i] = null;
+        }
+      }
+      while (++i < seqs.length);
+    }
+
+    return namedseqs;
+  }
+
+  /**
+   * core findIdMatch search method
+   * @param nam SeqIdName
+   * @return SequenceI
+   */
+  private SequenceI findIdMatch(jalview.analysis.SequenceIdMatcher.SeqIdName
+                                nam)
+  {
+    Vector matches = new Vector();
+    while (names.containsKey(nam))
+    {
+      matches.addElement(names.remove(nam));
+    }
+    return pickbestMatch(nam, matches);
+  }
+
+  private class SeqIdName
+  {
+    String id;
+
+    SeqIdName(String s)
+    {
+      if (s != null)
+      {
+        id = new String(s);
+      }
+      else
+      {
+        id = "";
+      }
+    }
+
+    public int hashCode()
+    {
+      return ( (id.length() >= 4) ? id.substring(0, 4).hashCode() : id.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;
+    }
+
+    /**
+     * Characters that define the end of a unique sequence ID at
+     * the beginning of an arbitrary ID string
+     * JBPNote: This is a heuristic that will fail for arbritrarily extended sequence id's
+     * (like portions of an aligned set of repeats from one sequence)
+     */
+    private String WORD_SEP = "~. |#\\/<>!\"£$%^*)}[@',?_";
+
+    /**
+     * matches if one ID properly contains another at a whitespace boundary.
+     * TODO: (JBPNote) These are not efficient. should use char[] for speed
+     * todo: (JBPNote) Set separator characters appropriately
+     * @param s SeqIdName
+     * @return boolean
+     */
+    public boolean equals(SeqIdName s)
+    {
+      if (id.length() > s.id.length())
+      {
+        return id.startsWith(s.id) ?
+            (WORD_SEP.indexOf(id.charAt(s.id.length())) > -1)
+            : false;
+      }
+      else
+      {
+        return s.id.startsWith(id) ?
+            (s.id.equals(id) ? true :
+             (WORD_SEP.indexOf(s.id.charAt(id.length())) > -1))
+            : false;
+      }
+    }
+
+    public boolean equals(String s)
+    {
+      if (id.length() > s.length())
+      {
+        return id.startsWith(s) ?
+            (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
+            : false;
+      }
+      else
+      {
+        return s.startsWith(id) ?
+            (s.equals(id) ? true :
+             (WORD_SEP.indexOf(s.charAt(id.length())) > -1))
+            : false;
+      }
+    }
+  }
+}
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 7c1ea3f..fc42a74 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index d7c2b43..13045f9 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.io.*;
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 33a73d3..602d29b 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 6b292e9..00388a0 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index c932962..a4cc0e7 100755
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 2d2d748..198cb21 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 909ce78..ef0dcbb 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 82a5911..1533530 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 78d7ba7..7c9d421 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,279 +1,278 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-
-public class CutAndPasteTransfer
-    extends Panel implements ActionListener, MouseListener
-{
-  boolean pdbImport = false;
-  boolean treeImport = false;
-  boolean annotationImport = false;
-  Sequence  seq;
-  AlignFrame alignFrame;
-
-  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-    this.alignFrame = alignFrame;
-
-    if (!forImport)
-    {
-      buttonPanel.setVisible(false);
-    }
-  }
-
-  public String getText()
-  {
-    return textarea.getText();
-  }
-
-  public void setText(String text)
-  {
-    textarea.setText(text);
-  }
-
-  public void setPDBImport(Sequence seq)
-  {
-    this.seq = seq;
-    accept.setLabel("Accept");
-    addSequences.setVisible(false);
-    pdbImport = true;
-  }
-
-  public void setTreeImport()
-  {
-    treeImport = true;
-    accept.setLabel("Accept");
-    addSequences.setVisible(false);
-  }
-
-  public void setAnnotationImport()
-  {
-    annotationImport = true;
-    accept.setLabel("Accept");
-    addSequences.setVisible(false);
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == accept)
-    {
-      ok(true);
-    }
-    else if (evt.getSource() == addSequences)
-    {
-      ok(false);
-    }
-    else if (evt.getSource() == cancel)
-    {
-      cancel();
-    }
-  }
-
-  protected void ok(boolean newWindow)
-  {
-    String text = getText();
-    int length = text.length();
-    textarea.append("\n");
-    if (textarea.getText().length() == length)
-    {
-      String warning =
-          "\n\n#################################################\n"
-          + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
-          + "\nCAN'T INPUT FULL ALIGNMENT"
-          + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
-          + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
-          + "\n#################################################\n";
-      textarea.setText(text.substring(0, text.length() - warning.length())
-                       + warning);
-
-      textarea.setCaretPosition(text.length());
-    }
-
-    if (pdbImport)
-    {
-      PDBEntry pdb = new PDBEntry();
-      pdb.setFile(text);
-
-      if ( alignFrame.alignPanel.av.applet.jmolAvailable )
-        new jalview.appletgui.AppletJmol(pdb,
-                                         new Sequence[]{seq},
-                                         null,
-                                         alignFrame.alignPanel,
-                                         AppletFormatAdapter.PASTE);
-      else
-
-        new MCview.AppletPDBViewer(pdb,
-                                   new Sequence[]{seq},
-                                   null,
-                                   alignFrame.alignPanel,
-                                   AppletFormatAdapter.PASTE);
-
-    }
-    else if (treeImport)
-    {
-      try
-      {
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
-            "Paste");
-
-        fin.parse();
-        if (fin.getTree() != null)
-        {
-          alignFrame.loadTree(fin, "Pasted tree file");
-        }
-
-      }
-      catch (Exception ex)
-      {
-        textarea.setText("Could not parse Newick file!\n" + ex);
-        return;
-      }
-    }
-    else if (annotationImport)
-    {
-      if (new AnnotationFile().readAnnotationFile(
-          alignFrame.viewport.alignment, textarea.getText(),
-          jalview.io.AppletFormatAdapter.PASTE))
-      {
-        alignFrame.alignPanel.fontChanged();
-        alignFrame.alignPanel.setScrollValues(0, 0);
-
-      }
-      else
-      {
-        alignFrame.parseFeaturesFile(textarea.getText(),
-                                     jalview.io.AppletFormatAdapter.PASTE);
-      }
-    }
-    else if (alignFrame != null)
-    {
-      Alignment al = null;
-
-      String format = new IdentifyFile().Identify(text,
-                                                  AppletFormatAdapter.PASTE);
-      try
-      {
-        al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE,
-                                                format);
-      }
-      catch (java.io.IOException ex)
-      {
-        ex.printStackTrace();
-      }
-
-      if (al != null)
-      {
-        if (newWindow)
-        {
-          AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
-                                         "Cut & Paste input - " + format,
-                                         false);
-          af.statusBar.setText("Successfully pasted alignment file");
-        }
-        else
-        {
-          alignFrame.addSequences(al.getSequencesArray());
-        }
-      }
-    }
-
-    if (this.getParent() instanceof Frame)
-    {
-      ( (Frame)this.getParent()).setVisible(false);
-    }
-    else
-    {
-      ( (Dialog)this.getParent()).setVisible(false);
-    }
-  }
-
-  protected void cancel()
-  {
-    textarea.setText("");
-    if (this.getParent() instanceof Frame)
-    {
-      ( (Frame)this.getParent()).setVisible(false);
-    }
-    else
-    {
-      ( (Dialog)this.getParent()).setVisible(false);
-    }
-  }
-
-  protected TextArea textarea = new TextArea();
-  Button accept = new Button("New Window");
-  Button addSequences = new Button("Add to Current Alignment");
-  Button cancel = new Button("Close");
-
-  protected Panel buttonPanel = new Panel();
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  private void jbInit()
-      throws Exception
-  {
-    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
-    textarea.setText("Paste your alignment file here");
-    textarea.addMouseListener(this);
-    this.setLayout(borderLayout1);
-    accept.addActionListener(this);
-    addSequences.addActionListener(this);
-    cancel.addActionListener(this);
-    this.add(buttonPanel, BorderLayout.SOUTH);
-    buttonPanel.add(accept, null);
-    buttonPanel.add(addSequences);
-    buttonPanel.add(cancel, null);
-    this.add(textarea, java.awt.BorderLayout.CENTER);
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    if (textarea.getText().startsWith("Paste your"))
-    {
-      textarea.setText("");
-    }
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {}
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-
-  public void mouseExited(MouseEvent evt)
-  {}
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class CutAndPasteTransfer
+    extends Panel implements ActionListener, MouseListener
+{
+  boolean pdbImport = false;
+  boolean treeImport = false;
+  boolean annotationImport = false;
+  Sequence  seq;
+  AlignFrame alignFrame;
+
+  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    this.alignFrame = alignFrame;
+
+    if (!forImport)
+    {
+      buttonPanel.setVisible(false);
+    }
+  }
+
+  public String getText()
+  {
+    return textarea.getText();
+  }
+
+  public void setText(String text)
+  {
+    textarea.setText(text);
+  }
+
+  public void setPDBImport(Sequence seq)
+  {
+    this.seq = seq;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+    pdbImport = true;
+  }
+
+  public void setTreeImport()
+  {
+    treeImport = true;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+  }
+
+  public void setAnnotationImport()
+  {
+    annotationImport = true;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == accept)
+    {
+      ok(true);
+    }
+    else if (evt.getSource() == addSequences)
+    {
+      ok(false);
+    }
+    else if (evt.getSource() == cancel)
+    {
+      cancel();
+    }
+  }
+
+  protected void ok(boolean newWindow)
+  {
+    String text = getText();
+    int length = text.length();
+    textarea.append("\n");
+    if (textarea.getText().length() == length)
+    {
+      String warning =
+          "\n\n#################################################\n"
+          + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
+          + "\nCAN'T INPUT FULL ALIGNMENT"
+          + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
+          + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
+          + "\n#################################################\n";
+      textarea.setText(text.substring(0, text.length() - warning.length())
+                       + warning);
+
+      textarea.setCaretPosition(text.length());
+    }
+
+    if (pdbImport)
+    {
+      PDBEntry pdb = new PDBEntry();
+      pdb.setFile(text);
+
+      if ( alignFrame.alignPanel.av.applet.jmolAvailable )
+        new jalview.appletgui.AppletJmol(pdb,
+                                         new Sequence[]{seq},
+                                         null,
+                                         alignFrame.alignPanel,
+                                         AppletFormatAdapter.PASTE);
+      else
+
+        new MCview.AppletPDBViewer(pdb,
+                                   new Sequence[]{seq},
+                                   null,
+                                   alignFrame.alignPanel,
+                                   AppletFormatAdapter.PASTE);
+
+    }
+    else if (treeImport)
+    {
+      try
+      {
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
+            "Paste");
+
+        fin.parse();
+        if (fin.getTree() != null)
+        {
+          alignFrame.loadTree(fin, "Pasted tree file");
+        }
+
+      }
+      catch (Exception ex)
+      {
+        textarea.setText("Could not parse Newick file!\n" + ex);
+        return;
+      }
+    }
+    else if (annotationImport)
+    {
+      if (new AnnotationFile().readAnnotationFile(
+          alignFrame.viewport.alignment, textarea.getText(),
+          jalview.io.AppletFormatAdapter.PASTE))
+      {
+        alignFrame.alignPanel.fontChanged();
+        alignFrame.alignPanel.setScrollValues(0, 0);
+
+      }
+      else
+      {
+        alignFrame.parseFeaturesFile(textarea.getText(),
+                                     jalview.io.AppletFormatAdapter.PASTE);
+      }
+    }
+    else if (alignFrame != null)
+    {
+      Alignment al = null;
+
+      String format = new IdentifyFile().Identify(text,
+                                                  AppletFormatAdapter.PASTE);
+      try
+      {
+        al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE,
+                                                format);
+      }
+      catch (java.io.IOException ex)
+      {
+        ex.printStackTrace();
+      }
+
+      if (al != null)
+      {
+        if (newWindow)
+        {
+          AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
+                                         "Cut & Paste input - " + format,
+                                         false);
+          af.statusBar.setText("Successfully pasted alignment file");
+        }
+        else
+        {
+          alignFrame.addSequences(al.getSequencesArray());
+        }
+      }
+    }
+
+    if (this.getParent() instanceof Frame)
+    {
+      ( (Frame)this.getParent()).setVisible(false);
+    }
+    else
+    {
+      ( (Dialog)this.getParent()).setVisible(false);
+    }
+  }
+
+  protected void cancel()
+  {
+    textarea.setText("");
+    if (this.getParent() instanceof Frame)
+    {
+      ( (Frame)this.getParent()).setVisible(false);
+    }
+    else
+    {
+      ( (Dialog)this.getParent()).setVisible(false);
+    }
+  }
+
+  protected TextArea textarea = new TextArea();
+  Button accept = new Button("New Window");
+  Button addSequences = new Button("Add to Current Alignment");
+  Button cancel = new Button("Close");
+
+  protected Panel buttonPanel = new Panel();
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  private void jbInit()
+      throws Exception
+  {
+    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
+    textarea.setText("Paste your alignment file here");
+    textarea.addMouseListener(this);
+    this.setLayout(borderLayout1);
+    accept.addActionListener(this);
+    addSequences.addActionListener(this);
+    cancel.addActionListener(this);
+    this.add(buttonPanel, BorderLayout.SOUTH);
+    buttonPanel.add(accept, null);
+    buttonPanel.add(addSequences);
+    buttonPanel.add(cancel, null);
+    this.add(textarea, java.awt.BorderLayout.CENTER);
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    if (textarea.getText().startsWith("Paste your"))
+    {
+      textarea.setText("");
+    }
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {}
+
+  public void mouseClicked(MouseEvent evt)
+  {}
+
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
+}
diff --git a/src/jalview/appletgui/EditNameDialog.java b/src/jalview/appletgui/EditNameDialog.java
index 46325d9..252ced6 100644
--- a/src/jalview/appletgui/EditNameDialog.java
+++ b/src/jalview/appletgui/EditNameDialog.java
@@ -1,84 +1,83 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-
-public class EditNameDialog extends JVDialog
-{
-  TextField id, description;
-
-  public String getName()
-  {
-    return id.getText();
-  }
-
-  public String getDescription()
-  {
-    if (description.getText().length() < 1)
-    {
-      return null;
-    }
-    else
-    {
-      return description.getText();
-    }
-  }
-
-  public EditNameDialog(String name,
-                        String desc,
-                        String label1,
-                        String label2,
-                        Frame owner,
-                        String title,
-                        int width, int height, boolean display)
-  {
-    super(owner, title, true, width, height);
-
-    Font mono = new Font("Monospaced", Font.PLAIN, 12);
-    Panel panel = new Panel(new BorderLayout());
-    Panel panel2 = new Panel(new BorderLayout());
-
-    id = new TextField(name, 40);
-    id.setFont(mono);
-    Label label = new Label(label1);
-    label.setFont(mono);
-
-    panel2.add(label, BorderLayout.WEST);
-    panel2.add(id, BorderLayout.CENTER);
-    panel.add(panel2, BorderLayout.NORTH);
-
-
-    if(label2!=null)
-    {
-      panel2 = new Panel(new BorderLayout());
-      description = new TextField(desc, 40);
-      description.setFont(mono);
-      label = new Label(label2);
-      label.setFont(mono);
-      panel2.add(label, BorderLayout.WEST);
-      panel2.add(description, BorderLayout.CENTER);
-      panel.add(panel2, BorderLayout.CENTER);
-    }
-    setMainPanel(panel);
-    setVisible(display);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
+
+
+public class EditNameDialog extends JVDialog
+{
+  TextField id, description;
+
+  public String getName()
+  {
+    return id.getText();
+  }
+
+  public String getDescription()
+  {
+    if (description.getText().length() < 1)
+    {
+      return null;
+    }
+    else
+    {
+      return description.getText();
+    }
+  }
+
+  public EditNameDialog(String name,
+                        String desc,
+                        String label1,
+                        String label2,
+                        Frame owner,
+                        String title,
+                        int width, int height, boolean display)
+  {
+    super(owner, title, true, width, height);
+
+    Font mono = new Font("Monospaced", Font.PLAIN, 12);
+    Panel panel = new Panel(new BorderLayout());
+    Panel panel2 = new Panel(new BorderLayout());
+
+    id = new TextField(name, 40);
+    id.setFont(mono);
+    Label label = new Label(label1);
+    label.setFont(mono);
+
+    panel2.add(label, BorderLayout.WEST);
+    panel2.add(id, BorderLayout.CENTER);
+    panel.add(panel2, BorderLayout.NORTH);
+
+
+    if(label2!=null)
+    {
+      panel2 = new Panel(new BorderLayout());
+      description = new TextField(desc, 40);
+      description.setFont(mono);
+      label = new Label(label2);
+      label.setFont(mono);
+      panel2.add(label, BorderLayout.WEST);
+      panel2.add(description, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.CENTER);
+    }
+    setMainPanel(panel);
+    setVisible(display);
+  }
+}
diff --git a/src/jalview/appletgui/EmbmenuFrame.java b/src/jalview/appletgui/EmbmenuFrame.java
index 23f6aa2..a138aa7 100644
--- a/src/jalview/appletgui/EmbmenuFrame.java
+++ b/src/jalview/appletgui/EmbmenuFrame.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.BorderLayout;
@@ -258,4 +276,4 @@ public class EmbmenuFrame extends Frame implements MouseListener
     embeddedMenu=null;
     super.finalize();
   }
-}
\ No newline at end of file
+}
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 5e65409..7e9003d 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 6670d2f..fc7ee2b 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 9e974e9..1c38a41 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java
index 87fa50f..a622ffd 100755
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
@@ -1,268 +1,267 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-public class FontChooser
-    extends Panel implements ActionListener, ItemListener
-{
-  AlignmentPanel ap;
-  TreePanel tp;
-  Font oldFont;
-  boolean init = true;
-  Frame frame;
-
-  public FontChooser(TreePanel tp)
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-    this.tp = tp;
-    oldFont = tp.getTreeFont();
-    init();
-  }
-
-  public FontChooser(AlignmentPanel ap)
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-    this.ap = ap;
-    oldFont = ap.av.getFont();
-    init();
-  }
-
-  void init()
-  {
-    String fonts[] = Toolkit.getDefaultToolkit().getFontList();
-    for (int i = 0; i < fonts.length; i++)
-    {
-      fontName.addItem(fonts[i]);
-    }
-
-    for (int i = 1; i < 31; i++)
-    {
-      fontSize.addItem(i + "");
-    }
-
-    fontStyle.addItem("plain");
-    fontStyle.addItem("bold");
-    fontStyle.addItem("italic");
-
-    fontName.select(oldFont.getName());
-    fontSize.select(oldFont.getSize() + "");
-    fontStyle.select(oldFont.getStyle());
-
-    Frame frame = new Frame();
-    this.frame = frame;
-    frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 115);
-
-    init = false;
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == ok)
-    {
-      ok_actionPerformed();
-    }
-    else if (evt.getSource() == cancel)
-    {
-      cancel_actionPerformed();
-    }
-  }
-
-  public void itemStateChanged(ItemEvent evt)
-  {
-    if (evt.getSource() == fontName)
-    {
-      fontName_actionPerformed();
-    }
-    else if (evt.getSource() == fontSize)
-    {
-      fontSize_actionPerformed();
-    }
-    else if (evt.getSource() == fontStyle)
-    {
-      fontStyle_actionPerformed();
-    }
-  }
-
-  protected void ok_actionPerformed()
-  {
-    frame.setVisible(false);
-    if (ap != null)
-    {
-      if (ap.getOverviewPanel() != null)
-      {
-        ap.getOverviewPanel().updateOverviewImage();
-      }
-    }
-
-  }
-
-  protected void cancel_actionPerformed()
-  {
-    if (ap != null)
-    {
-      ap.av.setFont(oldFont);
-      ap.paintAlignment(true);
-    }
-    else if (tp != null)
-    {
-      tp.setTreeFont(oldFont);
-      tp.treeCanvas.repaint();
-    }
-
-    fontName.select(oldFont.getName());
-    fontSize.select(oldFont.getSize() + "");
-    fontStyle.select(oldFont.getStyle());
-
-    frame.setVisible(false);
-  }
-
-  void changeFont()
-  {
-    Font newFont = new Font(fontName.getSelectedItem().toString(),
-                            fontStyle.getSelectedIndex(),
-                            Integer.parseInt(fontSize.getSelectedItem().
-                                             toString())
-        );
-    if (ap != null)
-    {
-      ap.av.setFont(newFont);
-      ap.fontChanged();
-    }
-    else if (tp != null)
-    {
-      tp.setTreeFont(newFont);
-    }
-  }
-
-  protected void fontName_actionPerformed()
-  {
-    if (init)
-    {
-      return;
-    }
-    changeFont();
-  }
-
-  protected void fontSize_actionPerformed()
-  {
-    if (init)
-    {
-      return;
-    }
-    changeFont();
-  }
-
-  protected void fontStyle_actionPerformed()
-  {
-    if (init)
-    {
-      return;
-    }
-    changeFont();
-  }
-
-  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();
-
-  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(this);
-    fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
-    fontStyle.addItemListener(this);
-    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(this);
-    ok.setFont(new java.awt.Font("Verdana", 0, 11));
-    ok.setLabel("OK");
-    ok.addActionListener(this);
-    cancel.setFont(new java.awt.Font("Verdana", 0, 11));
-    cancel.setLabel("Cancel");
-    cancel.addActionListener(this);
-    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);
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+public class FontChooser
+    extends Panel implements ActionListener, ItemListener
+{
+  AlignmentPanel ap;
+  TreePanel tp;
+  Font oldFont;
+  boolean init = true;
+  Frame frame;
+
+  public FontChooser(TreePanel tp)
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    this.tp = tp;
+    oldFont = tp.getTreeFont();
+    init();
+  }
+
+  public FontChooser(AlignmentPanel ap)
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    this.ap = ap;
+    oldFont = ap.av.getFont();
+    init();
+  }
+
+  void init()
+  {
+    String fonts[] = Toolkit.getDefaultToolkit().getFontList();
+    for (int i = 0; i < fonts.length; i++)
+    {
+      fontName.addItem(fonts[i]);
+    }
+
+    for (int i = 1; i < 31; i++)
+    {
+      fontSize.addItem(i + "");
+    }
+
+    fontStyle.addItem("plain");
+    fontStyle.addItem("bold");
+    fontStyle.addItem("italic");
+
+    fontName.select(oldFont.getName());
+    fontSize.select(oldFont.getSize() + "");
+    fontStyle.select(oldFont.getStyle());
+
+    Frame frame = new Frame();
+    this.frame = frame;
+    frame.add(this);
+    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 115);
+
+    init = false;
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == ok)
+    {
+      ok_actionPerformed();
+    }
+    else if (evt.getSource() == cancel)
+    {
+      cancel_actionPerformed();
+    }
+  }
+
+  public void itemStateChanged(ItemEvent evt)
+  {
+    if (evt.getSource() == fontName)
+    {
+      fontName_actionPerformed();
+    }
+    else if (evt.getSource() == fontSize)
+    {
+      fontSize_actionPerformed();
+    }
+    else if (evt.getSource() == fontStyle)
+    {
+      fontStyle_actionPerformed();
+    }
+  }
+
+  protected void ok_actionPerformed()
+  {
+    frame.setVisible(false);
+    if (ap != null)
+    {
+      if (ap.getOverviewPanel() != null)
+      {
+        ap.getOverviewPanel().updateOverviewImage();
+      }
+    }
+
+  }
+
+  protected void cancel_actionPerformed()
+  {
+    if (ap != null)
+    {
+      ap.av.setFont(oldFont);
+      ap.paintAlignment(true);
+    }
+    else if (tp != null)
+    {
+      tp.setTreeFont(oldFont);
+      tp.treeCanvas.repaint();
+    }
+
+    fontName.select(oldFont.getName());
+    fontSize.select(oldFont.getSize() + "");
+    fontStyle.select(oldFont.getStyle());
+
+    frame.setVisible(false);
+  }
+
+  void changeFont()
+  {
+    Font newFont = new Font(fontName.getSelectedItem().toString(),
+                            fontStyle.getSelectedIndex(),
+                            Integer.parseInt(fontSize.getSelectedItem().
+                                             toString())
+        );
+    if (ap != null)
+    {
+      ap.av.setFont(newFont);
+      ap.fontChanged();
+    }
+    else if (tp != null)
+    {
+      tp.setTreeFont(newFont);
+    }
+  }
+
+  protected void fontName_actionPerformed()
+  {
+    if (init)
+    {
+      return;
+    }
+    changeFont();
+  }
+
+  protected void fontSize_actionPerformed()
+  {
+    if (init)
+    {
+      return;
+    }
+    changeFont();
+  }
+
+  protected void fontStyle_actionPerformed()
+  {
+    if (init)
+    {
+      return;
+    }
+    changeFont();
+  }
+
+  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();
+
+  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(this);
+    fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));
+    fontStyle.addItemListener(this);
+    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(this);
+    ok.setFont(new java.awt.Font("Verdana", 0, 11));
+    ok.setLabel("OK");
+    ok.addActionListener(this);
+    cancel.setFont(new java.awt.Font("Verdana", 0, 11));
+    cancel.setLabel("Cancel");
+    cancel.addActionListener(this);
+    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);
+  }
+
+}
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index bec3c63..3093087 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 44a03ec..5bfde8d 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/IdwidthAdjuster.java b/src/jalview/appletgui/IdwidthAdjuster.java
index 052a95e..685ea60 100755
--- a/src/jalview/appletgui/IdwidthAdjuster.java
+++ b/src/jalview/appletgui/IdwidthAdjuster.java
@@ -1,104 +1,103 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-public class IdwidthAdjuster
-    extends Panel implements MouseListener, MouseMotionListener
-{
-  boolean active = false;
-  int oldX = 0;
-  Image image;
-  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);
-    }
-
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    oldX = evt.getX();
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {
-    active = true;
-    repaint();
-  }
-
-  public void mouseExited(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    active = true;
-    Dimension d = ap.idPanel.idCanvas.getSize();
-    int dif = evt.getX() - oldX;
-
-    if (d.width + dif > 20 || dif > 0)
-    {
-      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 paint(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getSize().width, getSize().height);
-    if (active)
-    {
-      if (image != null)
-      {
-        g.drawImage(image, getSize().width - 20, 2, this);
-      }
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+public class IdwidthAdjuster
+    extends Panel implements MouseListener, MouseMotionListener
+{
+  boolean active = false;
+  int oldX = 0;
+  Image image;
+  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);
+    }
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    oldX = evt.getX();
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    active = false;
+    repaint();
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+    active = true;
+    repaint();
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+    active = false;
+    repaint();
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    active = true;
+    Dimension d = ap.idPanel.idCanvas.getSize();
+    int dif = evt.getX() - oldX;
+
+    if (d.width + dif > 20 || dif > 0)
+    {
+      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 paint(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getSize().width, getSize().height);
+    if (active)
+    {
+      if (image != null)
+      {
+        g.drawImage(image, getSize().width - 20, 2, this);
+      }
+    }
+  }
+
+}
diff --git a/src/jalview/appletgui/JVDialog.java b/src/jalview/appletgui/JVDialog.java
index b8e0abc..520dc2e 100644
--- a/src/jalview/appletgui/JVDialog.java
+++ b/src/jalview/appletgui/JVDialog.java
@@ -1,79 +1,78 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-public class JVDialog extends Dialog implements ActionListener
-{
-  AlignmentPanel ap;
-  Panel buttonPanel;
-  Button ok = new Button("Accept");
-  Button cancel = new Button("Cancel");
-  boolean accept = false;
-  Frame owner;
-
-  public JVDialog(Frame owner,
-                  String title,
-                  boolean modal,
-                  int width, int height)
-  {
-      super(owner, title, modal);
-      this.owner = owner;
-
-      height += owner.getInsets().top + getInsets().bottom;
-
-      setBounds(owner.getBounds().x
-                + (owner.getSize().width - width) / 2,
-                owner.getBounds().y
-                + (owner.getSize().height - height) / 2,
-                width, height);
-  }
-
-  void setMainPanel(Panel panel)
-  {
-    add(panel, BorderLayout.NORTH);
-
-    buttonPanel = new Panel(new FlowLayout());
-
-    buttonPanel.add(ok);
-    buttonPanel.add(cancel);
-    ok.addActionListener(this);
-    cancel.addActionListener(this);
-
-    add(buttonPanel, BorderLayout.SOUTH);
-
-    pack();
-
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == ok)
-    {
-      accept = true;
-    }
-
-    setVisible(false);
-  }
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+public class JVDialog extends Dialog implements ActionListener
+{
+  AlignmentPanel ap;
+  Panel buttonPanel;
+  Button ok = new Button("Accept");
+  Button cancel = new Button("Cancel");
+  boolean accept = false;
+  Frame owner;
+
+  public JVDialog(Frame owner,
+                  String title,
+                  boolean modal,
+                  int width, int height)
+  {
+      super(owner, title, modal);
+      this.owner = owner;
+
+      height += owner.getInsets().top + getInsets().bottom;
+
+      setBounds(owner.getBounds().x
+                + (owner.getSize().width - width) / 2,
+                owner.getBounds().y
+                + (owner.getSize().height - height) / 2,
+                width, height);
+  }
+
+  void setMainPanel(Panel panel)
+  {
+    add(panel, BorderLayout.NORTH);
+
+    buttonPanel = new Panel(new FlowLayout());
+
+    buttonPanel.add(ok);
+    buttonPanel.add(cancel);
+    ok.addActionListener(this);
+    cancel.addActionListener(this);
+
+    add(buttonPanel, BorderLayout.SOUTH);
+
+    pack();
+
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == ok)
+    {
+      accept = true;
+    }
+
+    setVisible(false);
+  }
+
+
+}
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 7265489..3f20d16 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,449 +1,448 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-public class OverviewPanel
-    extends Panel implements Runnable, MouseMotionListener, MouseListener
-{
-  Image miniMe;
-  Image offscreen;
-  AlignViewport av;
-  AlignmentPanel ap;
-  float scalew = 1f;
-  float scaleh = 1f;
-
-  public int width, sequencesHeight;
-  int graphHeight = 20;
-  int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
-
-  boolean resizing = false;
-
-  // Can set different properties in this seqCanvas than
-  // main visible SeqCanvas
-  SequenceRenderer sr;
-  FeatureRenderer fr;
-
-  Frame nullFrame;
-
-  public OverviewPanel(AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-    setLayout(null);
-    nullFrame = new Frame();
-    nullFrame.addNotify();
-
-    sr = new SequenceRenderer(av);
-    sr.graphics = nullFrame.getGraphics();
-    sr.renderGaps = false;
-    sr.forOverview = true;
-    fr = new FeatureRenderer(av);
-    fr.overview = true;
-
-    // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.alignment.getWidth() /
-        (float) av.alignment.getHeight();
-
-    if (av.hconsensus == null)
-    {
-      graphHeight = 0;
-    }
-
-    if (av.alignment.getWidth() > av.alignment.getHeight())
-    {
-      // wider
-      width = 400;
-      sequencesHeight = (int) (400f / initialScale);
-      if (sequencesHeight < 40)
-      {
-        sequencesHeight = 40;
-      }
-    }
-    else
-    {
-      // taller
-      width = (int) (400f * initialScale);
-      sequencesHeight = 300;
-      if (width < 120)
-      {
-        width = 120;
-      }
-    }
-
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-    addComponentListener(new ComponentAdapter()
-    {
-
-      public void componentResized(ComponentEvent evt)
-      {
-        if (getSize().width != width ||
-            getSize().height != sequencesHeight + graphHeight)
-        {
-          updateOverviewImage();
-        }
-      }
-    });
-
-    addMouseMotionListener(this);
-
-    addMouseListener(this);
-
-    updateOverviewImage();
-
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-
-  public void mouseExited(MouseEvent evt)
-  {}
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void mouseMoved(MouseEvent evt)
-  {}
-
-  public void mousePressed(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-  }
-
-  void checkValid()
-  {
-    if (boxY < 0)
-    {
-      boxY = 0;
-    }
-
-    if (boxY > (sequencesHeight - boxHeight))
-    {
-      boxY = sequencesHeight - boxHeight + 1;
-    }
-
-    if (boxX < 0)
-    {
-      boxX = 0;
-    }
-
-    if (boxX > (width - boxWidth))
-    {
-      if (av.hasHiddenColumns)
-      {
-        //Try smallest possible box
-        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
-                          av.getCharWidth() * scalew);
-      }
-      boxX = width - boxWidth;
-    }
-
-    int col = (int) (boxX / scalew / av.getCharWidth());
-    int row = (int) (boxY / scaleh / av.getCharHeight());
-
-    if (av.hasHiddenColumns)
-    {
-      if (!av.getColumnSelection().isVisible(col))
-      {
-        return;
-      }
-
-      col = av.getColumnSelection().findColumnPosition(col);
-    }
-
-    if (av.hasHiddenRows)
-    {
-      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
-    }
-
-    ap.setScrollValues(col, row);
-    ap.paintAlignment(false);
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateOverviewImage()
-  {
-    if (resizing)
-    {
-      resizeAgain = true;
-      return;
-    }
-
-    if (av.showSequenceFeatures)
-    {
-      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().
-          featureGroups;
-      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().
-          featureColours;
-    }
-
-    resizing = true;
-
-    if ( (getSize().width > 0) && (getSize().height > 0))
-    {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
-    }
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    Thread thread = new Thread(this);
-    thread.start();
-    repaint();
-  }
-
-  // This is set true if the user resizes whilst
-  // the overview is being calculated
-  boolean resizeAgain = false;
-
-  public void run()
-  {
-    miniMe = null;
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight();
-
-    if (av.showSequenceFeatures)
-    {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    if (getSize().width > 0 && getSize().height > 0)
-    {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
-    }
-
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
-    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
-
-    Graphics mg = miniMe.getGraphics();
-    float sampleCol = (float) alwidth / (float) width;
-    float sampleRow = (float) alheight / (float) sequencesHeight;
-
-    int lastcol = 0, lastrow = 0;
-    int xstart = 0, ystart = 0;
-    Color color = Color.yellow;
-    int row, col, sameRow = 0, sameCol = 0;
-    jalview.datamodel.SequenceI seq;
-    boolean hiddenRow = false;
-    for (row = 0; row <= sequencesHeight; row++)
-    {
-      if ( (int) (row * sampleRow) == lastrow)
-      {
-        sameRow++;
-        continue;
-      }
-
-      hiddenRow = false;
-      if (av.hasHiddenRows)
-      {
-        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
-        if (seq == null)
-        {
-          int index =
-              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
-              lastrow);
-
-          seq = av.alignment.getSequenceAt(index);
-        }
-        else
-        {
-          hiddenRow = true;
-        }
-      }
-      else
-      {
-        seq = av.alignment.getSequenceAt(lastrow);
-      }
-
-      for (col = 0; col < width; col++)
-      {
-        if ( (int) (col * sampleCol) == lastcol &&
-            (int) (row * sampleRow) == lastrow)
-        {
-          sameCol++;
-          continue;
-        }
-
-        lastcol = (int) (col * sampleCol);
-
-        if (seq.getLength() > lastcol)
-        {
-          color = sr.getResidueBoxColour(
-              seq, lastcol);
-
-          if (av.showSequenceFeatures)
-          {
-            color = fr.findFeatureColour(color, seq, lastcol);
-          }
-        }
-        else
-        {
-          color = Color.white; //White
-        }
-
-        if (hiddenRow ||
-            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
-        {
-          color = color.darker().darker();
-        }
-
-        mg.setColor(color);
-        if (sameCol == 1 && sameRow == 1)
-        {
-          mg.drawLine(xstart, ystart, xstart, ystart);
-        }
-        else
-        {
-          mg.fillRect(xstart, ystart, sameCol, sameRow);
-        }
-
-        xstart = col;
-        sameCol = 1;
-      }
-      lastrow = (int) (row * sampleRow);
-      ystart = row;
-      sameRow = 1;
-    }
-
-    if (av.conservation != null)
-    {
-      for (col = 0; col < width; col++)
-      {
-        lastcol = (int) (col * sampleCol);
-        {
-          mg.translate(col, sequencesHeight);
-          ap.annotationPanel.drawGraph(mg, av.conservation,
-                                       (int) (sampleCol) + 1,
-                                       graphHeight,
-                                       (int) (col * sampleCol),
-                                       (int) (col * sampleCol) + 1);
-          mg.translate( -col, -sequencesHeight);
-        }
-      }
-    }
-    System.gc();
-
-    resizing = false;
-
-    setBoxPosition();
-
-    if (resizeAgain)
-    {
-      resizeAgain = false;
-      updateOverviewImage();
-    }
-  }
-
-  public void setBoxPosition()
-  {
-    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.alignment.getHeight()
-                          + av.alignment.getHiddenSequences().getSize()) *
-        av.getCharHeight();
-
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
-
-    if (av.hasHiddenColumns)
-    {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
-
-    int startSeq = av.startSeq;
-    int endSeq = av.endSeq;
-
-    if (av.hasHiddenRows)
-    {
-      startSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
-
-      endSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
-
-    }
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    boxX = (int) (startRes * av.getCharWidth() * scalew);
-    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
-
-    if (av.hasHiddenColumns)
-    {
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-    else
-    {
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-
-    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
-
-    repaint();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    Graphics og = offscreen.getGraphics();
-    if (miniMe != null)
-    {
-      og.drawImage(miniMe, 0, 0, this);
-      og.setColor(Color.red);
-      og.drawRect(boxX, boxY, boxWidth, boxHeight);
-      og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-      g.drawImage(offscreen, 0, 0, this);
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+public class OverviewPanel
+    extends Panel implements Runnable, MouseMotionListener, MouseListener
+{
+  Image miniMe;
+  Image offscreen;
+  AlignViewport av;
+  AlignmentPanel ap;
+  float scalew = 1f;
+  float scaleh = 1f;
+
+  public int width, sequencesHeight;
+  int graphHeight = 20;
+  int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
+
+  boolean resizing = false;
+
+  // Can set different properties in this seqCanvas than
+  // main visible SeqCanvas
+  SequenceRenderer sr;
+  FeatureRenderer fr;
+
+  Frame nullFrame;
+
+  public OverviewPanel(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+    setLayout(null);
+    nullFrame = new Frame();
+    nullFrame.addNotify();
+
+    sr = new SequenceRenderer(av);
+    sr.graphics = nullFrame.getGraphics();
+    sr.renderGaps = false;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(av);
+    fr.overview = true;
+
+    // scale the initial size of overviewpanel to shape of alignment
+    float initialScale = (float) av.alignment.getWidth() /
+        (float) av.alignment.getHeight();
+
+    if (av.hconsensus == null)
+    {
+      graphHeight = 0;
+    }
+
+    if (av.alignment.getWidth() > av.alignment.getHeight())
+    {
+      // wider
+      width = 400;
+      sequencesHeight = (int) (400f / initialScale);
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
+    }
+    else
+    {
+      // taller
+      width = (int) (400f * initialScale);
+      sequencesHeight = 300;
+      if (width < 120)
+      {
+        width = 120;
+      }
+    }
+
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
+    addComponentListener(new ComponentAdapter()
+    {
+
+      public void componentResized(ComponentEvent evt)
+      {
+        if (getSize().width != width ||
+            getSize().height != sequencesHeight + graphHeight)
+        {
+          updateOverviewImage();
+        }
+      }
+    });
+
+    addMouseMotionListener(this);
+
+    addMouseListener(this);
+
+    updateOverviewImage();
+
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
+
+  public void mouseClicked(MouseEvent evt)
+  {}
+
+  public void mouseMoved(MouseEvent evt)
+  {}
+
+  public void mousePressed(MouseEvent evt)
+  {
+    boxX = evt.getX();
+    boxY = evt.getY();
+    checkValid();
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    boxX = evt.getX();
+    boxY = evt.getY();
+    checkValid();
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    boxX = evt.getX();
+    boxY = evt.getY();
+    checkValid();
+  }
+
+  void checkValid()
+  {
+    if (boxY < 0)
+    {
+      boxY = 0;
+    }
+
+    if (boxY > (sequencesHeight - boxHeight))
+    {
+      boxY = sequencesHeight - boxHeight + 1;
+    }
+
+    if (boxX < 0)
+    {
+      boxX = 0;
+    }
+
+    if (boxX > (width - boxWidth))
+    {
+      if (av.hasHiddenColumns)
+      {
+        //Try smallest possible box
+        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
+                          av.getCharWidth() * scalew);
+      }
+      boxX = width - boxWidth;
+    }
+
+    int col = (int) (boxX / scalew / av.getCharWidth());
+    int row = (int) (boxY / scaleh / av.getCharHeight());
+
+    if (av.hasHiddenColumns)
+    {
+      if (!av.getColumnSelection().isVisible(col))
+      {
+        return;
+      }
+
+      col = av.getColumnSelection().findColumnPosition(col);
+    }
+
+    if (av.hasHiddenRows)
+    {
+      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
+    }
+
+    ap.setScrollValues(col, row);
+    ap.paintAlignment(false);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateOverviewImage()
+  {
+    if (resizing)
+    {
+      resizeAgain = true;
+      return;
+    }
+
+    if (av.showSequenceFeatures)
+    {
+      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureGroups;
+      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().
+          featureColours;
+    }
+
+    resizing = true;
+
+    if ( (getSize().width > 0) && (getSize().height > 0))
+    {
+      width = getSize().width;
+      sequencesHeight = getSize().height - graphHeight;
+    }
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
+
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
+  }
+
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  boolean resizeAgain = false;
+
+  public void run()
+  {
+    miniMe = null;
+    int alwidth = av.alignment.getWidth();
+    int alheight = av.alignment.getHeight();
+
+    if (av.showSequenceFeatures)
+    {
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+    }
+
+    if (getSize().width > 0 && getSize().height > 0)
+    {
+      width = getSize().width;
+      sequencesHeight = getSize().height - graphHeight;
+    }
+
+    setSize(new Dimension(width, sequencesHeight + graphHeight));
+
+    int fullsizeWidth = alwidth * av.getCharWidth();
+    int fullsizeHeight = alheight * av.getCharHeight();
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
+    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
+
+    Graphics mg = miniMe.getGraphics();
+    float sampleCol = (float) alwidth / (float) width;
+    float sampleRow = (float) alheight / (float) sequencesHeight;
+
+    int lastcol = 0, lastrow = 0;
+    int xstart = 0, ystart = 0;
+    Color color = Color.yellow;
+    int row, col, sameRow = 0, sameCol = 0;
+    jalview.datamodel.SequenceI seq;
+    boolean hiddenRow = false;
+    for (row = 0; row <= sequencesHeight; row++)
+    {
+      if ( (int) (row * sampleRow) == lastrow)
+      {
+        sameRow++;
+        continue;
+      }
+
+      hiddenRow = false;
+      if (av.hasHiddenRows)
+      {
+        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        if (seq == null)
+        {
+          int index =
+              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+              lastrow);
+
+          seq = av.alignment.getSequenceAt(index);
+        }
+        else
+        {
+          hiddenRow = true;
+        }
+      }
+      else
+      {
+        seq = av.alignment.getSequenceAt(lastrow);
+      }
+
+      for (col = 0; col < width; col++)
+      {
+        if ( (int) (col * sampleCol) == lastcol &&
+            (int) (row * sampleRow) == lastrow)
+        {
+          sameCol++;
+          continue;
+        }
+
+        lastcol = (int) (col * sampleCol);
+
+        if (seq.getLength() > lastcol)
+        {
+          color = sr.getResidueBoxColour(
+              seq, lastcol);
+
+          if (av.showSequenceFeatures)
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
+        }
+        else
+        {
+          color = Color.white; //White
+        }
+
+        if (hiddenRow ||
+            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+        {
+          color = color.darker().darker();
+        }
+
+        mg.setColor(color);
+        if (sameCol == 1 && sameRow == 1)
+        {
+          mg.drawLine(xstart, ystart, xstart, ystart);
+        }
+        else
+        {
+          mg.fillRect(xstart, ystart, sameCol, sameRow);
+        }
+
+        xstart = col;
+        sameCol = 1;
+      }
+      lastrow = (int) (row * sampleRow);
+      ystart = row;
+      sameRow = 1;
+    }
+
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
+        {
+          mg.translate(col, sequencesHeight);
+          ap.annotationPanel.drawGraph(mg, av.conservation,
+                                       (int) (sampleCol) + 1,
+                                       graphHeight,
+                                       (int) (col * sampleCol),
+                                       (int) (col * sampleCol) + 1);
+          mg.translate( -col, -sequencesHeight);
+        }
+      }
+    }
+    System.gc();
+
+    resizing = false;
+
+    setBoxPosition();
+
+    if (resizeAgain)
+    {
+      resizeAgain = false;
+      updateOverviewImage();
+    }
+  }
+
+  public void setBoxPosition()
+  {
+    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
+    int fullsizeHeight = (av.alignment.getHeight()
+                          + av.alignment.getHiddenSequences().getSize()) *
+        av.getCharHeight();
+
+    int startRes = av.getStartRes();
+    int endRes = av.getEndRes();
+
+    if (av.hasHiddenColumns)
+    {
+      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
+      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+    }
+
+    int startSeq = av.startSeq;
+    int endSeq = av.endSeq;
+
+    if (av.hasHiddenRows)
+    {
+      startSeq =
+          av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
+
+      endSeq =
+          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
+
+    }
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    boxX = (int) (startRes * av.getCharWidth() * scalew);
+    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+
+    if (av.hasHiddenColumns)
+    {
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
+    else
+    {
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
+
+    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
+
+    repaint();
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    Graphics og = offscreen.getGraphics();
+    if (miniMe != null)
+    {
+      og.drawImage(miniMe, 0, 0, this);
+      og.setColor(Color.red);
+      og.drawRect(boxX, boxY, boxWidth, boxHeight);
+      og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+      g.drawImage(offscreen, 0, 0, this);
+    }
+  }
+
+}
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index ee54478..fac7ad2 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 7e0edf7..422257b 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,228 +1,228 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class PaintRefresher
-{
-  static Hashtable components;
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param comp DOCUMENT ME!
-   * @param al DOCUMENT ME!
-   */
-  public static void Register(Component comp, String seqSetId)
-  {
-    if (components == null)
-    {
-      components = new Hashtable();
-    }
-
-    if (components.containsKey(seqSetId))
-    {
-      Vector comps = (Vector) components.get(seqSetId);
-      if (!comps.contains(comp))
-      {
-        comps.addElement(comp);
-      }
-    }
-    else
-    {
-      Vector vcoms = new Vector();
-      vcoms.addElement(comp);
-      components.put(seqSetId, vcoms);
-    }
-  }
-
-  public static void RemoveComponent(Component comp)
-  {
-    if (components == null)
-    {
-      return;
-    }
-
-    Enumeration en = components.keys();
-    while (en.hasMoreElements())
-    {
-      String id = en.nextElement().toString();
-      Vector comps = (Vector) components.get(id);
-      comps.removeElement(comp);
-      if (comps.size() == 0)
-      {
-        components.remove(id);
-      }
-    }
-  }
-
-  public static void Refresh(Component source, String id)
-  {
-    Refresh(source, id, false, false);
-  }
-
-  public static void Refresh(Component source,
-                             String id,
-                             boolean alignmentChanged,
-                             boolean validateSequences)
-  {
-    if (components == null)
-    {
-      return;
-    }
-
-    Component comp;
-    Vector comps = (Vector) components.get(id);
-
-    if (comps == null)
-    {
-      return;
-    }
-
-    Enumeration e = comps.elements();
-    while (e.hasMoreElements())
-    {
-      comp = (Component) e.nextElement();
-
-      if (comp == source)
-      {
-        continue;
-      }
-
-      if (!comp.isValid())
-      {
-        comps.removeElement(comp);
-      }
-      else if (validateSequences
-               && comp instanceof AlignmentPanel
-               && source instanceof AlignmentPanel)
-      {
-        validateSequences( ( (AlignmentPanel) source).av.alignment,
-                          ( (AlignmentPanel) comp).av.alignment);
-      }
-
-      if (comp instanceof AlignmentPanel && alignmentChanged)
-      {
-        ( (AlignmentPanel) comp).alignmentChanged();
-      }
-
-      comp.repaint();
-    }
-  }
-
-  static void validateSequences(AlignmentI source, AlignmentI comp)
-  {
-    SequenceI[] a1;
-    if (source.getHiddenSequences().getSize() > 0)
-    {
-      a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();
-    }
-    else
-    {
-      a1 = source.getSequencesArray();
-    }
-
-    SequenceI[] a2;
-    if (comp.getHiddenSequences().getSize() > 0)
-    {
-      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-    }
-    else
-    {
-      a2 = comp.getSequencesArray();
-    }
-
-    int i, iSize = a1.length, j, jSize = a2.length;
-
-    if (iSize == jSize)
-    {
-      return;
-    }
-
-    boolean exists = false;
-    for (i = 0; i < iSize; i++)
-    {
-      exists = false;
-
-      for (j = 0; j < jSize; j++)
-      {
-        if (a2[j] == a1[i])
-        {
-          exists = true;
-          break;
-        }
-      }
-
-      if (!exists)
-      {
-        if (i < comp.getHeight())
-        {
-          comp.getSequences().insertElementAt(a1[i], i);
-        }
-        else
-        {
-          comp.addSequence(a1[i]);
-        }
-
-        if (comp.getHiddenSequences().getSize() > 0)
-        {
-          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-        }
-        else
-        {
-          a2 = comp.getSequencesArray();
-        }
-
-        jSize = a2.length;
-      }
-    }
-
-    iSize = a1.length;
-    jSize = a2.length;
-
-    for (j = 0; j < jSize; j++)
-    {
-      exists = false;
-      for (i = 0; i < iSize; i++)
-      {
-        if (a2[j] == a1[i])
-        {
-          exists = true;
-          break;
-        }
-      }
-
-      if (!exists)
-      {
-        comp.deleteSequence(a2[j]);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PaintRefresher
+{
+  static Hashtable components;
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param comp DOCUMENT ME!
+   * @param al DOCUMENT ME!
+   */
+  public static void Register(Component comp, String seqSetId)
+  {
+    if (components == null)
+    {
+      components = new Hashtable();
+    }
+
+    if (components.containsKey(seqSetId))
+    {
+      Vector comps = (Vector) components.get(seqSetId);
+      if (!comps.contains(comp))
+      {
+        comps.addElement(comp);
+      }
+    }
+    else
+    {
+      Vector vcoms = new Vector();
+      vcoms.addElement(comp);
+      components.put(seqSetId, vcoms);
+    }
+  }
+
+  public static void RemoveComponent(Component comp)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Enumeration en = components.keys();
+    while (en.hasMoreElements())
+    {
+      String id = en.nextElement().toString();
+      Vector comps = (Vector) components.get(id);
+      comps.removeElement(comp);
+      if (comps.size() == 0)
+      {
+        components.remove(id);
+      }
+    }
+  }
+
+  public static void Refresh(Component source, String id)
+  {
+    Refresh(source, id, false, false);
+  }
+
+  public static void Refresh(Component source,
+                             String id,
+                             boolean alignmentChanged,
+                             boolean validateSequences)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Component comp;
+    Vector comps = (Vector) components.get(id);
+
+    if (comps == null)
+    {
+      return;
+    }
+
+    Enumeration e = comps.elements();
+    while (e.hasMoreElements())
+    {
+      comp = (Component) e.nextElement();
+
+      if (comp == source)
+      {
+        continue;
+      }
+
+      if (!comp.isValid())
+      {
+        comps.removeElement(comp);
+      }
+      else if (validateSequences
+               && comp instanceof AlignmentPanel
+               && source instanceof AlignmentPanel)
+      {
+        validateSequences( ( (AlignmentPanel) source).av.alignment,
+                          ( (AlignmentPanel) comp).av.alignment);
+      }
+
+      if (comp instanceof AlignmentPanel && alignmentChanged)
+      {
+        ( (AlignmentPanel) comp).alignmentChanged();
+      }
+
+      comp.repaint();
+    }
+  }
+
+  static void validateSequences(AlignmentI source, AlignmentI comp)
+  {
+    SequenceI[] a1;
+    if (source.getHiddenSequences().getSize() > 0)
+    {
+      a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a1 = source.getSequencesArray();
+    }
+
+    SequenceI[] a2;
+    if (comp.getHiddenSequences().getSize() > 0)
+    {
+      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a2 = comp.getSequencesArray();
+    }
+
+    int i, iSize = a1.length, j, jSize = a2.length;
+
+    if (iSize == jSize)
+    {
+      return;
+    }
+
+    boolean exists = false;
+    for (i = 0; i < iSize; i++)
+    {
+      exists = false;
+
+      for (j = 0; j < jSize; j++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        if (i < comp.getHeight())
+        {
+          comp.getSequences().insertElementAt(a1[i], i);
+        }
+        else
+        {
+          comp.addSequence(a1[i]);
+        }
+
+        if (comp.getHiddenSequences().getSize() > 0)
+        {
+          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+        }
+        else
+        {
+          a2 = comp.getSequencesArray();
+        }
+
+        jSize = a2.length;
+      }
+    }
+
+    iSize = a1.length;
+    jSize = a2.length;
+
+    for (j = 0; j < jSize; j++)
+    {
+      exists = false;
+      for (i = 0; i < iSize; i++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        comp.deleteSequence(a2[j]);
+      }
+    }
+  }
+}
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 05372a4..31f1340 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index 9881b64..8415153 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index a2463e8..dc53d15 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -1,622 +1,621 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.math.*;
-import jalview.util.*;
-
-public class RotatableCanvas
-    extends Panel implements MouseListener,
-    MouseMotionListener,
-    KeyListener
-{
-  RotatableMatrix idmat = new RotatableMatrix(3, 3);
-  RotatableMatrix objmat = new RotatableMatrix(3, 3);
-  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
-  String tooltip;
-  int toolx, tooly;
-
-  //RubberbandRectangle rubberband;
-
-  boolean drawAxes = true;
-
-  int omx = 0;
-  int mx = 0;
-  int omy = 0;
-  int my = 0;
-
-  Image img;
-  Graphics ig;
-
-  Dimension prefsize;
-
-  float centre[] = new float[3];
-  float width[] = new float[3];
-
-  float max[] = new float[3];
-  float min[] = new float[3];
-
-  float maxwidth;
-  float scale;
-
-  int npoint;
-
-  Vector points;
-  float[][] orig;
-  float[][] axes;
-
-  int startx;
-  int starty;
-
-  int lastx;
-  int lasty;
-
-  int rectx1;
-  int recty1;
-  int rectx2;
-  int recty2;
-
-  float scalefactor = 1;
-
-  AlignViewport av;
-  boolean showLabels = false;
-
-  public RotatableCanvas(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  public void showLabels(boolean b)
-  {
-    showLabels = b;
-    repaint();
-  }
-
-  public void setPoints(Vector points, int npoint)
-  {
-    this.points = points;
-    this.npoint = npoint;
-    PaintRefresher.Register(this, av.getSequenceSetId());
-
-    prefsize = getPreferredSize();
-    orig = new float[npoint][3];
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      for (int j = 0; j < 3; j++)
-      {
-        orig[i][j] = sp.coord[j];
-      }
-    }
-    //Initialize the matrices to identity
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        if (i != j)
-        {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
-        }
-        else
-        {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
-        }
-      }
-    }
-
-    axes = new float[3][3];
-    initAxes();
-
-    findCentre();
-    findWidth();
-
-    scale = findScale();
-
-    //    System.out.println("Scale factor = " + scale);
-
-    addMouseListener(this);
-    addKeyListener(this);
-    // if (getParent() != null) {
-    //   getParent().addKeyListener(this);
-    //}
-    addMouseMotionListener(this);
-
-    // Add rubberband
-    //   rubberband  = new RubberbandRectangle(this);
-    //  rubberband.setActive(true);
-    //   rubberband.addListener(this);
-  }
-
-  /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
-     redrawneeded = true;
-     repaint();
-     return true;
-   }
-
-   public void removeNotify() {
-     controller.removeListener(this);
-     super.removeNotify();
-   }*/
-
-  public void initAxes()
-  {
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        if (i != j)
-        {
-          axes[i][j] = 0;
-        }
-        else
-        {
-          axes[i][j] = 1;
-        }
-      }
-    }
-  }
-
-  public void findWidth()
-  {
-    max = new float[3];
-    min = new float[3];
-
-    max[0] = (float) - 1e30;
-    max[1] = (float) - 1e30;
-    max[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])
-        {
-          max[i] = sp.coord[i];
-        }
-        if (sp.coord[i] <= min[i])
-        {
-          min[i] = sp.coord[i];
-        }
-      }
-    }
-
-    //    System.out.println("xmax " + max[0] + " min " + min[0]);
-    //System.out.println("ymax " + max[1] + " min " + min[1]);
-    //System.out.println("zmax " + max[2] + " min " + min[2]);
-
-    width[0] = Math.abs(max[0] - min[0]);
-    width[1] = Math.abs(max[1] - min[1]);
-    width[2] = Math.abs(max[2] - min[2]);
-
-    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 (getSize().width != 0)
-    {
-      width = getSize().width;
-      height = getSize().height;
-    }
-    else
-    {
-      width = prefsize.width;
-      height = prefsize.height;
-    }
-
-    if (width < height)
-    {
-      dim = width;
-    }
-    else
-    {
-      dim = height;
-    }
-
-    return (float) (dim * scalefactor / (2 * maxwidth));
-  }
-
-  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;
-
-    //    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)
-    {
-      return prefsize;
-    }
-    else
-    {
-      return new Dimension(400, 400);
-    }
-  }
-
-  public Dimension getMinimumSize()
-  {
-    return getPreferredSize();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    if (points == null)
-    {
-      g.setFont(new Font("Verdana", Font.PLAIN, 18));
-      g.drawString("Calculating PCA....", 20, getSize().height / 2);
-    }
-    else
-    {
-
-      //Only create the image at the beginning -
-      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);
-        ig = img.getGraphics();
-
-      }
-
-      drawBackground(ig, Color.black);
-      drawScene(ig);
-      if (drawAxes == true)
-      {
-        drawAxes(ig);
-      }
-
-      if (tooltip != null)
-      {
-        ig.setColor(Color.red);
-        ig.drawString(tooltip, toolx, tooly);
-      }
-
-      g.drawImage(img, 0, 0, this);
-    }
-  }
-
-  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));
-    }
-  }
-
-  public void drawBackground(Graphics g, Color col)
-  {
-    g.setColor(col);
-    g.fillRect(0, 0, prefsize.width, prefsize.height);
-  }
-
-  public void drawScene(Graphics g)
-  {
-    //boolean darker = false;
-
-    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;
-      float z = sp.coord[1] - centre[2];
-
-      if (av.getSequenceColour(sp.sequence) == Color.black)
-      {
-        g.setColor(Color.white);
-      }
-      else
-      {
-        g.setColor(av.getSequenceColour(sp.sequence));
-      }
-
-      if (av.getSelectionGroup() != null)
-      {
-        if (av.getSelectionGroup().getSequences(null).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);
-      if (showLabels)
-      {
-        g.setColor(Color.red);
-        g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.
-                     getName(),
-                     x - 3, y - 4);
-      }
-    }
-  }
-
-  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)
-  {
-    if (evt.getKeyCode() == KeyEvent.VK_UP)
-    {
-      scalefactor = (float) (scalefactor * 1.1);
-      scale = findScale();
-    }
-    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
-    {
-      scalefactor = (float) (scalefactor * 0.9);
-      scale = findScale();
-    }
-    else if (evt.getKeyChar() == 's')
-    {
-      System.err.println("DEBUG: Rectangle selection"); // log.debug
-      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]);
-      }
-      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 mousePressed(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int y = evt.getY();
-
-    mx = x;
-    my = y;
-
-    omx = mx;
-    omy = my;
-
-    startx = x;
-    starty = y;
-
-    rectx1 = x;
-    recty1 = y;
-
-    rectx2 = -1;
-    recty2 = -1;
-
-    SequenceI found = findPoint(x, y);
-
-    if (found != null)
-    {
-      if (av.getSelectionGroup() != null)
-      {
-        av.getSelectionGroup().addOrRemove(found, true);
-        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
-        PaintRefresher.Refresh(this, av.getSequenceSetId());
-      }
-      else
-      {
-        av.setSelectionGroup(new SequenceGroup());
-        av.getSelectionGroup().addOrRemove(found, true);
-        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
-
-      }
-    }
-    repaint();
-  }
-
-  public void mouseMoved(MouseEvent evt)
-  {
-    SequenceI found = findPoint(evt.getX(), evt.getY());
-    if (found == null)
-    {
-      tooltip = null;
-    }
-    else
-    {
-      tooltip = found.getName();
-      toolx = evt.getX();
-      tooly = evt.getY();
-    }
-    repaint();
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    mx = evt.getX();
-    my = evt.getY();
-
-    rotmat.setIdentity();
-
-    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);
-      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);
-
-      //Now translate back again
-      sp.coord[0] += centre[0];
-      sp.coord[1] += centre[1];
-      sp.coord[2] += centre[2];
-    }
-
-    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)
-  {
-    //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);
-
-      if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
-      {
-        if (av != null)
-        {
-          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
-          {
-            av.getSelectionGroup().addSequence(sp.sequence, true);
-          }
-        }
-      }
-    }
-  }
-
-  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;
-
-      if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
-      {
-        found = i;
-      }
-    }
-    if (found != -1)
-    {
-      return ( (SequencePoint) points.elementAt(found)).sequence;
-    }
-    else
-    {
-      return null;
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 jalview.math.*;
+import jalview.util.*;
+
+public class RotatableCanvas
+    extends Panel implements MouseListener,
+    MouseMotionListener,
+    KeyListener
+{
+  RotatableMatrix idmat = new RotatableMatrix(3, 3);
+  RotatableMatrix objmat = new RotatableMatrix(3, 3);
+  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+  String tooltip;
+  int toolx, tooly;
+
+  //RubberbandRectangle rubberband;
+
+  boolean drawAxes = true;
+
+  int omx = 0;
+  int mx = 0;
+  int omy = 0;
+  int my = 0;
+
+  Image img;
+  Graphics ig;
+
+  Dimension prefsize;
+
+  float centre[] = new float[3];
+  float width[] = new float[3];
+
+  float max[] = new float[3];
+  float min[] = new float[3];
+
+  float maxwidth;
+  float scale;
+
+  int npoint;
+
+  Vector points;
+  float[][] orig;
+  float[][] axes;
+
+  int startx;
+  int starty;
+
+  int lastx;
+  int lasty;
+
+  int rectx1;
+  int recty1;
+  int rectx2;
+  int recty2;
+
+  float scalefactor = 1;
+
+  AlignViewport av;
+  boolean showLabels = false;
+
+  public RotatableCanvas(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  public void showLabels(boolean b)
+  {
+    showLabels = b;
+    repaint();
+  }
+
+  public void setPoints(Vector points, int npoint)
+  {
+    this.points = points;
+    this.npoint = npoint;
+    PaintRefresher.Register(this, av.getSequenceSetId());
+
+    prefsize = getPreferredSize();
+    orig = new float[npoint][3];
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      for (int j = 0; j < 3; j++)
+      {
+        orig[i][j] = sp.coord[j];
+      }
+    }
+    //Initialize the matrices to identity
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
+        {
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
+        }
+        else
+        {
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
+        }
+      }
+    }
+
+    axes = new float[3][3];
+    initAxes();
+
+    findCentre();
+    findWidth();
+
+    scale = findScale();
+
+    //    System.out.println("Scale factor = " + scale);
+
+    addMouseListener(this);
+    addKeyListener(this);
+    // if (getParent() != null) {
+    //   getParent().addKeyListener(this);
+    //}
+    addMouseMotionListener(this);
+
+    // Add rubberband
+    //   rubberband  = new RubberbandRectangle(this);
+    //  rubberband.setActive(true);
+    //   rubberband.addListener(this);
+  }
+
+  /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
+     redrawneeded = true;
+     repaint();
+     return true;
+   }
+
+   public void removeNotify() {
+     controller.removeListener(this);
+     super.removeNotify();
+   }*/
+
+  public void initAxes()
+  {
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
+        {
+          axes[i][j] = 0;
+        }
+        else
+        {
+          axes[i][j] = 1;
+        }
+      }
+    }
+  }
+
+  public void findWidth()
+  {
+    max = new float[3];
+    min = new float[3];
+
+    max[0] = (float) - 1e30;
+    max[1] = (float) - 1e30;
+    max[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])
+        {
+          max[i] = sp.coord[i];
+        }
+        if (sp.coord[i] <= min[i])
+        {
+          min[i] = sp.coord[i];
+        }
+      }
+    }
+
+    //    System.out.println("xmax " + max[0] + " min " + min[0]);
+    //System.out.println("ymax " + max[1] + " min " + min[1]);
+    //System.out.println("zmax " + max[2] + " min " + min[2]);
+
+    width[0] = Math.abs(max[0] - min[0]);
+    width[1] = Math.abs(max[1] - min[1]);
+    width[2] = Math.abs(max[2] - min[2]);
+
+    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 (getSize().width != 0)
+    {
+      width = getSize().width;
+      height = getSize().height;
+    }
+    else
+    {
+      width = prefsize.width;
+      height = prefsize.height;
+    }
+
+    if (width < height)
+    {
+      dim = width;
+    }
+    else
+    {
+      dim = height;
+    }
+
+    return (float) (dim * scalefactor / (2 * maxwidth));
+  }
+
+  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;
+
+    //    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)
+    {
+      return prefsize;
+    }
+    else
+    {
+      return new Dimension(400, 400);
+    }
+  }
+
+  public Dimension getMinimumSize()
+  {
+    return getPreferredSize();
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    if (points == null)
+    {
+      g.setFont(new Font("Verdana", Font.PLAIN, 18));
+      g.drawString("Calculating PCA....", 20, getSize().height / 2);
+    }
+    else
+    {
+
+      //Only create the image at the beginning -
+      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);
+        ig = img.getGraphics();
+
+      }
+
+      drawBackground(ig, Color.black);
+      drawScene(ig);
+      if (drawAxes == true)
+      {
+        drawAxes(ig);
+      }
+
+      if (tooltip != null)
+      {
+        ig.setColor(Color.red);
+        ig.drawString(tooltip, toolx, tooly);
+      }
+
+      g.drawImage(img, 0, 0, this);
+    }
+  }
+
+  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));
+    }
+  }
+
+  public void drawBackground(Graphics g, Color col)
+  {
+    g.setColor(col);
+    g.fillRect(0, 0, prefsize.width, prefsize.height);
+  }
+
+  public void drawScene(Graphics g)
+  {
+    //boolean darker = false;
+
+    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;
+      float z = sp.coord[1] - centre[2];
+
+      if (av.getSequenceColour(sp.sequence) == Color.black)
+      {
+        g.setColor(Color.white);
+      }
+      else
+      {
+        g.setColor(av.getSequenceColour(sp.sequence));
+      }
+
+      if (av.getSelectionGroup() != null)
+      {
+        if (av.getSelectionGroup().getSequences(null).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);
+      if (showLabels)
+      {
+        g.setColor(Color.red);
+        g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.
+                     getName(),
+                     x - 3, y - 4);
+      }
+    }
+  }
+
+  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)
+  {
+    if (evt.getKeyCode() == KeyEvent.VK_UP)
+    {
+      scalefactor = (float) (scalefactor * 1.1);
+      scale = findScale();
+    }
+    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+    {
+      scalefactor = (float) (scalefactor * 0.9);
+      scale = findScale();
+    }
+    else if (evt.getKeyChar() == 's')
+    {
+      System.err.println("DEBUG: Rectangle selection"); // log.debug
+      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]);
+      }
+      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 mousePressed(MouseEvent evt)
+  {
+    int x = evt.getX();
+    int y = evt.getY();
+
+    mx = x;
+    my = y;
+
+    omx = mx;
+    omy = my;
+
+    startx = x;
+    starty = y;
+
+    rectx1 = x;
+    recty1 = y;
+
+    rectx2 = -1;
+    recty2 = -1;
+
+    SequenceI found = findPoint(x, y);
+
+    if (found != null)
+    {
+      if (av.getSelectionGroup() != null)
+      {
+        av.getSelectionGroup().addOrRemove(found, true);
+        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+        PaintRefresher.Refresh(this, av.getSequenceSetId());
+      }
+      else
+      {
+        av.setSelectionGroup(new SequenceGroup());
+        av.getSelectionGroup().addOrRemove(found, true);
+        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+
+      }
+    }
+    repaint();
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {
+    SequenceI found = findPoint(evt.getX(), evt.getY());
+    if (found == null)
+    {
+      tooltip = null;
+    }
+    else
+    {
+      tooltip = found.getName();
+      toolx = evt.getX();
+      tooly = evt.getY();
+    }
+    repaint();
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    mx = evt.getX();
+    my = evt.getY();
+
+    rotmat.setIdentity();
+
+    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);
+      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);
+
+      //Now translate back again
+      sp.coord[0] += centre[0];
+      sp.coord[1] += centre[1];
+      sp.coord[2] += centre[2];
+    }
+
+    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)
+  {
+    //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);
+
+      if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
+      {
+        if (av != null)
+        {
+          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
+          {
+            av.getSelectionGroup().addSequence(sp.sequence, true);
+          }
+        }
+      }
+    }
+  }
+
+  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;
+
+      if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
+      {
+        found = i;
+      }
+    }
+    if (found != -1)
+    {
+      return ( (SequencePoint) points.elementAt(found)).sequence;
+    }
+    else
+    {
+      return null;
+    }
+  }
+
+}
diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index a1d0bf7..b938cb8 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,453 +1,452 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class ScalePanel
-    extends Panel implements MouseMotionListener, MouseListener
-{
-
-  protected int offy = 4;
-  public int width;
-
-  protected AlignViewport av;
-  AlignmentPanel ap;
-
-  boolean stretchingGroup = false;
-  int min; //used by mouseDragged to see if user
-  int max; //used by mouseDragged to see if user
-  boolean mouseDragging = false;
-  int[] reveal;
-
-  public ScalePanel(AlignViewport av, AlignmentPanel ap)
-  {
-    setLayout(null);
-    this.av = av;
-    this.ap = ap;
-
-    addMouseListener(this);
-    addMouseMotionListener(this);
-
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    final int res;
-
-    if (av.hasHiddenColumns)
-    {
-      res = av.getColumnSelection().adjustForHiddenColumns(x);
-    }
-    else
-    {
-      res = x;
-    }
-
-    min = res;
-    max = res;
-    if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK)
-        == InputEvent.BUTTON3_MASK)
-    {
-      PopupMenu pop = new PopupMenu();
-      if (reveal != null)
-      {
-        MenuItem item = new MenuItem("Reveal");
-        item.addActionListener(new ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            av.showColumn(reveal[0]);
-            reveal = null;
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
-          }
-        });
-        pop.add(item);
-
-        if (av.getColumnSelection().getHiddenColumns().size() > 1)
-        {
-          item = new MenuItem("Reveal All");
-          item.addActionListener(new ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-              av.showAllHiddenColumns();
-              reveal = null;
-              ap.paintAlignment(true);
-              if (ap.overviewPanel != null)
-              {
-                ap.overviewPanel.updateOverviewImage();
-              }
-            }
-          });
-          pop.add(item);
-        }
-        this.add(pop);
-        pop.show(this, evt.getX(), evt.getY());
-      }
-      else if (av.getColumnSelection().contains(res))
-      {
-        MenuItem item = new MenuItem("Hide Columns");
-        item.addActionListener(new ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            av.hideColumns(res, res);
-            if (av.getSelectionGroup() != null
-                &&
-                av.getSelectionGroup().getSize() == av.alignment.getHeight())
-            {
-              av.setSelectionGroup(null);
-            }
-
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
-          }
-        });
-        pop.add(item);
-        this.add(pop);
-        pop.show(this, evt.getX(), evt.getY());
-      }
-    }
-    else // LEFT MOUSE TO SELECT
-    {
-      if (!evt.isControlDown() && !evt.isShiftDown())
-      {
-        av.getColumnSelection().clear();
-      }
-
-      av.getColumnSelection().addElement(res);
-      SequenceGroup sg = new SequenceGroup();
-      for (int i = 0; i < av.alignment.getSequences().size(); i++)
-      {
-        sg.addSequence(av.alignment.getSequenceAt(i), false);
-      }
-
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-      av.setSelectionGroup(sg);
-
-      if (evt.isShiftDown())
-      {
-        int min = Math.min(av.getColumnSelection().getMin(), res);
-        int max = Math.max(av.getColumnSelection().getMax(), res);
-        for (int i = min; i < max; i++)
-        {
-          av.getColumnSelection().addElement(i);
-        }
-        sg.setStartRes(min);
-        sg.setEndRes(max);
-      }
-    }
-
-    ap.paintAlignment(true);
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-    mouseDragging = false;
-
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
-    if (res > av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth() - 1;
-    }
-
-    if (av.hasHiddenColumns)
-    {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
-    }
-
-    if (!stretchingGroup)
-    {
-      ap.paintAlignment(false);
-
-      return;
-    }
-
-    SequenceGroup sg = av.getSelectionGroup();
-
-    if (res > sg.getStartRes())
-    {
-      sg.setEndRes(res);
-    }
-    else if (res < sg.getStartRes())
-    {
-      sg.setStartRes(res);
-    }
-
-    stretchingGroup = false;
-    ap.paintAlignment(false);
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    mouseDragging = true;
-
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    if (res < 0)
-    {
-      res = 0;
-    }
-
-    if (av.hasHiddenColumns)
-    {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
-    }
-
-    if (res > av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth() - 1;
-    }
-
-    if (res < min)
-    {
-      min = res;
-    }
-
-    if (res > max)
-    {
-      max = res;
-    }
-
-    SequenceGroup sg = av.getSelectionGroup();
-
-    if (sg != null)
-    {
-      stretchingGroup = true;
-
-      if (!av.getColumnSelection().contains(res))
-      {
-        av.getColumnSelection().addElement(res);
-      }
-
-      if (res > sg.getStartRes())
-      {
-        sg.setEndRes(res);
-      }
-      if (res < sg.getStartRes())
-      {
-        sg.setStartRes(res);
-      }
-
-      int col;
-      for (int i = min; i <= max; i++)
-      {
-        col = av.getColumnSelection().adjustForHiddenColumns(i);
-
-        if ( (col < sg.getStartRes()) || (col > sg.getEndRes()))
-        {
-          av.getColumnSelection().removeElement(col);
-        }
-        else
-        {
-          av.getColumnSelection().addElement(col);
-        }
-      }
-
-      ap.paintAlignment(false);
-    }
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {
-    if (mouseDragging)
-    {
-      ap.seqPanel.scrollCanvas(null);
-    }
-  }
-
-  public void mouseExited(MouseEvent evt)
-  {
-    if (mouseDragging)
-    {
-      ap.seqPanel.scrollCanvas(evt);
-    }
-  }
-
-  public void mouseClicked(MouseEvent evt)
-  {
-
-  }
-
-  public void mouseMoved(MouseEvent evt)
-  {
-    if (!av.hasHiddenColumns)
-    {
-      return;
-    }
-
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
-    res = av.getColumnSelection().adjustForHiddenColumns(res);
-
-    reveal = null;
-    for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
-    {
-      int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
-          elementAt(i);
-      if (res + 1 == region[0] || res - 1 == region[1])
-      {
-        reveal = region;
-        break;
-      }
-    }
-
-    repaint();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    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)
-  {
-    gg.setFont(av.getFont());
-
-    //Fill in the background
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, width, height);
-    gg.setColor(Color.black);
-
-    //Fill the selected columns
-    ColumnSelection cs = av.getColumnSelection();
-    gg.setColor(new Color(220, 0, 0));
-
-    for (int i = 0; i < cs.size(); i++)
-    {
-      int sel = cs.columnAt(i);
-      if (av.hasHiddenColumns)
-      {
-        sel = av.getColumnSelection().findColumnPosition(sel);
-      }
-
-      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;
-
-    FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = av.charHeight - fm.getDescent();
-
-    if ( (scalestartx % 10) == 0)
-    {
-      scalestartx += 5;
-    }
-
-    String string;
-    int maxX = 0;
-
-    for (int i = scalestartx; i < endx; i += 5)
-    {
-      if ( (i % 10) == 0)
-      {
-        string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(
-            i));
-        if ( (i - startx - 1) * av.charWidth > maxX)
-        {
-          gg.drawString(string,
-                        (i - startx - 1) * av.charWidth, y);
-          maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
-        }
-
-        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));
-      }
-    }
-
-    if (av.hasHiddenColumns)
-    {
-      gg.setColor(Color.blue);
-      int res;
-      if (av.getShowHiddenMarkers())
-      {
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
-             i++)
-        {
-
-          res = av.getColumnSelection().findHiddenRegionPosition(i) -
-              startx;
-
-          if (res < 0 || res > endx - scalestartx)
-          {
-            continue;
-          }
-
-          gg.fillPolygon(new int[]
-                         {res * av.charWidth - av.charHeight / 4,
-                         res * av.charWidth + av.charHeight / 4,
-                         res * av.charWidth},
-                         new int[]
-                         {
-                         y - av.charHeight / 2, y - av.charHeight / 2,
-                         y + 8
-          }, 3);
-
-        }
-      }
-
-      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
-      {
-        gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);
-      }
-    }
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+
+public class ScalePanel
+    extends Panel implements MouseMotionListener, MouseListener
+{
+
+  protected int offy = 4;
+  public int width;
+
+  protected AlignViewport av;
+  AlignmentPanel ap;
+
+  boolean stretchingGroup = false;
+  int min; //used by mouseDragged to see if user
+  int max; //used by mouseDragged to see if user
+  boolean mouseDragging = false;
+  int[] reveal;
+
+  public ScalePanel(AlignViewport av, AlignmentPanel ap)
+  {
+    setLayout(null);
+    this.av = av;
+    this.ap = ap;
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    final int res;
+
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(x);
+    }
+    else
+    {
+      res = x;
+    }
+
+    min = res;
+    max = res;
+    if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK)
+        == InputEvent.BUTTON3_MASK)
+    {
+      PopupMenu pop = new PopupMenu();
+      if (reveal != null)
+      {
+        MenuItem item = new MenuItem("Reveal");
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            av.showColumn(reveal[0]);
+            reveal = null;
+            ap.paintAlignment(true);
+            if (ap.overviewPanel != null)
+            {
+              ap.overviewPanel.updateOverviewImage();
+            }
+          }
+        });
+        pop.add(item);
+
+        if (av.getColumnSelection().getHiddenColumns().size() > 1)
+        {
+          item = new MenuItem("Reveal All");
+          item.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              av.showAllHiddenColumns();
+              reveal = null;
+              ap.paintAlignment(true);
+              if (ap.overviewPanel != null)
+              {
+                ap.overviewPanel.updateOverviewImage();
+              }
+            }
+          });
+          pop.add(item);
+        }
+        this.add(pop);
+        pop.show(this, evt.getX(), evt.getY());
+      }
+      else if (av.getColumnSelection().contains(res))
+      {
+        MenuItem item = new MenuItem("Hide Columns");
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            av.hideColumns(res, res);
+            if (av.getSelectionGroup() != null
+                &&
+                av.getSelectionGroup().getSize() == av.alignment.getHeight())
+            {
+              av.setSelectionGroup(null);
+            }
+
+            ap.paintAlignment(true);
+            if (ap.overviewPanel != null)
+            {
+              ap.overviewPanel.updateOverviewImage();
+            }
+          }
+        });
+        pop.add(item);
+        this.add(pop);
+        pop.show(this, evt.getX(), evt.getY());
+      }
+    }
+    else // LEFT MOUSE TO SELECT
+    {
+      if (!evt.isControlDown() && !evt.isShiftDown())
+      {
+        av.getColumnSelection().clear();
+      }
+
+      av.getColumnSelection().addElement(res);
+      SequenceGroup sg = new SequenceGroup();
+      for (int i = 0; i < av.alignment.getSequences().size(); i++)
+      {
+        sg.addSequence(av.alignment.getSequenceAt(i), false);
+      }
+
+      sg.setStartRes(res);
+      sg.setEndRes(res);
+      av.setSelectionGroup(sg);
+
+      if (evt.isShiftDown())
+      {
+        int min = Math.min(av.getColumnSelection().getMin(), res);
+        int max = Math.max(av.getColumnSelection().getMax(), res);
+        for (int i = min; i < max; i++)
+        {
+          av.getColumnSelection().addElement(i);
+        }
+        sg.setStartRes(min);
+        sg.setEndRes(max);
+      }
+    }
+
+    ap.paintAlignment(true);
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    mouseDragging = false;
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
+
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
+
+    if (!stretchingGroup)
+    {
+      ap.paintAlignment(false);
+
+      return;
+    }
+
+    SequenceGroup sg = av.getSelectionGroup();
+
+    if (res > sg.getStartRes())
+    {
+      sg.setEndRes(res);
+    }
+    else if (res < sg.getStartRes())
+    {
+      sg.setStartRes(res);
+    }
+
+    stretchingGroup = false;
+    ap.paintAlignment(false);
+  }
+
+  public void mouseDragged(MouseEvent evt)
+  {
+    mouseDragging = true;
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    if (res < 0)
+    {
+      res = 0;
+    }
+
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
+
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
+
+    if (res < min)
+    {
+      min = res;
+    }
+
+    if (res > max)
+    {
+      max = res;
+    }
+
+    SequenceGroup sg = av.getSelectionGroup();
+
+    if (sg != null)
+    {
+      stretchingGroup = true;
+
+      if (!av.getColumnSelection().contains(res))
+      {
+        av.getColumnSelection().addElement(res);
+      }
+
+      if (res > sg.getStartRes())
+      {
+        sg.setEndRes(res);
+      }
+      if (res < sg.getStartRes())
+      {
+        sg.setStartRes(res);
+      }
+
+      int col;
+      for (int i = min; i <= max; i++)
+      {
+        col = av.getColumnSelection().adjustForHiddenColumns(i);
+
+        if ( (col < sg.getStartRes()) || (col > sg.getEndRes()))
+        {
+          av.getColumnSelection().removeElement(col);
+        }
+        else
+        {
+          av.getColumnSelection().addElement(col);
+        }
+      }
+
+      ap.paintAlignment(false);
+    }
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (mouseDragging)
+    {
+      ap.seqPanel.scrollCanvas(null);
+    }
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+    if (mouseDragging)
+    {
+      ap.seqPanel.scrollCanvas(evt);
+    }
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {
+    if (!av.hasHiddenColumns)
+    {
+      return;
+    }
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+    res = av.getColumnSelection().adjustForHiddenColumns(res);
+
+    reveal = null;
+    for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+    {
+      int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
+          elementAt(i);
+      if (res + 1 == region[0] || res - 1 == region[1])
+      {
+        reveal = region;
+        break;
+      }
+    }
+
+    repaint();
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    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)
+  {
+    gg.setFont(av.getFont());
+
+    //Fill in the background
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, width, height);
+    gg.setColor(Color.black);
+
+    //Fill the selected columns
+    ColumnSelection cs = av.getColumnSelection();
+    gg.setColor(new Color(220, 0, 0));
+
+    for (int i = 0; i < cs.size(); i++)
+    {
+      int sel = cs.columnAt(i);
+      if (av.hasHiddenColumns)
+      {
+        sel = av.getColumnSelection().findColumnPosition(sel);
+      }
+
+      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;
+
+    FontMetrics fm = gg.getFontMetrics(av.getFont());
+    int y = av.charHeight - fm.getDescent();
+
+    if ( (scalestartx % 10) == 0)
+    {
+      scalestartx += 5;
+    }
+
+    String string;
+    int maxX = 0;
+
+    for (int i = scalestartx; i < endx; i += 5)
+    {
+      if ( (i % 10) == 0)
+      {
+        string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(
+            i));
+        if ( (i - startx - 1) * av.charWidth > maxX)
+        {
+          gg.drawString(string,
+                        (i - startx - 1) * av.charWidth, y);
+          maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
+        }
+
+        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));
+      }
+    }
+
+    if (av.hasHiddenColumns)
+    {
+      gg.setColor(Color.blue);
+      int res;
+      if (av.getShowHiddenMarkers())
+      {
+        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
+             i++)
+        {
+
+          res = av.getColumnSelection().findHiddenRegionPosition(i) -
+              startx;
+
+          if (res < 0 || res > endx - scalestartx)
+          {
+            continue;
+          }
+
+          gg.fillPolygon(new int[]
+                         {res * av.charWidth - av.charHeight / 4,
+                         res * av.charWidth + av.charHeight / 4,
+                         res * av.charWidth},
+                         new int[]
+                         {
+                         y - av.charHeight / 2, y - av.charHeight / 2,
+                         y + 8
+          }, 3);
+
+        }
+      }
+
+      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
+      {
+        gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);
+      }
+    }
+
+  }
+
+}
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 5fb956c..dcf205e 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,825 +1,824 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class SeqCanvas
-    extends Panel
-{
-  FeatureRenderer fr;
-  SequenceRenderer sr;
-  Image img;
-  Graphics gg;
-  int imgWidth;
-  int imgHeight;
-
-  AlignViewport av;
-
-  SearchResults searchResults = null;
-
-  boolean fastPaint = false;
-
-  int cursorX = 0;
-  int cursorY = 0;
-
-  public SeqCanvas(AlignViewport av)
-  {
-    this.av = av;
-    fr = new FeatureRenderer(av);
-    sr = new SequenceRenderer(av);
-    PaintRefresher.Register(this, av.getSequenceSetId());
-  }
-
-  public AlignViewport getViewport()
-  {
-    return av;
-  }
-
-  public FeatureRenderer getFeatureRenderer()
-  {
-    return fr;
-  }
-
-  public SequenceRenderer getSequenceRenderer()
-  {
-    return sr;
-  }
-
-  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
-  {
-    int scalestartx = startx - startx % 10 + 10;
-
-    g.setColor(Color.black);
-
-    // NORTH SCALE
-    for (int i = scalestartx; i < endx; i += 10)
-    {
-      int value = i;
-      if (av.hasHiddenColumns)
-      {
-        value = av.getColumnSelection().adjustForHiddenColumns(value);
-      }
-
-      g.drawString(String.valueOf(value), (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);
-    }
-  }
-
-  void drawWestScale(Graphics g, int startx, int endx, int ypos)
-  {
-    FontMetrics fm = getFontMetrics(av.getFont());
-    ypos += av.charHeight;
-    if (av.hasHiddenColumns)
-    {
-      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
-      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
-    }
-
-    int maxwidth = av.alignment.getWidth();
-    if (av.hasHiddenColumns)
-    {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-    }
-
-    // WEST 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)
-      {
-        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) -
-            av.charWidth / 2;
-        g.drawString(value + "", x,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-      }
-    }
-  }
-
-  void drawEastScale(Graphics g, int startx, int endx, int ypos)
-  {
-    ypos += av.charHeight;
-
-    if (av.hasHiddenColumns)
-    {
-      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
-    }
-
-    SequenceI seq;
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
-    {
-      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 = seq.findPosition(index);
-
-        break;
-      }
-
-      if (value != -1)
-      {
-        g.drawString(String.valueOf(value), 0,
-                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
-      }
-    }
-  }
-
-  int lastsr = 0;
-  void fastPaint(int horizontal, int vertical)
-  {
-    if (fastPaint || gg == null)
-    {
-      return;
-    }
-
-    // Its possible on certain browsers that the call to fastpaint
-    // is faster than it can paint, so this check here catches
-    // this possibility
-    if (lastsr + horizontal != av.startRes)
-    {
-      horizontal = av.startRes - lastsr;
-    }
-
-    lastsr = av.startRes;
-
-    fastPaint = true;
-    gg.copyArea(horizontal * av.charWidth,
-                vertical * av.charHeight,
-                imgWidth - horizontal * av.charWidth,
-                imgHeight - vertical * av.charHeight,
-                -horizontal * av.charWidth,
-                -vertical * av.charHeight);
-
-    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
-        transX = 0, transY = 0;
-
-    if (horizontal > 0) // scrollbar pulled right, image to the left
-    {
-      transX = (er - sr - horizontal) * av.charWidth;
-      sr = er - horizontal;
-    }
-    else if (horizontal < 0)
-    {
-      er = sr - horizontal;
-    }
-
-    else if (vertical > 0) // scroll down
-    {
-      ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
-      {
-        ss = av.startSeq;
-      }
-      else
-      {
-        transY = imgHeight - vertical * av.charHeight;
-      }
-    }
-    else if (vertical < 0)
-    {
-      es = ss - vertical;
-      if (es > av.endSeq)
-      {
-        es = av.endSeq;
-      }
-    }
-
-    gg.translate(transX, transY);
-
-    drawPanel(gg, sr, er, ss, es, 0);
-    gg.translate( -transX, -transY);
-
-    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.
-   */
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-
-    if (img != null && (fastPaint
-                        || (getSize().width != g.getClipBounds().width)
-                        || (getSize().height != g.getClipBounds().height)))
-    {
-      g.drawImage(img, 0, 0, this);
-      fastPaint = false;
-      return;
-    }
-
-    if (fastPaint)
-    {
-      g.drawImage(img, 0, 0, this);
-      fastPaint = false;
-      return;
-    }
-
-    // this draws the whole of the alignment
-    imgWidth = this.getSize().width;
-    imgHeight = this.getSize().height;
-
-    imgWidth -= imgWidth % av.charWidth;
-    imgHeight -= imgHeight % av.charHeight;
-
-    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());
-    }
-
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, imgWidth, imgHeight);
-
-    if (av.getWrapAlignment())
-    {
-      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
-    }
-    else
-    {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
-    }
-
-    g.drawImage(img, 0, 0, this);
-
-  }
-
-  int LABEL_WEST, LABEL_EAST;
-  public int getWrappedCanvasWidth(int cwidth)
-  {
-    cwidth -= cwidth % av.charWidth;
-
-    FontMetrics fm = getFontMetrics(av.getFont());
-
-    LABEL_EAST = 0;
-    LABEL_WEST = 0;
-
-    if (av.scaleRightWrapped)
-    {
-      LABEL_EAST = fm.stringWidth(getMask());
-    }
-
-    if (av.scaleLeftWrapped)
-    {
-      LABEL_WEST = fm.stringWidth(getMask());
-    }
-
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-  }
-
-  /**
-   * Generates a string of zeroes.
-   * @return String
-   */
-  String getMask()
-  {
-    String mask = "0";
-    int maxWidth = 0;
-    int tmp;
-    for (int i = 0; i < av.alignment.getHeight(); i++)
-    {
-      tmp = av.alignment.getSequenceAt(i).getEnd();
-      if (tmp > maxWidth)
-      {
-        maxWidth = tmp;
-      }
-    }
-
-    for (int i = maxWidth; i > 0; i /= 10)
-    {
-      mask += "0";
-    }
-    return mask;
-  }
-
-  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
-                               int startRes)
-  {
-    AlignmentI al = av.getAlignment();
-
-    FontMetrics fm = getFontMetrics(av.getFont());
-
-    if (av.scaleRightWrapped)
-    {
-      LABEL_EAST = fm.stringWidth(getMask());
-    }
-
-    if (av.scaleLeftWrapped)
-    {
-      LABEL_WEST = fm.stringWidth(getMask());
-    }
-
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
-    {
-      hgap += av.charHeight;
-    }
-
-    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-    int cHeight = av.getAlignment().getHeight() * av.charHeight;
-
-    av.setWrappedWidth(cWidth);
-
-    av.endRes = av.startRes + cWidth;
-
-    int endx;
-    int ypos = hgap;
-
-    int maxwidth = av.alignment.getWidth() - 1;
-
-    if (av.hasHiddenColumns)
-    {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-    }
-
-    while ( (ypos <= canvasHeight) && (startRes < maxwidth))
-    {
-      endx = startRes + cWidth - 1;
-
-      if (endx > maxwidth)
-      {
-        endx = maxwidth;
-      }
-
-      g.setColor(Color.black);
-
-      if (av.scaleLeftWrapped)
-      {
-        drawWestScale(g, startRes, endx, ypos);
-      }
-
-      if (av.scaleRightWrapped)
-      {
-        g.translate(canvasWidth - LABEL_EAST, 0);
-        drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST), 0);
-      }
-
-      g.translate(LABEL_WEST, 0);
-
-      if (av.scaleAboveWrapped)
-      {
-        drawNorthScale(g, startRes, endx, ypos);
-      }
-      if (av.hasHiddenColumns && av.showHiddenMarkers)
-      {
-        g.setColor(Color.blue);
-        int res;
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
-             i++)
-        {
-          res = av.getColumnSelection().findHiddenRegionPosition(i) -
-              startRes;
-
-          if (res < 0 || res > endx - startRes)
-          {
-            continue;
-          }
-
-          gg.fillPolygon(new int[]
-                         {res * av.charWidth - av.charHeight / 4,
-                         res * av.charWidth + av.charHeight / 4,
-                         res * av.charWidth},
-                         new int[]
-                         {
-                         ypos - (av.charHeight / 2),
-                         ypos - (av.charHeight / 2),
-                         ypos - (av.charHeight / 2) + 8
-          }, 3);
-
-        }
-      }
-
-      if (g.getClip() == null)
-      {
-        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
-      }
-
-      drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
-      g.setClip(null);
-
-      if (av.showAnnotation)
-      {
-        g.translate(0, cHeight + ypos + 4);
-        if (annotations == null)
-        {
-          annotations = new AnnotationPanel(av);
-        }
-
-        annotations.drawComponent(g, startRes, endx + 1);
-        g.translate(0, -cHeight - ypos - 4);
-      }
-      g.translate( -LABEL_WEST, 0);
-
-      ypos += cHeight + getAnnotationHeight() + hgap;
-
-      startRes += cWidth;
-    }
-
-  }
-
-  AnnotationPanel annotations;
-  int getAnnotationHeight()
-  {
-    if (!av.showAnnotation)
-    {
-      return 0;
-    }
-
-    if (annotations == null)
-    {
-      annotations = new AnnotationPanel(av);
-    }
-
-    return annotations.adjustPanelHeight();
-  }
-
-  void drawPanel(Graphics g1, int startRes, int endRes,
-                 int startSeq, int endSeq, int offset)
-  {
-    if (!av.hasHiddenColumns)
-    {
-      draw(g1, startRes, endRes, startSeq, endSeq, offset);
-    }
-    else
-    {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
-
-      int screenY = 0;
-      int blockStart = startRes;
-      int blockEnd = endRes;
-
-      for (int i = 0; i < regions.size(); i++)
-      {
-        int[] region = (int[]) regions.elementAt(i);
-        int hideStart = region[0];
-        int hideEnd = region[1];
-
-        if (hideStart <= blockStart)
-        {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
-
-        blockEnd = hideStart - 1;
-
-        g1.translate(screenY * av.charWidth, 0);
-
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
-        if (av.getShowHiddenMarkers())
-        {
-          g1.setColor(Color.blue);
-          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
-                      0 + offset,
-                      (blockEnd - blockStart + 1) * av.charWidth - 1,
-                      (endSeq - startSeq) * av.charHeight + offset);
-        }
-
-        g1.translate( -screenY * av.charWidth, 0);
-        screenY += blockEnd - blockStart + 1;
-        blockStart = hideEnd + 1;
-      }
-
-      if (screenY <= (endRes - startRes))
-      {
-        blockEnd = blockStart + (endRes - startRes) - screenY;
-        g1.translate(screenY * av.charWidth, 0);
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
-        g1.translate( -screenY * av.charWidth, 0);
-      }
-    }
-
-  }
-
-  //int startRes, int endRes, int startSeq, int endSeq, int x, int y,
-  // int x1, int x2, int y1, int y2, int startx, int starty,
-  void draw(Graphics g,
-            int startRes, int endRes,
-            int startSeq, int endSeq,
-            int offset)
-  {
-    g.setFont(av.getFont());
-    sr.prepare(g, av.renderGaps);
-
-    SequenceI nextSeq;
-
-    /// First draw the sequences
-    /////////////////////////////
-    for (int i = startSeq; i < endSeq; i++)
-    {
-      nextSeq = av.alignment.getSequenceAt(i);
-
-      if (nextSeq == null)
-      {
-        continue;
-      }
-
-      sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
-                      startRes, endRes,
-                      offset + ( (i - startSeq) * av.charHeight));
-
-      if (av.showSequenceFeatures)
-      {
-        fr.drawSequence(g, nextSeq, startRes, endRes,
-                        offset + ( (i - startSeq) * av.charHeight));
-      }
-
-      /// Highlight search Results once all sequences have been drawn
-      //////////////////////////////////////////////////////////
-      if (searchResults != null)
-      {
-        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
-            endRes);
-        if (visibleResults != null)
-        {
-          for (int r = 0; r < visibleResults.length; r += 2)
-          {
-            sr.drawHighlightedText(nextSeq, visibleResults[r],
-                                   visibleResults[r + 1],
-                                   (visibleResults[r] - startRes) *
-                                   av.charWidth,
-                                   offset + ( (i - startSeq) * av.charHeight));
-          }
-        }
-      }
-
-      if (av.cursorMode && cursorY == i
-          && cursorX >= startRes && cursorX <= endRes)
-      {
-        sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
-                      offset + ( (i - startSeq) * av.charHeight));
-      }
-    }
-
-    if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0)
-    {
-      drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
-    }
-
-  }
-
-  void drawGroupsBoundaries(Graphics g,
-                            int startRes, int endRes,
-                            int startSeq, int endSeq,
-                            int offset)
-  {
-    //
-    /////////////////////////////////////
-    // Now outline any areas if necessary
-    /////////////////////////////////////
-    SequenceGroup group = av.getSelectionGroup();
-
-    int sx = -1;
-    int sy = -1;
-    int ex = -1;
-    int groupIndex = -1;
-
-    if ( (group == null) && (av.alignment.getGroups().size() > 0))
-    {
-      group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
-      groupIndex = 0;
-    }
-
-    if (group != null)
-    {
-      do
-      {
-        int oldY = -1;
-        int i = 0;
-        boolean inGroup = false;
-        int top = -1;
-        int bottom = -1;
-        int alHeight = av.alignment.getHeight() - 1;
-
-        for (i = startSeq; i < endSeq; i++)
-        {
-          sx = (group.getStartRes() - startRes) * av.charWidth;
-          sy = offset + ( (i - startSeq) * av.charHeight);
-          ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *
-                av.charWidth) -
-              1;
-
-          if (sx + ex < 0 || sx > imgWidth)
-          {
-            continue;
-          }
-
-          if ( (sx <= (endRes - startRes) * av.charWidth) &&
-              group.getSequences(null).
-              contains(av.alignment.getSequenceAt(i)))
-          {
-            if ( (bottom == -1) &&
-                (i >= alHeight ||
-                 !group.getSequences(null).contains(
-                     av.alignment.getSequenceAt(i + 1))))
-            {
-              bottom = sy + av.charHeight;
-            }
-
-            if (!inGroup)
-            {
-              if ( ( (top == -1) && (i == 0)) ||
-                  !group.getSequences(null).contains(
-                      av.alignment.getSequenceAt(i - 1)))
-              {
-                top = sy;
-              }
-
-              oldY = sy;
-              inGroup = true;
-
-              if (group == av.getSelectionGroup())
-              {
-                g.setColor(Color.red);
-              }
-              else
-              {
-                g.setColor(group.getOutlineColour());
-              }
-            }
-          }
-          else
-          {
-            if (inGroup)
-            {
-              if (sx >= 0 && sx < imgWidth)
-              {
-                g.drawLine(sx, oldY, sx, sy);
-              }
-
-              if (sx + ex < imgWidth)
-              {
-                g.drawLine(sx + ex, oldY, sx + ex, sy);
-              }
-
-              if (sx < 0)
-              {
-                ex += sx;
-                sx = 0;
-              }
-
-              if (sx + ex > imgWidth)
-              {
-                ex = imgWidth;
-              }
-
-              else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
-              {
-                ex = (endRes - startRes + 1) * av.charWidth;
-              }
-
-              if (top != -1)
-              {
-                g.drawLine(sx, top, sx + ex, top);
-                top = -1;
-              }
-
-              if (bottom != -1)
-              {
-                g.drawLine(sx, bottom, sx + ex, bottom);
-                bottom = -1;
-              }
-
-              inGroup = false;
-            }
-          }
-        }
-
-        if (inGroup)
-        {
-          sy = offset + ( (i - startSeq) * av.charHeight);
-          if (sx >= 0 && sx < imgWidth)
-          {
-            g.drawLine(sx, oldY, sx, sy);
-          }
-
-          if (sx + ex < imgWidth)
-          {
-            g.drawLine(sx + ex, oldY, sx + ex, sy);
-          }
-
-          if (sx < 0)
-          {
-            ex += sx;
-            sx = 0;
-          }
-
-          if (sx + ex > imgWidth)
-          {
-            ex = imgWidth;
-          }
-          else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
-          {
-            ex = (endRes - startRes + 1) * av.charWidth;
-          }
-
-          if (top != -1)
-          {
-            g.drawLine(sx, top, sx + ex, top);
-            top = -1;
-          }
-
-          if (bottom != -1)
-          {
-            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
-            bottom = -1;
-          }
-
-          inGroup = false;
-        }
-
-        groupIndex++;
-
-        if (groupIndex >= av.alignment.getGroups().size())
-        {
-          break;
-        }
-
-        group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
-      }
-      while (groupIndex < av.alignment.getGroups().size());
-
-    }
-  }
-
-  public void highlightSearchResults(SearchResults results)
-  {
-    searchResults = results;
-
-    repaint();
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
+
+public class SeqCanvas
+    extends Panel
+{
+  FeatureRenderer fr;
+  SequenceRenderer sr;
+  Image img;
+  Graphics gg;
+  int imgWidth;
+  int imgHeight;
+
+  AlignViewport av;
+
+  SearchResults searchResults = null;
+
+  boolean fastPaint = false;
+
+  int cursorX = 0;
+  int cursorY = 0;
+
+  public SeqCanvas(AlignViewport av)
+  {
+    this.av = av;
+    fr = new FeatureRenderer(av);
+    sr = new SequenceRenderer(av);
+    PaintRefresher.Register(this, av.getSequenceSetId());
+  }
+
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return fr;
+  }
+
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return sr;
+  }
+
+  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  {
+    int scalestartx = startx - startx % 10 + 10;
+
+    g.setColor(Color.black);
+
+    // NORTH SCALE
+    for (int i = scalestartx; i < endx; i += 10)
+    {
+      int value = i;
+      if (av.hasHiddenColumns)
+      {
+        value = av.getColumnSelection().adjustForHiddenColumns(value);
+      }
+
+      g.drawString(String.valueOf(value), (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);
+    }
+  }
+
+  void drawWestScale(Graphics g, int startx, int endx, int ypos)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
+    ypos += av.charHeight;
+    if (av.hasHiddenColumns)
+    {
+      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+    }
+
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
+
+    // WEST 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)
+      {
+        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) -
+            av.charWidth / 2;
+        g.drawString(value + "", x,
+                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+      }
+    }
+  }
+
+  void drawEastScale(Graphics g, int startx, int endx, int ypos)
+  {
+    ypos += av.charHeight;
+
+    if (av.hasHiddenColumns)
+    {
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+    }
+
+    SequenceI seq;
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      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 = seq.findPosition(index);
+
+        break;
+      }
+
+      if (value != -1)
+      {
+        g.drawString(String.valueOf(value), 0,
+                     (ypos + (i * av.charHeight)) - (av.charHeight / 5));
+      }
+    }
+  }
+
+  int lastsr = 0;
+  void fastPaint(int horizontal, int vertical)
+  {
+    if (fastPaint || gg == null)
+    {
+      return;
+    }
+
+    // Its possible on certain browsers that the call to fastpaint
+    // is faster than it can paint, so this check here catches
+    // this possibility
+    if (lastsr + horizontal != av.startRes)
+    {
+      horizontal = av.startRes - lastsr;
+    }
+
+    lastsr = av.startRes;
+
+    fastPaint = true;
+    gg.copyArea(horizontal * av.charWidth,
+                vertical * av.charHeight,
+                imgWidth - horizontal * av.charWidth,
+                imgHeight - vertical * av.charHeight,
+                -horizontal * av.charWidth,
+                -vertical * av.charHeight);
+
+    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
+        transX = 0, transY = 0;
+
+    if (horizontal > 0) // scrollbar pulled right, image to the left
+    {
+      transX = (er - sr - horizontal) * av.charWidth;
+      sr = er - horizontal;
+    }
+    else if (horizontal < 0)
+    {
+      er = sr - horizontal;
+    }
+
+    else if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
+      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      {
+        ss = av.startSeq;
+      }
+      else
+      {
+        transY = imgHeight - vertical * av.charHeight;
+      }
+    }
+    else if (vertical < 0)
+    {
+      es = ss - vertical;
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
+
+    gg.translate(transX, transY);
+
+    drawPanel(gg, sr, er, ss, es, 0);
+    gg.translate( -transX, -transY);
+
+    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.
+   */
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+
+    if (img != null && (fastPaint
+                        || (getSize().width != g.getClipBounds().width)
+                        || (getSize().height != g.getClipBounds().height)))
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    if (fastPaint)
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    // this draws the whole of the alignment
+    imgWidth = this.getSize().width;
+    imgHeight = this.getSize().height;
+
+    imgWidth -= imgWidth % av.charWidth;
+    imgHeight -= imgHeight % av.charHeight;
+
+    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());
+    }
+
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
+
+    if (av.getWrapAlignment())
+    {
+      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+    }
+    else
+    {
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+    }
+
+    g.drawImage(img, 0, 0, this);
+
+  }
+
+  int LABEL_WEST, LABEL_EAST;
+  public int getWrappedCanvasWidth(int cwidth)
+  {
+    cwidth -= cwidth % av.charWidth;
+
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    LABEL_EAST = 0;
+    LABEL_WEST = 0;
+
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(getMask());
+    }
+
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(getMask());
+    }
+
+    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+  }
+
+  /**
+   * Generates a string of zeroes.
+   * @return String
+   */
+  String getMask()
+  {
+    String mask = "0";
+    int maxWidth = 0;
+    int tmp;
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      tmp = av.alignment.getSequenceAt(i).getEnd();
+      if (tmp > maxWidth)
+      {
+        maxWidth = tmp;
+      }
+    }
+
+    for (int i = maxWidth; i > 0; i /= 10)
+    {
+      mask += "0";
+    }
+    return mask;
+  }
+
+  public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
+                               int startRes)
+  {
+    AlignmentI al = av.getAlignment();
+
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(getMask());
+    }
+
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(getMask());
+    }
+
+    int hgap = av.charHeight;
+    if (av.scaleAboveWrapped)
+    {
+      hgap += av.charHeight;
+    }
+
+    int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+    int cHeight = av.getAlignment().getHeight() * av.charHeight;
+
+    av.setWrappedWidth(cWidth);
+
+    av.endRes = av.startRes + cWidth;
+
+    int endx;
+    int ypos = hgap;
+
+    int maxwidth = av.alignment.getWidth() - 1;
+
+    if (av.hasHiddenColumns)
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
+
+    while ( (ypos <= canvasHeight) && (startRes < maxwidth))
+    {
+      endx = startRes + cWidth - 1;
+
+      if (endx > maxwidth)
+      {
+        endx = maxwidth;
+      }
+
+      g.setColor(Color.black);
+
+      if (av.scaleLeftWrapped)
+      {
+        drawWestScale(g, startRes, endx, ypos);
+      }
+
+      if (av.scaleRightWrapped)
+      {
+        g.translate(canvasWidth - LABEL_EAST, 0);
+        drawEastScale(g, startRes, endx, ypos);
+        g.translate( - (canvasWidth - LABEL_EAST), 0);
+      }
+
+      g.translate(LABEL_WEST, 0);
+
+      if (av.scaleAboveWrapped)
+      {
+        drawNorthScale(g, startRes, endx, ypos);
+      }
+      if (av.hasHiddenColumns && av.showHiddenMarkers)
+      {
+        g.setColor(Color.blue);
+        int res;
+        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
+             i++)
+        {
+          res = av.getColumnSelection().findHiddenRegionPosition(i) -
+              startRes;
+
+          if (res < 0 || res > endx - startRes)
+          {
+            continue;
+          }
+
+          gg.fillPolygon(new int[]
+                         {res * av.charWidth - av.charHeight / 4,
+                         res * av.charWidth + av.charHeight / 4,
+                         res * av.charWidth},
+                         new int[]
+                         {
+                         ypos - (av.charHeight / 2),
+                         ypos - (av.charHeight / 2),
+                         ypos - (av.charHeight / 2) + 8
+          }, 3);
+
+        }
+      }
+
+      if (g.getClip() == null)
+      {
+        g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+      }
+
+      drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+      g.setClip(null);
+
+      if (av.showAnnotation)
+      {
+        g.translate(0, cHeight + ypos + 4);
+        if (annotations == null)
+        {
+          annotations = new AnnotationPanel(av);
+        }
+
+        annotations.drawComponent(g, startRes, endx + 1);
+        g.translate(0, -cHeight - ypos - 4);
+      }
+      g.translate( -LABEL_WEST, 0);
+
+      ypos += cHeight + getAnnotationHeight() + hgap;
+
+      startRes += cWidth;
+    }
+
+  }
+
+  AnnotationPanel annotations;
+  int getAnnotationHeight()
+  {
+    if (!av.showAnnotation)
+    {
+      return 0;
+    }
+
+    if (annotations == null)
+    {
+      annotations = new AnnotationPanel(av);
+    }
+
+    return annotations.adjustPanelHeight();
+  }
+
+  void drawPanel(Graphics g1, int startRes, int endRes,
+                 int startSeq, int endSeq, int offset)
+  {
+    if (!av.hasHiddenColumns)
+    {
+      draw(g1, startRes, endRes, startSeq, endSeq, offset);
+    }
+    else
+    {
+      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+
+      int screenY = 0;
+      int blockStart = startRes;
+      int blockEnd = endRes;
+
+      for (int i = 0; i < regions.size(); i++)
+      {
+        int[] region = (int[]) regions.elementAt(i);
+        int hideStart = region[0];
+        int hideEnd = region[1];
+
+        if (hideStart <= blockStart)
+        {
+          blockStart += (hideEnd - hideStart) + 1;
+          continue;
+        }
+
+        blockEnd = hideStart - 1;
+
+        g1.translate(screenY * av.charWidth, 0);
+
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+        if (av.getShowHiddenMarkers())
+        {
+          g1.setColor(Color.blue);
+          g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
+                      0 + offset,
+                      (blockEnd - blockStart + 1) * av.charWidth - 1,
+                      (endSeq - startSeq) * av.charHeight + offset);
+        }
+
+        g1.translate( -screenY * av.charWidth, 0);
+        screenY += blockEnd - blockStart + 1;
+        blockStart = hideEnd + 1;
+      }
+
+      if (screenY <= (endRes - startRes))
+      {
+        blockEnd = blockStart + (endRes - startRes) - screenY;
+        g1.translate(screenY * av.charWidth, 0);
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+        g1.translate( -screenY * av.charWidth, 0);
+      }
+    }
+
+  }
+
+  //int startRes, int endRes, int startSeq, int endSeq, int x, int y,
+  // int x1, int x2, int y1, int y2, int startx, int starty,
+  void draw(Graphics g,
+            int startRes, int endRes,
+            int startSeq, int endSeq,
+            int offset)
+  {
+    g.setFont(av.getFont());
+    sr.prepare(g, av.renderGaps);
+
+    SequenceI nextSeq;
+
+    /// First draw the sequences
+    /////////////////////////////
+    for (int i = startSeq; i < endSeq; i++)
+    {
+      nextSeq = av.alignment.getSequenceAt(i);
+
+      if (nextSeq == null)
+      {
+        continue;
+      }
+
+      sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+                      startRes, endRes,
+                      offset + ( (i - startSeq) * av.charHeight));
+
+      if (av.showSequenceFeatures)
+      {
+        fr.drawSequence(g, nextSeq, startRes, endRes,
+                        offset + ( (i - startSeq) * av.charHeight));
+      }
+
+      /// Highlight search Results once all sequences have been drawn
+      //////////////////////////////////////////////////////////
+      if (searchResults != null)
+      {
+        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+            endRes);
+        if (visibleResults != null)
+        {
+          for (int r = 0; r < visibleResults.length; r += 2)
+          {
+            sr.drawHighlightedText(nextSeq, visibleResults[r],
+                                   visibleResults[r + 1],
+                                   (visibleResults[r] - startRes) *
+                                   av.charWidth,
+                                   offset + ( (i - startSeq) * av.charHeight));
+          }
+        }
+      }
+
+      if (av.cursorMode && cursorY == i
+          && cursorX >= startRes && cursorX <= endRes)
+      {
+        sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
+                      offset + ( (i - startSeq) * av.charHeight));
+      }
+    }
+
+    if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0)
+    {
+      drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+    }
+
+  }
+
+  void drawGroupsBoundaries(Graphics g,
+                            int startRes, int endRes,
+                            int startSeq, int endSeq,
+                            int offset)
+  {
+    //
+    /////////////////////////////////////
+    // Now outline any areas if necessary
+    /////////////////////////////////////
+    SequenceGroup group = av.getSelectionGroup();
+
+    int sx = -1;
+    int sy = -1;
+    int ex = -1;
+    int groupIndex = -1;
+
+    if ( (group == null) && (av.alignment.getGroups().size() > 0))
+    {
+      group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+      groupIndex = 0;
+    }
+
+    if (group != null)
+    {
+      do
+      {
+        int oldY = -1;
+        int i = 0;
+        boolean inGroup = false;
+        int top = -1;
+        int bottom = -1;
+        int alHeight = av.alignment.getHeight() - 1;
+
+        for (i = startSeq; i < endSeq; i++)
+        {
+          sx = (group.getStartRes() - startRes) * av.charWidth;
+          sy = offset + ( (i - startSeq) * av.charHeight);
+          ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *
+                av.charWidth) -
+              1;
+
+          if (sx + ex < 0 || sx > imgWidth)
+          {
+            continue;
+          }
+
+          if ( (sx <= (endRes - startRes) * av.charWidth) &&
+              group.getSequences(null).
+              contains(av.alignment.getSequenceAt(i)))
+          {
+            if ( (bottom == -1) &&
+                (i >= alHeight ||
+                 !group.getSequences(null).contains(
+                     av.alignment.getSequenceAt(i + 1))))
+            {
+              bottom = sy + av.charHeight;
+            }
+
+            if (!inGroup)
+            {
+              if ( ( (top == -1) && (i == 0)) ||
+                  !group.getSequences(null).contains(
+                      av.alignment.getSequenceAt(i - 1)))
+              {
+                top = sy;
+              }
+
+              oldY = sy;
+              inGroup = true;
+
+              if (group == av.getSelectionGroup())
+              {
+                g.setColor(Color.red);
+              }
+              else
+              {
+                g.setColor(group.getOutlineColour());
+              }
+            }
+          }
+          else
+          {
+            if (inGroup)
+            {
+              if (sx >= 0 && sx < imgWidth)
+              {
+                g.drawLine(sx, oldY, sx, sy);
+              }
+
+              if (sx + ex < imgWidth)
+              {
+                g.drawLine(sx + ex, oldY, sx + ex, sy);
+              }
+
+              if (sx < 0)
+              {
+                ex += sx;
+                sx = 0;
+              }
+
+              if (sx + ex > imgWidth)
+              {
+                ex = imgWidth;
+              }
+
+              else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+              {
+                ex = (endRes - startRes + 1) * av.charWidth;
+              }
+
+              if (top != -1)
+              {
+                g.drawLine(sx, top, sx + ex, top);
+                top = -1;
+              }
+
+              if (bottom != -1)
+              {
+                g.drawLine(sx, bottom, sx + ex, bottom);
+                bottom = -1;
+              }
+
+              inGroup = false;
+            }
+          }
+        }
+
+        if (inGroup)
+        {
+          sy = offset + ( (i - startSeq) * av.charHeight);
+          if (sx >= 0 && sx < imgWidth)
+          {
+            g.drawLine(sx, oldY, sx, sy);
+          }
+
+          if (sx + ex < imgWidth)
+          {
+            g.drawLine(sx + ex, oldY, sx + ex, sy);
+          }
+
+          if (sx < 0)
+          {
+            ex += sx;
+            sx = 0;
+          }
+
+          if (sx + ex > imgWidth)
+          {
+            ex = imgWidth;
+          }
+          else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+          {
+            ex = (endRes - startRes + 1) * av.charWidth;
+          }
+
+          if (top != -1)
+          {
+            g.drawLine(sx, top, sx + ex, top);
+            top = -1;
+          }
+
+          if (bottom != -1)
+          {
+            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+            bottom = -1;
+          }
+
+          inGroup = false;
+        }
+
+        groupIndex++;
+
+        if (groupIndex >= av.alignment.getGroups().size())
+        {
+          break;
+        }
+
+        group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
+      }
+      while (groupIndex < av.alignment.getGroups().size());
+
+    }
+  }
+
+  public void highlightSearchResults(SearchResults results)
+  {
+    searchResults = results;
+
+    repaint();
+  }
+
+}
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 158f0ab..39309fd 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index daf971d..2885a62 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,333 +1,332 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class SequenceRenderer
-{
-  AlignViewport av;
-  FontMetrics fm;
-  boolean renderGaps = true;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup[] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
-  boolean forOverview = false;
-
-  public SequenceRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void prepare(Graphics g, boolean renderGaps)
-  {
-    graphics = g;
-    fm = g.getFontMetrics();
-
-    this.renderGaps = renderGaps;
-  }
-
-  public Color getResidueBoxColour(SequenceI seq, int i)
-  {
-    allGroups = av.alignment.findAllGroups(seq);
-
-    if (inCurrentSequenceGroup(i))
-    {
-      if (currentSequenceGroup.getDisplayBoxes())
-      {
-        getBoxColour(currentSequenceGroup.cs, seq, i);
-      }
-    }
-    else if (av.getShowBoxes())
-    {
-      getBoxColour(av.globalColourScheme, seq, i);
-    }
-
-    return resBoxColour;
-  }
-
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    if (cs != null)
-    {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
-    }
-    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
-    {
-      resBoxColour = Color.lightGray;
-    }
-    else
-    {
-      resBoxColour = Color.white;
-    }
-
-  }
-
-  public Color findSequenceColour(SequenceI seq, int i)
-  {
-    allGroups = av.alignment.findAllGroups(seq);
-    drawBoxes(seq, i, i, 0);
-    return resBoxColour;
-  }
-
-  public void drawSequence(SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int y1)
-  {
-    if (seq == null)
-    {
-      return;
-    }
-
-    allGroups = sg;
-
-    drawBoxes(seq, start, end, y1);
-
-    if (av.validCharWidth)
-    {
-      drawText(seq, start, end, y1);
-    }
-  }
-
-  public void drawBoxes(SequenceI seq, int start, int end, int y1)
-  {
-    int i = start;
-    int length = seq.getLength();
-
-    int curStart = -1;
-    int curWidth = av.charWidth;
-
-    Color tempColour = null;
-    while (i <= end)
-    {
-      resBoxColour = Color.white;
-      if (i < length)
-      {
-        if (inCurrentSequenceGroup(i))
-        {
-          if (currentSequenceGroup.getDisplayBoxes())
-          {
-            getBoxColour(currentSequenceGroup.cs, seq, i);
-          }
-        }
-        else if (av.getShowBoxes())
-        {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
-        }
-      }
-
-      if (resBoxColour != tempColour)
-      {
-        if (tempColour != null)
-        {
-          graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-                            av.charHeight);
-        }
-        graphics.setColor(resBoxColour);
-
-        curStart = i;
-        curWidth = av.charWidth;
-        tempColour = resBoxColour;
-
-      }
-      else
-      {
-        curWidth += av.charWidth;
-      }
-
-      i++;
-    }
-
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-                      av.charHeight);
-  }
-
-  public void drawText(SequenceI seq, int start, int end, int y1)
-  {
-    Font boldFont = null;
-    boolean bold = false;
-    if (av.upperCasebold)
-    {
-      boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
-
-      graphics.setFont(av.getFont());
-    }
-
-    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
-
-    int charOffset = 0;
-
-    // Need to find the sequence position here.
-    if (end + 1 >= seq.getLength())
-    {
-      end = seq.getLength() - 1;
-    }
-
-    char s = ' ';
-
-    for (int i = start; i <= end; i++)
-    {
-      graphics.setColor(Color.black);
-
-      s = seq.getCharAt(i);
-      if (!renderGaps && jalview.util.Comparison.isGap(s))
-      {
-        continue;
-      }
-
-      if (inCurrentSequenceGroup(i))
-      {
-        if (!currentSequenceGroup.getDisplayText())
-        {
-          continue;
-        }
-
-        if (currentSequenceGroup.getColourText())
-        {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
-          graphics.setColor(resBoxColour.darker());
-        }
-      }
-      else
-      {
-        if (!av.getShowText())
-        {
-          continue;
-        }
-
-        if (av.getColourText())
-        {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
-          if (av.getShowBoxes())
-          {
-            graphics.setColor(resBoxColour.darker());
-          }
-          else
-          {
-            graphics.setColor(resBoxColour);
-          }
-        }
-      }
-
-      if (av.upperCasebold)
-      {
-        fm = graphics.getFontMetrics();
-        if ('A' <= s && s <= 'Z')
-        {
-          if (!bold)
-          {
-
-            graphics.setFont(boldFont);
-          }
-          bold = true;
-        }
-        else if (bold)
-        {
-          graphics.setFont(av.font);
-          bold = false;
-        }
-
-      }
-
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + av.charWidth * (i - start),
-                          y1);
-    }
-
-  }
-
-  boolean inCurrentSequenceGroup(int res)
-  {
-    if (allGroups == null)
-    {
-      return false;
-    }
-
-    for (int i = 0; i < allGroups.length; i++)
-    {
-      if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
-      {
-        currentSequenceGroup = allGroups[i];
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
-                                  int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
-    graphics.setColor(Color.white);
-
-    char s = '~';
-    // Need to find the sequence position here.
-    if (av.validCharWidth)
-    {
-      for (int i = start; i <= end; i++)
-      {
-        if (i < seq.getLength())
-        {
-          s = seq.getCharAt(i);
-        }
-
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s),
-                            charOffset + x1 + av.charWidth * (i - start),
-                            y1 + av.charHeight - pady);
-      }
-    }
-  }
-
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
-    graphics.setColor(Color.white);
-
-    graphics.setColor(Color.white);
-
-    char s = seq.getCharAt(res);
-    if (av.validCharWidth)
-    {
-
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + x1,
-                          (y1 + av.charHeight) - pady);
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
+
+public class SequenceRenderer
+{
+  AlignViewport av;
+  FontMetrics fm;
+  boolean renderGaps = true;
+  SequenceGroup currentSequenceGroup = null;
+  SequenceGroup[] allGroups = null;
+  Color resBoxColour;
+  Graphics graphics;
+  boolean forOverview = false;
+
+  public SequenceRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void prepare(Graphics g, boolean renderGaps)
+  {
+    graphics = g;
+    fm = g.getFontMetrics();
+
+    this.renderGaps = renderGaps;
+  }
+
+  public Color getResidueBoxColour(SequenceI seq, int i)
+  {
+    allGroups = av.alignment.findAllGroups(seq);
+
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+      getBoxColour(av.globalColourScheme, seq, i);
+    }
+
+    return resBoxColour;
+  }
+
+  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  {
+    if (cs != null)
+    {
+      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+    }
+    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+      resBoxColour = Color.lightGray;
+    }
+    else
+    {
+      resBoxColour = Color.white;
+    }
+
+  }
+
+  public Color findSequenceColour(SequenceI seq, int i)
+  {
+    allGroups = av.alignment.findAllGroups(seq);
+    drawBoxes(seq, i, i, 0);
+    return resBoxColour;
+  }
+
+  public void drawSequence(SequenceI seq, SequenceGroup[] sg,
+                           int start, int end, int y1)
+  {
+    if (seq == null)
+    {
+      return;
+    }
+
+    allGroups = sg;
+
+    drawBoxes(seq, start, end, y1);
+
+    if (av.validCharWidth)
+    {
+      drawText(seq, start, end, y1);
+    }
+  }
+
+  public void drawBoxes(SequenceI seq, int start, int end, int y1)
+  {
+    int i = start;
+    int length = seq.getLength();
+
+    int curStart = -1;
+    int curWidth = av.charWidth;
+
+    Color tempColour = null;
+    while (i <= end)
+    {
+      resBoxColour = Color.white;
+      if (i < length)
+      {
+        if (inCurrentSequenceGroup(i))
+        {
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+          }
+        }
+        else if (av.getShowBoxes())
+        {
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
+        }
+      }
+
+      if (resBoxColour != tempColour)
+      {
+        if (tempColour != null)
+        {
+          graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                            av.charHeight);
+        }
+        graphics.setColor(resBoxColour);
+
+        curStart = i;
+        curWidth = av.charWidth;
+        tempColour = resBoxColour;
+
+      }
+      else
+      {
+        curWidth += av.charWidth;
+      }
+
+      i++;
+    }
+
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                      av.charHeight);
+  }
+
+  public void drawText(SequenceI seq, int start, int end, int y1)
+  {
+    Font boldFont = null;
+    boolean bold = false;
+    if (av.upperCasebold)
+    {
+      boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+
+      graphics.setFont(av.getFont());
+    }
+
+    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+
+    int charOffset = 0;
+
+    // Need to find the sequence position here.
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
+
+    char s = ' ';
+
+    for (int i = start; i <= end; i++)
+    {
+      graphics.setColor(Color.black);
+
+      s = seq.getCharAt(i);
+      if (!renderGaps && jalview.util.Comparison.isGap(s))
+      {
+        continue;
+      }
+
+      if (inCurrentSequenceGroup(i))
+      {
+        if (!currentSequenceGroup.getDisplayText())
+        {
+          continue;
+        }
+
+        if (currentSequenceGroup.getColourText())
+        {
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+          graphics.setColor(resBoxColour.darker());
+        }
+      }
+      else
+      {
+        if (!av.getShowText())
+        {
+          continue;
+        }
+
+        if (av.getColourText())
+        {
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
+          if (av.getShowBoxes())
+          {
+            graphics.setColor(resBoxColour.darker());
+          }
+          else
+          {
+            graphics.setColor(resBoxColour);
+          }
+        }
+      }
+
+      if (av.upperCasebold)
+      {
+        fm = graphics.getFontMetrics();
+        if ('A' <= s && s <= 'Z')
+        {
+          if (!bold)
+          {
+
+            graphics.setFont(boldFont);
+          }
+          bold = true;
+        }
+        else if (bold)
+        {
+          graphics.setFont(av.font);
+          bold = false;
+        }
+
+      }
+
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s),
+                          charOffset + av.charWidth * (i - start),
+                          y1);
+    }
+
+  }
+
+  boolean inCurrentSequenceGroup(int res)
+  {
+    if (allGroups == null)
+    {
+      return false;
+    }
+
+    for (int i = 0; i < allGroups.length; i++)
+    {
+      if (allGroups[i].getStartRes() <= res && allGroups[i].getEndRes() >= res)
+      {
+        currentSequenceGroup = allGroups[i];
+        return true;
+      }
+    }
+
+    return false;
+  }
+
+  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+                                  int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
+    graphics.setColor(Color.white);
+
+    char s = '~';
+    // Need to find the sequence position here.
+    if (av.validCharWidth)
+    {
+      for (int i = start; i <= end; i++)
+      {
+        if (i < seq.getLength())
+        {
+          s = seq.getCharAt(i);
+        }
+
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                            charOffset + x1 + av.charWidth * (i - start),
+                            y1 + av.charHeight - pady);
+      }
+    }
+  }
+
+  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+    graphics.setColor(Color.white);
+
+    graphics.setColor(Color.white);
+
+    char s = seq.getCharAt(res);
+    if (av.validCharWidth)
+    {
+
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s),
+                          charOffset + x1,
+                          (y1 + av.charHeight) - pady);
+    }
+  }
+
+}
diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 8507331..b898b2c 100755
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -1,363 +1,362 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class SliderPanel
-    extends Panel implements ActionListener,
-    AdjustmentListener,
-    MouseListener
-{
-  AlignmentPanel ap;
-  boolean forConservation = true;
-  ColourSchemeI cs;
-
-  static Frame conservationSlider;
-  static Frame PIDSlider;
-
-  public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs,
-                                          String source)
-  {
-    SliderPanel sp = null;
-
-    if (conservationSlider == null)
-    {
-      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
-      conservationSlider = new Frame();
-      conservationSlider.add(sp);
-    }
-    else
-    {
-      sp = (SliderPanel) conservationSlider.getComponent(0);
-      sp.cs = cs;
-    }
-
-    conservationSlider.setTitle("Conservation Colour Increment  (" + source +
-                                ")");
-    if (ap.av.alignment.getGroups() != null)
-    {
-      sp.setAllGroupsCheckEnabled(true);
-    }
-    else
-    {
-      sp.setAllGroupsCheckEnabled(false);
-    }
-
-    return sp.getValue();
-  }
-
-  public static void showConservationSlider()
-  {
-    try
-    {
-      PIDSlider.setVisible(false);
-      PIDSlider = null;
-    }
-    catch (Exception ex)
-    {}
-
-    if (!conservationSlider.isVisible())
-    {
-      jalview.bin.JalviewLite.addFrame(conservationSlider,
-                                       conservationSlider.getTitle(), 420, 100);
-      conservationSlider.addWindowListener(new WindowAdapter()
-      {
-        public void windowClosing(WindowEvent e)
-        {
-          conservationSlider = null;
-        }
-      });
-
-    }
-
-  }
-
-  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)
-        {
-          PIDSlider = null;
-        }
-      });
-    }
-
-  }
-
-  public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
-                     ColourSchemeI cs)
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-    this.ap = ap;
-    this.cs = cs;
-    forConservation = forConserve;
-    undoButton.setVisible(false);
-    applyButton.setVisible(false);
-    if (forConservation)
-    {
-      label.setText("Modify conservation visibility");
-      slider.setMinimum(0);
-      slider.setMaximum(50 + slider.getVisibleAmount());
-      slider.setUnitIncrement(1);
-    }
-    else
-    {
-      label.setText("Colour residues above % occurence");
-      slider.setMinimum(0);
-      slider.setMaximum(100 + slider.getVisibleAmount());
-      slider.setBlockIncrement(1);
-    }
-
-    slider.addAdjustmentListener(this);
-    slider.addMouseListener(this);
-
-    slider.setValue(value);
-    valueField.setText(value + "");
-  }
-
-  public void valueChanged(int i)
-  {
-    if (cs == null)
-    {
-      return;
-    }
-
-    ColourSchemeI toChange = null;
-    Vector allGroups = null;
-    int groupIndex = 0;
-
-    if (allGroupsCheck.getState())
-    {
-      allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size() - 1;
-    }
-    else
-    {
-      toChange = cs;
-    }
-
-    while (groupIndex > -1)
-    {
-      if (allGroups != null)
-      {
-        toChange = ( (SequenceGroup) allGroups.elementAt(groupIndex)).cs;
-      }
-
-      if (forConservation)
-      {
-        toChange.setConservationInc(i);
-      }
-      else
-      {
-        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
-      }
-
-      groupIndex--;
-    }
-
-    ap.seqPanel.seqCanvas.repaint();
-
-  }
-
-  public void setAllGroupsCheckEnabled(boolean b)
-  {
-    allGroupsCheck.setEnabled(b);
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == applyButton)
-    {
-      applyButton_actionPerformed();
-    }
-    else if (evt.getSource() == undoButton)
-    {
-      undoButton_actionPerformed();
-    }
-    else if (evt.getSource() == valueField)
-    {
-      valueField_actionPerformed();
-    }
-  }
-
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    valueField.setText(slider.getValue() + "");
-    valueChanged(slider.getValue());
-  }
-
-  public void valueField_actionPerformed()
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    }
-    catch (Exception ex)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-
-  public void setValue(int value)
-  {
-    slider.setValue(value);
-  }
-
-  public int getValue()
-  {
-    return Integer.parseInt(valueField.getText());
-  }
-
-  // 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();
-
-  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(this);
-    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(this);
-    undoButton.setEnabled(false);
-    undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    undoButton.setLabel("Undo");
-    undoButton.addActionListener(this);
-    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");
-    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 applyButton_actionPerformed()
-  {}
-
-  protected void undoButton_actionPerformed()
-  {}
-
-  public void mousePressed(MouseEvent evt)
-  {}
-
-  public void mouseReleased(MouseEvent evt)
-  {
-      ap.paintAlignment(true);
-  }
-
-  public void mouseClicked(MouseEvent evt)
-  {}
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-
-  public void mouseExited(MouseEvent evt)
-  {}
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 jalview.schemes.*;
+
+public class SliderPanel
+    extends Panel implements ActionListener,
+    AdjustmentListener,
+    MouseListener
+{
+  AlignmentPanel ap;
+  boolean forConservation = true;
+  ColourSchemeI cs;
+
+  static Frame conservationSlider;
+  static Frame PIDSlider;
+
+  public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs,
+                                          String source)
+  {
+    SliderPanel sp = null;
+
+    if (conservationSlider == null)
+    {
+      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+      conservationSlider = new Frame();
+      conservationSlider.add(sp);
+    }
+    else
+    {
+      sp = (SliderPanel) conservationSlider.getComponent(0);
+      sp.cs = cs;
+    }
+
+    conservationSlider.setTitle("Conservation Colour Increment  (" + source +
+                                ")");
+    if (ap.av.alignment.getGroups() != null)
+    {
+      sp.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      sp.setAllGroupsCheckEnabled(false);
+    }
+
+    return sp.getValue();
+  }
+
+  public static void showConservationSlider()
+  {
+    try
+    {
+      PIDSlider.setVisible(false);
+      PIDSlider = null;
+    }
+    catch (Exception ex)
+    {}
+
+    if (!conservationSlider.isVisible())
+    {
+      jalview.bin.JalviewLite.addFrame(conservationSlider,
+                                       conservationSlider.getTitle(), 420, 100);
+      conservationSlider.addWindowListener(new WindowAdapter()
+      {
+        public void windowClosing(WindowEvent e)
+        {
+          conservationSlider = null;
+        }
+      });
+
+    }
+
+  }
+
+  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)
+        {
+          PIDSlider = null;
+        }
+      });
+    }
+
+  }
+
+  public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
+                     ColourSchemeI cs)
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    this.ap = ap;
+    this.cs = cs;
+    forConservation = forConserve;
+    undoButton.setVisible(false);
+    applyButton.setVisible(false);
+    if (forConservation)
+    {
+      label.setText("Modify conservation visibility");
+      slider.setMinimum(0);
+      slider.setMaximum(50 + slider.getVisibleAmount());
+      slider.setUnitIncrement(1);
+    }
+    else
+    {
+      label.setText("Colour residues above % occurence");
+      slider.setMinimum(0);
+      slider.setMaximum(100 + slider.getVisibleAmount());
+      slider.setBlockIncrement(1);
+    }
+
+    slider.addAdjustmentListener(this);
+    slider.addMouseListener(this);
+
+    slider.setValue(value);
+    valueField.setText(value + "");
+  }
+
+  public void valueChanged(int i)
+  {
+    if (cs == null)
+    {
+      return;
+    }
+
+    ColourSchemeI toChange = null;
+    Vector allGroups = null;
+    int groupIndex = 0;
+
+    if (allGroupsCheck.getState())
+    {
+      allGroups = ap.av.alignment.getGroups();
+      groupIndex = allGroups.size() - 1;
+    }
+    else
+    {
+      toChange = cs;
+    }
+
+    while (groupIndex > -1)
+    {
+      if (allGroups != null)
+      {
+        toChange = ( (SequenceGroup) allGroups.elementAt(groupIndex)).cs;
+      }
+
+      if (forConservation)
+      {
+        toChange.setConservationInc(i);
+      }
+      else
+      {
+        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+      }
+
+      groupIndex--;
+    }
+
+    ap.seqPanel.seqCanvas.repaint();
+
+  }
+
+  public void setAllGroupsCheckEnabled(boolean b)
+  {
+    allGroupsCheck.setEnabled(b);
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == applyButton)
+    {
+      applyButton_actionPerformed();
+    }
+    else if (evt.getSource() == undoButton)
+    {
+      undoButton_actionPerformed();
+    }
+    else if (evt.getSource() == valueField)
+    {
+      valueField_actionPerformed();
+    }
+  }
+
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    valueField.setText(slider.getValue() + "");
+    valueChanged(slider.getValue());
+  }
+
+  public void valueField_actionPerformed()
+  {
+    try
+    {
+      int i = Integer.parseInt(valueField.getText());
+      slider.setValue(i);
+    }
+    catch (Exception ex)
+    {
+      valueField.setText(slider.getValue() + "");
+    }
+  }
+
+  public void setValue(int value)
+  {
+    slider.setValue(value);
+  }
+
+  public int getValue()
+  {
+    return Integer.parseInt(valueField.getText());
+  }
+
+  // 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();
+
+  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(this);
+    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(this);
+    undoButton.setEnabled(false);
+    undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    undoButton.setLabel("Undo");
+    undoButton.addActionListener(this);
+    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");
+    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 applyButton_actionPerformed()
+  {}
+
+  protected void undoButton_actionPerformed()
+  {}
+
+  public void mousePressed(MouseEvent evt)
+  {}
+
+  public void mouseReleased(MouseEvent evt)
+  {
+      ap.paintAlignment(true);
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {}
+
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
+}
diff --git a/src/jalview/appletgui/Tooltip.java b/src/jalview/appletgui/Tooltip.java
index 7de5193..cfc6bcc 100755
--- a/src/jalview/appletgui/Tooltip.java
+++ b/src/jalview/appletgui/Tooltip.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.applet.*;
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 425c7a9..d312fbf 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 6ab01aa..71fe134 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 6e14146..68cb610 100755
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -1,589 +1,588 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class UserDefinedColours
-    extends Panel implements ActionListener, AdjustmentListener
-{
-
-  AlignmentPanel ap;
-  SequenceGroup seqGroup;
-  Button selectedButton;
-  Vector oldColours = new Vector();
-  ColourSchemeI oldColourScheme;
-  Frame frame;
-  MCview.AppletPDBCanvas pdbcanvas;
-  AppletJmol jmol;
-
-  Dialog dialog;
-  Object caller;
-  String originalLabel;
-  Color originalColour;
-
-  int R = 0, G = 0, B = 0;
-
-  public ColourSchemeI loadDefaultColours()
-  {
-    // NOT IMPLEMENTED YET IN APPLET VERSION
-    return null;
-  }
-
-  public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
-  {
-    this.ap = ap;
-    seqGroup = sg;
-
-    if (seqGroup != null)
-    {
-      oldColourScheme = seqGroup.cs;
-    }
-    else
-    {
-      oldColourScheme = ap.av.getGlobalColourScheme();
-    }
-
-    init();
-  }
-
-  public UserDefinedColours(MCview.AppletPDBCanvas pdb)
-  {
-    this.pdbcanvas = pdb;
-    init();
-  }
-
-  public UserDefinedColours(AppletJmol jmol)
-  {
-    this.jmol = jmol;
-    init();
-  }
-
-  public UserDefinedColours(FeatureRenderer fr, Frame alignframe)
-  {
-    caller = fr;
-    originalColour = fr.colourPanel.getBackground();
-    originalLabel = "Feature Colour";
-    setForDialog("Select Feature Colour", alignframe);
-    setTargetColour(fr.colourPanel.getBackground());
-    dialog.setVisible(true);
-  }
-
-  public UserDefinedColours(Component caller,
-                            Color col1,
-                            Frame alignframe)
-  {
-    this.caller = caller;
-    originalColour = col1;
-    originalLabel = "Select Colour";
-    setForDialog("Select Colour", alignframe);
-    setTargetColour(col1);
-    dialog.setVisible(true);
-  }
-
-
-  public UserDefinedColours(Object caller,
-                            String label,
-                            Color colour)
-  {
-    this.caller = caller;
-    originalColour = colour;
-    originalLabel = label;
-    init();
-    remove(buttonPanel);
-
-    setTargetColour(colour);
-
-    okcancelPanel.setBounds(new Rectangle(0, 113, 400, 35));
-    frame.setTitle("User Defined Colours - " + label);
-    frame.setSize(420, 200);
-  }
-
-  void setForDialog(String title, Frame alignframe)
-  {
-    init();
-    frame.setVisible(false);
-    remove(buttonPanel);
-    dialog = new Dialog(alignframe, title, true);
-
-    dialog.add(this);
-    this.setSize(400,123);
-    okcancelPanel.setBounds(new Rectangle(0, 123, 400, 35));
-    int height = 160 + alignframe.getInsets().top + getInsets().bottom;
-    int width = 400;
-
-    dialog.setBounds(alignframe.getBounds().x
-              + (alignframe.getSize().width - width) / 2,
-              alignframe.getBounds().y
-              + (alignframe.getSize().height - height) / 2,
-              width, height);
-
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == okButton)
-    {
-      okButton_actionPerformed();
-    }
-    else if (evt.getSource() == applyButton)
-    {
-      applyButton_actionPerformed();
-    }
-    else if (evt.getSource() == cancelButton)
-    {
-      cancelButton_actionPerformed();
-    }
-    else if (evt.getSource() == rText)
-    {
-      rText_actionPerformed();
-    }
-    else if (evt.getSource() == gText)
-    {
-      gText_actionPerformed();
-    }
-    else if (evt.getSource() == bText)
-    {
-      bText_actionPerformed();
-    }
-  }
-
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    if (evt.getSource() == rScroller)
-    {
-      rScroller_adjustmentValueChanged();
-    }
-    else if (evt.getSource() == gScroller)
-    {
-      gScroller_adjustmentValueChanged();
-    }
-    else if (evt.getSource() == bScroller)
-    {
-      bScroller_adjustmentValueChanged();
-    }
-  }
-
-  void init()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-    frame = new Frame();
-    frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);
-
-    if (seqGroup != null)
-    {
-      frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
-    }
-
-    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", "'.','-',' '");
-
-    validate();
-  }
-
-  protected void rText_actionPerformed()
-  {
-    try
-    {
-      int i = Integer.parseInt(rText.getText());
-      rScroller.setValue(i);
-      rScroller_adjustmentValueChanged();
-    }
-    catch (NumberFormatException ex)
-    {}
-  }
-
-  protected void gText_actionPerformed()
-  {
-    try
-    {
-      int i = Integer.parseInt(gText.getText());
-      gScroller.setValue(i);
-      gScroller_adjustmentValueChanged();
-    }
-    catch (NumberFormatException ex)
-    {}
-
-  }
-
-  protected void bText_actionPerformed()
-  {
-    try
-    {
-      int i = Integer.parseInt(bText.getText());
-      bScroller.setValue(i);
-      bScroller_adjustmentValueChanged();
-    }
-    catch (NumberFormatException ex)
-    {}
-
-  }
-
-  protected void rScroller_adjustmentValueChanged()
-  {
-    R = rScroller.getValue();
-    rText.setText(R + "");
-    colourChanged();
-  }
-
-  protected void gScroller_adjustmentValueChanged()
-  {
-    G = gScroller.getValue();
-    gText.setText(G + "");
-    colourChanged();
-  }
-
-  protected void bScroller_adjustmentValueChanged()
-  {
-    B = bScroller.getValue();
-    bText.setText(B + "");
-    colourChanged();
-  }
-
-  public void colourChanged()
-  {
-    Color col = new Color(R, G, B);
-    target.setBackground(col);
-    target.repaint();
-
-    if (selectedButton != null)
-    {
-      selectedButton.setBackground(col);
-      selectedButton.repaint();
-    }
-  }
-
-  void setTargetColour(Color col)
-  {
-    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();
-  }
-
-  public void colourButtonPressed(MouseEvent e)
-  {
-    selectedButton = (Button) e.getSource();
-    setTargetColour(selectedButton.getBackground());
-  }
-
-  void makeButton(String label, String aa)
-  {
-    final Button button = new Button();
-    Color col = Color.white;
-
-    try
-    {
-      col = oldColourScheme.findColour(aa.charAt(0), -1);
-    }
-    catch (Exception ex)
-    {}
-
-    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()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        colourButtonPressed(e);
-      }
-    });
-
-    buttonPanel.add(button, null);
-  }
-
-  protected void okButton_actionPerformed()
-  {
-    applyButton_actionPerformed();
-    if (dialog != null)
-      dialog.setVisible(false);
-
-    frame.setVisible(false);
-  }
-
-  public Color getColor()
-  {
-    return new Color(R, G, B);
-  }
-
-  protected void applyButton_actionPerformed()
-  {
-    if (caller != null)
-    {
-      if (caller instanceof FeatureSettings)
-      {
-        ( (FeatureSettings) caller).setUserColour
-            (originalLabel, getColor());
-      }
-      else if (caller instanceof AnnotationColourChooser)
-      {
-        if (originalLabel.equals("Min Colour"))
-        {
-          ( (AnnotationColourChooser) caller).minColour_actionPerformed
-              (getColor());
-        }
-        else
-        {
-          ( (AnnotationColourChooser) caller).maxColour_actionPerformed
-              (getColor());
-        }
-      }
-      else if(caller instanceof FeatureRenderer)
-      {
-        ((FeatureRenderer)caller).colourPanel.setBackground(getColor());
-      }
-
-      return;
-    }
-
-    Color[] newColours = new Color[24];
-    for (int i = 0; i < 24; i++)
-    {
-      Button button = (Button) buttonPanel.getComponent(i);
-      newColours[i] = button.getBackground();
-    }
-
-    UserColourScheme ucs = new UserColourScheme(newColours);
-    if (ap != null)
-    {
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
-    }
-
-    if (ap != null)
-    {
-      if (seqGroup != null)
-      {
-        seqGroup.cs = ucs;
-      }
-      else
-      {
-        ap.av.setGlobalColourScheme(ucs);
-      }
-      ap.seqPanel.seqCanvas.img = null;
-      ap.paintAlignment(true);
-    }
-    else if(jmol!=null)
-    {
-      jmol.setJalviewColourScheme(ucs);
-    }
-    else if (pdbcanvas != null)
-    {
-      pdbcanvas.setColours(ucs);
-    }
-  }
-
-  protected void cancelButton_actionPerformed()
-  {
-    if (caller != null)
-    {
-      if (caller instanceof FeatureSettings)
-      {
-        ( (FeatureSettings) caller).setUserColour
-            (originalLabel, originalColour);
-      }
-      else if (caller instanceof AnnotationColourChooser)
-      {
-        if (originalLabel.equals("Min Colour"))
-        {
-          ( (AnnotationColourChooser) caller).minColour_actionPerformed
-              (originalColour);
-        }
-        else
-        {
-          ( (AnnotationColourChooser) caller).maxColour_actionPerformed
-              (originalColour);
-        }
-      }
-      else if (caller instanceof FeatureRenderer)
-      {
-        ( (FeatureRenderer) caller).colourPanel.setBackground(originalColour);
-
-      }
-
-      if(dialog!=null)
-        dialog.setVisible(false);
-
-      frame.setVisible(false);
-      return;
-    }
-
-    Color[] newColours = new Color[24];
-    for (int i = 0; i < 24; i++)
-    {
-      newColours[i] = (Color) oldColours.elementAt(i);
-      buttonPanel.getComponent(i).setBackground(newColours[i]);
-    }
-
-    UserColourScheme ucs = new UserColourScheme(newColours);
-
-    if (ap != null)
-    {
-      if (seqGroup != null)
-      {
-        seqGroup.cs = ucs;
-      }
-      else
-      {
-        ap.av.setGlobalColourScheme(ucs);
-      }
-      ap.paintAlignment(true);
-    }
-    else if(jmol !=null)
-    {
-      jmol.setJalviewColourScheme(ucs);
-    }
-    else if (pdbcanvas != null)
-    {
-      pdbcanvas.pdb.setColours(ucs);
-    }
-
-    frame.setVisible(false);
-  }
-
-  protected Panel buttonPanel = new Panel();
-  protected GridLayout gridLayout = new GridLayout();
-  Panel okcancelPanel = 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();
-  protected TextField rText = new TextField();
-  Label label4 = new Label();
-  protected Scrollbar gScroller = new Scrollbar();
-  protected TextField gText = new TextField();
-  Label label5 = new Label();
-  protected Scrollbar bScroller = new Scrollbar();
-  protected TextField bText = new TextField();
-  protected Panel target = new Panel();
-
-  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(this);
-    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    applyButton.setLabel("Apply");
-    applyButton.addActionListener(this);
-    cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    cancelButton.setLabel("Cancel");
-    cancelButton.addActionListener(this);
-    this.setBackground(new Color(212, 208, 223));
-    okcancelPanel.setBounds(new Rectangle(0, 265, 400, 35));
-    buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));
-    rScroller.setMaximum(256);
-    rScroller.setMinimum(0);
-    rScroller.setOrientation(0);
-    rScroller.setUnitIncrement(1);
-    rScroller.setVisibleAmount(1);
-    rScroller.setBounds(new Rectangle(36, 27, 119, 19));
-    rScroller.addAdjustmentListener(this);
-    label1.setAlignment(Label.RIGHT);
-    label1.setText("R");
-    label1.setBounds(new Rectangle(19, 30, 16, 15));
-    rText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
-    rText.setText("0        ");
-    rText.setBounds(new Rectangle(156, 27, 53, 19));
-    rText.addActionListener(this);
-    label4.setAlignment(Label.RIGHT);
-    label4.setText("G");
-    label4.setBounds(new Rectangle(15, 56, 20, 15));
-    gScroller.setMaximum(256);
-    gScroller.setMinimum(0);
-    gScroller.setOrientation(0);
-    gScroller.setUnitIncrement(1);
-    gScroller.setVisibleAmount(1);
-    gScroller.setBounds(new Rectangle(35, 52, 120, 20));
-    gScroller.addAdjustmentListener(this);
-    gText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
-    gText.setText("0        ");
-    gText.setBounds(new Rectangle(156, 52, 53, 20));
-    gText.addActionListener(this);
-    label5.setAlignment(Label.RIGHT);
-    label5.setText("B");
-    label5.setBounds(new Rectangle(14, 82, 20, 15));
-    bScroller.setMaximum(256);
-    bScroller.setMinimum(0);
-    bScroller.setOrientation(0);
-    bScroller.setUnitIncrement(1);
-    bScroller.setVisibleAmount(1);
-    bScroller.setBounds(new Rectangle(35, 78, 120, 20));
-    bScroller.addAdjustmentListener(this);
-    bText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
-    bText.setText("0        ");
-    bText.setBounds(new Rectangle(157, 78, 52, 20));
-    bText.addActionListener(this);
-    target.setBackground(Color.black);
-    target.setBounds(new Rectangle(229, 26, 134, 79));
-    this.add(okcancelPanel, null);
-    okcancelPanel.add(okButton, null);
-    okcancelPanel.add(applyButton, null);
-    okcancelPanel.add(cancelButton, null);
-    this.add(buttonPanel, null);
-    this.add(target, null);
-    this.add(gScroller);
-    this.add(rScroller);
-    this.add(bScroller);
-    this.add(label5);
-    this.add(label4);
-    this.add(label1);
-    this.add(gText);
-    this.add(rText);
-    this.add(bText);
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 jalview.schemes.*;
+
+public class UserDefinedColours
+    extends Panel implements ActionListener, AdjustmentListener
+{
+
+  AlignmentPanel ap;
+  SequenceGroup seqGroup;
+  Button selectedButton;
+  Vector oldColours = new Vector();
+  ColourSchemeI oldColourScheme;
+  Frame frame;
+  MCview.AppletPDBCanvas pdbcanvas;
+  AppletJmol jmol;
+
+  Dialog dialog;
+  Object caller;
+  String originalLabel;
+  Color originalColour;
+
+  int R = 0, G = 0, B = 0;
+
+  public ColourSchemeI loadDefaultColours()
+  {
+    // NOT IMPLEMENTED YET IN APPLET VERSION
+    return null;
+  }
+
+  public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
+  {
+    this.ap = ap;
+    seqGroup = sg;
+
+    if (seqGroup != null)
+    {
+      oldColourScheme = seqGroup.cs;
+    }
+    else
+    {
+      oldColourScheme = ap.av.getGlobalColourScheme();
+    }
+
+    init();
+  }
+
+  public UserDefinedColours(MCview.AppletPDBCanvas pdb)
+  {
+    this.pdbcanvas = pdb;
+    init();
+  }
+
+  public UserDefinedColours(AppletJmol jmol)
+  {
+    this.jmol = jmol;
+    init();
+  }
+
+  public UserDefinedColours(FeatureRenderer fr, Frame alignframe)
+  {
+    caller = fr;
+    originalColour = fr.colourPanel.getBackground();
+    originalLabel = "Feature Colour";
+    setForDialog("Select Feature Colour", alignframe);
+    setTargetColour(fr.colourPanel.getBackground());
+    dialog.setVisible(true);
+  }
+
+  public UserDefinedColours(Component caller,
+                            Color col1,
+                            Frame alignframe)
+  {
+    this.caller = caller;
+    originalColour = col1;
+    originalLabel = "Select Colour";
+    setForDialog("Select Colour", alignframe);
+    setTargetColour(col1);
+    dialog.setVisible(true);
+  }
+
+
+  public UserDefinedColours(Object caller,
+                            String label,
+                            Color colour)
+  {
+    this.caller = caller;
+    originalColour = colour;
+    originalLabel = label;
+    init();
+    remove(buttonPanel);
+
+    setTargetColour(colour);
+
+    okcancelPanel.setBounds(new Rectangle(0, 113, 400, 35));
+    frame.setTitle("User Defined Colours - " + label);
+    frame.setSize(420, 200);
+  }
+
+  void setForDialog(String title, Frame alignframe)
+  {
+    init();
+    frame.setVisible(false);
+    remove(buttonPanel);
+    dialog = new Dialog(alignframe, title, true);
+
+    dialog.add(this);
+    this.setSize(400,123);
+    okcancelPanel.setBounds(new Rectangle(0, 123, 400, 35));
+    int height = 160 + alignframe.getInsets().top + getInsets().bottom;
+    int width = 400;
+
+    dialog.setBounds(alignframe.getBounds().x
+              + (alignframe.getSize().width - width) / 2,
+              alignframe.getBounds().y
+              + (alignframe.getSize().height - height) / 2,
+              width, height);
+
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == okButton)
+    {
+      okButton_actionPerformed();
+    }
+    else if (evt.getSource() == applyButton)
+    {
+      applyButton_actionPerformed();
+    }
+    else if (evt.getSource() == cancelButton)
+    {
+      cancelButton_actionPerformed();
+    }
+    else if (evt.getSource() == rText)
+    {
+      rText_actionPerformed();
+    }
+    else if (evt.getSource() == gText)
+    {
+      gText_actionPerformed();
+    }
+    else if (evt.getSource() == bText)
+    {
+      bText_actionPerformed();
+    }
+  }
+
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    if (evt.getSource() == rScroller)
+    {
+      rScroller_adjustmentValueChanged();
+    }
+    else if (evt.getSource() == gScroller)
+    {
+      gScroller_adjustmentValueChanged();
+    }
+    else if (evt.getSource() == bScroller)
+    {
+      bScroller_adjustmentValueChanged();
+    }
+  }
+
+  void init()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    frame = new Frame();
+    frame.add(this);
+    jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);
+
+    if (seqGroup != null)
+    {
+      frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
+    }
+
+    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", "'.','-',' '");
+
+    validate();
+  }
+
+  protected void rText_actionPerformed()
+  {
+    try
+    {
+      int i = Integer.parseInt(rText.getText());
+      rScroller.setValue(i);
+      rScroller_adjustmentValueChanged();
+    }
+    catch (NumberFormatException ex)
+    {}
+  }
+
+  protected void gText_actionPerformed()
+  {
+    try
+    {
+      int i = Integer.parseInt(gText.getText());
+      gScroller.setValue(i);
+      gScroller_adjustmentValueChanged();
+    }
+    catch (NumberFormatException ex)
+    {}
+
+  }
+
+  protected void bText_actionPerformed()
+  {
+    try
+    {
+      int i = Integer.parseInt(bText.getText());
+      bScroller.setValue(i);
+      bScroller_adjustmentValueChanged();
+    }
+    catch (NumberFormatException ex)
+    {}
+
+  }
+
+  protected void rScroller_adjustmentValueChanged()
+  {
+    R = rScroller.getValue();
+    rText.setText(R + "");
+    colourChanged();
+  }
+
+  protected void gScroller_adjustmentValueChanged()
+  {
+    G = gScroller.getValue();
+    gText.setText(G + "");
+    colourChanged();
+  }
+
+  protected void bScroller_adjustmentValueChanged()
+  {
+    B = bScroller.getValue();
+    bText.setText(B + "");
+    colourChanged();
+  }
+
+  public void colourChanged()
+  {
+    Color col = new Color(R, G, B);
+    target.setBackground(col);
+    target.repaint();
+
+    if (selectedButton != null)
+    {
+      selectedButton.setBackground(col);
+      selectedButton.repaint();
+    }
+  }
+
+  void setTargetColour(Color col)
+  {
+    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();
+  }
+
+  public void colourButtonPressed(MouseEvent e)
+  {
+    selectedButton = (Button) e.getSource();
+    setTargetColour(selectedButton.getBackground());
+  }
+
+  void makeButton(String label, String aa)
+  {
+    final Button button = new Button();
+    Color col = Color.white;
+
+    try
+    {
+      col = oldColourScheme.findColour(aa.charAt(0), -1);
+    }
+    catch (Exception ex)
+    {}
+
+    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()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        colourButtonPressed(e);
+      }
+    });
+
+    buttonPanel.add(button, null);
+  }
+
+  protected void okButton_actionPerformed()
+  {
+    applyButton_actionPerformed();
+    if (dialog != null)
+      dialog.setVisible(false);
+
+    frame.setVisible(false);
+  }
+
+  public Color getColor()
+  {
+    return new Color(R, G, B);
+  }
+
+  protected void applyButton_actionPerformed()
+  {
+    if (caller != null)
+    {
+      if (caller instanceof FeatureSettings)
+      {
+        ( (FeatureSettings) caller).setUserColour
+            (originalLabel, getColor());
+      }
+      else if (caller instanceof AnnotationColourChooser)
+      {
+        if (originalLabel.equals("Min Colour"))
+        {
+          ( (AnnotationColourChooser) caller).minColour_actionPerformed
+              (getColor());
+        }
+        else
+        {
+          ( (AnnotationColourChooser) caller).maxColour_actionPerformed
+              (getColor());
+        }
+      }
+      else if(caller instanceof FeatureRenderer)
+      {
+        ((FeatureRenderer)caller).colourPanel.setBackground(getColor());
+      }
+
+      return;
+    }
+
+    Color[] newColours = new Color[24];
+    for (int i = 0; i < 24; i++)
+    {
+      Button button = (Button) buttonPanel.getComponent(i);
+      newColours[i] = button.getBackground();
+    }
+
+    UserColourScheme ucs = new UserColourScheme(newColours);
+    if (ap != null)
+    {
+      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+    }
+
+    if (ap != null)
+    {
+      if (seqGroup != null)
+      {
+        seqGroup.cs = ucs;
+      }
+      else
+      {
+        ap.av.setGlobalColourScheme(ucs);
+      }
+      ap.seqPanel.seqCanvas.img = null;
+      ap.paintAlignment(true);
+    }
+    else if(jmol!=null)
+    {
+      jmol.setJalviewColourScheme(ucs);
+    }
+    else if (pdbcanvas != null)
+    {
+      pdbcanvas.setColours(ucs);
+    }
+  }
+
+  protected void cancelButton_actionPerformed()
+  {
+    if (caller != null)
+    {
+      if (caller instanceof FeatureSettings)
+      {
+        ( (FeatureSettings) caller).setUserColour
+            (originalLabel, originalColour);
+      }
+      else if (caller instanceof AnnotationColourChooser)
+      {
+        if (originalLabel.equals("Min Colour"))
+        {
+          ( (AnnotationColourChooser) caller).minColour_actionPerformed
+              (originalColour);
+        }
+        else
+        {
+          ( (AnnotationColourChooser) caller).maxColour_actionPerformed
+              (originalColour);
+        }
+      }
+      else if (caller instanceof FeatureRenderer)
+      {
+        ( (FeatureRenderer) caller).colourPanel.setBackground(originalColour);
+
+      }
+
+      if(dialog!=null)
+        dialog.setVisible(false);
+
+      frame.setVisible(false);
+      return;
+    }
+
+    Color[] newColours = new Color[24];
+    for (int i = 0; i < 24; i++)
+    {
+      newColours[i] = (Color) oldColours.elementAt(i);
+      buttonPanel.getComponent(i).setBackground(newColours[i]);
+    }
+
+    UserColourScheme ucs = new UserColourScheme(newColours);
+
+    if (ap != null)
+    {
+      if (seqGroup != null)
+      {
+        seqGroup.cs = ucs;
+      }
+      else
+      {
+        ap.av.setGlobalColourScheme(ucs);
+      }
+      ap.paintAlignment(true);
+    }
+    else if(jmol !=null)
+    {
+      jmol.setJalviewColourScheme(ucs);
+    }
+    else if (pdbcanvas != null)
+    {
+      pdbcanvas.pdb.setColours(ucs);
+    }
+
+    frame.setVisible(false);
+  }
+
+  protected Panel buttonPanel = new Panel();
+  protected GridLayout gridLayout = new GridLayout();
+  Panel okcancelPanel = 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();
+  protected TextField rText = new TextField();
+  Label label4 = new Label();
+  protected Scrollbar gScroller = new Scrollbar();
+  protected TextField gText = new TextField();
+  Label label5 = new Label();
+  protected Scrollbar bScroller = new Scrollbar();
+  protected TextField bText = new TextField();
+  protected Panel target = new Panel();
+
+  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(this);
+    applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    applyButton.setLabel("Apply");
+    applyButton.addActionListener(this);
+    cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));
+    cancelButton.setLabel("Cancel");
+    cancelButton.addActionListener(this);
+    this.setBackground(new Color(212, 208, 223));
+    okcancelPanel.setBounds(new Rectangle(0, 265, 400, 35));
+    buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));
+    rScroller.setMaximum(256);
+    rScroller.setMinimum(0);
+    rScroller.setOrientation(0);
+    rScroller.setUnitIncrement(1);
+    rScroller.setVisibleAmount(1);
+    rScroller.setBounds(new Rectangle(36, 27, 119, 19));
+    rScroller.addAdjustmentListener(this);
+    label1.setAlignment(Label.RIGHT);
+    label1.setText("R");
+    label1.setBounds(new Rectangle(19, 30, 16, 15));
+    rText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
+    rText.setText("0        ");
+    rText.setBounds(new Rectangle(156, 27, 53, 19));
+    rText.addActionListener(this);
+    label4.setAlignment(Label.RIGHT);
+    label4.setText("G");
+    label4.setBounds(new Rectangle(15, 56, 20, 15));
+    gScroller.setMaximum(256);
+    gScroller.setMinimum(0);
+    gScroller.setOrientation(0);
+    gScroller.setUnitIncrement(1);
+    gScroller.setVisibleAmount(1);
+    gScroller.setBounds(new Rectangle(35, 52, 120, 20));
+    gScroller.addAdjustmentListener(this);
+    gText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
+    gText.setText("0        ");
+    gText.setBounds(new Rectangle(156, 52, 53, 20));
+    gText.addActionListener(this);
+    label5.setAlignment(Label.RIGHT);
+    label5.setText("B");
+    label5.setBounds(new Rectangle(14, 82, 20, 15));
+    bScroller.setMaximum(256);
+    bScroller.setMinimum(0);
+    bScroller.setOrientation(0);
+    bScroller.setUnitIncrement(1);
+    bScroller.setVisibleAmount(1);
+    bScroller.setBounds(new Rectangle(35, 78, 120, 20));
+    bScroller.addAdjustmentListener(this);
+    bText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));
+    bText.setText("0        ");
+    bText.setBounds(new Rectangle(157, 78, 52, 20));
+    bText.addActionListener(this);
+    target.setBackground(Color.black);
+    target.setBounds(new Rectangle(229, 26, 134, 79));
+    this.add(okcancelPanel, null);
+    okcancelPanel.add(okButton, null);
+    okcancelPanel.add(applyButton, null);
+    okcancelPanel.add(cancelButton, null);
+    this.add(buttonPanel, null);
+    this.add(target, null);
+    this.add(gScroller);
+    this.add(rScroller);
+    this.add(bScroller);
+    this.add(label5);
+    this.add(label4);
+    this.add(label1);
+    this.add(gText);
+    this.add(rText);
+    this.add(bText);
+  }
+
+}
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 0744cd9..65ff8c5 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 4f383a0..cf3ac30 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 393476d..8f2b3d4 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 5b107b5..3a90ca9 100755
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java
index 108d3ad..2608d9d 100755
--- a/src/jalview/binding/Annotation.java
+++ b/src/jalview/binding/Annotation.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java
index d133fe0..7293790 100755
--- a/src/jalview/binding/AnnotationElement.java
+++ b/src/jalview/binding/AnnotationElement.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
index 488ff98..f0a0ec2 100755
--- a/src/jalview/binding/Colour.java
+++ b/src/jalview/binding/Colour.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java
index d429df3..de40051 100755
--- a/src/jalview/binding/Feature.java
+++ b/src/jalview/binding/Feature.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java
index f3d06be..87b12ef 100755
--- a/src/jalview/binding/FeatureSettings.java
+++ b/src/jalview/binding/FeatureSettings.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Features.java b/src/jalview/binding/Features.java
index e50ae7c..0ca7e53 100755
--- a/src/jalview/binding/Features.java
+++ b/src/jalview/binding/Features.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java
index 862eebd..fe15b16 100755
--- a/src/jalview/binding/JGroup.java
+++ b/src/jalview/binding/JGroup.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
index 14b1f2f..0a967bd 100755
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java
index 21f8be9..e49546a 100755
--- a/src/jalview/binding/JalviewModel.java
+++ b/src/jalview/binding/JalviewModel.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 5ebcee6..784af77 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java
index b5d0335..3aa2f76 100755
--- a/src/jalview/binding/JalviewUserColours.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java
index cac4cf6..341d498 100755
--- a/src/jalview/binding/Pdbentry.java
+++ b/src/jalview/binding/Pdbentry.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java
index 83bc40a..2299e41 100755
--- a/src/jalview/binding/PdbentryItem.java
+++ b/src/jalview/binding/PdbentryItem.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
 /**
diff --git a/src/jalview/binding/Pdbids.java b/src/jalview/binding/Pdbids.java
index b4745a2..ed6fd8f 100755
--- a/src/jalview/binding/Pdbids.java
+++ b/src/jalview/binding/Pdbids.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Property.java b/src/jalview/binding/Property.java
index f1114f7..c05e3c4 100755
--- a/src/jalview/binding/Property.java
+++ b/src/jalview/binding/Property.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java
index 9c8cbc2..7370668 100755
--- a/src/jalview/binding/Sequence.java
+++ b/src/jalview/binding/Sequence.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
index 13a9020..32c2f0f 100755
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java
index 1bb2a62..32d09ea 100755
--- a/src/jalview/binding/SequenceType.java
+++ b/src/jalview/binding/SequenceType.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java
index 9cd84b4..253c77f 100755
--- a/src/jalview/binding/Setting.java
+++ b/src/jalview/binding/Setting.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java
index 5f138d0..afebcf6 100755
--- a/src/jalview/binding/Tree.java
+++ b/src/jalview/binding/Tree.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java
index 24c97ff..6d81bac 100755
--- a/src/jalview/binding/UserColourScheme.java
+++ b/src/jalview/binding/UserColourScheme.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java
index bdefe05..ae14b12 100755
--- a/src/jalview/binding/UserColours.java
+++ b/src/jalview/binding/UserColours.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index 1c92bd3..19440c1 100755
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java
index 5fda35e..2901305 100755
--- a/src/jalview/binding/VamsasModel.java
+++ b/src/jalview/binding/VamsasModel.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java
index 643c323..34d8f69 100755
--- a/src/jalview/binding/Viewport.java
+++ b/src/jalview/binding/Viewport.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.binding;
 
   //---------------------------------/
diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 976be92..64bffbc 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/commands/CommandI.java b/src/jalview/commands/CommandI.java
index 97675e7..9fe508b 100644
--- a/src/jalview/commands/CommandI.java
+++ b/src/jalview/commands/CommandI.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index e859e3e..a50cdc4 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/commands/OrderCommand.java b/src/jalview/commands/OrderCommand.java
index b331690..13328b8 100644
--- a/src/jalview/commands/OrderCommand.java
+++ b/src/jalview/commands/OrderCommand.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index a874f71..ecd2cba 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.commands;
 
 /*
diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index 5639fa5..fffea86 100644
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.commands;
 
 /*
diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java
index 9b9c99e..ff5742b 100644
--- a/src/jalview/commands/SlideSequencesCommand.java
+++ b/src/jalview/commands/SlideSequencesCommand.java
@@ -1,23 +1,21 @@
-
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.commands;
 
 import jalview.datamodel.*;
diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 4110bd1..81b5dca 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 6c6c26e..3f05d5f 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 import java.util.Enumeration;
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index a88fa9e..82bc8db 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index f2864db..07fbfa5 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index f89602f..eb27908 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index b149749..3f806b6 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,316 +1,316 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-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;
-     }
-   */
-
-  /** DOCUMENT ME!! */
-  public static final int FILE = 0;
-
-  /** DOCUMENT ME!! */
-  public static final int MSA = 1;
-
-  /** DOCUMENT ME!! */
-  public static final int USER = 2;
-  private int Type = 0;
-  private String Name;
-  private Vector Order = null;
-
-  /**
-   * Creates a new AlignmentOrder object.
-   */
-  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));
-    }
-  }
-
-  /**
-   * Creates a new AlignmentOrder object.
-   *
-   * @param orderFrom DOCUMENT ME!
-   */
-  public AlignmentOrder(SequenceI[] orderFrom)
-  {
-    Order = new Vector();
-
-    for (int i = 0, ns = orderFrom.length; i < ns; i++)
-    {
-      Order.addElement(orderFrom[i]);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param Type DOCUMENT ME!
-   */
-  public void setType(int Type)
-  {
-    this.Type = Type;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getType()
-  {
-    return Type;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param Name DOCUMENT ME!
-   */
-  public void setName(String Name)
-  {
-    this.Name = Name;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String getName()
-  {
-    return Name;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param Order DOCUMENT ME!
-   */
-  public void setOrder(Vector Order)
-  {
-    this.Order = Order;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Vector getOrder()
-  {
-    return Order;
-  }
-
-  /**
-   * replaces oldref with newref in the alignment order.
-   * @param oldref
-   * @param newref
-   * @return true if oldref was contained in order and replaced with newref
-   */
-  public boolean updateSequence(SequenceI oldref, SequenceI newref)
-  {
-    int found = Order.indexOf(oldref);
-    if (found > -1)
-    {
-      Order.setElementAt(newref, found);
-    }
-    return found > -1;
-  }
-
-  /**
-   * Exact equivalence of two AlignmentOrders
-   * @param o
-   * @return true if o orders the same sequenceI objects in the same way
-   */
-  public boolean equals(AlignmentOrder o)
-  {
-    return equals(o, true);
-  }
-
-  /**
-   * Exact equivalence of two AlignmentOrders
-   *  // TODO: Weak SequenceI equivalence - will throw Error at moment
-   * @param o
-   * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)
-   * @return true if o orders equivalent sequenceI objects in the same way
-   */
-  public boolean equals(AlignmentOrder o, boolean identity)
-  {
-    if (o != this)
-    {
-      if (o == null)
-      {
-        return false;
-      }
-      if (Order != null && o.Order != null && Order.size() == o.Order.size())
-      {
-        if (!identity)
-        {
-          throw new Error("Weak sequenceI equivalence not yet implemented.");
-        }
-        else
-        {
-          for (int i = 0, j = o.Order.size(); i < j; i++)
-          {
-            if (Order.elementAt(i) != o.Order.elementAt(i))
-            {
-              return false;
-            }
-          }
-        }
-      }
-      else
-      {
-        return false;
-      }
-    }
-    return true;
-  }
-
-  /**
-   * Consistency test for alignmentOrders
-   * @param o
-   * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way
-   */
-  public boolean isConsistent(AlignmentOrder o)
-  {
-    return isConsistent(o, true);
-  }
-
-  /**
-   * Consistency test for alignmentOrders
-   * @param o
-   *  // TODO: Weak SequenceI equivalence - will throw Error at moment
-   * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)
-   * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way
-   */
-  public boolean isConsistent(AlignmentOrder o, boolean identity)
-  {
-    if (o != this)
-    {
-      if (o == null)
-      {
-        return false;
-      }
-      if (Order != null && o.Order != null)
-      {
-        Vector c, s;
-        if (o.Order.size() > Order.size())
-        {
-          c = o.Order;
-          s = Order;
-        }
-        else
-        {
-          c = Order;
-          s = o.Order;
-        }
-        if (!identity)
-        {
-          throw new Error("Weak sequenceI equivalence not yet implemented.");
-        }
-        else
-        {
-          // test if c contains s and order in s is conserved in c
-          int last = -1;
-          for (int i = 0, j = s.size(); i < j; i++)
-          {
-            int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by incremental position search
-            if (pos > last)
-            {
-              last = pos;
-            }
-            else
-            {
-              return false;
-            }
-          }
-        }
-      }
-      else
-      {
-        return false;
-      }
-    }
-    return true;
-  }
-  /**
-   * 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
-
-   } */
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+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;
+     }
+   */
+
+  /** DOCUMENT ME!! */
+  public static final int FILE = 0;
+
+  /** DOCUMENT ME!! */
+  public static final int MSA = 1;
+
+  /** DOCUMENT ME!! */
+  public static final int USER = 2;
+  private int Type = 0;
+  private String Name;
+  private Vector Order = null;
+
+  /**
+   * Creates a new AlignmentOrder object.
+   */
+  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));
+    }
+  }
+
+  /**
+   * Creates a new AlignmentOrder object.
+   *
+   * @param orderFrom DOCUMENT ME!
+   */
+  public AlignmentOrder(SequenceI[] orderFrom)
+  {
+    Order = new Vector();
+
+    for (int i = 0, ns = orderFrom.length; i < ns; i++)
+    {
+      Order.addElement(orderFrom[i]);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Type DOCUMENT ME!
+   */
+  public void setType(int Type)
+  {
+    this.Type = Type;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getType()
+  {
+    return Type;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Name DOCUMENT ME!
+   */
+  public void setName(String Name)
+  {
+    this.Name = Name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return Name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Order DOCUMENT ME!
+   */
+  public void setOrder(Vector Order)
+  {
+    this.Order = Order;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Vector getOrder()
+  {
+    return Order;
+  }
+
+  /**
+   * replaces oldref with newref in the alignment order.
+   * @param oldref
+   * @param newref
+   * @return true if oldref was contained in order and replaced with newref
+   */
+  public boolean updateSequence(SequenceI oldref, SequenceI newref)
+  {
+    int found = Order.indexOf(oldref);
+    if (found > -1)
+    {
+      Order.setElementAt(newref, found);
+    }
+    return found > -1;
+  }
+
+  /**
+   * Exact equivalence of two AlignmentOrders
+   * @param o
+   * @return true if o orders the same sequenceI objects in the same way
+   */
+  public boolean equals(AlignmentOrder o)
+  {
+    return equals(o, true);
+  }
+
+  /**
+   * Exact equivalence of two AlignmentOrders
+   *  // TODO: Weak SequenceI equivalence - will throw Error at moment
+   * @param o
+   * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)
+   * @return true if o orders equivalent sequenceI objects in the same way
+   */
+  public boolean equals(AlignmentOrder o, boolean identity)
+  {
+    if (o != this)
+    {
+      if (o == null)
+      {
+        return false;
+      }
+      if (Order != null && o.Order != null && Order.size() == o.Order.size())
+      {
+        if (!identity)
+        {
+          throw new Error("Weak sequenceI equivalence not yet implemented.");
+        }
+        else
+        {
+          for (int i = 0, j = o.Order.size(); i < j; i++)
+          {
+            if (Order.elementAt(i) != o.Order.elementAt(i))
+            {
+              return false;
+            }
+          }
+        }
+      }
+      else
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  /**
+   * Consistency test for alignmentOrders
+   * @param o
+   * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way
+   */
+  public boolean isConsistent(AlignmentOrder o)
+  {
+    return isConsistent(o, true);
+  }
+
+  /**
+   * Consistency test for alignmentOrders
+   * @param o
+   *  // TODO: Weak SequenceI equivalence - will throw Error at moment
+   * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)
+   * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way
+   */
+  public boolean isConsistent(AlignmentOrder o, boolean identity)
+  {
+    if (o != this)
+    {
+      if (o == null)
+      {
+        return false;
+      }
+      if (Order != null && o.Order != null)
+      {
+        Vector c, s;
+        if (o.Order.size() > Order.size())
+        {
+          c = o.Order;
+          s = Order;
+        }
+        else
+        {
+          c = Order;
+          s = o.Order;
+        }
+        if (!identity)
+        {
+          throw new Error("Weak sequenceI equivalence not yet implemented.");
+        }
+        else
+        {
+          // test if c contains s and order in s is conserved in c
+          int last = -1;
+          for (int i = 0, j = s.size(); i < j; i++)
+          {
+            int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by incremental position search
+            if (pos > last)
+            {
+              last = pos;
+            }
+            else
+            {
+              return false;
+            }
+          }
+        }
+      }
+      else
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+  /**
+   * 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/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 79e0ba2..ad4e895 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,510 +1,510 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class AlignmentView
-{
-  /**
-   * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
-   */
-  private SeqCigar[] sequences = null;
-  private int[] contigs = null;
-  private int width = 0;
-  private int firstCol = 0;
-  public AlignmentView(CigarArray seqcigararray)
-  {
-    if (!seqcigararray.isSeqCigarArray())
-    {
-      throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences.");
-    }
-    //contigs = seqcigararray.applyDeletions();
-    contigs = seqcigararray.getDeletedRegions();
-    sequences = seqcigararray.getSeqCigarArray();
-    width = seqcigararray.getWidth(); // visible width
-  }
-
-  /**
-   * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment
-   * @param sdata
-   * @param firstcol
-   */
-  public AlignmentView(CigarArray sdata, int firstcol)
-  {
-    this(sdata);
-    firstCol = firstcol;
-  }
-
-  public void setSequences(SeqCigar[] sequences)
-  {
-    this.sequences = sequences;
-  }
-
-  public void setContigs(int[] contigs)
-  {
-    this.contigs = contigs;
-  }
-
-  public SeqCigar[] getSequences()
-  {
-    return sequences;
-  }
-
-  /**
-   * @see CigarArray.getDeletedRegions
-   * @return int[] { vis_start, sym_start, length }
-   */
-  public int[] getContigs()
-  {
-    return contigs;
-  }
-
-  /**
-   * get the full alignment and a columnselection object marking the hidden regions
-   * @param gapCharacter char
-   * @return Object[] { SequenceI[], ColumnSelection}
-   */
-  public Object[] getAlignmentAndColumnSelection(char gapCharacter)
-  {
-    ColumnSelection colsel = new ColumnSelection();
-
-    return new Object[]
-        {
-        SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
-                                          contigs), colsel};
-  }
-
-  /**
-   * getSequenceStrings
-   *
-   * @param c char
-   * @return String[]
-   */
-  public String[] getSequenceStrings(char c)
-  {
-    String[] seqs = new String[sequences.length];
-    for (int n = 0; n < sequences.length; n++)
-    {
-      String fullseq = sequences[n].getSequenceString(c);
-      if (contigs != null)
-      {
-        seqs[n] = "";
-        int p = 0;
-        for (int h = 0; h < contigs.length; h += 3)
-        {
-          seqs[n] += fullseq.substring(p, contigs[h + 1]);
-          p = contigs[h + 1] + contigs[h + 2];
-        }
-        seqs[n] += fullseq.substring(p);
-      }
-      else
-      {
-        seqs[n] = fullseq;
-      }
-    }
-    return seqs;
-  }
-
-  /**
-   *
-   * @return visible number of columns in alignment view
-   */
-  public int getWidth()
-  {
-    return width;
-  }
-
-  protected void setWidth(int width)
-  {
-    this.width = width;
-  }
-
-  /**
-   * get the contiguous subalignments in an alignment view.
-   * @param gapCharacter char
-   * @return SequenceI[][]
-   */
-  public SequenceI[][] getVisibleContigs(char gapCharacter)
-  {
-    SequenceI[][] smsa;
-    int njobs = 1;
-    if (sequences == null || width <= 0)
-    {
-      return null;
-    }
-    if (contigs != null && contigs.length > 0)
-    {
-      int start = 0;
-      njobs = 0;
-      int fwidth = width;
-      for (int contig = 0; contig < contigs.length; contig += 3)
-      {
-        if ( (contigs[contig + 1] - start) > 0)
-        {
-          njobs++;
-        }
-        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
-        start = contigs[contig + 1] + contigs[contig + 2];
-      }
-      if (start < fwidth)
-      {
-        njobs++;
-      }
-      smsa = new SequenceI[njobs][];
-      start = 0;
-      int j = 0;
-      for (int contig = 0; contig < contigs.length; contig += 3)
-      {
-        if (contigs[contig + 1] - start > 0)
-        {
-          SequenceI mseq[] = new SequenceI[sequences.length];
-          for (int s = 0; s < mseq.length; s++)
-          {
-            mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
-                contigs[contig + 1]);
-          }
-          smsa[j] = mseq;
-          j++;
-        }
-        start = contigs[contig + 1] + contigs[contig + 2];
-      }
-      if (start < fwidth)
-      {
-        SequenceI mseq[] = new SequenceI[sequences.length];
-        for (int s = 0; s < mseq.length; s++)
-        {
-          mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
-              fwidth + 1);
-        }
-        smsa[j] = mseq;
-        j++;
-      }
-    }
-    else
-    {
-      smsa = new SequenceI[1][];
-      smsa[0] = new SequenceI[sequences.length];
-      for (int s = 0; s < sequences.length; s++)
-      {
-        smsa[0][s] = sequences[s].getSeq(gapCharacter);
-      }
-    }
-    return smsa;
-  }
-
-  /**
-   * return full msa and hidden regions with visible blocks replaced with new sub alignments
-   * @param nvismsa SequenceI[][]
-   * @param orders AlignmentOrder[] corresponding to each SequenceI[] block.
-   * @return Object[]
-   */
-  public Object[] getUpdatedView(SequenceI[][] nvismsa, AlignmentOrder[] orders,
-                                 char gapCharacter)
-  {
-    if (sequences == null || width <= 0)
-    {
-      throw new Error("empty view cannot be updated.");
-    }
-    if (nvismsa == null)
-    {
-      throw new Error(
-          "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
-    }
-    if (contigs != null && contigs.length > 0)
-    {
-      SequenceI[] alignment = new SequenceI[sequences.length];
-      ColumnSelection columnselection = new ColumnSelection();
-      if (contigs != null && contigs.length > 0)
-      {
-        int start = 0;
-        int nwidth = 0;
-        int owidth = width;
-        int j = 0;
-        for (int contig = 0; contig < contigs.length; contig += 3)
-        {
-          owidth += contigs[contig + 2]; // recover final column width
-          if (contigs[contig + 1] - start > 0)
-          {
-            int swidth = 0; // subalignment width
-            if (nvismsa[j] != null)
-            {
-              SequenceI mseq[] = nvismsa[j];
-              AlignmentOrder order = (orders == null) ? null : orders[j];
-              j++;
-              if (mseq.length != sequences.length)
-              {
-                throw new Error(
-                    "Mismatch between number of sequences in block " + j + " (" +
-                    mseq.length + ") and the original view (" +
-                    sequences.length + ")");
-              }
-              swidth = mseq[0].getLength(); // JBPNote: could ensure padded here.
-              for (int s = 0; s < mseq.length; s++)
-              {
-                if (alignment[s] == null)
-                {
-                  alignment[s] = mseq[s];
-                }
-                else
-                {
-                  alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                           mseq[s].getSequenceAsString());
-                  if (mseq[s].getStart() <= mseq[s].getEnd())
-                  {
-                    alignment[s].setEnd(mseq[s].getEnd());
-                  }
-                  if (order != null)
-                  {
-                    order.updateSequence(mseq[s], alignment[s]);
-                  }
-                }
-              }
-            }
-            else
-            {
-              // recover original alignment block or place gaps
-              if (true)
-              {
-                // recover input data
-                for (int s = 0; s < sequences.length; s++)
-                {
-                  SequenceI oseq = sequences[s].getSeq(gapCharacter).
-                      getSubSequence(start,
-                                     contigs[contig + 1]);
-                  if (swidth < oseq.getLength())
-                  {
-                    swidth = oseq.getLength();
-                  }
-                  if (alignment[s] == null)
-                  {
-                    alignment[s] = oseq;
-                  }
-                  else
-                  {
-                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                             oseq.getSequenceAsString());
-                    if (oseq.getEnd() >= oseq.getStart())
-                    {
-                      alignment[s].setEnd(oseq.getEnd());
-                    }
-                  }
-                }
-
-              }
-              j++;
-            }
-            nwidth += swidth;
-          }
-          // advance to begining of visible region
-          start = contigs[contig + 1] + contigs[contig + 2];
-          // add hidden segment to right of next region
-          for (int s = 0; s < sequences.length; s++)
-          {
-            SequenceI hseq = sequences[s].getSeq(gapCharacter).getSubSequence(
-                contigs[contig +
-                1], start);
-            if (alignment[s] == null)
-            {
-              alignment[s] = hseq;
-            }
-            else
-            {
-              alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                       hseq.getSequenceAsString());
-              if (hseq.getEnd() >= hseq.getStart())
-              {
-                alignment[s].setEnd(hseq.getEnd());
-              }
-            }
-          }
-          // mark hidden segment as hidden in the new alignment
-          columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
-          nwidth += contigs[contig + 2];
-        }
-        // Do final segment - if it exists
-        if (j < nvismsa.length)
-        {
-          int swidth = 0;
-          if (nvismsa[j] != null)
-          {
-            SequenceI mseq[] = nvismsa[j];
-            AlignmentOrder order = (orders != null) ? orders[j] : null;
-            swidth = mseq[0].getLength();
-            for (int s = 0; s < mseq.length; s++)
-            {
-              if (alignment[s] == null)
-              {
-                alignment[s] = mseq[s];
-              }
-              else
-              {
-                alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                         mseq[s].getSequenceAsString());
-                if (mseq[s].getEnd() >= mseq[s].getStart())
-                {
-                  alignment[s].setEnd(mseq[s].getEnd());
-                }
-                if (order != null)
-                {
-                  order.updateSequence(mseq[s], alignment[s]);
-                }
-              }
-            }
-          }
-          else
-          {
-            if (start < owidth)
-            {
-              // recover input data or place gaps
-              if (true)
-              {
-                // recover input data
-                for (int s = 0; s < sequences.length; s++)
-                {
-                  SequenceI oseq = sequences[s].getSeq(gapCharacter).
-                      getSubSequence(start,
-                                     owidth + 1);
-                  if (swidth < oseq.getLength())
-                  {
-                    swidth = oseq.getLength();
-                  }
-                  if (alignment[s] == null)
-                  {
-                    alignment[s] = oseq;
-                  }
-                  else
-                  {
-                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
-                                             oseq.getSequenceAsString());
-                    if (oseq.getEnd() >= oseq.getStart())
-                    {
-                      alignment[s].setEnd(oseq.getEnd());
-                    }
-                  }
-                }
-                nwidth += swidth;
-              }
-              else
-              {
-                // place gaps.
-                throw new Error("Padding not yet implemented.");
-              }
-            }
-          }
-        }
-      }
-      return new Object[]
-          {
-          alignment, columnselection};
-    }
-    else
-    {
-      if (nvismsa.length != 1)
-      {
-        throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks=" +
-                        nvismsa.length);
-      }
-      if (nvismsa[0] != null)
-      {
-        return new Object[]
-            {
-            nvismsa[0], new ColumnSelection()};
-      }
-      else
-      {
-        return getAlignmentAndColumnSelection(gapCharacter);
-      }
-    }
-  }
-
-  /**
-   * returns simple array of start end positions of visible range on alignment.
-   * vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment.
-   * @return int[] { start_i, end_i } for 1<i<n visible regions.
-   */
-  public int[] getVisibleContigs()
-  {
-    if (contigs != null && contigs.length > 0)
-    {
-      int start = 0;
-      int nvis = 0;
-      int fwidth = width;
-      for (int contig = 0; contig < contigs.length; contig += 3)
-      {
-        if ( (contigs[contig + 1] - start) > 0)
-        {
-          nvis++;
-        }
-        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
-        start = contigs[contig + 1] + contigs[contig + 2];
-      }
-      if (start < fwidth)
-      {
-        nvis++;
-      }
-      int viscontigs[] = new int[nvis * 2];
-      nvis = 0;
-      start = 0;
-      for (int contig = 0; contig < contigs.length; contig += 3)
-      {
-        if ( (contigs[contig + 1] - start) > 0)
-        {
-          viscontigs[nvis] = start;
-          viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
-          nvis += 2;
-        }
-        start = contigs[contig + 1] + contigs[contig + 2];
-      }
-      if (start < fwidth)
-      {
-        viscontigs[nvis] = start;
-        viscontigs[nvis + 1] = fwidth; // end is inclusive
-        nvis += 2;
-      }
-      return viscontigs;
-    }
-    else
-    {
-      return new int[]
-          {
-          0, width};
-    }
-  }
-
-  /**
-   *
-   * @return position of first visible column of AlignmentView within its parent's alignment reference frame
-   */
-  public int getAlignmentOrigin()
-  {
-    // TODO Auto-generated method stub
-    return firstCol;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public class AlignmentView
+{
+  /**
+   * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
+   */
+  private SeqCigar[] sequences = null;
+  private int[] contigs = null;
+  private int width = 0;
+  private int firstCol = 0;
+  public AlignmentView(CigarArray seqcigararray)
+  {
+    if (!seqcigararray.isSeqCigarArray())
+    {
+      throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences.");
+    }
+    //contigs = seqcigararray.applyDeletions();
+    contigs = seqcigararray.getDeletedRegions();
+    sequences = seqcigararray.getSeqCigarArray();
+    width = seqcigararray.getWidth(); // visible width
+  }
+
+  /**
+   * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment
+   * @param sdata
+   * @param firstcol
+   */
+  public AlignmentView(CigarArray sdata, int firstcol)
+  {
+    this(sdata);
+    firstCol = firstcol;
+  }
+
+  public void setSequences(SeqCigar[] sequences)
+  {
+    this.sequences = sequences;
+  }
+
+  public void setContigs(int[] contigs)
+  {
+    this.contigs = contigs;
+  }
+
+  public SeqCigar[] getSequences()
+  {
+    return sequences;
+  }
+
+  /**
+   * @see CigarArray.getDeletedRegions
+   * @return int[] { vis_start, sym_start, length }
+   */
+  public int[] getContigs()
+  {
+    return contigs;
+  }
+
+  /**
+   * get the full alignment and a columnselection object marking the hidden regions
+   * @param gapCharacter char
+   * @return Object[] { SequenceI[], ColumnSelection}
+   */
+  public Object[] getAlignmentAndColumnSelection(char gapCharacter)
+  {
+    ColumnSelection colsel = new ColumnSelection();
+
+    return new Object[]
+        {
+        SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
+                                          contigs), colsel};
+  }
+
+  /**
+   * getSequenceStrings
+   *
+   * @param c char
+   * @return String[]
+   */
+  public String[] getSequenceStrings(char c)
+  {
+    String[] seqs = new String[sequences.length];
+    for (int n = 0; n < sequences.length; n++)
+    {
+      String fullseq = sequences[n].getSequenceString(c);
+      if (contigs != null)
+      {
+        seqs[n] = "";
+        int p = 0;
+        for (int h = 0; h < contigs.length; h += 3)
+        {
+          seqs[n] += fullseq.substring(p, contigs[h + 1]);
+          p = contigs[h + 1] + contigs[h + 2];
+        }
+        seqs[n] += fullseq.substring(p);
+      }
+      else
+      {
+        seqs[n] = fullseq;
+      }
+    }
+    return seqs;
+  }
+
+  /**
+   *
+   * @return visible number of columns in alignment view
+   */
+  public int getWidth()
+  {
+    return width;
+  }
+
+  protected void setWidth(int width)
+  {
+    this.width = width;
+  }
+
+  /**
+   * get the contiguous subalignments in an alignment view.
+   * @param gapCharacter char
+   * @return SequenceI[][]
+   */
+  public SequenceI[][] getVisibleContigs(char gapCharacter)
+  {
+    SequenceI[][] smsa;
+    int njobs = 1;
+    if (sequences == null || width <= 0)
+    {
+      return null;
+    }
+    if (contigs != null && contigs.length > 0)
+    {
+      int start = 0;
+      njobs = 0;
+      int fwidth = width;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          njobs++;
+        }
+        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        njobs++;
+      }
+      smsa = new SequenceI[njobs][];
+      start = 0;
+      int j = 0;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if (contigs[contig + 1] - start > 0)
+        {
+          SequenceI mseq[] = new SequenceI[sequences.length];
+          for (int s = 0; s < mseq.length; s++)
+          {
+            mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+                contigs[contig + 1]);
+          }
+          smsa[j] = mseq;
+          j++;
+        }
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        SequenceI mseq[] = new SequenceI[sequences.length];
+        for (int s = 0; s < mseq.length; s++)
+        {
+          mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+              fwidth + 1);
+        }
+        smsa[j] = mseq;
+        j++;
+      }
+    }
+    else
+    {
+      smsa = new SequenceI[1][];
+      smsa[0] = new SequenceI[sequences.length];
+      for (int s = 0; s < sequences.length; s++)
+      {
+        smsa[0][s] = sequences[s].getSeq(gapCharacter);
+      }
+    }
+    return smsa;
+  }
+
+  /**
+   * return full msa and hidden regions with visible blocks replaced with new sub alignments
+   * @param nvismsa SequenceI[][]
+   * @param orders AlignmentOrder[] corresponding to each SequenceI[] block.
+   * @return Object[]
+   */
+  public Object[] getUpdatedView(SequenceI[][] nvismsa, AlignmentOrder[] orders,
+                                 char gapCharacter)
+  {
+    if (sequences == null || width <= 0)
+    {
+      throw new Error("empty view cannot be updated.");
+    }
+    if (nvismsa == null)
+    {
+      throw new Error(
+          "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+    }
+    if (contigs != null && contigs.length > 0)
+    {
+      SequenceI[] alignment = new SequenceI[sequences.length];
+      ColumnSelection columnselection = new ColumnSelection();
+      if (contigs != null && contigs.length > 0)
+      {
+        int start = 0;
+        int nwidth = 0;
+        int owidth = width;
+        int j = 0;
+        for (int contig = 0; contig < contigs.length; contig += 3)
+        {
+          owidth += contigs[contig + 2]; // recover final column width
+          if (contigs[contig + 1] - start > 0)
+          {
+            int swidth = 0; // subalignment width
+            if (nvismsa[j] != null)
+            {
+              SequenceI mseq[] = nvismsa[j];
+              AlignmentOrder order = (orders == null) ? null : orders[j];
+              j++;
+              if (mseq.length != sequences.length)
+              {
+                throw new Error(
+                    "Mismatch between number of sequences in block " + j + " (" +
+                    mseq.length + ") and the original view (" +
+                    sequences.length + ")");
+              }
+              swidth = mseq[0].getLength(); // JBPNote: could ensure padded here.
+              for (int s = 0; s < mseq.length; s++)
+              {
+                if (alignment[s] == null)
+                {
+                  alignment[s] = mseq[s];
+                }
+                else
+                {
+                  alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                           mseq[s].getSequenceAsString());
+                  if (mseq[s].getStart() <= mseq[s].getEnd())
+                  {
+                    alignment[s].setEnd(mseq[s].getEnd());
+                  }
+                  if (order != null)
+                  {
+                    order.updateSequence(mseq[s], alignment[s]);
+                  }
+                }
+              }
+            }
+            else
+            {
+              // recover original alignment block or place gaps
+              if (true)
+              {
+                // recover input data
+                for (int s = 0; s < sequences.length; s++)
+                {
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter).
+                      getSubSequence(start,
+                                     contigs[contig + 1]);
+                  if (swidth < oseq.getLength())
+                  {
+                    swidth = oseq.getLength();
+                  }
+                  if (alignment[s] == null)
+                  {
+                    alignment[s] = oseq;
+                  }
+                  else
+                  {
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                             oseq.getSequenceAsString());
+                    if (oseq.getEnd() >= oseq.getStart())
+                    {
+                      alignment[s].setEnd(oseq.getEnd());
+                    }
+                  }
+                }
+
+              }
+              j++;
+            }
+            nwidth += swidth;
+          }
+          // advance to begining of visible region
+          start = contigs[contig + 1] + contigs[contig + 2];
+          // add hidden segment to right of next region
+          for (int s = 0; s < sequences.length; s++)
+          {
+            SequenceI hseq = sequences[s].getSeq(gapCharacter).getSubSequence(
+                contigs[contig +
+                1], start);
+            if (alignment[s] == null)
+            {
+              alignment[s] = hseq;
+            }
+            else
+            {
+              alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                       hseq.getSequenceAsString());
+              if (hseq.getEnd() >= hseq.getStart())
+              {
+                alignment[s].setEnd(hseq.getEnd());
+              }
+            }
+          }
+          // mark hidden segment as hidden in the new alignment
+          columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
+          nwidth += contigs[contig + 2];
+        }
+        // Do final segment - if it exists
+        if (j < nvismsa.length)
+        {
+          int swidth = 0;
+          if (nvismsa[j] != null)
+          {
+            SequenceI mseq[] = nvismsa[j];
+            AlignmentOrder order = (orders != null) ? orders[j] : null;
+            swidth = mseq[0].getLength();
+            for (int s = 0; s < mseq.length; s++)
+            {
+              if (alignment[s] == null)
+              {
+                alignment[s] = mseq[s];
+              }
+              else
+              {
+                alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                         mseq[s].getSequenceAsString());
+                if (mseq[s].getEnd() >= mseq[s].getStart())
+                {
+                  alignment[s].setEnd(mseq[s].getEnd());
+                }
+                if (order != null)
+                {
+                  order.updateSequence(mseq[s], alignment[s]);
+                }
+              }
+            }
+          }
+          else
+          {
+            if (start < owidth)
+            {
+              // recover input data or place gaps
+              if (true)
+              {
+                // recover input data
+                for (int s = 0; s < sequences.length; s++)
+                {
+                  SequenceI oseq = sequences[s].getSeq(gapCharacter).
+                      getSubSequence(start,
+                                     owidth + 1);
+                  if (swidth < oseq.getLength())
+                  {
+                    swidth = oseq.getLength();
+                  }
+                  if (alignment[s] == null)
+                  {
+                    alignment[s] = oseq;
+                  }
+                  else
+                  {
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                             oseq.getSequenceAsString());
+                    if (oseq.getEnd() >= oseq.getStart())
+                    {
+                      alignment[s].setEnd(oseq.getEnd());
+                    }
+                  }
+                }
+                nwidth += swidth;
+              }
+              else
+              {
+                // place gaps.
+                throw new Error("Padding not yet implemented.");
+              }
+            }
+          }
+        }
+      }
+      return new Object[]
+          {
+          alignment, columnselection};
+    }
+    else
+    {
+      if (nvismsa.length != 1)
+      {
+        throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks=" +
+                        nvismsa.length);
+      }
+      if (nvismsa[0] != null)
+      {
+        return new Object[]
+            {
+            nvismsa[0], new ColumnSelection()};
+      }
+      else
+      {
+        return getAlignmentAndColumnSelection(gapCharacter);
+      }
+    }
+  }
+
+  /**
+   * returns simple array of start end positions of visible range on alignment.
+   * vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment.
+   * @return int[] { start_i, end_i } for 1<i<n visible regions.
+   */
+  public int[] getVisibleContigs()
+  {
+    if (contigs != null && contigs.length > 0)
+    {
+      int start = 0;
+      int nvis = 0;
+      int fwidth = width;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          nvis++;
+        }
+        fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        nvis++;
+      }
+      int viscontigs[] = new int[nvis * 2];
+      nvis = 0;
+      start = 0;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
+          viscontigs[nvis] = start;
+          viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
+          nvis += 2;
+        }
+        start = contigs[contig + 1] + contigs[contig + 2];
+      }
+      if (start < fwidth)
+      {
+        viscontigs[nvis] = start;
+        viscontigs[nvis + 1] = fwidth; // end is inclusive
+        nvis += 2;
+      }
+      return viscontigs;
+    }
+    else
+    {
+      return new int[]
+          {
+          0, width};
+    }
+  }
+
+  /**
+   *
+   * @return position of first visible column of AlignmentView within its parent's alignment reference frame
+   */
+  public int getAlignmentOrigin()
+  {
+    // TODO Auto-generated method stub
+    return firstCol;
+  }
+}
diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 9fc69bb..b332fb4 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index a7e8254..da63613 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,284 +1,284 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class BinaryNode
-{
-  Object element;
-  String name;
-  BinaryNode left;
-  BinaryNode right;
-  BinaryNode parent;
-
-  /** DOCUMENT ME!! */
-  public int bootstrap;
-
-  /**
-   * Creates a new BinaryNode object.
-   */
-  public BinaryNode()
-  {
-    left = right = parent = null;
-    bootstrap = 0;
-  }
-
-  /**
-   * Creates a new BinaryNode object.
-   *
-   * @param element DOCUMENT ME!
-   * @param parent DOCUMENT ME!
-   * @param name DOCUMENT ME!
-   */
-  public BinaryNode(Object element, BinaryNode parent, String name)
-  {
-    this.element = element;
-    this.parent = parent;
-    this.name = name;
-
-    left = right = null;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Object element()
-  {
-    return element;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param v DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Object setElement(Object v)
-  {
-    return element = v;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode left()
-  {
-    return left;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode setLeft(BinaryNode n)
-  {
-    return left = n;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode right()
-  {
-    return right;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode setRight(BinaryNode n)
-  {
-    return right = n;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode parent()
-  {
-    return parent;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public BinaryNode setParent(BinaryNode n)
-  {
-    return parent = n;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public boolean isLeaf()
-  {
-    return (left == null) && (right == null);
-  }
-
-  /**
-   * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)
-   * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to  NULL - you  should use
-   * setChild(null), or detach() for this.
-   *
-   */
-  public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
-  {
-    if (leftchild != null)
-    {
-      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;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param name DOCUMENT ME!
-   */
-  public void setName(String name)
-  {
-    this.name = name;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String getName()
-  {
-    return this.name;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param boot DOCUMENT ME!
-   */
-  public void setBootstrap(int boot)
-  {
-    this.bootstrap = boot;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getBootstrap()
-  {
-    return bootstrap;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BinaryNode
+{
+  Object element;
+  String name;
+  BinaryNode left;
+  BinaryNode right;
+  BinaryNode parent;
+
+  /** DOCUMENT ME!! */
+  public int bootstrap;
+
+  /**
+   * Creates a new BinaryNode object.
+   */
+  public BinaryNode()
+  {
+    left = right = parent = null;
+    bootstrap = 0;
+  }
+
+  /**
+   * Creates a new BinaryNode object.
+   *
+   * @param element DOCUMENT ME!
+   * @param parent DOCUMENT ME!
+   * @param name DOCUMENT ME!
+   */
+  public BinaryNode(Object element, BinaryNode parent, String name)
+  {
+    this.element = element;
+    this.parent = parent;
+    this.name = name;
+
+    left = right = null;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Object element()
+  {
+    return element;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param v DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Object setElement(Object v)
+  {
+    return element = v;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode left()
+  {
+    return left;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode setLeft(BinaryNode n)
+  {
+    return left = n;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode right()
+  {
+    return right;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode setRight(BinaryNode n)
+  {
+    return right = n;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode parent()
+  {
+    return parent;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode setParent(BinaryNode n)
+  {
+    return parent = n;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean isLeaf()
+  {
+    return (left == null) && (right == null);
+  }
+
+  /**
+   * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)
+   * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to  NULL - you  should use
+   * setChild(null), or detach() for this.
+   *
+   */
+  public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
+  {
+    if (leftchild != null)
+    {
+      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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param name DOCUMENT ME!
+   */
+  public void setName(String name)
+  {
+    this.name = name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return this.name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param boot DOCUMENT ME!
+   */
+  public void setBootstrap(int boot)
+  {
+    this.bootstrap = boot;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getBootstrap()
+  {
+    return bootstrap;
+  }
+}
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 1cdc934..596fb60 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index c17e01e..fdd3bff 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index d44d599..4ca2720 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/CigarCigar.java b/src/jalview/datamodel/CigarCigar.java
index 83cce19..a47c5eb 100644
--- a/src/jalview/datamodel/CigarCigar.java
+++ b/src/jalview/datamodel/CigarCigar.java
@@ -1,59 +1,59 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-public class CigarCigar
-    extends CigarSimple
-{
-  SeqCigar refCigar;
-  /**
-   * Apply CIGAR operations to the result of another cigar
-   * @param cigar Cigar
-   */
-  CigarCigar(SeqCigar cigar)
-  {
-    super();
-    refCigar = cigar;
-  }
-
-  /**
-   *
-   * @return String formed by applying CIGAR operations to the reference object
-   * @param GapChar char
-   * @todo Implement this jalview.datamodel.Cigar method
-   */
-  public String getSequenceString(char GapChar)
-  {
-    if (length == 0)
-    {
-      return "";
-    }
-    String refString = refCigar.getSequenceString(GapChar);
-    if (refString != null)
-    {
-      return (length == 0) ? "" :
-          (String) getSequenceAndDeletions(refString, GapChar)[0];
-    }
-    else
-    {
-      return null;
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class CigarCigar
+    extends CigarSimple
+{
+  SeqCigar refCigar;
+  /**
+   * Apply CIGAR operations to the result of another cigar
+   * @param cigar Cigar
+   */
+  CigarCigar(SeqCigar cigar)
+  {
+    super();
+    refCigar = cigar;
+  }
+
+  /**
+   *
+   * @return String formed by applying CIGAR operations to the reference object
+   * @param GapChar char
+   * @todo Implement this jalview.datamodel.Cigar method
+   */
+  public String getSequenceString(char GapChar)
+  {
+    if (length == 0)
+    {
+      return "";
+    }
+    String refString = refCigar.getSequenceString(GapChar);
+    if (refString != null)
+    {
+      return (length == 0) ? "" :
+          (String) getSequenceAndDeletions(refString, GapChar)[0];
+    }
+    else
+    {
+      return null;
+    }
+  }
+
+}
diff --git a/src/jalview/datamodel/CigarSimple.java b/src/jalview/datamodel/CigarSimple.java
index 3891687..2616d74 100644
--- a/src/jalview/datamodel/CigarSimple.java
+++ b/src/jalview/datamodel/CigarSimple.java
@@ -1,43 +1,43 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public abstract class CigarSimple
-    extends CigarBase
-{
-  /**
-   * Return a symbol sequence with edits (gaps, insertions and deletions) applied
-   * @param GapChar char
-   * @return String
-   */
-  public abstract String getSequenceString(char GapChar);
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public abstract class CigarSimple
+    extends CigarBase
+{
+  /**
+   * Return a symbol sequence with edits (gaps, insertions and deletions) applied
+   * @param GapChar char
+   * @return String
+   */
+  public abstract String getSequenceString(char GapChar);
+
+}
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 74f4cda..9ec4270 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index b6c3192..f827bad 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 0552b2c..1aabf70 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,102 +1,102 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-/**
- * Defines internal constants for unambiguous annotation
- * of DbRefEntry source strings and describing the data
- * retrieved from external database sources (see jalview.ws.DbSourcProxy)
- * @author JimP
- *
- */
-public class DBRefSource
-{
-  /**
-   * UNIPROT Accession Number
-   */
-  public static String UNIPROT = "UNIPROT";
-  /**
-   * UNIPROT Entry Name
-   */
-  public static String UP_NAME = "UNIPROT_NAME";
-  /**
-   * Uniprot Knowledgebase/TrEMBL
-   * as served from EMBL protein products.
-   */
-  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
-  /**
-   * PDB Entry Code
-   */
-  public static String PDB = "PDB";
-  /**
-   * EMBL ID
-   */
-  public static String EMBL = "EMBL";
-  /**
-   * EMBLCDS ID
-   */
-  public static String EMBLCDS = "EMBLCDS";
-  /**
-   * PFAM ID
-   */
-  public static String PFAM = "PFAM";
-  /**
-   * GeneDB ID
-   */
-  public static final String GENEDB = "GeneDB";
-
-  /**
-   * List of databases whose sequences might have coding regions annotated
-   */
-  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB};
-  public static final String[] CODINGDBS = { EMBLCDS, GENEDB};
-  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB};
-  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB};
-  public static final String[] PROTEINSTR = { PDB };
-  public static final String[] DOMAINDBS = { PFAM };
-  /**
-   * set of unique DBRefSource property constants.
-   * These could be used to reconstruct the above groupings
-   */
-  public static final Object SEQDB = "SQ";
-  /**
-   * database of nucleic acid sequences
-   */
-  public static final Object DNASEQDB = "NASQ";
-  /**
-   * database of amino acid sequences
-   */
-  public static final Object PROTSEQDB = "PROTSQ";
-  /**
-   * database of cDNA sequences
-   */
-  public static final Object CODINGSEQDB = "CODING";
-  /**
-   * database of na sequences with exon annotation
-   */
-  public static final Object DNACODINGSEQDB = "XONCODING";
-  /**
-   * DB returns several sequences associated with a protein domain
-   */
-  public static final Object DOMAINDB = "DOMAIN";
-  /**
-   * DB query can take multiple accession codes concatenated
-   * by a separator. Value of property indicates maximum number of accession codes to send at a time.
-   */
-  public static final Object MULTIACC = "MULTIACC";
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+/**
+ * Defines internal constants for unambiguous annotation
+ * of DbRefEntry source strings and describing the data
+ * retrieved from external database sources (see jalview.ws.DbSourcProxy)
+ * @author JimP
+ *
+ */
+public class DBRefSource
+{
+  /**
+   * UNIPROT Accession Number
+   */
+  public static String UNIPROT = "UNIPROT";
+  /**
+   * UNIPROT Entry Name
+   */
+  public static String UP_NAME = "UNIPROT_NAME";
+  /**
+   * Uniprot Knowledgebase/TrEMBL
+   * as served from EMBL protein products.
+   */
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
+  /**
+   * PDB Entry Code
+   */
+  public static String PDB = "PDB";
+  /**
+   * EMBL ID
+   */
+  public static String EMBL = "EMBL";
+  /**
+   * EMBLCDS ID
+   */
+  public static String EMBLCDS = "EMBLCDS";
+  /**
+   * PFAM ID
+   */
+  public static String PFAM = "PFAM";
+  /**
+   * GeneDB ID
+   */
+  public static final String GENEDB = "GeneDB";
+
+  /**
+   * List of databases whose sequences might have coding regions annotated
+   */
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB};
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB};
+  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB};
+  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB};
+  public static final String[] PROTEINSTR = { PDB };
+  public static final String[] DOMAINDBS = { PFAM };
+  /**
+   * set of unique DBRefSource property constants.
+   * These could be used to reconstruct the above groupings
+   */
+  public static final Object SEQDB = "SQ";
+  /**
+   * database of nucleic acid sequences
+   */
+  public static final Object DNASEQDB = "NASQ";
+  /**
+   * database of amino acid sequences
+   */
+  public static final Object PROTSEQDB = "PROTSQ";
+  /**
+   * database of cDNA sequences
+   */
+  public static final Object CODINGSEQDB = "CODING";
+  /**
+   * database of na sequences with exon annotation
+   */
+  public static final Object DNACODINGSEQDB = "XONCODING";
+  /**
+   * DB returns several sequences associated with a protein domain
+   */
+  public static final Object DOMAINDB = "DOMAIN";
+  /**
+   * DB query can take multiple accession codes concatenated
+   * by a separator. Value of property indicates maximum number of accession codes to send at a time.
+   */
+  public static final Object MULTIACC = "MULTIACC";
+}
diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index d81a31c..e5c56b9 100644
--- a/src/jalview/datamodel/FeatureProperties.java
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 /**
diff --git a/src/jalview/datamodel/GraphLine.java b/src/jalview/datamodel/GraphLine.java
index 77b7ef5..7791ead 100755
--- a/src/jalview/datamodel/GraphLine.java
+++ b/src/jalview/datamodel/GraphLine.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 21dcce1..d64e8e0 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.datamodel;
 
 import java.util.*;
diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 835400e..7440fd0 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 import java.util.Vector;
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 69f0d68..5c98874 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/Provenance.java b/src/jalview/datamodel/Provenance.java
index f8afedf..46e4fe3 100755
--- a/src/jalview/datamodel/Provenance.java
+++ b/src/jalview/datamodel/Provenance.java
@@ -1,47 +1,47 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-public class Provenance
-{
-  Vector entries = new Vector();
-  public Provenance()
-  {
-
-  }
-
-  public ProvenanceEntry[] getEntries()
-  {
-    ProvenanceEntry[] ret = new ProvenanceEntry[entries.size()];
-    for (int i = 0; i < entries.size(); i++)
-    {
-      ret[i] = (ProvenanceEntry) entries.elementAt(i);
-    }
-    return ret;
-  }
-
-  public void addEntry(String user, String action, java.util.Date date,
-                       String id)
-  {
-    entries.addElement(new ProvenanceEntry(user, action, date, id));
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+public class Provenance
+{
+  Vector entries = new Vector();
+  public Provenance()
+  {
+
+  }
+
+  public ProvenanceEntry[] getEntries()
+  {
+    ProvenanceEntry[] ret = new ProvenanceEntry[entries.size()];
+    for (int i = 0; i < entries.size(); i++)
+    {
+      ret[i] = (ProvenanceEntry) entries.elementAt(i);
+    }
+    return ret;
+  }
+
+  public void addEntry(String user, String action, java.util.Date date,
+                       String id)
+  {
+    entries.addElement(new ProvenanceEntry(user, action, date, id));
+  }
+
+}
diff --git a/src/jalview/datamodel/ProvenanceEntry.java b/src/jalview/datamodel/ProvenanceEntry.java
index b08dd6d..de3b2d5 100755
--- a/src/jalview/datamodel/ProvenanceEntry.java
+++ b/src/jalview/datamodel/ProvenanceEntry.java
@@ -1,52 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-public class ProvenanceEntry
-{
-  String user, action, id;
-  java.util.Date date;
-  public ProvenanceEntry(String u, String a, java.util.Date d, String i)
-  {
-    user = u;
-    action = a;
-    date = d;
-    id = i;
-  }
-
-  public String getUser()
-  {
-    return user;
-  }
-
-  public String getAction()
-  {
-    return action;
-  }
-
-  public java.util.Date getDate()
-  {
-    return date;
-  }
-
-  public String getID()
-  {
-    return id;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class ProvenanceEntry
+{
+  String user, action, id;
+  java.util.Date date;
+  public ProvenanceEntry(String u, String a, java.util.Date d, String i)
+  {
+    user = u;
+    action = a;
+    date = d;
+    id = i;
+  }
+
+  public String getUser()
+  {
+    return user;
+  }
+
+  public String getAction()
+  {
+    return action;
+  }
+
+  public java.util.Date getDate()
+  {
+    return date;
+  }
+
+  public String getID()
+  {
+    return id;
+  }
+}
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index b9176b4..c5f8e6f 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 9ed0388..da8fada 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 56a829c..53dffbf 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 1f34b8b..3e1c2b7 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6ded8bd..292f9e7 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index d9ffc81..b610bbe 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index ca09301..d847510 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index f105cc8..e2fb924 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/UniprotEntry.java b/src/jalview/datamodel/UniprotEntry.java
index b963022..41e75d7 100755
--- a/src/jalview/datamodel/UniprotEntry.java
+++ b/src/jalview/datamodel/UniprotEntry.java
@@ -1,93 +1,93 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-public class UniprotEntry
-{
-
-  UniprotSequence sequence;
-  Vector name;
-  Vector accession;
-  Vector feature;
-  Vector dbrefs;
-  UniprotProteinName protName;
-
-  public void setAccession(Vector items)
-  {
-    accession = items;
-  }
-
-  public void setFeature(Vector items)
-  {
-    feature = items;
-  }
-
-  public Vector getFeature()
-  {
-    return feature;
-  }
-
-  public Vector getAccession()
-  {
-    return accession;
-  }
-
-  public void setProtein(UniprotProteinName names)
-  {
-    protName = names;
-  }
-
-  public UniprotProteinName getProtein()
-  {
-    return protName;
-  }
-
-  public void setName(Vector na)
-  {
-    name = na;
-  }
-
-  public Vector getName()
-  {
-    return name;
-  }
-
-  public UniprotSequence getUniprotSequence()
-  {
-    return sequence;
-  }
-
-  public void setUniprotSequence(UniprotSequence seq)
-  {
-    sequence = seq;
-  }
-
-  public Vector getDbReference()
-  {
-    return dbrefs;
-  }
-
-  public void setDbReference(Vector dbref)
-  {
-    this.dbrefs = dbref;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+public class UniprotEntry
+{
+
+  UniprotSequence sequence;
+  Vector name;
+  Vector accession;
+  Vector feature;
+  Vector dbrefs;
+  UniprotProteinName protName;
+
+  public void setAccession(Vector items)
+  {
+    accession = items;
+  }
+
+  public void setFeature(Vector items)
+  {
+    feature = items;
+  }
+
+  public Vector getFeature()
+  {
+    return feature;
+  }
+
+  public Vector getAccession()
+  {
+    return accession;
+  }
+
+  public void setProtein(UniprotProteinName names)
+  {
+    protName = names;
+  }
+
+  public UniprotProteinName getProtein()
+  {
+    return protName;
+  }
+
+  public void setName(Vector na)
+  {
+    name = na;
+  }
+
+  public Vector getName()
+  {
+    return name;
+  }
+
+  public UniprotSequence getUniprotSequence()
+  {
+    return sequence;
+  }
+
+  public void setUniprotSequence(UniprotSequence seq)
+  {
+    sequence = seq;
+  }
+
+  public Vector getDbReference()
+  {
+    return dbrefs;
+  }
+
+  public void setDbReference(Vector dbref)
+  {
+    this.dbrefs = dbref;
+  }
+
+}
diff --git a/src/jalview/datamodel/UniprotFile.java b/src/jalview/datamodel/UniprotFile.java
index b088ec2..6df0bad 100755
--- a/src/jalview/datamodel/UniprotFile.java
+++ b/src/jalview/datamodel/UniprotFile.java
@@ -1,36 +1,36 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-public class UniprotFile
-{
-  Vector _items;
-
-  public void setUniprotEntries(Vector items)
-  {
-    _items = items;
-  }
-
-  public Vector getUniprotEntries()
-  {
-    return _items;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+public class UniprotFile
+{
+  Vector _items;
+
+  public void setUniprotEntries(Vector items)
+  {
+    _items = items;
+  }
+
+  public Vector getUniprotEntries()
+  {
+    return _items;
+  }
+}
diff --git a/src/jalview/datamodel/UniprotProteinName.java b/src/jalview/datamodel/UniprotProteinName.java
index bb9a628..ebdf7d7 100755
--- a/src/jalview/datamodel/UniprotProteinName.java
+++ b/src/jalview/datamodel/UniprotProteinName.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/datamodel/UniprotSequence.java b/src/jalview/datamodel/UniprotSequence.java
index d5262e3..410f7b8 100755
--- a/src/jalview/datamodel/UniprotSequence.java
+++ b/src/jalview/datamodel/UniprotSequence.java
@@ -1,46 +1,46 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-public class UniprotSequence
-{
-  /**
-   * internal content storage
-   */
-  private java.lang.String _content = "";
-
-  public void setContent(String seq)
-  {
-    StringBuffer sb = new StringBuffer();
-    for (int i = 0; i < seq.length(); i++)
-    {
-      if (seq.charAt(i) != ' ')
-      {
-        sb.append(seq.charAt(i));
-      }
-    }
-    _content = sb.toString();
-  }
-
-  public String getContent()
-  {
-    return _content;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+public class UniprotSequence
+{
+  /**
+   * internal content storage
+   */
+  private java.lang.String _content = "";
+
+  public void setContent(String seq)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < seq.length(); i++)
+    {
+      if (seq.charAt(i) != ' ')
+      {
+        sb.append(seq.charAt(i));
+      }
+    }
+    _content = sb.toString();
+  }
+
+  public String getContent()
+  {
+    return _content;
+  }
+
+}
diff --git a/src/jalview/datamodel/xdb/embl/BasePosition.java b/src/jalview/datamodel/xdb/embl/BasePosition.java
index e0fe833..a0ff2e6 100644
--- a/src/jalview/datamodel/xdb/embl/BasePosition.java
+++ b/src/jalview/datamodel/xdb/embl/BasePosition.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 public class BasePosition {
diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index d08ee0a..73ffeef 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 import jalview.datamodel.DBRefEntry;
diff --git a/src/jalview/datamodel/xdb/embl/EmblError.java b/src/jalview/datamodel/xdb/embl/EmblError.java
index 3db5eca..29b6e65 100644
--- a/src/jalview/datamodel/xdb/embl/EmblError.java
+++ b/src/jalview/datamodel/xdb/embl/EmblError.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 public class EmblError {
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeature.java b/src/jalview/datamodel/xdb/embl/EmblFeature.java
index e2997fb..babc96d 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeature.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeature.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 import java.util.Hashtable;
 import java.util.Vector;
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
index 09d27fe..9ac59e3 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocElement.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 public class EmblFeatureLocElement {
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index 0341ec3..632ca21 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 import java.util.Enumeration;
@@ -109,4 +127,4 @@ public class EmblFeatureLocations {
     }
     return se;
     }
-}
\ No newline at end of file
+}
diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index 691cbad..b731d4b 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 
diff --git a/src/jalview/datamodel/xdb/embl/EmblSequence.java b/src/jalview/datamodel/xdb/embl/EmblSequence.java
index c68bcc5..5501a00 100644
--- a/src/jalview/datamodel/xdb/embl/EmblSequence.java
+++ b/src/jalview/datamodel/xdb/embl/EmblSequence.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 public class EmblSequence {
diff --git a/src/jalview/datamodel/xdb/embl/Qualifier.java b/src/jalview/datamodel/xdb/embl/Qualifier.java
index 37a0239..f94f88c 100644
--- a/src/jalview/datamodel/xdb/embl/Qualifier.java
+++ b/src/jalview/datamodel/xdb/embl/Qualifier.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 public class Qualifier {
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 648f94c..1320aa0 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,19 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 Softwarechang
+ * 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;
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index f798671..96dfc1c 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 95b4220..d81de9b 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 83a8a12..9ca5d66 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,517 +1,517 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.Dimension;
-
-public class AnnotationColourChooser
-    extends JPanel
-{
-  JInternalFrame frame;
-  AlignViewport av;
-  AlignmentPanel ap;
-  ColourSchemeI oldcs;
-  Hashtable oldgroupColours;
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
-  boolean adjusting = false;
-
-  public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
-  {
-    oldcs = av.getGlobalColourScheme();
-    if (av.alignment.getGroups() != null)
-    {
-      oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-        if (sg.cs != null)
-        {
-          oldgroupColours.put(sg, sg.cs);
-        }
-      }
-    }
-    this.av = av;
-    this.ap = ap;
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
-
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        if (!adjusting)
-        {
-          thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
-          valueChanged();
-        }
-      }
-    });
-    slider.addMouseListener(new MouseAdapter()
-        {
-          public void mouseReleased(MouseEvent evt)
-          {
-            ap.paintAlignment(true);
-          }
-        });
-
-    if (av.alignment.getAlignmentAnnotation() == null)
-    {
-      return;
-    }
-
-    if (oldcs instanceof AnnotationColourGradient)
-    {
-      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      minColour.setBackground(acg.getMinColour());
-      maxColour.setBackground(acg.getMaxColour());
-    }
-    else
-    {
-      minColour.setBackground(Color.orange);
-      maxColour.setBackground(Color.red);
-    }
-
-    adjusting = true;
-    Vector list = new Vector();
-    int index = 1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
-    {
-      String label = av.alignment.getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-        list.addElement(label);
-      else
-        list.addElement(label+"_"+(index++));
-    }
-
-    annotations = new JComboBox(list);
-
-    threshold.addItem("No Threshold");
-    threshold.addItem("Above Threshold");
-    threshold.addItem("Below Threshold");
-
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {}
-
-    adjusting = false;
-
-    changeColour();
-
-  }
-
-  public AnnotationColourChooser()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    minColour.setBorder(BorderFactory.createEtchedBorder());
-    minColour.setPreferredSize(new Dimension(40, 20));
-    minColour.setToolTipText("Minimum Colour");
-    minColour.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        if (minColour.isEnabled())
-        {
-          minColour_actionPerformed();
-        }
-      }
-    });
-    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    maxColour.setBorder(BorderFactory.createEtchedBorder());
-    maxColour.setPreferredSize(new Dimension(40, 20));
-    maxColour.setToolTipText("Maximum Colour");
-    maxColour.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        if (maxColour.isEnabled())
-        {
-          maxColour_actionPerformed();
-        }
-      }
-    });
-    ok.setOpaque(false);
-    ok.setText("OK");
-    ok.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setOpaque(false);
-    cancel.setText("Cancel");
-    cancel.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    this.setLayout(borderLayout1);
-    jPanel2.setLayout(flowLayout1);
-    annotations.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        annotations_actionPerformed(e);
-      }
-    });
-    jPanel1.setBackground(Color.white);
-    jPanel2.setBackground(Color.white);
-    threshold.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        threshold_actionPerformed(e);
-      }
-    });
-    jPanel3.setLayout(flowLayout2);
-    thresholdValue.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdValue_actionPerformed(e);
-      }
-    });
-    slider.setPaintLabels(false);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(100, 32));
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(7);
-    jPanel3.setBackground(Color.white);
-    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    currentColours.setOpaque(false);
-    currentColours.setText("Use Original Colours");
-    currentColours.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        currentColours_actionPerformed(e);
-      }
-    });
-    thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setText("Threshold is Min/Max");
-    thresholdIsMin.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        thresholdIsMin_actionPerformed(actionEvent);
-      }
-    });
-    jPanel1.add(ok);
-    jPanel1.add(cancel);
-    jPanel2.add(annotations);
-    jPanel2.add(currentColours);
-    jPanel2.add(minColour);
-    jPanel2.add(maxColour);
-    this.add(jPanel3, java.awt.BorderLayout.CENTER);
-    jPanel3.add(threshold);
-    jPanel3.add(slider);
-    jPanel3.add(thresholdValue);
-    jPanel3.add(thresholdIsMin);
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-    this.add(jPanel2, java.awt.BorderLayout.NORTH);
-  }
-
-  JComboBox annotations;
-  JPanel minColour = new JPanel();
-  JPanel maxColour = new JPanel();
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JPanel jPanel1 = new JPanel();
-  JPanel jPanel2 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  JComboBox threshold = new JComboBox();
-  FlowLayout flowLayout1 = new FlowLayout();
-  JPanel jPanel3 = new JPanel();
-  FlowLayout flowLayout2 = new FlowLayout();
-  JSlider slider = new JSlider();
-  JTextField thresholdValue = new JTextField(20);
-  JCheckBox currentColours = new JCheckBox();
-  JCheckBox thresholdIsMin = new JCheckBox();
-
-  public void minColour_actionPerformed()
-  {
-    Color col = JColorChooser.showDialog(this,
-                                         "Select Colour for Minimum Value",
-                                         minColour.getBackground());
-    if (col != null)
-    {
-      minColour.setBackground(col);
-    }
-    minColour.repaint();
-    changeColour();
-  }
-
-  public void maxColour_actionPerformed()
-  {
-    Color col = JColorChooser.showDialog(this,
-                                         "Select Colour for Maximum Value",
-                                         maxColour.getBackground());
-    if (col != null)
-    {
-      maxColour.setBackground(col);
-    }
-    maxColour.repaint();
-    changeColour();
-  }
-
-  void changeColour()
-  {
-    // Check if combobox is still adjusting
-    if (adjusting)
-    {
-      return;
-    }
-
-
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];
-
-    int aboveThreshold = -1;
-    if (threshold.getSelectedItem().equals("Above Threshold"))
-    {
-      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
-    }
-    else if (threshold.getSelectedItem().equals("Below Threshold"))
-    {
-      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
-    }
-
-    slider.setEnabled(true);
-    thresholdValue.setEnabled(true);
-
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
-    {
-      slider.setEnabled(false);
-      thresholdValue.setEnabled(false);
-      thresholdValue.setText("");
-    }
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
-             currentAnnotation.threshold == null)
-    {
-      currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
-                                     ( (currentAnnotation.graphMax -
-                                        currentAnnotation.graphMin) / 2f,
-                                      "Threshold",
-                                      Color.black));
-    }
-
-    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
-    {
-      adjusting = true;
-      float range = currentAnnotation.graphMax * 1000 -
-          currentAnnotation.graphMin * 1000;
-
-      slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
-      slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
-      slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
-      thresholdValue.setText(currentAnnotation.threshold.value + "");
-      slider.setMajorTickSpacing( (int) (range / 10f));
-      slider.setEnabled(true);
-      thresholdValue.setEnabled(true);
-      adjusting = false;
-    }
-
-    AnnotationColourGradient acg = null;
-    if (currentColours.isSelected())
-    {
-      acg = new AnnotationColourGradient(
-          currentAnnotation,
-          av.getGlobalColourScheme(), aboveThreshold);
-    }
-    else
-    {
-      acg =
-          new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
-              aboveThreshold);
-    }
-
-    if(currentAnnotation.graphMin==0f&& currentAnnotation.graphMax==0f)
-    {
-      acg.predefinedColours = true;
-    }
-
-    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
-
-    av.setGlobalColourScheme(acg);
-
-    if (av.alignment.getGroups() != null)
-    {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        if (currentColours.isSelected())
-        {
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              sg.cs, aboveThreshold);
-        }
-        else
-        {
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
-              aboveThreshold);
-        }
-
-      }
-    }
-
-    ap.paintAlignment(false);
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {}
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    reset();
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {}
-  }
-
-  void reset()
-  {
-    av.setGlobalColourScheme(oldcs);
-    if (av.alignment.getGroups() != null)
-    {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
-      }
-    }
-  }
-
-  public void thresholdCheck_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-  public void threshold_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-  public void thresholdValue_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      float f = Float.parseFloat(thresholdValue.getText());
-      slider.setValue( (int) (f * 1000));
-    }
-    catch (NumberFormatException ex)
-    {}
-  }
-
-  public void valueChanged()
-  {
-    if (currentColours.isSelected()
-        && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
-    {
-      changeColour();
-    }
-
-    currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
-    ap.paintAlignment(false);
-  }
-
-  public void currentColours_actionPerformed(ActionEvent e)
-  {
-    if (currentColours.isSelected())
-    {
-      reset();
-    }
-
-    maxColour.setEnabled(!currentColours.isSelected());
-    minColour.setEnabled(!currentColours.isSelected());
-
-    changeColour();
-  }
-
-  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
-  {
-    changeColour();
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import java.awt.Dimension;
+
+public class AnnotationColourChooser
+    extends JPanel
+{
+  JInternalFrame frame;
+  AlignViewport av;
+  AlignmentPanel ap;
+  ColourSchemeI oldcs;
+  Hashtable oldgroupColours;
+  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  boolean adjusting = false;
+
+  public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
+  {
+    oldcs = av.getGlobalColourScheme();
+    if (av.alignment.getGroups() != null)
+    {
+      oldgroupColours = new Hashtable();
+      Vector allGroups = ap.av.alignment.getGroups();
+      SequenceGroup sg;
+      for (int g = 0; g < allGroups.size(); g++)
+      {
+        sg = (SequenceGroup) allGroups.get(g);
+        if (sg.cs != null)
+        {
+          oldgroupColours.put(sg, sg.cs);
+        }
+      }
+    }
+    this.av = av;
+    this.ap = ap;
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
+
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        if (!adjusting)
+        {
+          thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
+          valueChanged();
+        }
+      }
+    });
+    slider.addMouseListener(new MouseAdapter()
+        {
+          public void mouseReleased(MouseEvent evt)
+          {
+            ap.paintAlignment(true);
+          }
+        });
+
+    if (av.alignment.getAlignmentAnnotation() == null)
+    {
+      return;
+    }
+
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      minColour.setBackground(acg.getMinColour());
+      maxColour.setBackground(acg.getMaxColour());
+    }
+    else
+    {
+      minColour.setBackground(Color.orange);
+      maxColour.setBackground(Color.red);
+    }
+
+    adjusting = true;
+    Vector list = new Vector();
+    int index = 1;
+    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
+    {
+      String label = av.alignment.getAlignmentAnnotation()[i].label;
+      if (!list.contains(label))
+        list.addElement(label);
+      else
+        list.addElement(label+"_"+(index++));
+    }
+
+    annotations = new JComboBox(list);
+
+    threshold.addItem("No Threshold");
+    threshold.addItem("Above Threshold");
+    threshold.addItem("Below Threshold");
+
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {}
+
+    adjusting = false;
+
+    changeColour();
+
+  }
+
+  public AnnotationColourChooser()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    minColour.setBorder(BorderFactory.createEtchedBorder());
+    minColour.setPreferredSize(new Dimension(40, 20));
+    minColour.setToolTipText("Minimum Colour");
+    minColour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        if (minColour.isEnabled())
+        {
+          minColour_actionPerformed();
+        }
+      }
+    });
+    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    maxColour.setBorder(BorderFactory.createEtchedBorder());
+    maxColour.setPreferredSize(new Dimension(40, 20));
+    maxColour.setToolTipText("Maximum Colour");
+    maxColour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        if (maxColour.isEnabled())
+        {
+          maxColour_actionPerformed();
+        }
+      }
+    });
+    ok.setOpaque(false);
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setOpaque(false);
+    cancel.setText("Cancel");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    annotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotations_actionPerformed(e);
+      }
+    });
+    jPanel1.setBackground(Color.white);
+    jPanel2.setBackground(Color.white);
+    threshold.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed(e);
+      }
+    });
+    jPanel3.setLayout(flowLayout2);
+    thresholdValue.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        thresholdValue_actionPerformed(e);
+      }
+    });
+    slider.setPaintLabels(false);
+    slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setEnabled(false);
+    slider.setOpaque(false);
+    slider.setPreferredSize(new Dimension(100, 32));
+    thresholdValue.setEnabled(false);
+    thresholdValue.setColumns(7);
+    jPanel3.setBackground(Color.white);
+    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    currentColours.setOpaque(false);
+    currentColours.setText("Use Original Colours");
+    currentColours.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        currentColours_actionPerformed(e);
+      }
+    });
+    thresholdIsMin.setBackground(Color.white);
+    thresholdIsMin.setText("Threshold is Min/Max");
+    thresholdIsMin.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        thresholdIsMin_actionPerformed(actionEvent);
+      }
+    });
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+    jPanel2.add(annotations);
+    jPanel2.add(currentColours);
+    jPanel2.add(minColour);
+    jPanel2.add(maxColour);
+    this.add(jPanel3, java.awt.BorderLayout.CENTER);
+    jPanel3.add(threshold);
+    jPanel3.add(slider);
+    jPanel3.add(thresholdValue);
+    jPanel3.add(thresholdIsMin);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+    this.add(jPanel2, java.awt.BorderLayout.NORTH);
+  }
+
+  JComboBox annotations;
+  JPanel minColour = new JPanel();
+  JPanel maxColour = new JPanel();
+  JButton ok = new JButton();
+  JButton cancel = new JButton();
+  JPanel jPanel1 = new JPanel();
+  JPanel jPanel2 = new JPanel();
+  BorderLayout borderLayout1 = new BorderLayout();
+  JComboBox threshold = new JComboBox();
+  FlowLayout flowLayout1 = new FlowLayout();
+  JPanel jPanel3 = new JPanel();
+  FlowLayout flowLayout2 = new FlowLayout();
+  JSlider slider = new JSlider();
+  JTextField thresholdValue = new JTextField(20);
+  JCheckBox currentColours = new JCheckBox();
+  JCheckBox thresholdIsMin = new JCheckBox();
+
+  public void minColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+                                         "Select Colour for Minimum Value",
+                                         minColour.getBackground());
+    if (col != null)
+    {
+      minColour.setBackground(col);
+    }
+    minColour.repaint();
+    changeColour();
+  }
+
+  public void maxColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+                                         "Select Colour for Maximum Value",
+                                         maxColour.getBackground());
+    if (col != null)
+    {
+      maxColour.setBackground(col);
+    }
+    maxColour.repaint();
+    changeColour();
+  }
+
+  void changeColour()
+  {
+    // Check if combobox is still adjusting
+    if (adjusting)
+    {
+      return;
+    }
+
+
+    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];
+
+    int aboveThreshold = -1;
+    if (threshold.getSelectedItem().equals("Above Threshold"))
+    {
+      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+    }
+    else if (threshold.getSelectedItem().equals("Below Threshold"))
+    {
+      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+    }
+
+    slider.setEnabled(true);
+    thresholdValue.setEnabled(true);
+
+    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+    {
+      slider.setEnabled(false);
+      thresholdValue.setEnabled(false);
+      thresholdValue.setText("");
+    }
+    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
+             currentAnnotation.threshold == null)
+    {
+      currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
+                                     ( (currentAnnotation.graphMax -
+                                        currentAnnotation.graphMin) / 2f,
+                                      "Threshold",
+                                      Color.black));
+    }
+
+    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    {
+      adjusting = true;
+      float range = currentAnnotation.graphMax * 1000 -
+          currentAnnotation.graphMin * 1000;
+
+      slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
+      slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
+      slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
+      thresholdValue.setText(currentAnnotation.threshold.value + "");
+      slider.setMajorTickSpacing( (int) (range / 10f));
+      slider.setEnabled(true);
+      thresholdValue.setEnabled(true);
+      adjusting = false;
+    }
+
+    AnnotationColourGradient acg = null;
+    if (currentColours.isSelected())
+    {
+      acg = new AnnotationColourGradient(
+          currentAnnotation,
+          av.getGlobalColourScheme(), aboveThreshold);
+    }
+    else
+    {
+      acg =
+          new AnnotationColourGradient(
+              currentAnnotation,
+              minColour.getBackground(),
+              maxColour.getBackground(),
+              aboveThreshold);
+    }
+
+    if(currentAnnotation.graphMin==0f&& currentAnnotation.graphMax==0f)
+    {
+      acg.predefinedColours = true;
+    }
+
+    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+
+    av.setGlobalColourScheme(acg);
+
+    if (av.alignment.getGroups() != null)
+    {
+      Vector allGroups = ap.av.alignment.getGroups();
+      SequenceGroup sg;
+      for (int g = 0; g < allGroups.size(); g++)
+      {
+        sg = (SequenceGroup) allGroups.get(g);
+
+        if (sg.cs == null)
+        {
+          continue;
+        }
+
+        if (currentColours.isSelected())
+        {
+          sg.cs = new AnnotationColourGradient(
+              currentAnnotation,
+              sg.cs, aboveThreshold);
+        }
+        else
+        {
+          sg.cs = new AnnotationColourGradient(
+              currentAnnotation,
+              minColour.getBackground(),
+              maxColour.getBackground(),
+              aboveThreshold);
+        }
+
+      }
+    }
+
+    ap.paintAlignment(false);
+  }
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+    try
+    {
+      frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {}
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    reset();
+    try
+    {
+      frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {}
+  }
+
+  void reset()
+  {
+    av.setGlobalColourScheme(oldcs);
+    if (av.alignment.getGroups() != null)
+    {
+      Vector allGroups = ap.av.alignment.getGroups();
+      SequenceGroup sg;
+      for (int g = 0; g < allGroups.size(); g++)
+      {
+        sg = (SequenceGroup) allGroups.get(g);
+        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
+      }
+    }
+  }
+
+  public void thresholdCheck_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void annotations_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void threshold_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void thresholdValue_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      float f = Float.parseFloat(thresholdValue.getText());
+      slider.setValue( (int) (f * 1000));
+    }
+    catch (NumberFormatException ex)
+    {}
+  }
+
+  public void valueChanged()
+  {
+    if (currentColours.isSelected()
+        && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+    {
+      changeColour();
+    }
+
+    currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+    ap.paintAlignment(false);
+  }
+
+  public void currentColours_actionPerformed(ActionEvent e)
+  {
+    if (currentColours.isSelected())
+    {
+      reset();
+    }
+
+    maxColour.setEnabled(!currentColours.isSelected());
+    minColour.setEnabled(!currentColours.isSelected());
+
+    changeColour();
+  }
+
+  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+  {
+    changeColour();
+  }
+
+}
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index ab3f0d1..8354572 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 2eda839..8c42790 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 6371e86..410c84c 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 50e5644..6454c59 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index a3fa7c7..4212ae8 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,265 +1,265 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class CutAndPasteTransfer
-    extends GCutAndPasteTransfer
-{
-
-  AlignViewport viewport;
-
-  public CutAndPasteTransfer()
-  {
-    SwingUtilities.invokeLater(new Runnable()
-    {
-      public void run()
-      {
-        textarea.requestFocus();
-      }
-    });
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void setForInput(AlignViewport viewport)
-  {
-    this.viewport = viewport;
-    if (viewport != null)
-    {
-      ok.setText("Add");
-    }
-
-    getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String getText()
-  {
-    return textarea.getText();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param text DOCUMENT ME!
-   */
-  public void setText(String text)
-  {
-    textarea.setText(text);
-  }
-
-  public void appendText(String text)
-  {
-    textarea.append(text);
-  }
-
-  public void save_actionPerformed(ActionEvent e)
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-        jalview.bin.Cache.getProperty(
-            "LAST_DIRECTORY"));
-
-    chooser.setAcceptAllFileFilterUsed(false);
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Text to File");
-    chooser.setToolTipText("Save");
-
-    int value = chooser.showSaveDialog(this);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      try
-      {
-        java.io.PrintWriter out = new java.io.PrintWriter(
-            new java.io.FileWriter(chooser.getSelectedFile()));
-
-        out.print(getText());
-        out.close();
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
-
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void copyItem_actionPerformed(ActionEvent e)
-  {
-    textarea.getSelectedText();
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-    c.setContents(new StringSelection(textarea.getSelectedText()), null);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void pasteMenu_actionPerformed(ActionEvent e)
-  {
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-    Transferable contents = c.getContents(this);
-
-    if (contents == null)
-    {
-      return;
-    }
-
-    try
-    {
-      textarea.append( (String) contents.getTransferData(
-          DataFlavor.stringFlavor));
-    }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    String format = new IdentifyFile().Identify(getText(), "Paste");
-    Alignment al = null;
-
-    if (FormatAdapter.isValidFormat(format))
-    {
-      try
-      {
-        al = new FormatAdapter().readFile(getText(), "Paste", format);
-      }
-      catch (java.io.IOException ex)
-      {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                              "Couldn't read the pasted text.\n" +
-                                              ex.toString(),
-                                              "Error parsing text",
-                                              JOptionPane.WARNING_MESSAGE);
-      }
-    }
-
-    if (al != null)
-    {
-      if (viewport != null)
-      {
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-          viewport.getAlignment().addSequence(al.getSequenceAt(i));
-        }
-
-        viewport.firePropertyChange("alignment", null,
-                                    viewport.getAlignment().getSequences());
-      }
-      else
-      {
-        AlignFrame af = new AlignFrame(al,
-                                       AlignFrame.DEFAULT_WIDTH,
-                                       AlignFrame.DEFAULT_HEIGHT);
-        af.currentFileFormat = format;
-        Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
-                                 AlignFrame.DEFAULT_WIDTH,
-                                 AlignFrame.DEFAULT_HEIGHT);
-        af.statusBar.setText("Successfully pasted alignment file");
-
-        try
-        {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
-        }
-        catch (Exception ex)
-        {
-        }
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      this.setClosed(true);
-    }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  public void textarea_mousePressed(MouseEvent e)
-  {
-    if (SwingUtilities.isRightMouseButton(e))
-    {
-      JPopupMenu popup = new JPopupMenu("Edit");
-      JMenuItem item = new JMenuItem("Copy");
-      item.addActionListener(new ActionListener()
-      {
-        public void actionPerformed(ActionEvent e)
-        {
-          copyItem_actionPerformed(e);
-        }
-      });
-      popup.add(item);
-      item = new JMenuItem("Paste");
-      item.addActionListener(new ActionListener()
-      {
-        public void actionPerformed(ActionEvent e)
-        {
-          pasteMenu_actionPerformed(e);
-        }
-      });
-      popup.add(item);
-      popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);
-
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class CutAndPasteTransfer
+    extends GCutAndPasteTransfer
+{
+
+  AlignViewport viewport;
+
+  public CutAndPasteTransfer()
+  {
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        textarea.requestFocus();
+      }
+    });
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void setForInput(AlignViewport viewport)
+  {
+    this.viewport = viewport;
+    if (viewport != null)
+    {
+      ok.setText("Add");
+    }
+
+    getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getText()
+  {
+    return textarea.getText();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param text DOCUMENT ME!
+   */
+  public void setText(String text)
+  {
+    textarea.setText(text);
+  }
+
+  public void appendText(String text)
+  {
+    textarea.append(text);
+  }
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(
+        jalview.bin.Cache.getProperty(
+            "LAST_DIRECTORY"));
+
+    chooser.setAcceptAllFileFilterUsed(false);
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save Text to File");
+    chooser.setToolTipText("Save");
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      try
+      {
+        java.io.PrintWriter out = new java.io.PrintWriter(
+            new java.io.FileWriter(chooser.getSelectedFile()));
+
+        out.print(getText());
+        out.close();
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void copyItem_actionPerformed(ActionEvent e)
+  {
+    textarea.getSelectedText();
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    c.setContents(new StringSelection(textarea.getSelectedText()), null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void pasteMenu_actionPerformed(ActionEvent e)
+  {
+    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+    Transferable contents = c.getContents(this);
+
+    if (contents == null)
+    {
+      return;
+    }
+
+    try
+    {
+      textarea.append( (String) contents.getTransferData(
+          DataFlavor.stringFlavor));
+    }
+    catch (Exception ex)
+    {
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    String format = new IdentifyFile().Identify(getText(), "Paste");
+    Alignment al = null;
+
+    if (FormatAdapter.isValidFormat(format))
+    {
+      try
+      {
+        al = new FormatAdapter().readFile(getText(), "Paste", format);
+      }
+      catch (java.io.IOException ex)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              "Couldn't read the pasted text.\n" +
+                                              ex.toString(),
+                                              "Error parsing text",
+                                              JOptionPane.WARNING_MESSAGE);
+      }
+    }
+
+    if (al != null)
+    {
+      if (viewport != null)
+      {
+        for (int i = 0; i < al.getHeight(); i++)
+        {
+          viewport.getAlignment().addSequence(al.getSequenceAt(i));
+        }
+
+        viewport.firePropertyChange("alignment", null,
+                                    viewport.getAlignment().getSequences());
+      }
+      else
+      {
+        AlignFrame af = new AlignFrame(al,
+                                       AlignFrame.DEFAULT_WIDTH,
+                                       AlignFrame.DEFAULT_HEIGHT);
+        af.currentFileFormat = format;
+        Desktop.addInternalFrame(af, "Cut & Paste input - " + format,
+                                 AlignFrame.DEFAULT_WIDTH,
+                                 AlignFrame.DEFAULT_HEIGHT);
+        af.statusBar.setText("Successfully pasted alignment file");
+
+        try
+        {
+          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+        }
+        catch (Exception ex)
+        {
+        }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      this.setClosed(true);
+    }
+    catch (Exception ex)
+    {
+    }
+  }
+
+  public void textarea_mousePressed(MouseEvent e)
+  {
+    if (SwingUtilities.isRightMouseButton(e))
+    {
+      JPopupMenu popup = new JPopupMenu("Edit");
+      JMenuItem item = new JMenuItem("Copy");
+      item.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          copyItem_actionPerformed(e);
+        }
+      });
+      popup.add(item);
+      item = new JMenuItem("Paste");
+      item.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          pasteMenu_actionPerformed(e);
+        }
+      });
+      popup.add(item);
+      popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);
+
+    }
+  }
+
+}
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 807aa4b..91711dc 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 10687cd..310ec93 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/EPSOptions.java b/src/jalview/gui/EPSOptions.java
index dc7b650..a3339c1 100755
--- a/src/jalview/gui/EPSOptions.java
+++ b/src/jalview/gui/EPSOptions.java
@@ -1,143 +1,143 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-public class EPSOptions
-    extends JPanel
-{
-  JDialog dialog;
-  public boolean cancelled = false;
-  String value;
-
-  public EPSOptions()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-
-    ButtonGroup bg = new ButtonGroup();
-    bg.add(lineart);
-    bg.add(text);
-
-    JOptionPane pane = new JOptionPane(null,
-                                       JOptionPane.DEFAULT_OPTION,
-                                       JOptionPane.DEFAULT_OPTION,
-                                       null, new Object[]
-                                       {this});
-
-    dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");
-    dialog.setVisible(true);
-
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    lineart.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    lineart.setText("Lineart");
-    text.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    text.setText("Text");
-    text.setSelected(true);
-    askAgain.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    askAgain.setText("Don\'t ask me again");
-    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);
-      }
-    });
-    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    jLabel1.setText("Select EPS character rendering style");
-    this.setLayout(borderLayout1);
-    jPanel3.setBorder(BorderFactory.createEtchedBorder());
-    jPanel2.add(text);
-    jPanel2.add(lineart);
-    jPanel2.add(askAgain);
-    jPanel1.add(ok);
-    jPanel1.add(cancel);
-    jPanel3.add(jLabel1);
-    jPanel3.add(jPanel2);
-    this.add(jPanel3, java.awt.BorderLayout.CENTER);
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-  }
-
-  JRadioButton lineart = new JRadioButton();
-  JRadioButton text = new JRadioButton();
-  JCheckBox askAgain = new JCheckBox();
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JPanel jPanel1 = new JPanel();
-  JLabel jLabel1 = new JLabel();
-  JPanel jPanel2 = new JPanel();
-  JPanel jPanel3 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    if (lineart.isSelected())
-    {
-      value = "Lineart";
-    }
-    else
-    {
-      value = "Text";
-    }
-
-    if (!askAgain.isSelected())
-    {
-      jalview.bin.Cache.applicationProperties.remove("EPS_RENDERING");
-    }
-    else
-    {
-      jalview.bin.Cache.setProperty("EPS_RENDERING", value);
-    }
-
-    dialog.setVisible(false);
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    cancelled = true;
-    dialog.setVisible(false);
-  }
-
-  public String getValue()
-  {
-    return value;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
+
+public class EPSOptions
+    extends JPanel
+{
+  JDialog dialog;
+  public boolean cancelled = false;
+  String value;
+
+  public EPSOptions()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    ButtonGroup bg = new ButtonGroup();
+    bg.add(lineart);
+    bg.add(text);
+
+    JOptionPane pane = new JOptionPane(null,
+                                       JOptionPane.DEFAULT_OPTION,
+                                       JOptionPane.DEFAULT_OPTION,
+                                       null, new Object[]
+                                       {this});
+
+    dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");
+    dialog.setVisible(true);
+
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    lineart.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    lineart.setText("Lineart");
+    text.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    text.setText("Text");
+    text.setSelected(true);
+    askAgain.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    askAgain.setText("Don\'t ask me again");
+    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);
+      }
+    });
+    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    jLabel1.setText("Select EPS character rendering style");
+    this.setLayout(borderLayout1);
+    jPanel3.setBorder(BorderFactory.createEtchedBorder());
+    jPanel2.add(text);
+    jPanel2.add(lineart);
+    jPanel2.add(askAgain);
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+    jPanel3.add(jLabel1);
+    jPanel3.add(jPanel2);
+    this.add(jPanel3, java.awt.BorderLayout.CENTER);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+  }
+
+  JRadioButton lineart = new JRadioButton();
+  JRadioButton text = new JRadioButton();
+  JCheckBox askAgain = new JCheckBox();
+  JButton ok = new JButton();
+  JButton cancel = new JButton();
+  JPanel jPanel1 = new JPanel();
+  JLabel jLabel1 = new JLabel();
+  JPanel jPanel2 = new JPanel();
+  JPanel jPanel3 = new JPanel();
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    if (lineart.isSelected())
+    {
+      value = "Lineart";
+    }
+    else
+    {
+      value = "Text";
+    }
+
+    if (!askAgain.isSelected())
+    {
+      jalview.bin.Cache.applicationProperties.remove("EPS_RENDERING");
+    }
+    else
+    {
+      jalview.bin.Cache.setProperty("EPS_RENDERING", value);
+    }
+
+    dialog.setVisible(false);
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    cancelled = true;
+    dialog.setVisible(false);
+  }
+
+  public String getValue()
+  {
+    return value;
+  }
+}
diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java
index a3d2d47..10e329f 100644
--- a/src/jalview/gui/EditNameDialog.java
+++ b/src/jalview/gui/EditNameDialog.java
@@ -1,83 +1,82 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.gui;
-
-import java.awt.*;
-import javax.swing.*;
-
-public class EditNameDialog
-{
-  JTextField id, description;
-  JButton ok = new JButton("Accept");
-  JButton cancel = new JButton("Cancel");
-  boolean accept = false;
-
-  public String getName()
-  {
-    return id.getText();
-  }
-
-  public String getDescription()
-  {
-    if (description.getText().length() < 1)
-    {
-      return null;
-    }
-    else
-    {
-      return description.getText();
-    }
-  }
-
-  public EditNameDialog(String name,
-                        String desc,
-                        String label1,
-                        String label2,
-                        String title)
-  {
-    JLabel idlabel = new JLabel(label1);
-    JLabel desclabel = new JLabel(label2);
-    idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
-    desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
-    id = new JTextField(name, 40);
-    description = new JTextField(desc, 40);
-    JPanel panel = new JPanel(new BorderLayout());
-    JPanel panel2 = new JPanel(new BorderLayout());
-    panel2.add(idlabel, BorderLayout.WEST);
-    panel2.add(id, BorderLayout.CENTER);
-    panel.add(panel2, BorderLayout.NORTH);
-    if(desc!=null || label2!=null)
-    {
-      panel2 = new JPanel(new BorderLayout());
-      panel2.add(desclabel, BorderLayout.WEST);
-      panel2.add(description, BorderLayout.CENTER);
-      panel.add(panel2, BorderLayout.SOUTH);
-    }
-
-    int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-        panel, title,
-        JOptionPane.OK_CANCEL_OPTION);
-
-    if (reply == JOptionPane.OK_OPTION)
-    {
-      accept = true;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 javax.swing.*;
+
+public class EditNameDialog
+{
+  JTextField id, description;
+  JButton ok = new JButton("Accept");
+  JButton cancel = new JButton("Cancel");
+  boolean accept = false;
+
+  public String getName()
+  {
+    return id.getText();
+  }
+
+  public String getDescription()
+  {
+    if (description.getText().length() < 1)
+    {
+      return null;
+    }
+    else
+    {
+      return description.getText();
+    }
+  }
+
+  public EditNameDialog(String name,
+                        String desc,
+                        String label1,
+                        String label2,
+                        String title)
+  {
+    JLabel idlabel = new JLabel(label1);
+    JLabel desclabel = new JLabel(label2);
+    idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
+    desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
+    id = new JTextField(name, 40);
+    description = new JTextField(desc, 40);
+    JPanel panel = new JPanel(new BorderLayout());
+    JPanel panel2 = new JPanel(new BorderLayout());
+    panel2.add(idlabel, BorderLayout.WEST);
+    panel2.add(id, BorderLayout.CENTER);
+    panel.add(panel2, BorderLayout.NORTH);
+    if(desc!=null || label2!=null)
+    {
+      panel2 = new JPanel(new BorderLayout());
+      panel2.add(desclabel, BorderLayout.WEST);
+      panel2.add(description, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.SOUTH);
+    }
+
+    int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+        panel, title,
+        JOptionPane.OK_CANCEL_OPTION);
+
+    if (reply == JOptionPane.OK_OPTION)
+    {
+      accept = true;
+    }
+  }
+}
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index b643efb..fb0abd5 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index ea492e2..cd950ed 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5668b42..7d7ab0f 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index aaf0abc..5a4d219 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -1,259 +1,259 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.jbgui.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class FontChooser
-    extends GFontChooser
-{
-  AlignmentPanel ap;
-  TreePanel tp;
-  Font oldFont;
-  boolean init = true;
-  JInternalFrame frame;
-
-  /**
-   * Creates a new FontChooser object.
-   *
-   * @param ap DOCUMENT ME!
-   */
-  public FontChooser(TreePanel tp)
-  {
-    this.tp = tp;
-    ap = tp.treeCanvas.ap;
-    oldFont = tp.getTreeFont();
-    defaultButton.setVisible(false);
-    smoothFont.setEnabled(false);
-    init();
-  }
-
-  /**
-   * Creates a new FontChooser object.
-   *
-   * @param ap DOCUMENT ME!
-   */
-  public FontChooser(AlignmentPanel ap)
-  {
-    oldFont = ap.av.getFont();
-    this.ap = ap;
-    init();
-  }
-
-  void init()
-  {
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-
-    smoothFont.setSelected(ap.av.antiAlias);
-
-    if (tp != null)
-    {
-      Desktop.addInternalFrame(frame, "Change Font (Tree Panel)", 340, 170, false);
-    }
-    else
-    {
-      Desktop.addInternalFrame(frame, "Change Font", 340, 170, false);
-    }
-
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-
-    String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
-        .getAvailableFontFamilyNames();
-
-    for (int i = 0; i < fonts.length; i++)
-    {
-      fontName.addItem(fonts[i]);
-    }
-
-    for (int i = 1; i < 51; i++)
-    {
-      fontSize.addItem(i + "");
-    }
-
-    fontStyle.addItem("plain");
-    fontStyle.addItem("bold");
-    fontStyle.addItem("italic");
-
-    fontName.setSelectedItem(oldFont.getName());
-    fontSize.setSelectedItem(oldFont.getSize() + "");
-    fontStyle.setSelectedIndex(oldFont.getStyle());
-
-    FontMetrics fm = getGraphics().getFontMetrics(oldFont);
-    monospaced.setSelected(fm.getStringBounds("M", getGraphics()).getWidth()
-                           == fm.getStringBounds("|", getGraphics()).getWidth());
-
-    init = false;
-  }
-
-  public void smoothFont_actionPerformed(ActionEvent e)
-  {
-    ap.av.antiAlias = smoothFont.isSelected();
-    ap.annotationPanel.image = null;
-    ap.paintAlignment(true);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void ok_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {
-    }
-
-    if (ap != null)
-    {
-      if (ap.getOverviewPanel() != null)
-      {
-        ap.getOverviewPanel().updateOverviewImage();
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-    if (ap != null)
-    {
-      ap.av.setFont(oldFont);
-      ap.paintAlignment(true);
-    }
-    else if (tp != null)
-    {
-      tp.setTreeFont(oldFont);
-    }
-    fontName.setSelectedItem(oldFont.getName());
-    fontSize.setSelectedItem(oldFont.getSize() + "");
-    fontStyle.setSelectedIndex(oldFont.getStyle());
-
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  void changeFont()
-  {
-    Font newFont = new Font(fontName.getSelectedItem().toString(),
-                            fontStyle.getSelectedIndex(),
-                            Integer.parseInt(fontSize.getSelectedItem().
-                                             toString()));
-    if (tp != null)
-    {
-      tp.setTreeFont(newFont);
-    }
-    else if (ap != null)
-    {
-      ap.av.setFont(newFont);
-      ap.fontChanged();
-    }
-
-    FontMetrics fm = getGraphics().getFontMetrics(newFont);
-
-    monospaced.setSelected(fm.getStringBounds("M", getGraphics()).getWidth()
-                           == fm.getStringBounds("|", getGraphics()).getWidth());
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontName_actionPerformed(ActionEvent e)
-  {
-    if (init)
-    {
-      return;
-    }
-
-    changeFont();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-    if (init)
-    {
-      return;
-    }
-
-    changeFont();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontStyle_actionPerformed(ActionEvent e)
-  {
-    if (init)
-    {
-      return;
-    }
-
-    changeFont();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void defaultButton_actionPerformed(ActionEvent e)
-  {
-    Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
-    Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex() + "");
-    Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());
-    Cache.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.bin.*;
+import jalview.jbgui.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FontChooser
+    extends GFontChooser
+{
+  AlignmentPanel ap;
+  TreePanel tp;
+  Font oldFont;
+  boolean init = true;
+  JInternalFrame frame;
+
+  /**
+   * Creates a new FontChooser object.
+   *
+   * @param ap DOCUMENT ME!
+   */
+  public FontChooser(TreePanel tp)
+  {
+    this.tp = tp;
+    ap = tp.treeCanvas.ap;
+    oldFont = tp.getTreeFont();
+    defaultButton.setVisible(false);
+    smoothFont.setEnabled(false);
+    init();
+  }
+
+  /**
+   * Creates a new FontChooser object.
+   *
+   * @param ap DOCUMENT ME!
+   */
+  public FontChooser(AlignmentPanel ap)
+  {
+    oldFont = ap.av.getFont();
+    this.ap = ap;
+    init();
+  }
+
+  void init()
+  {
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+
+    smoothFont.setSelected(ap.av.antiAlias);
+
+    if (tp != null)
+    {
+      Desktop.addInternalFrame(frame, "Change Font (Tree Panel)", 340, 170, false);
+    }
+    else
+    {
+      Desktop.addInternalFrame(frame, "Change Font", 340, 170, false);
+    }
+
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+
+    String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
+        .getAvailableFontFamilyNames();
+
+    for (int i = 0; i < fonts.length; i++)
+    {
+      fontName.addItem(fonts[i]);
+    }
+
+    for (int i = 1; i < 51; i++)
+    {
+      fontSize.addItem(i + "");
+    }
+
+    fontStyle.addItem("plain");
+    fontStyle.addItem("bold");
+    fontStyle.addItem("italic");
+
+    fontName.setSelectedItem(oldFont.getName());
+    fontSize.setSelectedItem(oldFont.getSize() + "");
+    fontStyle.setSelectedIndex(oldFont.getStyle());
+
+    FontMetrics fm = getGraphics().getFontMetrics(oldFont);
+    monospaced.setSelected(fm.getStringBounds("M", getGraphics()).getWidth()
+                           == fm.getStringBounds("|", getGraphics()).getWidth());
+
+    init = false;
+  }
+
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+    ap.av.antiAlias = smoothFont.isSelected();
+    ap.annotationPanel.image = null;
+    ap.paintAlignment(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void ok_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {
+    }
+
+    if (ap != null)
+    {
+      if (ap.getOverviewPanel() != null)
+      {
+        ap.getOverviewPanel().updateOverviewImage();
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void cancel_actionPerformed(ActionEvent e)
+  {
+    if (ap != null)
+    {
+      ap.av.setFont(oldFont);
+      ap.paintAlignment(true);
+    }
+    else if (tp != null)
+    {
+      tp.setTreeFont(oldFont);
+    }
+    fontName.setSelectedItem(oldFont.getName());
+    fontSize.setSelectedItem(oldFont.getSize() + "");
+    fontStyle.setSelectedIndex(oldFont.getStyle());
+
+    try
+    {
+      frame.setClosed(true);
+    }
+    catch (Exception ex)
+    {
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  void changeFont()
+  {
+    Font newFont = new Font(fontName.getSelectedItem().toString(),
+                            fontStyle.getSelectedIndex(),
+                            Integer.parseInt(fontSize.getSelectedItem().
+                                             toString()));
+    if (tp != null)
+    {
+      tp.setTreeFont(newFont);
+    }
+    else if (ap != null)
+    {
+      ap.av.setFont(newFont);
+      ap.fontChanged();
+    }
+
+    FontMetrics fm = getGraphics().getFontMetrics(newFont);
+
+    monospaced.setSelected(fm.getStringBounds("M", getGraphics()).getWidth()
+                           == fm.getStringBounds("|", getGraphics()).getWidth());
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fontName_actionPerformed(ActionEvent e)
+  {
+    if (init)
+    {
+      return;
+    }
+
+    changeFont();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fontSize_actionPerformed(ActionEvent e)
+  {
+    if (init)
+    {
+      return;
+    }
+
+    changeFont();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fontStyle_actionPerformed(ActionEvent e)
+  {
+    if (init)
+    {
+      return;
+    }
+
+    changeFont();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void defaultButton_actionPerformed(ActionEvent e)
+  {
+    Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
+    Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex() + "");
+    Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());
+    Cache.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
+  }
+}
diff --git a/src/jalview/gui/IProgressIndicator.java b/src/jalview/gui/IProgressIndicator.java
index 4acaba9..d88c05f 100644
--- a/src/jalview/gui/IProgressIndicator.java
+++ b/src/jalview/gui/IProgressIndicator.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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;
 
 /**
@@ -15,4 +33,4 @@ public interface IProgressIndicator
    */
   public abstract void setProgressBar(String message, long id);
 
-}
\ No newline at end of file
+}
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 97b8669..17e7683 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,477 +1,477 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class IdCanvas
-    extends JPanel
-{
-  protected AlignViewport av;
-  protected boolean showScores = true;
-  protected int maxIdLength = -1;
-  protected String maxIdStr = null;
-  BufferedImage image;
-  Graphics2D gg;
-  int imgHeight = 0;
-  boolean fastPaint = false;
-  java.util.Vector searchResults;
-  FontMetrics fm;
-  AnnotationLabels labels = null;
-  AnnotationPanel ap;
-  Font idfont;
-
-  /**
-   * Creates a new IdCanvas object.
-   *
-   * @param av DOCUMENT ME!
-   */
-  public IdCanvas(AlignViewport av)
-  {
-    setLayout(new BorderLayout());
-    this.av = av;
-    PaintRefresher.Register(this, av.getSequenceSetId());
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param gg DOCUMENT ME!
-   * @param s DOCUMENT ME!
-   * @param i DOCUMENT ME!
-   * @param starty DOCUMENT ME!
-   * @param ypos DOCUMENT ME!
-   */
-  public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
-                           int ypos)
-  {
-    int xPos = 0;
-    int panelWidth = getWidth();
-    int charHeight = av.charHeight;
-
-    if ( (searchResults != null) && searchResults.contains(s))
-    {
-      gg.setColor(Color.black);
-      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
-                  charHeight);
-      gg.setColor(Color.white);
-    }
-    else if ( (av.getSelectionGroup() != null) &&
-             av.getSelectionGroup().getSequences(null).contains(s))
-    {
-      gg.setColor(Color.lightGray);
-      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
-                  charHeight);
-      gg.setColor(Color.white);
-    }
-    else
-    {
-      gg.setColor(av.getSequenceColour(s));
-      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
-                  charHeight);
-      gg.setColor(Color.black);
-    }
-
-    if (av.rightAlignIds)
-    {
-      xPos = panelWidth - fm.stringWidth(
-          s.getDisplayId(av.getShowJVSuffix())
-          ) - 4;
-    }
-
-    gg.drawString(s.getDisplayId(av.getShowJVSuffix()),
-                  xPos,
-                  ( ( (i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
-
-    if (av.hasHiddenRows && av.showHiddenMarkers)
-    {
-      drawMarker(i, starty, ypos);
-    }
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param vertical DOCUMENT ME!
-   */
-  public void fastPaint(int vertical)
-  {
-    if (gg == null)
-    {
-      repaint();
-
-      return;
-    }
-
-    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;
-
-      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);
-
-    drawIds(ss, es);
-
-    gg.translate(0, -transY);
-
-    fastPaint = true;
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-
-    if (fastPaint)
-    {
-      fastPaint = false;
-      g.drawImage(image, 0, 0, this);
-
-      return;
-    }
-
-    int oldHeight = imgHeight;
-
-    imgHeight = getHeight();
-    imgHeight -= (imgHeight % av.charHeight);
-
-    if (imgHeight < 1)
-    {
-      return;
-    }
-
-    if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
-    {
-      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);
-
-    drawIds(av.getStartSeq(), av.endSeq);
-
-    g.drawImage(image, 0, 0, this);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param starty DOCUMENT ME!
-   * @param endy DOCUMENT ME!
-   */
-  void drawIds(int starty, int endy)
-  {
-    if (av.seqNameItalics)
-    {
-      idfont = new Font(av.getFont().getName(), Font.ITALIC,
-                        av.getFont().getSize());
-    }
-    else
-    {
-      idfont = av.getFont();
-    }
-
-    gg.setFont(idfont);
-    fm = gg.getFontMetrics();
-
-    if (av.antiAlias)
-    {
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                          RenderingHints.VALUE_ANTIALIAS_ON);
-    }
-
-    Color currentColor = Color.white;
-    Color currentTextColor = Color.black;
-
-    if (av.getWrapAlignment())
-    {
-      int maxwidth = av.alignment.getWidth();
-      int alheight = av.alignment.getHeight();
-
-      if (av.hasHiddenColumns)
-      {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-      }
-
-      int annotationHeight = 0;
-
-      if (av.showAnnotation)
-      {
-        if (ap == null)
-        {
-          ap = new AnnotationPanel(av);
-        }
-
-        annotationHeight = ap.adjustPanelHeight();
-        if (labels == null)
-        {
-          labels = new AnnotationLabels(av);
-        }
-      }
-
-      int hgap = av.charHeight;
-      if (av.scaleAboveWrapped)
-      {
-        hgap += av.charHeight;
-      }
-
-      int cHeight = alheight * av.charHeight
-          + hgap
-          + annotationHeight;
-
-      int rowSize = av.getEndRes() - av.getStartRes();
-
-      // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes;
-           (ypos <= getHeight()) && (row < maxwidth);
-           ypos += cHeight, row += rowSize)
-      {
-        for (int i = starty; i < alheight; i++)
-        {
-          SequenceI s = av.alignment.getSequenceAt(i);
-          if (av.hasHiddenRows)
-          {
-            setHiddenFont(s);
-          }
-          else
-          {
-            gg.setFont(idfont);
-          }
-
-          drawIdString(gg, s, i, 0, ypos);
-        }
-
-        if (labels != null && av.showAnnotation)
-        {
-          gg.translate(0, ypos + (alheight * av.charHeight));
-          labels.drawComponent(gg, getWidth());
-          gg.translate(0, -ypos - (alheight * av.charHeight));
-        }
-      }
-    }
-    else
-    {
-      //No need to hang on to labels if we're not wrapped
-      labels = null;
-
-      //Now draw the id strings
-      int panelWidth = getWidth();
-      int xPos = 0;
-
-      SequenceI sequence;
-      //Now draw the id strings
-      for (int i = starty; i < endy; i++)
-      {
-        sequence = av.alignment.getSequenceAt(i);
-
-        if (sequence == null)
-        {
-          continue;
-        }
-
-        if (av.hasHiddenRows)
-        {
-          setHiddenFont(sequence);
-        }
-
-        // Selected sequence colours
-        if ( (searchResults != null) &&
-            searchResults.contains(sequence))
-        {
-          currentColor = Color.black;
-          currentTextColor = Color.white;
-        }
-        else if ( (av.getSelectionGroup() != null) &&
-                 av.getSelectionGroup().getSequences(null).contains(
-                     sequence))
-        {
-          currentColor = Color.lightGray;
-          currentTextColor = Color.black;
-        }
-        else
-        {
-          currentColor = av.getSequenceColour(sequence);
-          currentTextColor = Color.black;
-        }
-
-        gg.setColor(currentColor);
-
-        gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
-                    av.charHeight);
-
-        gg.setColor(currentTextColor);
-
-        String string = sequence.getDisplayId(av.getShowJVSuffix());
-
-        if (av.rightAlignIds)
-        {
-          xPos = panelWidth - fm.stringWidth(string) - 4;
-        }
-
-        gg.drawString(string, xPos,
-                      ( ( (i - starty) * av.charHeight) + av.charHeight) -
-                      (av.charHeight / 5));
-
-        if (av.hasHiddenRows && av.showHiddenMarkers)
-        {
-          drawMarker(i, starty, 0);
-        }
-
-      }
-
-    }
-  }
-
-  void drawMarker(int i, int starty, int yoffset)
-  {
-
-    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
-    //Use this method here instead of calling hiddenSeq adjust
-    //3 times.
-    int hSize = hseqs.length;
-
-    int hiddenIndex = i;
-    int lastIndex = i - 1;
-    int nextIndex = i + 1;
-
-    for (int j = 0; j < hSize; j++)
-    {
-      if (hseqs[j] != null)
-      {
-        if (j - 1 < hiddenIndex)
-        {
-          hiddenIndex++;
-        }
-        if (j - 1 < lastIndex)
-        {
-          lastIndex++;
-        }
-        if (j - 1 < nextIndex)
-        {
-          nextIndex++;
-        }
-      }
-    }
-
-    boolean below = (hiddenIndex > lastIndex + 1);
-    boolean above = (nextIndex > hiddenIndex + 1);
-
-    gg.setColor(Color.blue);
-    if (below)
-    {
-      gg.fillPolygon(new int[]
-                     {getWidth() - av.charHeight,
-                     getWidth() - av.charHeight,
-                     getWidth()},
-                     new int[]
-                     {
-                     (i - starty) * av.charHeight + yoffset,
-                     (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
-                     (i - starty) * av.charHeight + yoffset
-      }, 3);
-    }
-    if (above)
-    {
-      gg.fillPolygon(new int[]
-                     {getWidth() - av.charHeight,
-                     getWidth() - av.charHeight,
-                     getWidth()},
-                     new int[]
-                     {
-                     (i - starty + 1) * av.charHeight + yoffset,
-                     (i - starty + 1) * av.charHeight + yoffset -
-                     av.charHeight / 4,
-                     (i - starty + 1) * av.charHeight + yoffset
-      }, 3);
-
-    }
-  }
-
-  void setHiddenFont(SequenceI seq)
-  {
-    Font bold = new Font(av.getFont().getName(), Font.BOLD,
-                         av.getFont().getSize());
-
-    if (av.hiddenRepSequences != null &&
-        av.hiddenRepSequences.containsKey(seq))
-    {
-      gg.setFont(bold);
-    }
-    else
-    {
-      gg.setFont(idfont);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param found DOCUMENT ME!
-   */
-  public void setHighlighted(java.util.Vector found)
-  {
-    searchResults = found;
-    repaint();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdCanvas
+    extends JPanel
+{
+  protected AlignViewport av;
+  protected boolean showScores = true;
+  protected int maxIdLength = -1;
+  protected String maxIdStr = null;
+  BufferedImage image;
+  Graphics2D gg;
+  int imgHeight = 0;
+  boolean fastPaint = false;
+  java.util.Vector searchResults;
+  FontMetrics fm;
+  AnnotationLabels labels = null;
+  AnnotationPanel ap;
+  Font idfont;
+
+  /**
+   * Creates a new IdCanvas object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public IdCanvas(AlignViewport av)
+  {
+    setLayout(new BorderLayout());
+    this.av = av;
+    PaintRefresher.Register(this, av.getSequenceSetId());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param gg DOCUMENT ME!
+   * @param s DOCUMENT ME!
+   * @param i DOCUMENT ME!
+   * @param starty DOCUMENT ME!
+   * @param ypos DOCUMENT ME!
+   */
+  public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,
+                           int ypos)
+  {
+    int xPos = 0;
+    int panelWidth = getWidth();
+    int charHeight = av.charHeight;
+
+    if ( (searchResults != null) && searchResults.contains(s))
+    {
+      gg.setColor(Color.black);
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
+                  charHeight);
+      gg.setColor(Color.white);
+    }
+    else if ( (av.getSelectionGroup() != null) &&
+             av.getSelectionGroup().getSequences(null).contains(s))
+    {
+      gg.setColor(Color.lightGray);
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
+                  charHeight);
+      gg.setColor(Color.white);
+    }
+    else
+    {
+      gg.setColor(av.getSequenceColour(s));
+      gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),
+                  charHeight);
+      gg.setColor(Color.black);
+    }
+
+    if (av.rightAlignIds)
+    {
+      xPos = panelWidth - fm.stringWidth(
+          s.getDisplayId(av.getShowJVSuffix())
+          ) - 4;
+    }
+
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()),
+                  xPos,
+                  ( ( (i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+
+    if (av.hasHiddenRows && av.showHiddenMarkers)
+    {
+      drawMarker(i, starty, ypos);
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param vertical DOCUMENT ME!
+   */
+  public void fastPaint(int vertical)
+  {
+    if (gg == null)
+    {
+      repaint();
+
+      return;
+    }
+
+    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;
+
+      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);
+
+    drawIds(ss, es);
+
+    gg.translate(0, -transY);
+
+    fastPaint = true;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    if (fastPaint)
+    {
+      fastPaint = false;
+      g.drawImage(image, 0, 0, this);
+
+      return;
+    }
+
+    int oldHeight = imgHeight;
+
+    imgHeight = getHeight();
+    imgHeight -= (imgHeight % av.charHeight);
+
+    if (imgHeight < 1)
+    {
+      return;
+    }
+
+    if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
+    {
+      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);
+
+    drawIds(av.getStartSeq(), av.endSeq);
+
+    g.drawImage(image, 0, 0, this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param starty DOCUMENT ME!
+   * @param endy DOCUMENT ME!
+   */
+  void drawIds(int starty, int endy)
+  {
+    if (av.seqNameItalics)
+    {
+      idfont = new Font(av.getFont().getName(), Font.ITALIC,
+                        av.getFont().getSize());
+    }
+    else
+    {
+      idfont = av.getFont();
+    }
+
+    gg.setFont(idfont);
+    fm = gg.getFontMetrics();
+
+    if (av.antiAlias)
+    {
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
+    }
+
+    Color currentColor = Color.white;
+    Color currentTextColor = Color.black;
+
+    if (av.getWrapAlignment())
+    {
+      int maxwidth = av.alignment.getWidth();
+      int alheight = av.alignment.getHeight();
+
+      if (av.hasHiddenColumns)
+      {
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
+
+      int annotationHeight = 0;
+
+      if (av.showAnnotation)
+      {
+        if (ap == null)
+        {
+          ap = new AnnotationPanel(av);
+        }
+
+        annotationHeight = ap.adjustPanelHeight();
+        if (labels == null)
+        {
+          labels = new AnnotationLabels(av);
+        }
+      }
+
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+      {
+        hgap += av.charHeight;
+      }
+
+      int cHeight = alheight * av.charHeight
+          + hgap
+          + annotationHeight;
+
+      int rowSize = av.getEndRes() - av.getStartRes();
+
+      // Draw the rest of the panels
+      for (int ypos = hgap, row = av.startRes;
+           (ypos <= getHeight()) && (row < maxwidth);
+           ypos += cHeight, row += rowSize)
+      {
+        for (int i = starty; i < alheight; i++)
+        {
+          SequenceI s = av.alignment.getSequenceAt(i);
+          if (av.hasHiddenRows)
+          {
+            setHiddenFont(s);
+          }
+          else
+          {
+            gg.setFont(idfont);
+          }
+
+          drawIdString(gg, s, i, 0, ypos);
+        }
+
+        if (labels != null && av.showAnnotation)
+        {
+          gg.translate(0, ypos + (alheight * av.charHeight));
+          labels.drawComponent(gg, getWidth());
+          gg.translate(0, -ypos - (alheight * av.charHeight));
+        }
+      }
+    }
+    else
+    {
+      //No need to hang on to labels if we're not wrapped
+      labels = null;
+
+      //Now draw the id strings
+      int panelWidth = getWidth();
+      int xPos = 0;
+
+      SequenceI sequence;
+      //Now draw the id strings
+      for (int i = starty; i < endy; i++)
+      {
+        sequence = av.alignment.getSequenceAt(i);
+
+        if (sequence == null)
+        {
+          continue;
+        }
+
+        if (av.hasHiddenRows)
+        {
+          setHiddenFont(sequence);
+        }
+
+        // Selected sequence colours
+        if ( (searchResults != null) &&
+            searchResults.contains(sequence))
+        {
+          currentColor = Color.black;
+          currentTextColor = Color.white;
+        }
+        else if ( (av.getSelectionGroup() != null) &&
+                 av.getSelectionGroup().getSequences(null).contains(
+                     sequence))
+        {
+          currentColor = Color.lightGray;
+          currentTextColor = Color.black;
+        }
+        else
+        {
+          currentColor = av.getSequenceColour(sequence);
+          currentTextColor = Color.black;
+        }
+
+        gg.setColor(currentColor);
+
+        gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
+                    av.charHeight);
+
+        gg.setColor(currentTextColor);
+
+        String string = sequence.getDisplayId(av.getShowJVSuffix());
+
+        if (av.rightAlignIds)
+        {
+          xPos = panelWidth - fm.stringWidth(string) - 4;
+        }
+
+        gg.drawString(string, xPos,
+                      ( ( (i - starty) * av.charHeight) + av.charHeight) -
+                      (av.charHeight / 5));
+
+        if (av.hasHiddenRows && av.showHiddenMarkers)
+        {
+          drawMarker(i, starty, 0);
+        }
+
+      }
+
+    }
+  }
+
+  void drawMarker(int i, int starty, int yoffset)
+  {
+
+    SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+    //Use this method here instead of calling hiddenSeq adjust
+    //3 times.
+    int hSize = hseqs.length;
+
+    int hiddenIndex = i;
+    int lastIndex = i - 1;
+    int nextIndex = i + 1;
+
+    for (int j = 0; j < hSize; j++)
+    {
+      if (hseqs[j] != null)
+      {
+        if (j - 1 < hiddenIndex)
+        {
+          hiddenIndex++;
+        }
+        if (j - 1 < lastIndex)
+        {
+          lastIndex++;
+        }
+        if (j - 1 < nextIndex)
+        {
+          nextIndex++;
+        }
+      }
+    }
+
+    boolean below = (hiddenIndex > lastIndex + 1);
+    boolean above = (nextIndex > hiddenIndex + 1);
+
+    gg.setColor(Color.blue);
+    if (below)
+    {
+      gg.fillPolygon(new int[]
+                     {getWidth() - av.charHeight,
+                     getWidth() - av.charHeight,
+                     getWidth()},
+                     new int[]
+                     {
+                     (i - starty) * av.charHeight + yoffset,
+                     (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
+                     (i - starty) * av.charHeight + yoffset
+      }, 3);
+    }
+    if (above)
+    {
+      gg.fillPolygon(new int[]
+                     {getWidth() - av.charHeight,
+                     getWidth() - av.charHeight,
+                     getWidth()},
+                     new int[]
+                     {
+                     (i - starty + 1) * av.charHeight + yoffset,
+                     (i - starty + 1) * av.charHeight + yoffset -
+                     av.charHeight / 4,
+                     (i - starty + 1) * av.charHeight + yoffset
+      }, 3);
+
+    }
+  }
+
+  void setHiddenFont(SequenceI seq)
+  {
+    Font bold = new Font(av.getFont().getName(), Font.BOLD,
+                         av.getFont().getSize());
+
+    if (av.hiddenRepSequences != null &&
+        av.hiddenRepSequences.containsKey(seq))
+    {
+      gg.setFont(bold);
+    }
+    else
+    {
+      gg.setFont(idfont);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param found DOCUMENT ME!
+   */
+  public void setHighlighted(java.util.Vector found)
+  {
+    searchResults = found;
+    repaint();
+  }
+}
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 4741974..a9c3f21 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 1c7d215..47df3ae 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -1,161 +1,161 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class IdwidthAdjuster
-    extends JPanel implements MouseListener,
-    MouseMotionListener
-{
-  boolean active = false;
-  int oldX = 0;
-  Image image;
-  AlignmentPanel ap;
-
-  /**
-   * Creates a new IdwidthAdjuster object.
-   *
-   * @param ap DOCUMENT ME!
-   */
-  public IdwidthAdjuster(AlignmentPanel ap)
-  {
-    this.ap = ap;
-
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-
-    if (url != null)
-    {
-      image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-    }
-
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mousePressed(MouseEvent evt)
-  {
-    oldX = evt.getX();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseReleased(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseEntered(MouseEvent evt)
-  {
-    active = true;
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseExited(MouseEvent evt)
-  {
-    active = false;
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseDragged(MouseEvent evt)
-  {
-    active = true;
-
-    Dimension d = ap.idPanel.idCanvas.getPreferredSize();
-    int dif = evt.getX() - oldX;
-
-    if ( ( (d.width + dif) > 20) || (dif > 0))
-    {
-      ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,
-          d.height));
-      ap.paintAlignment(true);
-    }
-
-    oldX = evt.getX();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseMoved(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseClicked(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-
-    if (active)
-    {
-      if (image != null)
-      {
-        g.drawImage(image, getWidth() - 20, 2, this);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdwidthAdjuster
+    extends JPanel implements MouseListener,
+    MouseMotionListener
+{
+  boolean active = false;
+  int oldX = 0;
+  Image image;
+  AlignmentPanel ap;
+
+  /**
+   * Creates a new IdwidthAdjuster object.
+   *
+   * @param ap DOCUMENT ME!
+   */
+  public IdwidthAdjuster(AlignmentPanel ap)
+  {
+    this.ap = ap;
+
+    java.net.URL url = getClass().getResource("/images/idwidth.gif");
+
+    if (url != null)
+    {
+      image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+    }
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    oldX = evt.getX();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+    active = false;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent evt)
+  {
+    active = true;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent evt)
+  {
+    active = false;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    active = true;
+
+    Dimension d = ap.idPanel.idCanvas.getPreferredSize();
+    int dif = evt.getX() - oldX;
+
+    if ( ( (d.width + dif) > 20) || (dif > 0))
+    {
+      ap.idPanel.idCanvas.setPreferredSize(new Dimension(d.width + dif,
+          d.height));
+      ap.paintAlignment(true);
+    }
+
+    oldX = evt.getX();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    if (active)
+    {
+      if (image != null)
+      {
+        g.drawImage(image, getWidth() - 20, 2, this);
+      }
+    }
+  }
+}
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ebf7aba..85b7f86 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index fe17dff..32b93db 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 04e5f13..545e0cd 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,447 +1,447 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class OverviewPanel
-    extends JPanel implements Runnable
-{
-  BufferedImage miniMe;
-  AlignViewport av;
-  AlignmentPanel ap;
-  float scalew = 1f;
-  float scaleh = 1f;
-  int width;
-  int sequencesHeight;
-  int graphHeight = 20;
-  int boxX = -1;
-  int boxY = -1;
-  int boxWidth = -1;
-  int boxHeight = -1;
-  boolean resizing = false;
-
-  // Can set different properties in this seqCanvas than
-  // main visible SeqCanvas
-  SequenceRenderer sr;
-  FeatureRenderer fr;
-
-  /**
-   * Creates a new OverviewPanel object.
-   *
-   * @param ap DOCUMENT ME!
-   */
-  public OverviewPanel(AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-    setLayout(null);
-
-    sr = new SequenceRenderer(av);
-    sr.renderGaps = false;
-    sr.forOverview = true;
-    fr = new FeatureRenderer(ap);
-
-    // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.alignment.getWidth() /
-        (float) av.alignment.getHeight();
-
-    if (av.conservation == null)
-    {
-      graphHeight = 0;
-    }
-
-    if (av.alignment.getWidth() > av.alignment.getHeight())
-    {
-      // wider
-      width = 400;
-      sequencesHeight = (int) (400f / initialScale);
-      if (sequencesHeight < 40)
-      {
-        sequencesHeight = 40;
-      }
-    }
-    else
-    {
-      // taller
-      width = (int) (400f * initialScale);
-      sequencesHeight = 300;
-
-      if (width < 120)
-      {
-        width = 120;
-      }
-    }
-
-    addComponentListener(new ComponentAdapter()
-    {
-      public void componentResized(ComponentEvent evt)
-      {
-        if ( (getWidth() != width) ||
-            (getHeight() != (sequencesHeight + graphHeight)))
-        {
-          updateOverviewImage();
-        }
-      }
-    });
-
-    addMouseMotionListener(new MouseMotionAdapter()
-    {
-      public void mouseDragged(MouseEvent evt)
-      {
-        if (!av.wrapAlignment)
-        {
-          boxX = evt.getX();
-          boxY = evt.getY();
-          checkValid();
-        }
-      }
-    });
-
-    addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
-      {
-        if (!av.wrapAlignment)
-        {
-          boxX = evt.getX();
-          boxY = evt.getY();
-          checkValid();
-        }
-      }
-    });
-
-    updateOverviewImage();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  void checkValid()
-  {
-    if (boxY < 0)
-    {
-      boxY = 0;
-    }
-
-    if (boxY > (sequencesHeight - boxHeight))
-    {
-      boxY = sequencesHeight - boxHeight + 1;
-    }
-
-    if (boxX < 0)
-    {
-      boxX = 0;
-    }
-
-    if (boxX > (width - boxWidth))
-    {
-      if (av.hasHiddenColumns)
-      {
-        //Try smallest possible box
-        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
-                          av.getCharWidth() * scalew);
-      }
-      boxX = width - boxWidth;
-    }
-
-    int col = (int) (boxX / scalew / av.getCharWidth());
-    int row = (int) (boxY / scaleh / av.getCharHeight());
-
-    if (av.hasHiddenColumns)
-    {
-      if (!av.getColumnSelection().isVisible(col))
-      {
-        return;
-      }
-
-      col = av.getColumnSelection().findColumnPosition(col);
-    }
-
-    if (av.hasHiddenRows)
-    {
-      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
-    }
-
-    ap.setScrollValues(col, row);
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateOverviewImage()
-  {
-    if (resizing)
-    {
-      resizeAgain = true;
-      return;
-    }
-
-    resizing = true;
-
-    if ( (getWidth() > 0) && (getHeight() > 0))
-    {
-      width = getWidth();
-      sequencesHeight = getHeight() - graphHeight;
-    }
-
-    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    Thread thread = new Thread(this);
-    thread.start();
-    repaint();
-  }
-
-  // This is set true if the user resizes whilst
-  // the overview is being calculated
-  boolean resizeAgain = false;
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void run()
-  {
-    miniMe = null;
-
-    if (av.showSequenceFeatures)
-    {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight()
-        + av.alignment.getHiddenSequences().getSize();
-
-    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
-                               BufferedImage.TYPE_INT_RGB);
-
-    Graphics mg = miniMe.getGraphics();
-    mg.setColor(Color.orange);
-    mg.fillRect(0, 0, width, miniMe.getHeight());
-
-    float sampleCol = (float) alwidth / (float) width;
-    float sampleRow = (float) alheight / (float) sequencesHeight;
-
-    int lastcol = -1, lastrow = -1;
-    int color = Color.white.getRGB();
-    int row, col;
-    jalview.datamodel.SequenceI seq;
-    boolean hiddenRow = false;
-    for (row = 0; row < sequencesHeight; row++)
-    {
-      if ( (int) (row * sampleRow) == lastrow)
-      {
-        //No need to recalculate the colours,
-        //Just copy from the row above
-        for (col = 0; col < width; col++)
-        {
-          miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
-        }
-        continue;
-      }
-
-      lastrow = (int) (row * sampleRow);
-
-      hiddenRow = false;
-      if (av.hasHiddenRows)
-      {
-        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
-        if (seq == null)
-        {
-          int index =
-              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
-              lastrow);
-
-          seq = av.alignment.getSequenceAt(index);
-        }
-        else
-        {
-          hiddenRow = true;
-        }
-      }
-      else
-      {
-        seq = av.alignment.getSequenceAt(lastrow);
-      }
-
-      if (seq == null)
-      {
-        System.out.println(lastrow + " null");
-        continue;
-      }
-
-      for (col = 0; col < width; col++)
-      {
-        if ( (int) (col * sampleCol) == lastcol &&
-            (int) (row * sampleRow) == lastrow)
-        {
-          miniMe.setRGB(col, row, color);
-          continue;
-        }
-
-        lastcol = (int) (col * sampleCol);
-
-        if (seq.getLength() > lastcol)
-        {
-          color = sr.getResidueBoxColour(
-              seq, lastcol).getRGB();
-
-          if (av.showSequenceFeatures)
-          {
-            color = fr.findFeatureColour(color, seq, lastcol);
-          }
-        }
-        else
-        {
-          color = -1; //White
-        }
-
-        if (hiddenRow ||
-            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
-        {
-          color = new Color(color).darker().darker().getRGB();
-        }
-
-        miniMe.setRGB(col, row, color);
-
-      }
-    }
-
-    if (av.conservation != null)
-    {
-      for (col = 0; col < width; col++)
-      {
-        lastcol = (int) (col * sampleCol);
-        {
-          mg.translate(col, sequencesHeight);
-          ap.annotationPanel.drawGraph(mg, av.conservation,
-                                       (int) (sampleCol) + 1,
-                                       graphHeight,
-                                       (int) (col * sampleCol),
-                                       (int) (col * sampleCol) + 1);
-          mg.translate( -col, -sequencesHeight);
-        }
-      }
-    }
-    System.gc();
-
-    resizing = false;
-
-    setBoxPosition();
-
-    if (resizeAgain)
-    {
-      resizeAgain = false;
-      updateOverviewImage();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void setBoxPosition()
-  {
-    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.alignment.getHeight()
-                          + av.alignment.getHiddenSequences().getSize()) *
-        av.getCharHeight();
-
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
-
-    if (av.hasHiddenColumns)
-    {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
-
-    int startSeq = av.startSeq;
-    int endSeq = av.endSeq;
-
-    if (av.hasHiddenRows)
-    {
-      startSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
-
-      endSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
-
-    }
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    boxX = (int) (startRes * av.getCharWidth() * scalew);
-    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
-
-    if (av.hasHiddenColumns)
-    {
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-    else
-    {
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-    }
-
-    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
-
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void paintComponent(Graphics g)
-  {
-    if(resizing)
-    {
-      g.setColor(Color.white);
-      g.fillRect(0,0,getWidth(),getHeight());
-    }
-    else if (miniMe != null)
-    {
-      g.drawImage(miniMe, 0, 0, this);
-    }
-
-    g.setColor(Color.red);
-    g.drawRect(boxX, boxY, boxWidth, boxHeight);
-    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 java.awt.image.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class OverviewPanel
+    extends JPanel implements Runnable
+{
+  BufferedImage miniMe;
+  AlignViewport av;
+  AlignmentPanel ap;
+  float scalew = 1f;
+  float scaleh = 1f;
+  int width;
+  int sequencesHeight;
+  int graphHeight = 20;
+  int boxX = -1;
+  int boxY = -1;
+  int boxWidth = -1;
+  int boxHeight = -1;
+  boolean resizing = false;
+
+  // Can set different properties in this seqCanvas than
+  // main visible SeqCanvas
+  SequenceRenderer sr;
+  FeatureRenderer fr;
+
+  /**
+   * Creates a new OverviewPanel object.
+   *
+   * @param ap DOCUMENT ME!
+   */
+  public OverviewPanel(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+    setLayout(null);
+
+    sr = new SequenceRenderer(av);
+    sr.renderGaps = false;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(ap);
+
+    // scale the initial size of overviewpanel to shape of alignment
+    float initialScale = (float) av.alignment.getWidth() /
+        (float) av.alignment.getHeight();
+
+    if (av.conservation == null)
+    {
+      graphHeight = 0;
+    }
+
+    if (av.alignment.getWidth() > av.alignment.getHeight())
+    {
+      // wider
+      width = 400;
+      sequencesHeight = (int) (400f / initialScale);
+      if (sequencesHeight < 40)
+      {
+        sequencesHeight = 40;
+      }
+    }
+    else
+    {
+      // taller
+      width = (int) (400f * initialScale);
+      sequencesHeight = 300;
+
+      if (width < 120)
+      {
+        width = 120;
+      }
+    }
+
+    addComponentListener(new ComponentAdapter()
+    {
+      public void componentResized(ComponentEvent evt)
+      {
+        if ( (getWidth() != width) ||
+            (getHeight() != (sequencesHeight + graphHeight)))
+        {
+          updateOverviewImage();
+        }
+      }
+    });
+
+    addMouseMotionListener(new MouseMotionAdapter()
+    {
+      public void mouseDragged(MouseEvent evt)
+      {
+        if (!av.wrapAlignment)
+        {
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
+        }
+      }
+    });
+
+    addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        if (!av.wrapAlignment)
+        {
+          boxX = evt.getX();
+          boxY = evt.getY();
+          checkValid();
+        }
+      }
+    });
+
+    updateOverviewImage();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  void checkValid()
+  {
+    if (boxY < 0)
+    {
+      boxY = 0;
+    }
+
+    if (boxY > (sequencesHeight - boxHeight))
+    {
+      boxY = sequencesHeight - boxHeight + 1;
+    }
+
+    if (boxX < 0)
+    {
+      boxX = 0;
+    }
+
+    if (boxX > (width - boxWidth))
+    {
+      if (av.hasHiddenColumns)
+      {
+        //Try smallest possible box
+        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
+                          av.getCharWidth() * scalew);
+      }
+      boxX = width - boxWidth;
+    }
+
+    int col = (int) (boxX / scalew / av.getCharWidth());
+    int row = (int) (boxY / scaleh / av.getCharHeight());
+
+    if (av.hasHiddenColumns)
+    {
+      if (!av.getColumnSelection().isVisible(col))
+      {
+        return;
+      }
+
+      col = av.getColumnSelection().findColumnPosition(col);
+    }
+
+    if (av.hasHiddenRows)
+    {
+      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
+    }
+
+    ap.setScrollValues(col, row);
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateOverviewImage()
+  {
+    if (resizing)
+    {
+      resizeAgain = true;
+      return;
+    }
+
+    resizing = true;
+
+    if ( (getWidth() > 0) && (getHeight() > 0))
+    {
+      width = getWidth();
+      sequencesHeight = getHeight() - graphHeight;
+    }
+
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
+  }
+
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  boolean resizeAgain = false;
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+    miniMe = null;
+
+    if (av.showSequenceFeatures)
+    {
+      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+    }
+
+    int alwidth = av.alignment.getWidth();
+    int alheight = av.alignment.getHeight()
+        + av.alignment.getHiddenSequences().getSize();
+
+    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+
+    int fullsizeWidth = alwidth * av.getCharWidth();
+    int fullsizeHeight = alheight * av.getCharHeight();
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+                               BufferedImage.TYPE_INT_RGB);
+
+    Graphics mg = miniMe.getGraphics();
+    mg.setColor(Color.orange);
+    mg.fillRect(0, 0, width, miniMe.getHeight());
+
+    float sampleCol = (float) alwidth / (float) width;
+    float sampleRow = (float) alheight / (float) sequencesHeight;
+
+    int lastcol = -1, lastrow = -1;
+    int color = Color.white.getRGB();
+    int row, col;
+    jalview.datamodel.SequenceI seq;
+    boolean hiddenRow = false;
+    for (row = 0; row < sequencesHeight; row++)
+    {
+      if ( (int) (row * sampleRow) == lastrow)
+      {
+        //No need to recalculate the colours,
+        //Just copy from the row above
+        for (col = 0; col < width; col++)
+        {
+          miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
+        }
+        continue;
+      }
+
+      lastrow = (int) (row * sampleRow);
+
+      hiddenRow = false;
+      if (av.hasHiddenRows)
+      {
+        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+        if (seq == null)
+        {
+          int index =
+              av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+              lastrow);
+
+          seq = av.alignment.getSequenceAt(index);
+        }
+        else
+        {
+          hiddenRow = true;
+        }
+      }
+      else
+      {
+        seq = av.alignment.getSequenceAt(lastrow);
+      }
+
+      if (seq == null)
+      {
+        System.out.println(lastrow + " null");
+        continue;
+      }
+
+      for (col = 0; col < width; col++)
+      {
+        if ( (int) (col * sampleCol) == lastcol &&
+            (int) (row * sampleRow) == lastrow)
+        {
+          miniMe.setRGB(col, row, color);
+          continue;
+        }
+
+        lastcol = (int) (col * sampleCol);
+
+        if (seq.getLength() > lastcol)
+        {
+          color = sr.getResidueBoxColour(
+              seq, lastcol).getRGB();
+
+          if (av.showSequenceFeatures)
+          {
+            color = fr.findFeatureColour(color, seq, lastcol);
+          }
+        }
+        else
+        {
+          color = -1; //White
+        }
+
+        if (hiddenRow ||
+            (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
+        {
+          color = new Color(color).darker().darker().getRGB();
+        }
+
+        miniMe.setRGB(col, row, color);
+
+      }
+    }
+
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
+        {
+          mg.translate(col, sequencesHeight);
+          ap.annotationPanel.drawGraph(mg, av.conservation,
+                                       (int) (sampleCol) + 1,
+                                       graphHeight,
+                                       (int) (col * sampleCol),
+                                       (int) (col * sampleCol) + 1);
+          mg.translate( -col, -sequencesHeight);
+        }
+      }
+    }
+    System.gc();
+
+    resizing = false;
+
+    setBoxPosition();
+
+    if (resizeAgain)
+    {
+      resizeAgain = false;
+      updateOverviewImage();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void setBoxPosition()
+  {
+    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
+    int fullsizeHeight = (av.alignment.getHeight()
+                          + av.alignment.getHiddenSequences().getSize()) *
+        av.getCharHeight();
+
+    int startRes = av.getStartRes();
+    int endRes = av.getEndRes();
+
+    if (av.hasHiddenColumns)
+    {
+      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
+      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+    }
+
+    int startSeq = av.startSeq;
+    int endSeq = av.endSeq;
+
+    if (av.hasHiddenRows)
+    {
+      startSeq =
+          av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
+
+      endSeq =
+          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
+
+    }
+
+    scalew = (float) width / (float) fullsizeWidth;
+    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
+
+    boxX = (int) (startRes * av.getCharWidth() * scalew);
+    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+
+    if (av.hasHiddenColumns)
+    {
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
+    else
+    {
+      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
+    }
+
+    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
+
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    if(resizing)
+    {
+      g.setColor(Color.white);
+      g.fillRect(0,0,getWidth(),getHeight());
+    }
+    else if (miniMe != null)
+    {
+      g.drawImage(miniMe, 0, 0, this);
+    }
+
+    g.setColor(Color.red);
+    g.drawRect(boxX, boxY, boxWidth, boxHeight);
+    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+
+  }
+}
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 06f1b25..00d3105 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index c6d3b58..915e4aa 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,243 +1,243 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class PaintRefresher
-{
-  static Hashtable components;
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param comp DOCUMENT ME!
-   * @param al DOCUMENT ME!
-   */
-  public static void Register(Component comp, String seqSetId)
-  {
-    if (components == null)
-    {
-      components = new Hashtable();
-    }
-
-    if (components.containsKey(seqSetId))
-    {
-      Vector comps = (Vector) components.get(seqSetId);
-      if (!comps.contains(comp))
-      {
-        comps.addElement(comp);
-      }
-    }
-    else
-    {
-      Vector vcoms = new Vector();
-      vcoms.addElement(comp);
-      components.put(seqSetId, vcoms);
-    }
-  }
-
-  public static void RemoveComponent(Component comp)
-  {
-    if (components == null)
-    {
-      return;
-    }
-
-    Enumeration en = components.keys();
-    while (en.hasMoreElements())
-    {
-      String id = en.nextElement().toString();
-      Vector comps = (Vector) components.get(id);
-      comps.remove(comp);
-      if (comps.size() == 0)
-      {
-        components.remove(id);
-      }
-    }
-  }
-
-  public static void Refresh(Component source, String id)
-  {
-    Refresh(source, id, false, false);
-  }
-
-  public static void Refresh(Component source,
-                             String id,
-                             boolean alignmentChanged,
-                             boolean validateSequences)
-  {
-    if (components == null)
-    {
-      return;
-    }
-
-    Component comp;
-    Vector comps = (Vector) components.get(id);
-
-    if (comps == null)
-    {
-      return;
-    }
-
-    Enumeration e = comps.elements();
-    while (e.hasMoreElements())
-    {
-      comp = (Component) e.nextElement();
-
-      if (comp == source)
-      {
-        continue;
-      }
-
-      if (validateSequences
-          && comp instanceof AlignmentPanel
-          && source instanceof AlignmentPanel)
-      {
-        validateSequences( ( (AlignmentPanel) source).av.alignment,
-                          ( (AlignmentPanel) comp).av.alignment);
-      }
-
-      if (comp instanceof AlignmentPanel && alignmentChanged)
-      {
-        ( (AlignmentPanel) comp).alignmentChanged();
-      }
-
-      comp.repaint();
-    }
-  }
-
-  static void validateSequences(AlignmentI source, AlignmentI comp)
-  {
-    SequenceI[] a1;
-    if (source.getHiddenSequences().getSize() > 0)
-    {
-      a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();
-    }
-    else
-    {
-      a1 = source.getSequencesArray();
-    }
-
-    SequenceI[] a2;
-    if (comp.getHiddenSequences().getSize() > 0)
-    {
-      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-    }
-    else
-    {
-      a2 = comp.getSequencesArray();
-    }
-
-    int i, iSize = a1.length, j, jSize = a2.length;
-
-    if (iSize == jSize)
-    {
-      return;
-    }
-
-    boolean exists = false;
-    for (i = 0; i < iSize; i++)
-    {
-      exists = false;
-
-      for (j = 0; j < jSize; j++)
-      {
-        if (a2[j] == a1[i])
-        {
-          exists = true;
-          break;
-        }
-      }
-
-      if (!exists)
-      {
-        if (i < comp.getHeight())
-        {
-          comp.getSequences().insertElementAt(a1[i], i);
-        }
-        else
-        {
-          comp.addSequence(a1[i]);
-        }
-
-        if (comp.getHiddenSequences().getSize() > 0)
-        {
-          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
-        }
-        else
-        {
-          a2 = comp.getSequencesArray();
-        }
-
-        jSize = a2.length;
-      }
-    }
-
-    iSize = a1.length;
-    jSize = a2.length;
-
-    for (j = 0; j < jSize; j++)
-    {
-      exists = false;
-      for (i = 0; i < iSize; i++)
-      {
-        if (a2[j] == a1[i])
-        {
-          exists = true;
-          break;
-        }
-      }
-
-      if (!exists)
-      {
-        comp.deleteSequence(a2[j]);
-      }
-    }
-  }
-
-  static AlignmentPanel[] getAssociatedPanels(String id)
-  {
-    Vector comps = (Vector) components.get(id);
-    Vector tmp = new Vector();
-    int i, iSize = comps.size();
-    for (i = 0; i < iSize; i++)
-    {
-      if (comps.elementAt(i) instanceof AlignmentPanel)
-      {
-        tmp.addElement( ( (AlignmentPanel) comps.elementAt(i)));
-      }
-    }
-    AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
-    tmp.toArray(result);
-
-    return result;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PaintRefresher
+{
+  static Hashtable components;
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param comp DOCUMENT ME!
+   * @param al DOCUMENT ME!
+   */
+  public static void Register(Component comp, String seqSetId)
+  {
+    if (components == null)
+    {
+      components = new Hashtable();
+    }
+
+    if (components.containsKey(seqSetId))
+    {
+      Vector comps = (Vector) components.get(seqSetId);
+      if (!comps.contains(comp))
+      {
+        comps.addElement(comp);
+      }
+    }
+    else
+    {
+      Vector vcoms = new Vector();
+      vcoms.addElement(comp);
+      components.put(seqSetId, vcoms);
+    }
+  }
+
+  public static void RemoveComponent(Component comp)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Enumeration en = components.keys();
+    while (en.hasMoreElements())
+    {
+      String id = en.nextElement().toString();
+      Vector comps = (Vector) components.get(id);
+      comps.remove(comp);
+      if (comps.size() == 0)
+      {
+        components.remove(id);
+      }
+    }
+  }
+
+  public static void Refresh(Component source, String id)
+  {
+    Refresh(source, id, false, false);
+  }
+
+  public static void Refresh(Component source,
+                             String id,
+                             boolean alignmentChanged,
+                             boolean validateSequences)
+  {
+    if (components == null)
+    {
+      return;
+    }
+
+    Component comp;
+    Vector comps = (Vector) components.get(id);
+
+    if (comps == null)
+    {
+      return;
+    }
+
+    Enumeration e = comps.elements();
+    while (e.hasMoreElements())
+    {
+      comp = (Component) e.nextElement();
+
+      if (comp == source)
+      {
+        continue;
+      }
+
+      if (validateSequences
+          && comp instanceof AlignmentPanel
+          && source instanceof AlignmentPanel)
+      {
+        validateSequences( ( (AlignmentPanel) source).av.alignment,
+                          ( (AlignmentPanel) comp).av.alignment);
+      }
+
+      if (comp instanceof AlignmentPanel && alignmentChanged)
+      {
+        ( (AlignmentPanel) comp).alignmentChanged();
+      }
+
+      comp.repaint();
+    }
+  }
+
+  static void validateSequences(AlignmentI source, AlignmentI comp)
+  {
+    SequenceI[] a1;
+    if (source.getHiddenSequences().getSize() > 0)
+    {
+      a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a1 = source.getSequencesArray();
+    }
+
+    SequenceI[] a2;
+    if (comp.getHiddenSequences().getSize() > 0)
+    {
+      a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+    }
+    else
+    {
+      a2 = comp.getSequencesArray();
+    }
+
+    int i, iSize = a1.length, j, jSize = a2.length;
+
+    if (iSize == jSize)
+    {
+      return;
+    }
+
+    boolean exists = false;
+    for (i = 0; i < iSize; i++)
+    {
+      exists = false;
+
+      for (j = 0; j < jSize; j++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        if (i < comp.getHeight())
+        {
+          comp.getSequences().insertElementAt(a1[i], i);
+        }
+        else
+        {
+          comp.addSequence(a1[i]);
+        }
+
+        if (comp.getHiddenSequences().getSize() > 0)
+        {
+          a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
+        }
+        else
+        {
+          a2 = comp.getSequencesArray();
+        }
+
+        jSize = a2.length;
+      }
+    }
+
+    iSize = a1.length;
+    jSize = a2.length;
+
+    for (j = 0; j < jSize; j++)
+    {
+      exists = false;
+      for (i = 0; i < iSize; i++)
+      {
+        if (a2[j] == a1[i])
+        {
+          exists = true;
+          break;
+        }
+      }
+
+      if (!exists)
+      {
+        comp.deleteSequence(a2[j]);
+      }
+    }
+  }
+
+  static AlignmentPanel[] getAssociatedPanels(String id)
+  {
+    Vector comps = (Vector) components.get(id);
+    Vector tmp = new Vector();
+    int i, iSize = comps.size();
+    for (i = 0; i < iSize; i++)
+    {
+      if (comps.elementAt(i) instanceof AlignmentPanel)
+      {
+        tmp.addElement( ( (AlignmentPanel) comps.elementAt(i)));
+      }
+    }
+    AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
+    tmp.toArray(result);
+
+    return result;
+  }
+
+}
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 190dcb0..7347f0a 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 056a983..ce71034 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 7226283..ae23ba1 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 1e51879..366922b 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 32c4adc..feaabf6 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,769 +1,769 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.math.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class RotatableCanvas
-    extends JPanel implements MouseListener,
-    MouseMotionListener, KeyListener
-{
-  RotatableMatrix idmat = new RotatableMatrix(3, 3);
-  RotatableMatrix objmat = new RotatableMatrix(3, 3);
-  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
-
-  //RubberbandRectangle rubberband;
-  boolean drawAxes = true;
-  int omx = 0;
-  int mx = 0;
-  int omy = 0;
-  int my = 0;
-  Image img;
-  Graphics ig;
-  Dimension prefsize;
-  float[] centre = new float[3];
-  float[] width = new float[3];
-  float[] max = new float[3];
-  float[] min = new float[3];
-  float maxwidth;
-  float scale;
-  int npoint;
-  Vector points;
-  float[][] orig;
-  float[][] axes;
-  int startx;
-  int starty;
-  int lastx;
-  int lasty;
-  int rectx1;
-  int recty1;
-  int rectx2;
-  int recty2;
-  float scalefactor = 1;
-  AlignViewport av;
-  AlignmentPanel ap;
-  boolean showLabels = false;
-  Color bgColour = Color.black;
-  boolean applyToAllViews = false;
-
-  //  Controller    controller;
-  public RotatableCanvas(AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-
-    addMouseWheelListener(new MouseWheelListener()
-    {
-      public void mouseWheelMoved(MouseWheelEvent e)
-      {
-        if (e.getWheelRotation() > 0)
-        {
-          scale = (float) (scale * 1.1);
-          repaint();
-        }
-
-        else
-        {
-          scale = (float) (scale * 0.9);
-          repaint();
-        }
-      }
-    });
-
-  }
-
-  public void showLabels(boolean b)
-  {
-    showLabels = b;
-    repaint();
-  }
-
-  public void setPoints(Vector points, int npoint)
-  {
-    this.points = points;
-    this.npoint = npoint;
-    ToolTipManager.sharedInstance().registerComponent(this);
-    ToolTipManager.sharedInstance().setInitialDelay(0);
-    ToolTipManager.sharedInstance().setDismissDelay(10000);
-
-    prefsize = getPreferredSize();
-    orig = new float[npoint][3];
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-
-      for (int j = 0; j < 3; j++)
-      {
-        orig[i][j] = sp.coord[j];
-      }
-    }
-
-    //Initialize the matrices to identity
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        if (i != j)
-        {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
-        }
-        else
-        {
-          idmat.addElement(i, j, 0);
-          objmat.addElement(i, j, 0);
-          rotmat.addElement(i, j, 0);
-        }
-      }
-    }
-
-    axes = new float[3][3];
-    initAxes();
-
-    findCentre();
-    findWidth();
-
-    scale = findScale();
-
-    addMouseListener(this);
-
-    addMouseMotionListener(this);
-
-  }
-
-  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
-        {
-          axes[i][j] = 1;
-        }
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void findWidth()
-  {
-    max = new float[3];
-    min = new float[3];
-
-    max[0] = (float) - 1e30;
-    max[1] = (float) - 1e30;
-    max[2] = (float) - 1e30;
-
-    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])
-        {
-          max[i] = sp.coord[i];
-        }
-
-        if (sp.coord[i] <= min[i])
-        {
-          min[i] = sp.coord[i];
-        }
-      }
-    }
-
-    //    System.out.println("xmax " + max[0] + " min " + min[0]);
-    //System.out.println("ymax " + max[1] + " min " + min[1]);
-    //System.out.println("zmax " + max[2] + " min " + min[2]);
-    width[0] = Math.abs(max[0] - min[0]);
-    width[1] = Math.abs(max[1] - min[1]);
-    width[2] = Math.abs(max[2] - min[2]);
-
-    maxwidth = width[0];
-
-    if (width[1] > width[0])
-    {
-      maxwidth = width[1];
-    }
-
-    if (width[2] > width[1])
-    {
-      maxwidth = width[2];
-    }
-
-    //System.out.println("Maxwidth = " + maxwidth);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public float findScale()
-  {
-    int dim;
-    int width;
-    int height;
-
-    if (getWidth() != 0)
-    {
-      width = getWidth();
-      height = getHeight();
-    }
-    else
-    {
-      width = prefsize.width;
-      height = prefsize.height;
-    }
-
-    if (width < height)
-    {
-      dim = width;
-    }
-    else
-    {
-      dim = height;
-    }
-
-    return (float) ( (dim * scalefactor) / (2 * maxwidth));
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  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;
-
-    //    System.out.println("Centre x " + centre[0]);
-    //System.out.println("Centre y " + centre[1]);
-    //System.out.println("Centre z " + centre[2]);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Dimension getPreferredSize()
-  {
-    if (prefsize != null)
-    {
-      return prefsize;
-    }
-    else
-    {
-      return new Dimension(400, 400);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Dimension getMinimumSize()
-  {
-    return getPreferredSize();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void paintComponent(Graphics g1)
-  {
-
-    Graphics2D g = (Graphics2D) g1;
-
-    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                       RenderingHints.VALUE_ANTIALIAS_ON);
-    if (points == null)
-    {
-      g.setFont(new Font("Verdana", Font.PLAIN, 18));
-      g.drawString("Calculating PCA....", 20, getHeight() / 2);
-    }
-    else
-    {
-      //Only create the image at the beginning -
-      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());
-        ig = img.getGraphics();
-      }
-
-      drawBackground(ig, bgColour);
-      drawScene(ig);
-
-      if (drawAxes == true)
-      {
-        drawAxes(ig);
-      }
-
-      g.drawImage(img, 0, 0, this);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  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)));
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param col DOCUMENT ME!
-   */
-  public void drawBackground(Graphics g, Color col)
-  {
-    g.setColor(col);
-    g.fillRect(0, 0, prefsize.width, prefsize.height);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   */
-  public void drawScene(Graphics g1)
-  {
-
-    Graphics2D g = (Graphics2D) g1;
-
-    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                       RenderingHints.VALUE_ANTIALIAS_ON);
-
-    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;
-      float z = sp.coord[1] - centre[2];
-
-      if (av.getSequenceColour(sp.sequence) == Color.black)
-      {
-        g.setColor(Color.white);
-      }
-      else
-      {
-        g.setColor(av.getSequenceColour(sp.sequence));
-      }
-
-      if (av.getSelectionGroup() != null)
-      {
-        if (av.getSelectionGroup().getSequences(null).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);
-      if (showLabels)
-      {
-        g.setColor(Color.red);
-        g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.
-                     getName(),
-                     x - 3, y - 4);
-      }
-    }
-
-    //    //Now the rectangle
-    //    if (rectx2 != -1 && recty2 != -1) {
-    //      g.setColor(Color.white);
-    //
-    //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
-    //    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Dimension minimumsize()
-  {
-    return prefsize;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Dimension preferredsize()
-  {
-    return prefsize;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void keyTyped(KeyEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void keyReleased(KeyEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void keyPressed(KeyEvent evt)
-  {
-    if (evt.getKeyCode() == KeyEvent.VK_UP)
-    {
-      scalefactor = (float) (scalefactor * 1.1);
-      scale = findScale();
-    }
-    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
-    {
-      scalefactor = (float) (scalefactor * 0.9);
-      scale = findScale();
-    }
-    else if (evt.getKeyChar() == 's')
-    {
-      System.err.println("DEBUG: Rectangle selection"); // log.debug
-
-      if ( (rectx2 != -1) && (recty2 != -1))
-      {
-        rectSelect(rectx1, recty1, rectx2, recty2);
-      }
-    }
-
-    repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseClicked(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseEntered(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseExited(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mouseReleased(MouseEvent evt)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  public void mousePressed(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int y = evt.getY();
-
-    mx = x;
-    my = y;
-
-    omx = mx;
-    omy = my;
-
-    startx = x;
-    starty = y;
-
-    rectx1 = x;
-    recty1 = y;
-
-    rectx2 = -1;
-    recty2 = -1;
-
-    SequenceI found = findPoint(x, y);
-
-    if (found != null)
-    {
-      AlignmentPanel[] aps = getAssociatedPanels();
-
-      for (int a = 0; a < aps.length; a++)
-      {
-        if (aps[a].av.getSelectionGroup() != null)
-        {
-          aps[a].av.getSelectionGroup().addOrRemove(found, true);
-        }
-        else
-        {
-          aps[a].av.setSelectionGroup(new SequenceGroup());
-          aps[a].av.getSelectionGroup().addOrRemove(found, true);
-          aps[a].av.getSelectionGroup().setEndRes(
-              aps[a].av.alignment.getWidth() - 1);
-        }
-      }
-
-      PaintRefresher.Refresh(this, av.getSequenceSetId());
-    }
-
-    repaint();
-  }
-
-  // private void fireSequenceSelectionEvent(Selection sel) {
-  //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
-  //}
-  public void mouseMoved(MouseEvent evt)
-  {
-    SequenceI found = findPoint(evt.getX(), evt.getY());
-
-    if (found != null)
-    {
-      this.setToolTipText(found.getName());
-    }
-    else
-    {
-      this.setToolTipText(null);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param evt DOCUMENT ME!
-   */
-  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
-    {
-      rotmat.setIdentity();
-
-      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);
-        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);
-
-        //Now translate back again
-        sp.coord[0] += centre[0];
-        sp.coord[1] += centre[1];
-        sp.coord[2] += centre[2];
-      }
-
-      for (int i = 0; i < 3; i++)
-      {
-        axes[i] = rotmat.vectorMultiply(axes[i]);
-      }
-
-      omx = mx;
-      omy = my;
-
-      paint(this.getGraphics());
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param x2 DOCUMENT ME!
-   * @param y2 DOCUMENT ME!
-   */
-  public void rectSelect(int x1, int y1, int x2, int y2)
-  {
-    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().getSequences(null).contains(sp.sequence))
-          {
-            av.getSelectionGroup().addSequence(sp.sequence, true);
-          }
-        }
-      }
-    }
-
-    // if (changedSel) {
-    //    fireSequenceSelectionEvent(av.getSelection());
-    // }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param x DOCUMENT ME!
-   * @param y DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public SequenceI findPoint(int x, int y)
-  {
-    int halfwidth = getWidth() / 2;
-    int halfheight = getHeight() / 2;
-
-    int found = -1;
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int px = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +
-          halfwidth;
-      int py = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +
-          halfheight;
-
-      if ( (Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
-      {
-        found = i;
-      }
-    }
-
-    if (found != -1)
-    {
-      return ( (SequencePoint) points.elementAt(found)).sequence;
-    }
-    else
-    {
-      return null;
-    }
-  }
-
-  AlignmentPanel[] getAssociatedPanels()
-  {
-    if (applyToAllViews)
-    {
-      return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
-    }
-    else
-    {
-      return new AlignmentPanel[]
-          {
-          ap};
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.math.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class RotatableCanvas
+    extends JPanel implements MouseListener,
+    MouseMotionListener, KeyListener
+{
+  RotatableMatrix idmat = new RotatableMatrix(3, 3);
+  RotatableMatrix objmat = new RotatableMatrix(3, 3);
+  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+
+  //RubberbandRectangle rubberband;
+  boolean drawAxes = true;
+  int omx = 0;
+  int mx = 0;
+  int omy = 0;
+  int my = 0;
+  Image img;
+  Graphics ig;
+  Dimension prefsize;
+  float[] centre = new float[3];
+  float[] width = new float[3];
+  float[] max = new float[3];
+  float[] min = new float[3];
+  float maxwidth;
+  float scale;
+  int npoint;
+  Vector points;
+  float[][] orig;
+  float[][] axes;
+  int startx;
+  int starty;
+  int lastx;
+  int lasty;
+  int rectx1;
+  int recty1;
+  int rectx2;
+  int recty2;
+  float scalefactor = 1;
+  AlignViewport av;
+  AlignmentPanel ap;
+  boolean showLabels = false;
+  Color bgColour = Color.black;
+  boolean applyToAllViews = false;
+
+  //  Controller    controller;
+  public RotatableCanvas(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+
+    addMouseWheelListener(new MouseWheelListener()
+    {
+      public void mouseWheelMoved(MouseWheelEvent e)
+      {
+        if (e.getWheelRotation() > 0)
+        {
+          scale = (float) (scale * 1.1);
+          repaint();
+        }
+
+        else
+        {
+          scale = (float) (scale * 0.9);
+          repaint();
+        }
+      }
+    });
+
+  }
+
+  public void showLabels(boolean b)
+  {
+    showLabels = b;
+    repaint();
+  }
+
+  public void setPoints(Vector points, int npoint)
+  {
+    this.points = points;
+    this.npoint = npoint;
+    ToolTipManager.sharedInstance().registerComponent(this);
+    ToolTipManager.sharedInstance().setInitialDelay(0);
+    ToolTipManager.sharedInstance().setDismissDelay(10000);
+
+    prefsize = getPreferredSize();
+    orig = new float[npoint][3];
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+
+      for (int j = 0; j < 3; j++)
+      {
+        orig[i][j] = sp.coord[j];
+      }
+    }
+
+    //Initialize the matrices to identity
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
+        {
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
+        }
+        else
+        {
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
+        }
+      }
+    }
+
+    axes = new float[3][3];
+    initAxes();
+
+    findCentre();
+    findWidth();
+
+    scale = findScale();
+
+    addMouseListener(this);
+
+    addMouseMotionListener(this);
+
+  }
+
+  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
+        {
+          axes[i][j] = 1;
+        }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void findWidth()
+  {
+    max = new float[3];
+    min = new float[3];
+
+    max[0] = (float) - 1e30;
+    max[1] = (float) - 1e30;
+    max[2] = (float) - 1e30;
+
+    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])
+        {
+          max[i] = sp.coord[i];
+        }
+
+        if (sp.coord[i] <= min[i])
+        {
+          min[i] = sp.coord[i];
+        }
+      }
+    }
+
+    //    System.out.println("xmax " + max[0] + " min " + min[0]);
+    //System.out.println("ymax " + max[1] + " min " + min[1]);
+    //System.out.println("zmax " + max[2] + " min " + min[2]);
+    width[0] = Math.abs(max[0] - min[0]);
+    width[1] = Math.abs(max[1] - min[1]);
+    width[2] = Math.abs(max[2] - min[2]);
+
+    maxwidth = width[0];
+
+    if (width[1] > width[0])
+    {
+      maxwidth = width[1];
+    }
+
+    if (width[2] > width[1])
+    {
+      maxwidth = width[2];
+    }
+
+    //System.out.println("Maxwidth = " + maxwidth);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findScale()
+  {
+    int dim;
+    int width;
+    int height;
+
+    if (getWidth() != 0)
+    {
+      width = getWidth();
+      height = getHeight();
+    }
+    else
+    {
+      width = prefsize.width;
+      height = prefsize.height;
+    }
+
+    if (width < height)
+    {
+      dim = width;
+    }
+    else
+    {
+      dim = height;
+    }
+
+    return (float) ( (dim * scalefactor) / (2 * maxwidth));
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  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;
+
+    //    System.out.println("Centre x " + centre[0]);
+    //System.out.println("Centre y " + centre[1]);
+    //System.out.println("Centre z " + centre[2]);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension getPreferredSize()
+  {
+    if (prefsize != null)
+    {
+      return prefsize;
+    }
+    else
+    {
+      return new Dimension(400, 400);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension getMinimumSize()
+  {
+    return getPreferredSize();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g1)
+  {
+
+    Graphics2D g = (Graphics2D) g1;
+
+    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                       RenderingHints.VALUE_ANTIALIAS_ON);
+    if (points == null)
+    {
+      g.setFont(new Font("Verdana", Font.PLAIN, 18));
+      g.drawString("Calculating PCA....", 20, getHeight() / 2);
+    }
+    else
+    {
+      //Only create the image at the beginning -
+      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());
+        ig = img.getGraphics();
+      }
+
+      drawBackground(ig, bgColour);
+      drawScene(ig);
+
+      if (drawAxes == true)
+      {
+        drawAxes(ig);
+      }
+
+      g.drawImage(img, 0, 0, this);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  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)));
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param col DOCUMENT ME!
+   */
+  public void drawBackground(Graphics g, Color col)
+  {
+    g.setColor(col);
+    g.fillRect(0, 0, prefsize.width, prefsize.height);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void drawScene(Graphics g1)
+  {
+
+    Graphics2D g = (Graphics2D) g1;
+
+    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                       RenderingHints.VALUE_ANTIALIAS_ON);
+
+    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;
+      float z = sp.coord[1] - centre[2];
+
+      if (av.getSequenceColour(sp.sequence) == Color.black)
+      {
+        g.setColor(Color.white);
+      }
+      else
+      {
+        g.setColor(av.getSequenceColour(sp.sequence));
+      }
+
+      if (av.getSelectionGroup() != null)
+      {
+        if (av.getSelectionGroup().getSequences(null).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);
+      if (showLabels)
+      {
+        g.setColor(Color.red);
+        g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.
+                     getName(),
+                     x - 3, y - 4);
+      }
+    }
+
+    //    //Now the rectangle
+    //    if (rectx2 != -1 && recty2 != -1) {
+    //      g.setColor(Color.white);
+    //
+    //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
+    //    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension minimumsize()
+  {
+    return prefsize;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension preferredsize()
+  {
+    return prefsize;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void keyTyped(KeyEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void keyReleased(KeyEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void keyPressed(KeyEvent evt)
+  {
+    if (evt.getKeyCode() == KeyEvent.VK_UP)
+    {
+      scalefactor = (float) (scalefactor * 1.1);
+      scale = findScale();
+    }
+    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+    {
+      scalefactor = (float) (scalefactor * 0.9);
+      scale = findScale();
+    }
+    else if (evt.getKeyChar() == 's')
+    {
+      System.err.println("DEBUG: Rectangle selection"); // log.debug
+
+      if ( (rectx2 != -1) && (recty2 != -1))
+      {
+        rectSelect(rectx1, recty1, rectx2, recty2);
+      }
+    }
+
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    int x = evt.getX();
+    int y = evt.getY();
+
+    mx = x;
+    my = y;
+
+    omx = mx;
+    omy = my;
+
+    startx = x;
+    starty = y;
+
+    rectx1 = x;
+    recty1 = y;
+
+    rectx2 = -1;
+    recty2 = -1;
+
+    SequenceI found = findPoint(x, y);
+
+    if (found != null)
+    {
+      AlignmentPanel[] aps = getAssociatedPanels();
+
+      for (int a = 0; a < aps.length; a++)
+      {
+        if (aps[a].av.getSelectionGroup() != null)
+        {
+          aps[a].av.getSelectionGroup().addOrRemove(found, true);
+        }
+        else
+        {
+          aps[a].av.setSelectionGroup(new SequenceGroup());
+          aps[a].av.getSelectionGroup().addOrRemove(found, true);
+          aps[a].av.getSelectionGroup().setEndRes(
+              aps[a].av.alignment.getWidth() - 1);
+        }
+      }
+
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
+    }
+
+    repaint();
+  }
+
+  // private void fireSequenceSelectionEvent(Selection sel) {
+  //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
+  //}
+  public void mouseMoved(MouseEvent evt)
+  {
+    SequenceI found = findPoint(evt.getX(), evt.getY());
+
+    if (found != null)
+    {
+      this.setToolTipText(found.getName());
+    }
+    else
+    {
+      this.setToolTipText(null);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  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
+    {
+      rotmat.setIdentity();
+
+      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);
+        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);
+
+        //Now translate back again
+        sp.coord[0] += centre[0];
+        sp.coord[1] += centre[1];
+        sp.coord[2] += centre[2];
+      }
+
+      for (int i = 0; i < 3; i++)
+      {
+        axes[i] = rotmat.vectorMultiply(axes[i]);
+      }
+
+      omx = mx;
+      omy = my;
+
+      paint(this.getGraphics());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param x1 DOCUMENT ME!
+   * @param y1 DOCUMENT ME!
+   * @param x2 DOCUMENT ME!
+   * @param y2 DOCUMENT ME!
+   */
+  public void rectSelect(int x1, int y1, int x2, int y2)
+  {
+    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().getSequences(null).contains(sp.sequence))
+          {
+            av.getSelectionGroup().addSequence(sp.sequence, true);
+          }
+        }
+      }
+    }
+
+    // if (changedSel) {
+    //    fireSequenceSelectionEvent(av.getSelection());
+    // }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param x DOCUMENT ME!
+   * @param y DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceI findPoint(int x, int y)
+  {
+    int halfwidth = getWidth() / 2;
+    int halfheight = getHeight() / 2;
+
+    int found = -1;
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int px = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +
+          halfwidth;
+      int py = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +
+          halfheight;
+
+      if ( (Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+      {
+        found = i;
+      }
+    }
+
+    if (found != -1)
+    {
+      return ( (SequencePoint) points.elementAt(found)).sequence;
+    }
+    else
+    {
+      return null;
+    }
+  }
+
+  AlignmentPanel[] getAssociatedPanels()
+  {
+    if (applyToAllViews)
+    {
+      return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
+    }
+    else
+    {
+      return new AlignmentPanel[]
+          {
+          ap};
+    }
+  }
+}
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index d8bdba3..88f0584 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/ScriptWindow.java b/src/jalview/gui/ScriptWindow.java
index 8e69584..1e8b201 100644
--- a/src/jalview/gui/ScriptWindow.java
+++ b/src/jalview/gui/ScriptWindow.java
@@ -1,616 +1,606 @@
-/* $RCSfile$
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2002-2005  The Jmol Development Team
- *
- * Contact: jmol-developers@lists.sf.net
- *
- *  This library is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public
- *  License as published by the Free Software Foundation; either
- *  version 2.1 of the License, or (at your option) any later version.
- *
- *  This library 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
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this library; if not, write to the Free Software
- *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
-
- *
- * Modified and added to Jalview by A Waterhouse to extend JInternalFrame
- *
-
- */
-package jalview.gui;
-
-import org.jmol.api.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.text.*;
-import java.util.Vector;
-
-import org.jmol.i18n.GT;
-import org.jmol.util.Logger;
-import org.jmol.util.CommandHistory;
-
-public final class ScriptWindow extends JPanel
-    implements ActionListener, EnterListener{
-
-  private ConsoleTextPane console;
-  private JButton closeButton;
-  private JButton runButton;
-  private JButton haltButton;
-  private JButton clearButton;
-  private JButton historyButton;
-  private JButton stateButton;
-   JmolViewer viewer;
-  AppJmol appJmol;
-
-  public ScriptWindow(AppJmol appJmol)
-  {
-    this.viewer = appJmol.viewer;
-    this.appJmol = appJmol;
-
-
-    setLayout(new BorderLayout());
-
-    console = new ConsoleTextPane(this);
-
-
-    console.setPrompt();
-    add(new JScrollPane(console)
-                         , BorderLayout.CENTER);
-
-    JPanel buttonPanel = new JPanel();
-    add(buttonPanel, BorderLayout.SOUTH);
-
-    runButton = new JButton(GT._("Run"));
-    haltButton = new JButton(GT._("Halt"));
-    runButton.addActionListener(this);
-   // buttonPanel.add(runButton);
-    haltButton.addActionListener(this);
-  //  buttonPanel.add(haltButton);
-    haltButton.setEnabled(false);
-
-    clearButton = new JButton(GT._("Clear"));
-    clearButton.addActionListener(this);
-    buttonPanel.add(clearButton);
-
-    historyButton = new JButton(GT._("History"));
-    historyButton.addActionListener(this);
-    buttonPanel.add(historyButton);
-
-    stateButton = new JButton(GT._("State"));
-    stateButton.addActionListener(this);
-    buttonPanel.add(stateButton);
-
-    closeButton = new JButton(GT._("Close"));
-    closeButton.addActionListener(this);
-    buttonPanel.add(closeButton);
-
-    for(int i=0; i<buttonPanel.getComponentCount(); i++)
-    {
-    //  ((JButton)buttonPanel.getComponent(i))
-    //      .setMargin(new Insets(0, 0, 0, 0));
-    }
-
-  }
-
-  public void sendConsoleEcho(String strEcho) {
-    if (strEcho != null && !isError) {
-
-      console.outputEcho(strEcho);
-
-    }
-    setError(false);
-  }
-
-  boolean isError = false;
-  void setError(boolean TF) {
-    isError = TF;
-    //if (isError)
-      //console.recallCommand(true);
-  }
-
-  public void sendConsoleMessage(String strStatus) {
-    if (strStatus == null) {
-      console.clearContent();
-      console.outputStatus("");
-    } else if (strStatus.indexOf("ERROR:") >= 0) {
-      console.outputError(strStatus);
-      isError = true;
-    } else if (!isError) {
-      console.outputStatus(strStatus);
-    }
-  }
-
-  public void notifyScriptTermination(String strMsg, int msWalltime) {
-    if (strMsg != null && strMsg.indexOf("ERROR") >= 0) {
-      console.outputError(strMsg);
-    }
-    runButton.setEnabled(true);
-    haltButton.setEnabled(false);
-  }
-
-  public void enterPressed() {
-    runButton.doClick(100);
-    //    executeCommand();
-  }
-
-
-  class ExecuteCommandThread extends Thread {
-
-    String strCommand;
-    ExecuteCommandThread (String command) {
-      strCommand = command;
-    }
-
-    public void run() {
-      try {
-        executeCommand(strCommand);
-      } catch (Exception ie) {
-        Logger.debug("execution command interrupted!"+ie);
-      }
-    }
-  }
-
-  ExecuteCommandThread execThread;
-  void executeCommandAsThread(){
-    String strCommand = console.getCommandString().trim();
-    if (strCommand.length() > 0) {
-      execThread = new ExecuteCommandThread(strCommand);
-      execThread.start();
-    }
-  }
-
-  void executeCommand(String strCommand) {
-    boolean doWait;
-    setError(false);
-    console.appendNewline();
-    console.setPrompt();
-    if (strCommand.length() > 0) {
-      String strErrorMessage = null;
-      doWait = (strCommand.indexOf("WAIT ") == 0);
-      if (doWait) { //for testing, mainly
-        // demonstrates using the statusManager system.
-        runButton.setEnabled(false);
-        haltButton.setEnabled(true);
-
-        Vector info = (Vector) viewer
-            .scriptWaitStatus(strCommand.substring(5),
-                "+fileLoaded,+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated");
-        runButton.setEnabled(true);
-        haltButton.setEnabled(false);
-        /*
-         * info = [ statusRecortSet0, statusRecortSet1, statusRecortSet2, ...]
-         * statusRecordSet = [ statusRecord0, statusRecord1, statusRecord2, ...]
-         * statusRecord = [int msgPtr, String statusName, int intInfo, String msg]
-         */
-        for (int i = 0; i < info.size(); i++) {
-          Vector statusRecordSet = (Vector) info.get(i);
-          for (int j = 0; j < statusRecordSet.size(); j++) {
-            Vector statusRecord = (Vector) statusRecordSet.get(j);
-            Logger.info("msg#=" + statusRecord.get(0) + " "
-                + statusRecord.get(1) + " intInfo=" + statusRecord.get(2)
-                + " stringInfo=" + statusRecord.get(3));
-          }
-        }
-        console.appendNewline();
-      } else {
-        boolean isScriptExecuting = viewer.isScriptExecuting();
-        if (viewer.checkHalt(strCommand))
-          strErrorMessage = (isScriptExecuting ? "string execution halted with " + strCommand : "no script was executing");
-        else
-          strErrorMessage = "";//viewer.scriptCheck(strCommand);
-        //the problem is that scriptCheck is synchronized, so these might get backed up.
-        if (strErrorMessage != null && strErrorMessage.length() > 0) {
-          console.outputError(strErrorMessage);
-        } else {
-          //runButton.setEnabled(false);
-          haltButton.setEnabled(true);
-          viewer.script(strCommand);
-        }
-      }
-    }
-    console.grabFocus();
-  }
-
-  public void actionPerformed(ActionEvent e) {
-    Object source = e.getSource();
-    if (source == closeButton) {
-      appJmol.showConsole(false);
-    } else if (source == runButton) {
-      executeCommandAsThread();
-    } else if (source == clearButton) {
-      console.clearContent();
-    } else if (source == historyButton) {
-      console.clearContent(viewer.getSetHistory(Integer.MAX_VALUE));
-    } else if (source == stateButton) {
-      console.clearContent(viewer.getStateInfo());
-    } else if (source == haltButton) {
-      viewer.haltScriptExecution();
-    }
-    console.grabFocus(); // always grab the focus (e.g., after clear)
-  }
-}
-
-class ConsoleTextPane extends JTextPane {
-
-  ConsoleDocument consoleDoc;
-  EnterListener enterListener;
-  JmolViewer viewer;
-
-  ConsoleTextPane(ScriptWindow scriptWindow) {
-    super(new ConsoleDocument());
-    consoleDoc = (ConsoleDocument)getDocument();
-    consoleDoc.setConsoleTextPane(this);
-    this.enterListener = (EnterListener) scriptWindow;
-    this.viewer = scriptWindow.viewer;
-  }
-
-  public String getCommandString() {
-    String cmd = consoleDoc.getCommandString();
-    return cmd;
-  }
-
-  public void setPrompt() {
-    consoleDoc.setPrompt();
-  }
-
-  public void appendNewline() {
-    consoleDoc.appendNewline();
-  }
-
-  public void outputError(String strError) {
-    consoleDoc.outputError(strError);
-  }
-
-  public void outputErrorForeground(String strError) {
-    consoleDoc.outputErrorForeground(strError);
-  }
-
-  public void outputEcho(String strEcho) {
-    consoleDoc.outputEcho(strEcho);
-  }
-
-  public void outputStatus(String strStatus) {
-    consoleDoc.outputStatus(strStatus);
-  }
-
-  public void enterPressed() {
-    if (enterListener != null)
-      enterListener.enterPressed();
-  }
-
-  public void clearContent() {
-    clearContent(null);
-  }
-  public void clearContent(String text) {
-    consoleDoc.clearContent();
-    if (text != null)
-      consoleDoc.outputEcho(text);
-    setPrompt();
-  }
-
-   /* (non-Javadoc)
-    * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)
-    */
-
-   /**
-    * Custom key event processing for command 0 implementation.
-    *
-    * Captures key up and key down strokes to call command history
-    * and redefines the same events with control down to allow
-    * caret vertical shift.
-    *
-    * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)
-    */
-   protected void processKeyEvent(KeyEvent ke)
-   {
-      // Id Control key is down, captures events does command
-      // history recall and inhibits caret vertical shift.
-      if (ke.getKeyCode() == KeyEvent.VK_UP
-         && ke.getID() == KeyEvent.KEY_PRESSED
-         && !ke.isControlDown())
-      {
-         recallCommand(true);
-      }
-      else if (
-         ke.getKeyCode() == KeyEvent.VK_DOWN
-            && ke.getID() == KeyEvent.KEY_PRESSED
-            && !ke.isControlDown())
-      {
-         recallCommand(false);
-      }
-      // If Control key is down, redefines the event as if it
-      // where a key up or key down stroke without modifiers.
-      // This allows to move the caret up and down
-      // with no command history recall.
-      else if (
-         (ke.getKeyCode() == KeyEvent.VK_DOWN
-            || ke.getKeyCode() == KeyEvent.VK_UP)
-            && ke.getID() == KeyEvent.KEY_PRESSED
-            && ke.isControlDown())
-      {
-         super
-            .processKeyEvent(new KeyEvent(
-               (Component) ke.getSource(),
-               ke.getID(),
-               ke.getWhen(),
-               0,         // No modifiers
-               ke.getKeyCode(),
-               ke.getKeyChar(),
-               ke.getKeyLocation()));
-      }
-      // Standard processing for other events.
-      else
-      {
-         super.processKeyEvent(ke);
-         //check command for compiler-identifyable syntax issues
-         //this may have to be taken out if people start complaining
-         //that only some of the commands are being checked
-         //that is -- that the script itself is not being fully checked
-
-         //not perfect -- help here?
-         if (ke.getID() == KeyEvent.KEY_RELEASED
-             && (ke.getKeyCode() > KeyEvent.VK_DOWN) || ke.getKeyCode() == KeyEvent.VK_BACK_SPACE)
-           checkCommand();
-      }
-   }
-
-   /**
-   * Recall command history.
-   *
-   * @param up - history up or down
-   */
-   void recallCommand(boolean up) {
-     String cmd = viewer.getSetHistory(up ? -1 : 1);
-    if (cmd == null) {
-      return;
-    }
-    try {
-      if (cmd.endsWith(CommandHistory.ERROR_FLAG)) {
-        cmd = cmd.substring(0, cmd.indexOf(CommandHistory.ERROR_FLAG));
-        consoleDoc.replaceCommand(cmd, true);
-      } else {
-        consoleDoc.replaceCommand(cmd, false);
-      }
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-   void checkCommand() {
-    String strCommand = consoleDoc.getCommandString();
-    if (strCommand.length() == 0)
-      return;
-    consoleDoc
-        .colorCommand(viewer.scriptCheck(strCommand) == null ? consoleDoc.attUserInput
-            : consoleDoc.attError);
-  }
-
-
-}
-
-class ConsoleDocument extends DefaultStyledDocument {
-
-  ConsoleTextPane consoleTextPane;
-
-  SimpleAttributeSet attError;
-  SimpleAttributeSet attEcho;
-  SimpleAttributeSet attPrompt;
-  SimpleAttributeSet attUserInput;
-  SimpleAttributeSet attStatus;
-
-  ConsoleDocument() {
-    super();
-
-    attError = new SimpleAttributeSet();
-    StyleConstants.setForeground(attError, Color.red);
-
-    attPrompt = new SimpleAttributeSet();
-    StyleConstants.setForeground(attPrompt, Color.magenta);
-
-    attUserInput = new SimpleAttributeSet();
-    StyleConstants.setForeground(attUserInput, Color.black);
-
-    attEcho = new SimpleAttributeSet();
-    StyleConstants.setForeground(attEcho, Color.blue);
-    StyleConstants.setBold(attEcho, true);
-
-    attStatus = new SimpleAttributeSet();
-    StyleConstants.setForeground(attStatus, Color.black);
-    StyleConstants.setItalic(attStatus, true);
-  }
-
-  void setConsoleTextPane(ConsoleTextPane consoleTextPane) {
-    this.consoleTextPane = consoleTextPane;
-  }
-
-  Position positionBeforePrompt; // starts at 0, so first time isn't tracked (at least on Mac OS X)
-  Position positionAfterPrompt;  // immediately after $, so this will track
-  int offsetAfterPrompt;         // only still needed for the insertString override and replaceCommand
-
-  /**
-   * Removes all content of the script window, and add a new prompt.
-   */
-  void clearContent() {
-      try {
-          super.remove(0, getLength());
-      } catch (BadLocationException exception) {
-          System.out.println("Could not clear script window content: " + exception.getMessage());
-      }
-  }
-
-  void setPrompt() {
-    try {
-      super.insertString(getLength(), "$ ", attPrompt);
-      setOffsetPositions();
-      consoleTextPane.setCaretPosition(offsetAfterPrompt);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  void setOffsetPositions() {
-    try {
-      offsetAfterPrompt = getLength();
-      positionBeforePrompt = createPosition(offsetAfterPrompt - 2);
-      // after prompt should be immediately after $ otherwise tracks the end
-      // of the line (and no command will be found) at least on Mac OS X it did.
-      positionAfterPrompt = createPosition(offsetAfterPrompt - 1);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  void setNoPrompt() {
-    try {
-      offsetAfterPrompt = getLength();
-      positionAfterPrompt = positionBeforePrompt = createPosition(offsetAfterPrompt);
-      consoleTextPane.setCaretPosition(offsetAfterPrompt);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  // it looks like the positionBeforePrompt does not track when it started out as 0
-  // and a insertString at location 0 occurs. It may be better to track the
-  // position after the prompt in stead
-  void outputBeforePrompt(String str, SimpleAttributeSet attribute) {
-    try {
-      int pt = consoleTextPane.getCaretPosition();
-      Position caretPosition = createPosition(pt);
-      pt = positionBeforePrompt.getOffset();
-      super.insertString(pt, str+"\n", attribute);
-      setOffsetPositions();
-      pt = caretPosition.getOffset();
-      consoleTextPane.setCaretPosition(pt);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  void outputError(String strError) {
-    outputBeforePrompt(strError, attError);
-  }
-
-  void outputErrorForeground(String strError) {
-    try {
-      super.insertString(getLength(), strError+"\n", attError);
-      consoleTextPane.setCaretPosition(getLength());
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-
-    }
-  }
-
-  void outputEcho(String strEcho) {
-    outputBeforePrompt(strEcho, attEcho);
-  }
-
-  void outputStatus(String strStatus) {
-    outputBeforePrompt(strStatus, attStatus);
-  }
-
-  void appendNewline() {
-    try {
-      super.insertString(getLength(), "\n", attUserInput);
-      consoleTextPane.setCaretPosition(getLength());
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-  }
-
-  // override the insertString to make sure everything typed ends up at the end
-  // or in the 'command line' using the proper font, and the newline is processed.
-  public void insertString(int offs, String str, AttributeSet a)
-    throws BadLocationException {
-    int ichNewline = str.indexOf('\n');
-    if (ichNewline > 0)
-      str = str.substring(0, ichNewline);
-    if (ichNewline != 0) {
-      if (offs < offsetAfterPrompt) {
-        offs = getLength();
-      }
-      super.insertString(offs, str, a == attError ? a : attUserInput);
-      consoleTextPane.setCaretPosition(offs+str.length());
-    }
-    if (ichNewline >= 0) {
-      consoleTextPane.enterPressed();
-    }
-  }
-
-  String getCommandString() {
-    String strCommand = "";
-    try {
-      int cmdStart = positionAfterPrompt.getOffset();
-      strCommand =  getText(cmdStart, getLength() - cmdStart);
-      while (strCommand.length() > 0 && strCommand.charAt(0) == ' ')
-        strCommand = strCommand.substring(1);
-    } catch (BadLocationException e) {
-      e.printStackTrace();
-    }
-    return strCommand;
-  }
-
-  public void remove(int offs, int len)
-    throws BadLocationException {
-    if (offs < offsetAfterPrompt) {
-      len -= offsetAfterPrompt - offs;
-      if (len <= 0)
-        return;
-      offs = offsetAfterPrompt;
-    }
-    super.remove(offs, len);
-//    consoleTextPane.setCaretPosition(offs);
-  }
-
-  public void replace(int offs, int length, String str, AttributeSet attrs)
-    throws BadLocationException {
-    if (offs < offsetAfterPrompt) {
-      if (offs + length < offsetAfterPrompt) {
-        offs = getLength();
-        length = 0;
-      } else {
-        length -= offsetAfterPrompt - offs;
-        offs = offsetAfterPrompt;
-      }
-    }
-    super.replace(offs, length, str, attrs);
-//    consoleTextPane.setCaretPosition(offs + str.length());
-  }
-
-   /**
-   * Replaces current command on script.
-   *
-   * @param newCommand new command value
-   * @param isError    true to set error color  ends with #??
-   *
-   * @throws BadLocationException
-   */
-  void replaceCommand(String newCommand, boolean isError) throws BadLocationException {
-    if (positionAfterPrompt == positionBeforePrompt)
-      return;
-    replace(offsetAfterPrompt, getLength() - offsetAfterPrompt, newCommand,
-        isError ? attError : attUserInput);
-  }
-
-  void colorCommand(SimpleAttributeSet att) {
-    if (positionAfterPrompt == positionBeforePrompt)
-      return;
-    setCharacterAttributes(offsetAfterPrompt, getLength() - offsetAfterPrompt, att, true);
-  }
-}
-
-interface EnterListener {
-  public void enterPressed();
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 org.jmol.api.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.text.*;
+import java.util.Vector;
+
+import org.jmol.i18n.GT;
+import org.jmol.util.Logger;
+import org.jmol.util.CommandHistory;
+
+public final class ScriptWindow extends JPanel
+    implements ActionListener, EnterListener{
+
+  private ConsoleTextPane console;
+  private JButton closeButton;
+  private JButton runButton;
+  private JButton haltButton;
+  private JButton clearButton;
+  private JButton historyButton;
+  private JButton stateButton;
+   JmolViewer viewer;
+  AppJmol appJmol;
+
+  public ScriptWindow(AppJmol appJmol)
+  {
+    this.viewer = appJmol.viewer;
+    this.appJmol = appJmol;
+
+
+    setLayout(new BorderLayout());
+
+    console = new ConsoleTextPane(this);
+
+
+    console.setPrompt();
+    add(new JScrollPane(console)
+                         , BorderLayout.CENTER);
+
+    JPanel buttonPanel = new JPanel();
+    add(buttonPanel, BorderLayout.SOUTH);
+
+    runButton = new JButton(GT._("Run"));
+    haltButton = new JButton(GT._("Halt"));
+    runButton.addActionListener(this);
+   // buttonPanel.add(runButton);
+    haltButton.addActionListener(this);
+  //  buttonPanel.add(haltButton);
+    haltButton.setEnabled(false);
+
+    clearButton = new JButton(GT._("Clear"));
+    clearButton.addActionListener(this);
+    buttonPanel.add(clearButton);
+
+    historyButton = new JButton(GT._("History"));
+    historyButton.addActionListener(this);
+    buttonPanel.add(historyButton);
+
+    stateButton = new JButton(GT._("State"));
+    stateButton.addActionListener(this);
+    buttonPanel.add(stateButton);
+
+    closeButton = new JButton(GT._("Close"));
+    closeButton.addActionListener(this);
+    buttonPanel.add(closeButton);
+
+    for(int i=0; i<buttonPanel.getComponentCount(); i++)
+    {
+    //  ((JButton)buttonPanel.getComponent(i))
+    //      .setMargin(new Insets(0, 0, 0, 0));
+    }
+
+  }
+
+  public void sendConsoleEcho(String strEcho) {
+    if (strEcho != null && !isError) {
+
+      console.outputEcho(strEcho);
+
+    }
+    setError(false);
+  }
+
+  boolean isError = false;
+  void setError(boolean TF) {
+    isError = TF;
+    //if (isError)
+      //console.recallCommand(true);
+  }
+
+  public void sendConsoleMessage(String strStatus) {
+    if (strStatus == null) {
+      console.clearContent();
+      console.outputStatus("");
+    } else if (strStatus.indexOf("ERROR:") >= 0) {
+      console.outputError(strStatus);
+      isError = true;
+    } else if (!isError) {
+      console.outputStatus(strStatus);
+    }
+  }
+
+  public void notifyScriptTermination(String strMsg, int msWalltime) {
+    if (strMsg != null && strMsg.indexOf("ERROR") >= 0) {
+      console.outputError(strMsg);
+    }
+    runButton.setEnabled(true);
+    haltButton.setEnabled(false);
+  }
+
+  public void enterPressed() {
+    runButton.doClick(100);
+    //    executeCommand();
+  }
+
+
+  class ExecuteCommandThread extends Thread {
+
+    String strCommand;
+    ExecuteCommandThread (String command) {
+      strCommand = command;
+    }
+
+    public void run() {
+      try {
+        executeCommand(strCommand);
+      } catch (Exception ie) {
+        Logger.debug("execution command interrupted!"+ie);
+      }
+    }
+  }
+
+  ExecuteCommandThread execThread;
+  void executeCommandAsThread(){
+    String strCommand = console.getCommandString().trim();
+    if (strCommand.length() > 0) {
+      execThread = new ExecuteCommandThread(strCommand);
+      execThread.start();
+    }
+  }
+
+  void executeCommand(String strCommand) {
+    boolean doWait;
+    setError(false);
+    console.appendNewline();
+    console.setPrompt();
+    if (strCommand.length() > 0) {
+      String strErrorMessage = null;
+      doWait = (strCommand.indexOf("WAIT ") == 0);
+      if (doWait) { //for testing, mainly
+        // demonstrates using the statusManager system.
+        runButton.setEnabled(false);
+        haltButton.setEnabled(true);
+
+        Vector info = (Vector) viewer
+            .scriptWaitStatus(strCommand.substring(5),
+                "+fileLoaded,+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated");
+        runButton.setEnabled(true);
+        haltButton.setEnabled(false);
+        /*
+         * info = [ statusRecortSet0, statusRecortSet1, statusRecortSet2, ...]
+         * statusRecordSet = [ statusRecord0, statusRecord1, statusRecord2, ...]
+         * statusRecord = [int msgPtr, String statusName, int intInfo, String msg]
+         */
+        for (int i = 0; i < info.size(); i++) {
+          Vector statusRecordSet = (Vector) info.get(i);
+          for (int j = 0; j < statusRecordSet.size(); j++) {
+            Vector statusRecord = (Vector) statusRecordSet.get(j);
+            Logger.info("msg#=" + statusRecord.get(0) + " "
+                + statusRecord.get(1) + " intInfo=" + statusRecord.get(2)
+                + " stringInfo=" + statusRecord.get(3));
+          }
+        }
+        console.appendNewline();
+      } else {
+        boolean isScriptExecuting = viewer.isScriptExecuting();
+        if (viewer.checkHalt(strCommand))
+          strErrorMessage = (isScriptExecuting ? "string execution halted with " + strCommand : "no script was executing");
+        else
+          strErrorMessage = "";//viewer.scriptCheck(strCommand);
+        //the problem is that scriptCheck is synchronized, so these might get backed up.
+        if (strErrorMessage != null && strErrorMessage.length() > 0) {
+          console.outputError(strErrorMessage);
+        } else {
+          //runButton.setEnabled(false);
+          haltButton.setEnabled(true);
+          viewer.script(strCommand);
+        }
+      }
+    }
+    console.grabFocus();
+  }
+
+  public void actionPerformed(ActionEvent e) {
+    Object source = e.getSource();
+    if (source == closeButton) {
+      appJmol.showConsole(false);
+    } else if (source == runButton) {
+      executeCommandAsThread();
+    } else if (source == clearButton) {
+      console.clearContent();
+    } else if (source == historyButton) {
+      console.clearContent(viewer.getSetHistory(Integer.MAX_VALUE));
+    } else if (source == stateButton) {
+      console.clearContent(viewer.getStateInfo());
+    } else if (source == haltButton) {
+      viewer.haltScriptExecution();
+    }
+    console.grabFocus(); // always grab the focus (e.g., after clear)
+  }
+}
+
+class ConsoleTextPane extends JTextPane {
+
+  ConsoleDocument consoleDoc;
+  EnterListener enterListener;
+  JmolViewer viewer;
+
+  ConsoleTextPane(ScriptWindow scriptWindow) {
+    super(new ConsoleDocument());
+    consoleDoc = (ConsoleDocument)getDocument();
+    consoleDoc.setConsoleTextPane(this);
+    this.enterListener = (EnterListener) scriptWindow;
+    this.viewer = scriptWindow.viewer;
+  }
+
+  public String getCommandString() {
+    String cmd = consoleDoc.getCommandString();
+    return cmd;
+  }
+
+  public void setPrompt() {
+    consoleDoc.setPrompt();
+  }
+
+  public void appendNewline() {
+    consoleDoc.appendNewline();
+  }
+
+  public void outputError(String strError) {
+    consoleDoc.outputError(strError);
+  }
+
+  public void outputErrorForeground(String strError) {
+    consoleDoc.outputErrorForeground(strError);
+  }
+
+  public void outputEcho(String strEcho) {
+    consoleDoc.outputEcho(strEcho);
+  }
+
+  public void outputStatus(String strStatus) {
+    consoleDoc.outputStatus(strStatus);
+  }
+
+  public void enterPressed() {
+    if (enterListener != null)
+      enterListener.enterPressed();
+  }
+
+  public void clearContent() {
+    clearContent(null);
+  }
+  public void clearContent(String text) {
+    consoleDoc.clearContent();
+    if (text != null)
+      consoleDoc.outputEcho(text);
+    setPrompt();
+  }
+
+   /* (non-Javadoc)
+    * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)
+    */
+
+   /**
+    * Custom key event processing for command 0 implementation.
+    *
+    * Captures key up and key down strokes to call command history
+    * and redefines the same events with control down to allow
+    * caret vertical shift.
+    *
+    * @see java.awt.Component#processKeyEvent(java.awt.event.KeyEvent)
+    */
+   protected void processKeyEvent(KeyEvent ke)
+   {
+      // Id Control key is down, captures events does command
+      // history recall and inhibits caret vertical shift.
+      if (ke.getKeyCode() == KeyEvent.VK_UP
+         && ke.getID() == KeyEvent.KEY_PRESSED
+         && !ke.isControlDown())
+      {
+         recallCommand(true);
+      }
+      else if (
+         ke.getKeyCode() == KeyEvent.VK_DOWN
+            && ke.getID() == KeyEvent.KEY_PRESSED
+            && !ke.isControlDown())
+      {
+         recallCommand(false);
+      }
+      // If Control key is down, redefines the event as if it
+      // where a key up or key down stroke without modifiers.
+      // This allows to move the caret up and down
+      // with no command history recall.
+      else if (
+         (ke.getKeyCode() == KeyEvent.VK_DOWN
+            || ke.getKeyCode() == KeyEvent.VK_UP)
+            && ke.getID() == KeyEvent.KEY_PRESSED
+            && ke.isControlDown())
+      {
+         super
+            .processKeyEvent(new KeyEvent(
+               (Component) ke.getSource(),
+               ke.getID(),
+               ke.getWhen(),
+               0,         // No modifiers
+               ke.getKeyCode(),
+               ke.getKeyChar(),
+               ke.getKeyLocation()));
+      }
+      // Standard processing for other events.
+      else
+      {
+         super.processKeyEvent(ke);
+         //check command for compiler-identifyable syntax issues
+         //this may have to be taken out if people start complaining
+         //that only some of the commands are being checked
+         //that is -- that the script itself is not being fully checked
+
+         //not perfect -- help here?
+         if (ke.getID() == KeyEvent.KEY_RELEASED
+             && (ke.getKeyCode() > KeyEvent.VK_DOWN) || ke.getKeyCode() == KeyEvent.VK_BACK_SPACE)
+           checkCommand();
+      }
+   }
+
+   /**
+   * Recall command history.
+   *
+   * @param up - history up or down
+   */
+   void recallCommand(boolean up) {
+     String cmd = viewer.getSetHistory(up ? -1 : 1);
+    if (cmd == null) {
+      return;
+    }
+    try {
+      if (cmd.endsWith(CommandHistory.ERROR_FLAG)) {
+        cmd = cmd.substring(0, cmd.indexOf(CommandHistory.ERROR_FLAG));
+        consoleDoc.replaceCommand(cmd, true);
+      } else {
+        consoleDoc.replaceCommand(cmd, false);
+      }
+    } catch (BadLocationException e) {
+      e.printStackTrace();
+    }
+  }
+
+   void checkCommand() {
+    String strCommand = consoleDoc.getCommandString();
+    if (strCommand.length() == 0)
+      return;
+    consoleDoc
+        .colorCommand(viewer.scriptCheck(strCommand) == null ? consoleDoc.attUserInput
+            : consoleDoc.attError);
+  }
+
+
+}
+
+class ConsoleDocument extends DefaultStyledDocument {
+
+  ConsoleTextPane consoleTextPane;
+
+  SimpleAttributeSet attError;
+  SimpleAttributeSet attEcho;
+  SimpleAttributeSet attPrompt;
+  SimpleAttributeSet attUserInput;
+  SimpleAttributeSet attStatus;
+
+  ConsoleDocument() {
+    super();
+
+    attError = new SimpleAttributeSet();
+    StyleConstants.setForeground(attError, Color.red);
+
+    attPrompt = new SimpleAttributeSet();
+    StyleConstants.setForeground(attPrompt, Color.magenta);
+
+    attUserInput = new SimpleAttributeSet();
+    StyleConstants.setForeground(attUserInput, Color.black);
+
+    attEcho = new SimpleAttributeSet();
+    StyleConstants.setForeground(attEcho, Color.blue);
+    StyleConstants.setBold(attEcho, true);
+
+    attStatus = new SimpleAttributeSet();
+    StyleConstants.setForeground(attStatus, Color.black);
+    StyleConstants.setItalic(attStatus, true);
+  }
+
+  void setConsoleTextPane(ConsoleTextPane consoleTextPane) {
+    this.consoleTextPane = consoleTextPane;
+  }
+
+  Position positionBeforePrompt; // starts at 0, so first time isn't tracked (at least on Mac OS X)
+  Position positionAfterPrompt;  // immediately after $, so this will track
+  int offsetAfterPrompt;         // only still needed for the insertString override and replaceCommand
+
+  /**
+   * Removes all content of the script window, and add a new prompt.
+   */
+  void clearContent() {
+      try {
+          super.remove(0, getLength());
+      } catch (BadLocationException exception) {
+          System.out.println("Could not clear script window content: " + exception.getMessage());
+      }
+  }
+
+  void setPrompt() {
+    try {
+      super.insertString(getLength(), "$ ", attPrompt);
+      setOffsetPositions();
+      consoleTextPane.setCaretPosition(offsetAfterPrompt);
+    } catch (BadLocationException e) {
+      e.printStackTrace();
+    }
+  }
+
+  void setOffsetPositions() {
+    try {
+      offsetAfterPrompt = getLength();
+      positionBeforePrompt = createPosition(offsetAfterPrompt - 2);
+      // after prompt should be immediately after $ otherwise tracks the end
+      // of the line (and no command will be found) at least on Mac OS X it did.
+      positionAfterPrompt = createPosition(offsetAfterPrompt - 1);
+    } catch (BadLocationException e) {
+      e.printStackTrace();
+    }
+  }
+
+  void setNoPrompt() {
+    try {
+      offsetAfterPrompt = getLength();
+      positionAfterPrompt = positionBeforePrompt = createPosition(offsetAfterPrompt);
+      consoleTextPane.setCaretPosition(offsetAfterPrompt);
+    } catch (BadLocationException e) {
+      e.printStackTrace();
+    }
+  }
+
+  // it looks like the positionBeforePrompt does not track when it started out as 0
+  // and a insertString at location 0 occurs. It may be better to track the
+  // position after the prompt in stead
+  void outputBeforePrompt(String str, SimpleAttributeSet attribute) {
+    try {
+      int pt = consoleTextPane.getCaretPosition();
+      Position caretPosition = createPosition(pt);
+      pt = positionBeforePrompt.getOffset();
+      super.insertString(pt, str+"\n", attribute);
+      setOffsetPositions();
+      pt = caretPosition.getOffset();
+      consoleTextPane.setCaretPosition(pt);
+    } catch (BadLocationException e) {
+      e.printStackTrace();
+    }
+  }
+
+  void outputError(String strError) {
+    outputBeforePrompt(strError, attError);
+  }
+
+  void outputErrorForeground(String strError) {
+    try {
+      super.insertString(getLength(), strError+"\n", attError);
+      consoleTextPane.setCaretPosition(getLength());
+    } catch (BadLocationException e) {
+      e.printStackTrace();
+
+    }
+  }
+
+  void outputEcho(String strEcho) {
+    outputBeforePrompt(strEcho, attEcho);
+  }
+
+  void outputStatus(String strStatus) {
+    outputBeforePrompt(strStatus, attStatus);
+  }
+
+  void appendNewline() {
+    try {
+      super.insertString(getLength(), "\n", attUserInput);
+      consoleTextPane.setCaretPosition(getLength());
+    } catch (BadLocationException e) {
+      e.printStackTrace();
+    }
+  }
+
+  // override the insertString to make sure everything typed ends up at the end
+  // or in the 'command line' using the proper font, and the newline is processed.
+  public void insertString(int offs, String str, AttributeSet a)
+    throws BadLocationException {
+    int ichNewline = str.indexOf('\n');
+    if (ichNewline > 0)
+      str = str.substring(0, ichNewline);
+    if (ichNewline != 0) {
+      if (offs < offsetAfterPrompt) {
+        offs = getLength();
+      }
+      super.insertString(offs, str, a == attError ? a : attUserInput);
+      consoleTextPane.setCaretPosition(offs+str.length());
+    }
+    if (ichNewline >= 0) {
+      consoleTextPane.enterPressed();
+    }
+  }
+
+  String getCommandString() {
+    String strCommand = "";
+    try {
+      int cmdStart = positionAfterPrompt.getOffset();
+      strCommand =  getText(cmdStart, getLength() - cmdStart);
+      while (strCommand.length() > 0 && strCommand.charAt(0) == ' ')
+        strCommand = strCommand.substring(1);
+    } catch (BadLocationException e) {
+      e.printStackTrace();
+    }
+    return strCommand;
+  }
+
+  public void remove(int offs, int len)
+    throws BadLocationException {
+    if (offs < offsetAfterPrompt) {
+      len -= offsetAfterPrompt - offs;
+      if (len <= 0)
+        return;
+      offs = offsetAfterPrompt;
+    }
+    super.remove(offs, len);
+//    consoleTextPane.setCaretPosition(offs);
+  }
+
+  public void replace(int offs, int length, String str, AttributeSet attrs)
+    throws BadLocationException {
+    if (offs < offsetAfterPrompt) {
+      if (offs + length < offsetAfterPrompt) {
+        offs = getLength();
+        length = 0;
+      } else {
+        length -= offsetAfterPrompt - offs;
+        offs = offsetAfterPrompt;
+      }
+    }
+    super.replace(offs, length, str, attrs);
+//    consoleTextPane.setCaretPosition(offs + str.length());
+  }
+
+   /**
+   * Replaces current command on script.
+   *
+   * @param newCommand new command value
+   * @param isError    true to set error color  ends with #??
+   *
+   * @throws BadLocationException
+   */
+  void replaceCommand(String newCommand, boolean isError) throws BadLocationException {
+    if (positionAfterPrompt == positionBeforePrompt)
+      return;
+    replace(offsetAfterPrompt, getLength() - offsetAfterPrompt, newCommand,
+        isError ? attError : attUserInput);
+  }
+
+  void colorCommand(SimpleAttributeSet att) {
+    if (positionAfterPrompt == positionBeforePrompt)
+      return;
+    setCharacterAttributes(offsetAfterPrompt, getLength() - offsetAfterPrompt, att, true);
+  }
+}
+
+interface EnterListener {
+  public void enterPressed();
+}
+
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index cd7c231..67f1ce0 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 7d451da..2b919e0 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index f594554..37bfc00 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 70f67d7..25bcb6d 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,434 +1,434 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SequenceRenderer
-{
-  AlignViewport av;
-  FontMetrics fm;
-  boolean renderGaps = true;
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup[] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
-  boolean monospacedFont;
-  boolean forOverview = false;
-
-  /**
-   * Creates a new SequenceRenderer object.
-   *
-   * @param av DOCUMENT ME!
-   */
-  public SequenceRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void prepare(Graphics g, boolean renderGaps)
-  {
-    graphics = g;
-    fm = g.getFontMetrics();
-
-    // If EPS graphics, stringWidth will be a double, not an int
-    double dwidth = fm.getStringBounds("M", g).getWidth();
-
-    monospacedFont =
-        (dwidth == fm.getStringBounds("|", g).getWidth()
-         && (float) av.charWidth == dwidth);
-
-    this.renderGaps = renderGaps;
-  }
-
-  public Color getResidueBoxColour(SequenceI seq, int i)
-  {
-    allGroups = av.alignment.findAllGroups(seq);
-
-    if (inCurrentSequenceGroup(i))
-    {
-      if (currentSequenceGroup.getDisplayBoxes())
-      {
-        getBoxColour(currentSequenceGroup.cs, seq, i);
-      }
-    }
-    else if (av.getShowBoxes())
-    {
-      getBoxColour(av.globalColourScheme, seq, i);
-    }
-
-    return resBoxColour;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param cs DOCUMENT ME!
-   * @param seq DOCUMENT ME!
-   * @param i DOCUMENT ME!
-   */
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
-  {
-    if (cs != null)
-    {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
-    }
-    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
-    {
-      resBoxColour = Color.lightGray;
-    }
-    else
-    {
-      resBoxColour = Color.white;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param g DOCUMENT ME!
-   * @param seq DOCUMENT ME!
-   * @param sg DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
-   */
-  public void drawSequence(SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int y1)
-  {
-    allGroups = sg;
-
-    drawBoxes(seq, start, end, y1);
-
-    if (av.validCharWidth)
-    {
-      drawText(seq, start, end, y1);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
-   */
-  public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
-  {
-    int i = start;
-    int length = seq.getLength();
-
-    int curStart = -1;
-    int curWidth = av.charWidth;
-
-    Color tempColour = null;
-
-    while (i <= end)
-    {
-      resBoxColour = Color.white;
-
-      if (i < length)
-      {
-        if (inCurrentSequenceGroup(i))
-        {
-          if (currentSequenceGroup.getDisplayBoxes())
-          {
-            getBoxColour(currentSequenceGroup.cs, seq, i);
-          }
-        }
-        else if (av.getShowBoxes())
-        {
-          getBoxColour(av.globalColourScheme, seq, i);
-        }
-
-      }
-
-      if (resBoxColour != tempColour)
-      {
-        if (tempColour != null)
-        {
-          graphics.fillRect(av.charWidth * (curStart - start), y1,
-                            curWidth, av.charHeight);
-        }
-
-        graphics.setColor(resBoxColour);
-
-        curStart = i;
-        curWidth = av.charWidth;
-        tempColour = resBoxColour;
-      }
-      else
-      {
-        curWidth += av.charWidth;
-      }
-
-      i++;
-    }
-
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-                      av.charHeight);
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
-   */
-  public void drawText(SequenceI seq, int start, int end, int y1)
-  {
-    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
-    int charOffset = 0;
-    char s;
-
-    if (end + 1 >= seq.getLength())
-    {
-      end = seq.getLength() - 1;
-    }
-    graphics.setColor(av.textColour);
-
-    if (monospacedFont
-        && av.showText
-        && allGroups.length == 0
-        && !av.getColourText()
-        && av.thresholdTextColour == 0)
-    {
-      if (av.renderGaps)
-      {
-        graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
-      }
-      else
-      {
-        char gap = av.getGapCharacter();
-        graphics.drawString(seq.getSequenceAsString(start, end + 1).replace(gap,
-            ' '), 0, y1);
-      }
-    }
-    else
-    {
-      boolean getboxColour = false;
-      for (int i = start; i <= end; i++)
-      {
-        graphics.setColor(av.textColour);
-        getboxColour = false;
-        s = seq.getCharAt(i);
-        if (!renderGaps && jalview.util.Comparison.isGap(s))
-        {
-          continue;
-        }
-
-        if (inCurrentSequenceGroup(i))
-        {
-          if (!currentSequenceGroup.getDisplayText())
-          {
-            continue;
-          }
-
-          if (currentSequenceGroup.thresholdTextColour > 0
-              || currentSequenceGroup.getColourText())
-          {
-            getboxColour = true;
-            getBoxColour(currentSequenceGroup.cs, seq, i);
-
-            if (currentSequenceGroup.getColourText())
-            {
-              graphics.setColor(resBoxColour.darker());
-            }
-
-            if (currentSequenceGroup.thresholdTextColour > 0)
-            {
-              if (resBoxColour.getRed() +
-                  resBoxColour.getBlue() +
-                  resBoxColour.getGreen() <
-                  currentSequenceGroup.thresholdTextColour)
-              {
-                graphics.setColor(currentSequenceGroup.textColour2);
-              }
-            }
-          }
-          else
-          {
-            graphics.setColor(currentSequenceGroup.textColour);
-          }
-
-        }
-        else
-        {
-          if (!av.getShowText())
-          {
-            continue;
-          }
-
-          if (av.getColourText())
-          {
-            getboxColour = true;
-            getBoxColour(av.globalColourScheme, seq, i);
-
-            if (av.getShowBoxes())
-            {
-              graphics.setColor(resBoxColour.darker());
-            }
-            else
-            {
-              graphics.setColor(resBoxColour);
-            }
-          }
-
-          if (av.thresholdTextColour > 0)
-          {
-            if (!getboxColour)
-            {
-              getBoxColour(av.globalColourScheme, seq, i);
-            }
-
-            if (resBoxColour.getRed() +
-                resBoxColour.getBlue() +
-                resBoxColour.getGreen() < av.thresholdTextColour)
-            {
-              graphics.setColor(av.textColour2);
-            }
-          }
-
-        }
-
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s),
-                            charOffset + av.charWidth * (i - start),
-                            y1);
-
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param res DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  boolean inCurrentSequenceGroup(int res)
-  {
-    if (allGroups == null)
-    {
-      return false;
-    }
-
-    for (int i = 0; i < allGroups.length; i++)
-    {
-      if ( (allGroups[i].getStartRes() <= res) &&
-          (allGroups[i].getEndRes() >= res))
-      {
-        currentSequenceGroup = allGroups[i];
-
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   * @param x1 DOCUMENT ME!
-   * @param y1 DOCUMENT ME!
-   * @param width DOCUMENT ME!
-   * @param height DOCUMENT ME!
-   */
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
-                                  int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.BLACK);
-    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
-    graphics.setColor(Color.white);
-
-    char s = '~';
-
-    // Need to find the sequence position here.
-    if (av.validCharWidth)
-    {
-      for (int i = start; i <= end; i++)
-      {
-        if (i < seq.getLength())
-        {
-          s = seq.getCharAt(i);
-        }
-
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s),
-                            charOffset + x1 + (av.charWidth * (i - start)),
-                            (y1 + av.charHeight) - pady);
-      }
-    }
-  }
-
-  public void drawCursor(SequenceI seq, int res, int x1, int y1)
-  {
-    int pady = av.charHeight / 5;
-    int charOffset = 0;
-    graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
-
-    if (av.validCharWidth)
-    {
-      graphics.setColor(Color.white);
-
-      char s = seq.getCharAt(res);
-
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s),
-                          charOffset + x1,
-                          (y1 + av.charHeight) - pady);
-    }
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceRenderer
+{
+  AlignViewport av;
+  FontMetrics fm;
+  boolean renderGaps = true;
+  SequenceGroup currentSequenceGroup = null;
+  SequenceGroup[] allGroups = null;
+  Color resBoxColour;
+  Graphics graphics;
+  boolean monospacedFont;
+  boolean forOverview = false;
+
+  /**
+   * Creates a new SequenceRenderer object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public SequenceRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void prepare(Graphics g, boolean renderGaps)
+  {
+    graphics = g;
+    fm = g.getFontMetrics();
+
+    // If EPS graphics, stringWidth will be a double, not an int
+    double dwidth = fm.getStringBounds("M", g).getWidth();
+
+    monospacedFont =
+        (dwidth == fm.getStringBounds("|", g).getWidth()
+         && (float) av.charWidth == dwidth);
+
+    this.renderGaps = renderGaps;
+  }
+
+  public Color getResidueBoxColour(SequenceI seq, int i)
+  {
+    allGroups = av.alignment.findAllGroups(seq);
+
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+      getBoxColour(av.globalColourScheme, seq, i);
+    }
+
+    return resBoxColour;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param cs DOCUMENT ME!
+   * @param seq DOCUMENT ME!
+   * @param i DOCUMENT ME!
+   */
+  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  {
+    if (cs != null)
+    {
+      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+    }
+    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+      resBoxColour = Color.lightGray;
+    }
+    else
+    {
+      resBoxColour = Color.white;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param seq DOCUMENT ME!
+   * @param sg DOCUMENT ME!
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   * @param x1 DOCUMENT ME!
+   * @param y1 DOCUMENT ME!
+   * @param width DOCUMENT ME!
+   * @param height DOCUMENT ME!
+   */
+  public void drawSequence(SequenceI seq, SequenceGroup[] sg,
+                           int start, int end, int y1)
+  {
+    allGroups = sg;
+
+    drawBoxes(seq, start, end, y1);
+
+    if (av.validCharWidth)
+    {
+      drawText(seq, start, end, y1);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   * @param x1 DOCUMENT ME!
+   * @param y1 DOCUMENT ME!
+   * @param width DOCUMENT ME!
+   * @param height DOCUMENT ME!
+   */
+  public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
+  {
+    int i = start;
+    int length = seq.getLength();
+
+    int curStart = -1;
+    int curWidth = av.charWidth;
+
+    Color tempColour = null;
+
+    while (i <= end)
+    {
+      resBoxColour = Color.white;
+
+      if (i < length)
+      {
+        if (inCurrentSequenceGroup(i))
+        {
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+          }
+        }
+        else if (av.getShowBoxes())
+        {
+          getBoxColour(av.globalColourScheme, seq, i);
+        }
+
+      }
+
+      if (resBoxColour != tempColour)
+      {
+        if (tempColour != null)
+        {
+          graphics.fillRect(av.charWidth * (curStart - start), y1,
+                            curWidth, av.charHeight);
+        }
+
+        graphics.setColor(resBoxColour);
+
+        curStart = i;
+        curWidth = av.charWidth;
+        tempColour = resBoxColour;
+      }
+      else
+      {
+        curWidth += av.charWidth;
+      }
+
+      i++;
+    }
+
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                      av.charHeight);
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   * @param x1 DOCUMENT ME!
+   * @param y1 DOCUMENT ME!
+   * @param width DOCUMENT ME!
+   * @param height DOCUMENT ME!
+   */
+  public void drawText(SequenceI seq, int start, int end, int y1)
+  {
+    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+    int charOffset = 0;
+    char s;
+
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
+    graphics.setColor(av.textColour);
+
+    if (monospacedFont
+        && av.showText
+        && allGroups.length == 0
+        && !av.getColourText()
+        && av.thresholdTextColour == 0)
+    {
+      if (av.renderGaps)
+      {
+        graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
+      }
+      else
+      {
+        char gap = av.getGapCharacter();
+        graphics.drawString(seq.getSequenceAsString(start, end + 1).replace(gap,
+            ' '), 0, y1);
+      }
+    }
+    else
+    {
+      boolean getboxColour = false;
+      for (int i = start; i <= end; i++)
+      {
+        graphics.setColor(av.textColour);
+        getboxColour = false;
+        s = seq.getCharAt(i);
+        if (!renderGaps && jalview.util.Comparison.isGap(s))
+        {
+          continue;
+        }
+
+        if (inCurrentSequenceGroup(i))
+        {
+          if (!currentSequenceGroup.getDisplayText())
+          {
+            continue;
+          }
+
+          if (currentSequenceGroup.thresholdTextColour > 0
+              || currentSequenceGroup.getColourText())
+          {
+            getboxColour = true;
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+
+            if (currentSequenceGroup.getColourText())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
+
+            if (currentSequenceGroup.thresholdTextColour > 0)
+            {
+              if (resBoxColour.getRed() +
+                  resBoxColour.getBlue() +
+                  resBoxColour.getGreen() <
+                  currentSequenceGroup.thresholdTextColour)
+              {
+                graphics.setColor(currentSequenceGroup.textColour2);
+              }
+            }
+          }
+          else
+          {
+            graphics.setColor(currentSequenceGroup.textColour);
+          }
+
+        }
+        else
+        {
+          if (!av.getShowText())
+          {
+            continue;
+          }
+
+          if (av.getColourText())
+          {
+            getboxColour = true;
+            getBoxColour(av.globalColourScheme, seq, i);
+
+            if (av.getShowBoxes())
+            {
+              graphics.setColor(resBoxColour.darker());
+            }
+            else
+            {
+              graphics.setColor(resBoxColour);
+            }
+          }
+
+          if (av.thresholdTextColour > 0)
+          {
+            if (!getboxColour)
+            {
+              getBoxColour(av.globalColourScheme, seq, i);
+            }
+
+            if (resBoxColour.getRed() +
+                resBoxColour.getBlue() +
+                resBoxColour.getGreen() < av.thresholdTextColour)
+            {
+              graphics.setColor(av.textColour2);
+            }
+          }
+
+        }
+
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                            charOffset + av.charWidth * (i - start),
+                            y1);
+
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param res DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  boolean inCurrentSequenceGroup(int res)
+  {
+    if (allGroups == null)
+    {
+      return false;
+    }
+
+    for (int i = 0; i < allGroups.length; i++)
+    {
+      if ( (allGroups[i].getStartRes() <= res) &&
+          (allGroups[i].getEndRes() >= res))
+      {
+        currentSequenceGroup = allGroups[i];
+
+        return true;
+      }
+    }
+
+    return false;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   * @param x1 DOCUMENT ME!
+   * @param y1 DOCUMENT ME!
+   * @param width DOCUMENT ME!
+   * @param height DOCUMENT ME!
+   */
+  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+                                  int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.BLACK);
+    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
+    graphics.setColor(Color.white);
+
+    char s = '~';
+
+    // Need to find the sequence position here.
+    if (av.validCharWidth)
+    {
+      for (int i = start; i <= end; i++)
+      {
+        if (i < seq.getLength())
+        {
+          s = seq.getCharAt(i);
+        }
+
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                            charOffset + x1 + (av.charWidth * (i - start)),
+                            (y1 + av.charHeight) - pady);
+      }
+    }
+  }
+
+  public void drawCursor(SequenceI seq, int res, int x1, int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+    if (av.validCharWidth)
+    {
+      graphics.setColor(Color.white);
+
+      char s = seq.getCharAt(res);
+
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s),
+                          charOffset + x1,
+                          (y1 + av.charHeight) - pady);
+    }
+
+  }
+}
diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 23b76e3..315935b 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,359 +1,359 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SliderPanel
-    extends GSliderPanel
-{
-  static JInternalFrame conservationSlider;
-  static JInternalFrame PIDSlider;
-  AlignmentPanel ap;
-  boolean forConservation = true;
-  ColourSchemeI cs;
-
-  /**
-   * Creates a new SliderPanel object.
-   *
-   * @param ap DOCUMENT ME!
-   * @param value DOCUMENT ME!
-   * @param forConserve DOCUMENT ME!
-   * @param cs DOCUMENT ME!
-   */
-  public SliderPanel(final AlignmentPanel ap, int value, boolean forConserve,
-                     ColourSchemeI cs)
-  {
-    this.ap = ap;
-    this.cs = cs;
-    forConservation = forConserve;
-    undoButton.setVisible(false);
-    applyButton.setVisible(false);
-
-    if (forConservation)
-    {
-      label.setText("Enter value to increase conservation visibility");
-      slider.setMinimum(0);
-      slider.setMaximum(100);
-    }
-    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.addMouseListener(new MouseAdapter()
-    {
-      public void mouseReleased(MouseEvent evt)
-      {
-         ap.paintAlignment(true);
-      }
-    });
-
-    slider.setValue(value);
-    valueField.setText(value + "");
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ap DOCUMENT ME!
-   * @param cs DOCUMENT ME!
-   * @param source DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public static int setConservationSlider(AlignmentPanel ap,
-                                          ColourSchemeI cs, String source)
-  {
-    SliderPanel sp = null;
-
-    if (conservationSlider == null)
-    {
-      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
-      conservationSlider = new JInternalFrame();
-      conservationSlider.setContentPane(sp);
-      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-    else
-    {
-      sp = (SliderPanel) conservationSlider.getContentPane();
-      sp.cs = cs;
-    }
-
-    conservationSlider.setTitle("Conservation Colour Increment  (" +
-                                source + ")");
-
-    if (ap.av.alignment.getGroups() != null)
-    {
-      sp.setAllGroupsCheckEnabled(true);
-    }
-    else
-    {
-      sp.setAllGroupsCheckEnabled(false);
-    }
-
-    return sp.getValue();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public static void showConservationSlider()
-  {
-    try
-    {
-      PIDSlider.setClosed(true);
-      PIDSlider = null;
-    }
-    catch (Exception ex)
-    {
-    }
-
-    if (!conservationSlider.isVisible())
-    {
-      Desktop.addInternalFrame(conservationSlider,
-                               conservationSlider.getTitle(), 420, 90, false);
-      conservationSlider.addInternalFrameListener(new javax.swing.event.
-                                                  InternalFrameAdapter()
-      {
-        public void internalFrameClosed(
-            javax.swing.event.InternalFrameEvent e)
-        {
-          conservationSlider = null;
-        }
-      });
-      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ap DOCUMENT ME!
-   * @param cs DOCUMENT ME!
-   * @param source DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
-                                       String source)
-  {
-    SliderPanel pid = null;
-
-    int threshold = 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();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  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);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   */
-  public void valueChanged(int i)
-  {
-    if (cs == null)
-    {
-      return;
-    }
-
-    ColourSchemeI toChange = null;
-    Vector allGroups = null;
-    int groupIndex = 0;
-
-    if (allGroupsCheck.isSelected())
-    {
-      allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size() - 1;
-    }
-    else
-    {
-      toChange = cs;
-    }
-
-    while (groupIndex > -1)
-    {
-      if (allGroups != null)
-      {
-        toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;
-
-        if (toChange == null)
-        {
-          groupIndex--;
-
-          continue;
-        }
-      }
-
-      if (forConservation)
-      {
-        if (toChange.conservationApplied())
-        {
-          toChange.setConservationInc(i);
-        }
-      }
-      else
-      {
-        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
-      }
-
-      groupIndex--;
-    }
-
-    ap.seqPanel.seqCanvas.repaint();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void setAllGroupsCheckEnabled(boolean b)
-  {
-    allGroupsCheck.setEnabled(b);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    }
-    catch (NumberFormatException ex)
-    {
-      valueField.setText(slider.getValue() + "");
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param value DOCUMENT ME!
-   */
-  public void setValue(int value)
-  {
-    slider.setValue(value);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getValue()
-  {
-    return Integer.parseInt(valueField.getText());
-  }
-
-  public void slider_mouseReleased(MouseEvent e)
-  {
-    if (ap.overviewPanel != null)
-    {
-      ap.overviewPanel.updateOverviewImage();
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SliderPanel
+    extends GSliderPanel
+{
+  static JInternalFrame conservationSlider;
+  static JInternalFrame PIDSlider;
+  AlignmentPanel ap;
+  boolean forConservation = true;
+  ColourSchemeI cs;
+
+  /**
+   * Creates a new SliderPanel object.
+   *
+   * @param ap DOCUMENT ME!
+   * @param value DOCUMENT ME!
+   * @param forConserve DOCUMENT ME!
+   * @param cs DOCUMENT ME!
+   */
+  public SliderPanel(final AlignmentPanel ap, int value, boolean forConserve,
+                     ColourSchemeI cs)
+  {
+    this.ap = ap;
+    this.cs = cs;
+    forConservation = forConserve;
+    undoButton.setVisible(false);
+    applyButton.setVisible(false);
+
+    if (forConservation)
+    {
+      label.setText("Enter value to increase conservation visibility");
+      slider.setMinimum(0);
+      slider.setMaximum(100);
+    }
+    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.addMouseListener(new MouseAdapter()
+    {
+      public void mouseReleased(MouseEvent evt)
+      {
+         ap.paintAlignment(true);
+      }
+    });
+
+    slider.setValue(value);
+    valueField.setText(value + "");
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ap DOCUMENT ME!
+   * @param cs DOCUMENT ME!
+   * @param source DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static int setConservationSlider(AlignmentPanel ap,
+                                          ColourSchemeI cs, String source)
+  {
+    SliderPanel sp = null;
+
+    if (conservationSlider == null)
+    {
+      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+      conservationSlider = new JInternalFrame();
+      conservationSlider.setContentPane(sp);
+      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+    else
+    {
+      sp = (SliderPanel) conservationSlider.getContentPane();
+      sp.cs = cs;
+    }
+
+    conservationSlider.setTitle("Conservation Colour Increment  (" +
+                                source + ")");
+
+    if (ap.av.alignment.getGroups() != null)
+    {
+      sp.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      sp.setAllGroupsCheckEnabled(false);
+    }
+
+    return sp.getValue();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public static void showConservationSlider()
+  {
+    try
+    {
+      PIDSlider.setClosed(true);
+      PIDSlider = null;
+    }
+    catch (Exception ex)
+    {
+    }
+
+    if (!conservationSlider.isVisible())
+    {
+      Desktop.addInternalFrame(conservationSlider,
+                               conservationSlider.getTitle(), 420, 90, false);
+      conservationSlider.addInternalFrameListener(new javax.swing.event.
+                                                  InternalFrameAdapter()
+      {
+        public void internalFrameClosed(
+            javax.swing.event.InternalFrameEvent e)
+        {
+          conservationSlider = null;
+        }
+      });
+      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ap DOCUMENT ME!
+   * @param cs DOCUMENT ME!
+   * @param source DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
+                                       String source)
+  {
+    SliderPanel pid = null;
+
+    int threshold = 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();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  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);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   */
+  public void valueChanged(int i)
+  {
+    if (cs == null)
+    {
+      return;
+    }
+
+    ColourSchemeI toChange = null;
+    Vector allGroups = null;
+    int groupIndex = 0;
+
+    if (allGroupsCheck.isSelected())
+    {
+      allGroups = ap.av.alignment.getGroups();
+      groupIndex = allGroups.size() - 1;
+    }
+    else
+    {
+      toChange = cs;
+    }
+
+    while (groupIndex > -1)
+    {
+      if (allGroups != null)
+      {
+        toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;
+
+        if (toChange == null)
+        {
+          groupIndex--;
+
+          continue;
+        }
+      }
+
+      if (forConservation)
+      {
+        if (toChange.conservationApplied())
+        {
+          toChange.setConservationInc(i);
+        }
+      }
+      else
+      {
+        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+      }
+
+      groupIndex--;
+    }
+
+    ap.seqPanel.seqCanvas.repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setAllGroupsCheckEnabled(boolean b)
+  {
+    allGroupsCheck.setEnabled(b);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void valueField_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      int i = Integer.parseInt(valueField.getText());
+      slider.setValue(i);
+    }
+    catch (NumberFormatException ex)
+    {
+      valueField.setText(slider.getValue() + "");
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param value DOCUMENT ME!
+   */
+  public void setValue(int value)
+  {
+    slider.setValue(value);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getValue()
+  {
+    return Integer.parseInt(valueField.getText());
+  }
+
+  public void slider_mouseReleased(MouseEvent e)
+  {
+    if (ap.overviewPanel != null)
+    {
+      ap.overviewPanel.updateOverviewImage();
+    }
+  }
+
+}
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index b72cc61..031e930 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index 8dd9d49..2f887cb 100644
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -1,213 +1,212 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-
-public class TextColourChooser
-{
-  AlignmentPanel ap;
-  SequenceGroup sg;
-
-  public void chooseColour(AlignmentPanel ap, SequenceGroup sg)
-  {
-    this.ap = ap;
-    this.sg = sg;
-
-    int original1, original2, originalThreshold;
-    if (sg == null)
-    {
-      original1 = ap.av.textColour.getRGB();
-      original2 = ap.av.textColour2.getRGB();
-      originalThreshold = ap.av.thresholdTextColour;
-    }
-    else
-    {
-      original1 = sg.textColour.getRGB();
-      original2 = sg.textColour2.getRGB();
-      originalThreshold = sg.thresholdTextColour;
-    }
-
-    final JSlider slider = new JSlider(0, 750, originalThreshold);
-    final JPanel col1 = new JPanel();
-    col1.setPreferredSize(new Dimension(40, 20));
-    col1.setBorder(BorderFactory.createEtchedBorder());
-    col1.setToolTipText("Dark Colour");
-    col1.setBackground(new Color(original1));
-    final JPanel col2 = new JPanel();
-    col2.setPreferredSize(new Dimension(40, 20));
-    col2.setBorder(BorderFactory.createEtchedBorder());
-    col2.setToolTipText("Light Colour");
-    col2.setBackground(new Color(original2));
-    final JPanel bigpanel = new JPanel(new BorderLayout());
-    JPanel panel = new JPanel();
-    bigpanel.add(panel, BorderLayout.CENTER);
-    bigpanel.add(new JLabel(
-        "<html><i>Select a dark and light text colour, then set the threshold to"
-        + "<br>switch between colours, based on background colour</i></html>"),
-                 BorderLayout.NORTH);
-    panel.add(col1);
-    panel.add(slider);
-    panel.add(col2);
-
-    col1.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        Color col = JColorChooser.showDialog(bigpanel,
-                                             "Select Colour for Text",
-                                             col1.getBackground());
-        if (col != null)
-        {
-          colour1Changed(col);
-          col1.setBackground(col);
-        }
-      }
-    });
-
-    col2.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        Color col = JColorChooser.showDialog(bigpanel,
-                                             "Select Colour for Text",
-                                             col2.getBackground());
-        if (col != null)
-        {
-          colour2Changed(col);
-          col2.setBackground(col);
-        }
-      }
-    });
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        thresholdChanged(slider.getValue());
-      }
-    });
-
-    int reply = JOptionPane.showInternalOptionDialog(
-        ap,
-        bigpanel,
-        "Adjust Foreground Text Colour Threshold",
-        JOptionPane.OK_CANCEL_OPTION,
-        JOptionPane.QUESTION_MESSAGE,
-        null,
-        null, null);
-
-    if (reply == JOptionPane.CANCEL_OPTION)
-    {
-      if (sg == null)
-      {
-        ap.av.textColour = new Color(original1);
-        ap.av.textColour2 = new Color(original2);
-        ap.av.thresholdTextColour = originalThreshold;
-      }
-      else
-      {
-        sg.textColour = new Color(original1);
-        sg.textColour2 = new Color(original2);
-        sg.thresholdTextColour = originalThreshold;
-      }
-    }
-  }
-
-  void colour1Changed(Color col)
-  {
-    if (sg == null)
-    {
-      ap.av.textColour = col;
-      if (ap.av.colourAppliesToAllGroups)
-      {
-        setGroupTextColour();
-      }
-    }
-    else
-    {
-      sg.textColour = col;
-    }
-
-    ap.paintAlignment(true);
-  }
-
-  void colour2Changed(Color col)
-  {
-    if (sg == null)
-    {
-      ap.av.textColour2 = col;
-      if (ap.av.colourAppliesToAllGroups)
-      {
-        setGroupTextColour();
-      }
-    }
-    else
-    {
-      sg.textColour2 = col;
-    }
-
-    ap.paintAlignment(true);
-  }
-
-  void thresholdChanged(int value)
-  {
-    if (sg == null)
-    {
-      ap.av.thresholdTextColour = value;
-      if (ap.av.colourAppliesToAllGroups)
-      {
-        setGroupTextColour();
-      }
-    }
-    else
-    {
-      sg.thresholdTextColour = value;
-    }
-
-    ap.paintAlignment(true);
-  }
-
-  void setGroupTextColour()
-  {
-    if (ap.av.alignment.getGroups() == null)
-    {
-      return;
-    }
-
-    Vector groups = ap.av.alignment.getGroups();
-
-    for (int i = 0; i < groups.size(); i++)
-    {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-      sg.textColour = ap.av.textColour;
-      sg.textColour2 = ap.av.textColour2;
-      sg.thresholdTextColour = ap.av.thresholdTextColour;
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.datamodel.*;
+
+public class TextColourChooser
+{
+  AlignmentPanel ap;
+  SequenceGroup sg;
+
+  public void chooseColour(AlignmentPanel ap, SequenceGroup sg)
+  {
+    this.ap = ap;
+    this.sg = sg;
+
+    int original1, original2, originalThreshold;
+    if (sg == null)
+    {
+      original1 = ap.av.textColour.getRGB();
+      original2 = ap.av.textColour2.getRGB();
+      originalThreshold = ap.av.thresholdTextColour;
+    }
+    else
+    {
+      original1 = sg.textColour.getRGB();
+      original2 = sg.textColour2.getRGB();
+      originalThreshold = sg.thresholdTextColour;
+    }
+
+    final JSlider slider = new JSlider(0, 750, originalThreshold);
+    final JPanel col1 = new JPanel();
+    col1.setPreferredSize(new Dimension(40, 20));
+    col1.setBorder(BorderFactory.createEtchedBorder());
+    col1.setToolTipText("Dark Colour");
+    col1.setBackground(new Color(original1));
+    final JPanel col2 = new JPanel();
+    col2.setPreferredSize(new Dimension(40, 20));
+    col2.setBorder(BorderFactory.createEtchedBorder());
+    col2.setToolTipText("Light Colour");
+    col2.setBackground(new Color(original2));
+    final JPanel bigpanel = new JPanel(new BorderLayout());
+    JPanel panel = new JPanel();
+    bigpanel.add(panel, BorderLayout.CENTER);
+    bigpanel.add(new JLabel(
+        "<html><i>Select a dark and light text colour, then set the threshold to"
+        + "<br>switch between colours, based on background colour</i></html>"),
+                 BorderLayout.NORTH);
+    panel.add(col1);
+    panel.add(slider);
+    panel.add(col2);
+
+    col1.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        Color col = JColorChooser.showDialog(bigpanel,
+                                             "Select Colour for Text",
+                                             col1.getBackground());
+        if (col != null)
+        {
+          colour1Changed(col);
+          col1.setBackground(col);
+        }
+      }
+    });
+
+    col2.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        Color col = JColorChooser.showDialog(bigpanel,
+                                             "Select Colour for Text",
+                                             col2.getBackground());
+        if (col != null)
+        {
+          colour2Changed(col);
+          col2.setBackground(col);
+        }
+      }
+    });
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        thresholdChanged(slider.getValue());
+      }
+    });
+
+    int reply = JOptionPane.showInternalOptionDialog(
+        ap,
+        bigpanel,
+        "Adjust Foreground Text Colour Threshold",
+        JOptionPane.OK_CANCEL_OPTION,
+        JOptionPane.QUESTION_MESSAGE,
+        null,
+        null, null);
+
+    if (reply == JOptionPane.CANCEL_OPTION)
+    {
+      if (sg == null)
+      {
+        ap.av.textColour = new Color(original1);
+        ap.av.textColour2 = new Color(original2);
+        ap.av.thresholdTextColour = originalThreshold;
+      }
+      else
+      {
+        sg.textColour = new Color(original1);
+        sg.textColour2 = new Color(original2);
+        sg.thresholdTextColour = originalThreshold;
+      }
+    }
+  }
+
+  void colour1Changed(Color col)
+  {
+    if (sg == null)
+    {
+      ap.av.textColour = col;
+      if (ap.av.colourAppliesToAllGroups)
+      {
+        setGroupTextColour();
+      }
+    }
+    else
+    {
+      sg.textColour = col;
+    }
+
+    ap.paintAlignment(true);
+  }
+
+  void colour2Changed(Color col)
+  {
+    if (sg == null)
+    {
+      ap.av.textColour2 = col;
+      if (ap.av.colourAppliesToAllGroups)
+      {
+        setGroupTextColour();
+      }
+    }
+    else
+    {
+      sg.textColour2 = col;
+    }
+
+    ap.paintAlignment(true);
+  }
+
+  void thresholdChanged(int value)
+  {
+    if (sg == null)
+    {
+      ap.av.thresholdTextColour = value;
+      if (ap.av.colourAppliesToAllGroups)
+      {
+        setGroupTextColour();
+      }
+    }
+    else
+    {
+      sg.thresholdTextColour = value;
+    }
+
+    ap.paintAlignment(true);
+  }
+
+  void setGroupTextColour()
+  {
+    if (ap.av.alignment.getGroups() == null)
+    {
+      return;
+    }
+
+    Vector groups = ap.av.alignment.getGroups();
+
+    for (int i = 0; i < groups.size(); i++)
+    {
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+      sg.textColour = ap.av.textColour;
+      sg.textColour2 = ap.av.textColour2;
+      sg.thresholdTextColour = ap.av.thresholdTextColour;
+    }
+  }
+
+}
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 3407c07..a022408 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index f85ad9c..1ebb24d 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 85f35cd..7a866ea 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/gui/UserQuestionnaireCheck.java b/src/jalview/gui/UserQuestionnaireCheck.java
index 0accc9c..9dc101a 100644
--- a/src/jalview/gui/UserQuestionnaireCheck.java
+++ b/src/jalview/gui/UserQuestionnaireCheck.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.*;
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 121a200..6967bac 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,5 +1,20 @@
-/**
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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;
 
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 5f02c09..a0eeedf 100755
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index e7e6d97..6aa5c01 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -1,100 +1,100 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import jalview.datamodel.*;
-
-public class AMSAFile
-    extends jalview.io.FastaFile
-{
-
-  AlignmentI al;
-  /**
-   * Creates a new AMSAFile object for output.
-   */
-  public AMSAFile(AlignmentI al)
-  {
-    this.al = al;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String print()
-  {
-    super.print(getSeqsAsArray());
-
-    AlignmentAnnotation aa;
-    if (al.getAlignmentAnnotation() != null)
-    {
-
-      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
-      {
-        aa = al.getAlignmentAnnotation()[i];
-
-
-        if (aa.autoCalculated || !aa.visible)
-        {
-          continue;
-        }
-
-        out.append(">#_" + aa.label);
-        if (aa.description != null)
-        {
-          out.append(" " + aa.description);
-        }
-
-        out.append("\n");
-
-        int nochunks = Math.min(aa.annotations.length, al.getWidth())
-                        / len + 1;
-
-        for (int j = 0; j < nochunks; j++)
-        {
-          int start = j * len;
-          int end = start + len;
-          if (end > aa.annotations.length)
-          {
-            end = aa.annotations.length;
-          }
-
-          String ch;
-          for (int k = start; k < end; k++)
-          {
-            if (aa.annotations[k] == null)
-            {
-              ch = " ";
-            }
-            else
-            {
-              ch = aa.annotations[k].displayCharacter;
-            }
-
-            out.append(ch);
-
-          }
-          out.append("\n");
-        }
-      }
-    }
-    return out.toString();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import jalview.datamodel.*;
+
+public class AMSAFile
+    extends jalview.io.FastaFile
+{
+
+  AlignmentI al;
+  /**
+   * Creates a new AMSAFile object for output.
+   */
+  public AMSAFile(AlignmentI al)
+  {
+    this.al = al;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
+    super.print(getSeqsAsArray());
+
+    AlignmentAnnotation aa;
+    if (al.getAlignmentAnnotation() != null)
+    {
+
+      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+      {
+        aa = al.getAlignmentAnnotation()[i];
+
+
+        if (aa.autoCalculated || !aa.visible)
+        {
+          continue;
+        }
+
+        out.append(">#_" + aa.label);
+        if (aa.description != null)
+        {
+          out.append(" " + aa.description);
+        }
+
+        out.append("\n");
+
+        int nochunks = Math.min(aa.annotations.length, al.getWidth())
+                        / len + 1;
+
+        for (int j = 0; j < nochunks; j++)
+        {
+          int start = j * len;
+          int end = start + len;
+          if (end > aa.annotations.length)
+          {
+            end = aa.annotations.length;
+          }
+
+          String ch;
+          for (int k = start; k < end; k++)
+          {
+            if (aa.annotations[k] == null)
+            {
+              ch = " ";
+            }
+            else
+            {
+              ch = aa.annotations[k].displayCharacter;
+            }
+
+            out.append(ch);
+
+          }
+          out.append("\n");
+        }
+      }
+    }
+    return out.toString();
+  }
+}
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 2ad32f0..c38fad3 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 288ce2f..ddf4348 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.io;
 
 import java.io.*;
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index c7b0575..370a45d 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index fa6f8e2..1d25d46 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/ClansFile.java b/src/jalview/io/ClansFile.java
index ee709e5..6347268 100644
--- a/src/jalview/io/ClansFile.java
+++ b/src/jalview/io/ClansFile.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io;
 
 /**
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index d62d185..387d576 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/DBRefFile.java b/src/jalview/io/DBRefFile.java
index f43a2a6..87e62b5 100644
--- a/src/jalview/io/DBRefFile.java
+++ b/src/jalview/io/DBRefFile.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io;
 
 import java.io.IOException;
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 1cb016c..b40460b 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 3e0314a..d7e2ef5 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 584840e..f185205 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.io;
 
 import java.util.*;
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 04a673c..cb3b122 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 983d02e..f22795e 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 8406f3d..e53f14c 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,389 +1,389 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.io.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
-
-public class HTMLOutput
-{
-  AlignViewport av;
-  SequenceRenderer sr;
-  FeatureRenderer fr;
-  Color color;
-
-  public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1)
-  {
-    this.av = ap.av;
-    this.sr = sr;
-
-    fr = new FeatureRenderer(ap);
-    fr.transferSettings(fr1);
-
-    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();
-      }
-    }
-  }
-
-  void drawUnwrappedAlignment(PrintWriter out)
-  {
-    out.println("<table border=\"1\"><tr><td>\n");
-    out.println(
-        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
-
-    //////////////
-    SequenceI seq;
-    AlignmentI alignment = av.getAlignment();
-
-    // 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);
-
-      String id = seq.getDisplayId(av.getShowJVSuffix());
-
-      out.println("<tr><td nowrap>" + id +
-                  "&nbsp;&nbsp;</td>");
-
-      for (int res = 0; res < seq.getLength(); res++)
-      {
-        if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
-        {
-          color = sr.getResidueBoxColour(seq, res);
-
-          color = fr.findFeatureColour(color, seq, res);
-        }
-        else
-        {
-          color = Color.white;
-        }
-
-        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();
-    SequenceI seq;
-    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.getWrappedWidth())
-    {
-      int endRes = startRes + av.getWrappedWidth();
-
-      if (endRes > al.getWidth())
-      {
-        endRes = al.getWidth();
-      }
-
-      if (av.getScaleAboveWrapped())
-      {
-        out.println("<tr>");
-
-        if (av.getScaleLeftWrapped())
-        {
-          out.println("<td colspan=\"7\">&nbsp;</td>");
-        }
-        else
-        {
-          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("</tr>");
-      }
-
-      int startPos, endPos;
-      for (int s = 0; s < al.getHeight(); s++)
-      {
-        out.println("<tr>");
-        seq = al.getSequenceAt(s);
-
-        startPos = seq.findPosition(startRes);
-        endPos = seq.findPosition(endRes) - 1;
-
-        String id = seq.getDisplayId(av.getShowJVSuffix());
-
-        out.println("<td nowrap>" + id +
-                    "&nbsp;&nbsp;</td>");
-
-        if (av.getScaleLeftWrapped())
-        {
-          if (startPos > seq.getEnd() || endPos == 0)
-          {
-            out.println("<td nowrap>&nbsp;</td>");
-          }
-          else
-          {
-            out.println("<td nowrap>" + startPos +
-                        "&nbsp;&nbsp;</td>");
-          }
-        }
-
-        for (int res = startRes; res < endRes; res++)
-        {
-          if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
-          {
-            color = sr.getResidueBoxColour(seq, res);
-
-            color = fr.findFeatureColour(color, seq, res);
-          }
-          else
-          {
-            color = Color.white;
-          }
-
-          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>");
-          }
-
-        }
-
-        if (av.getScaleRightWrapped() &&
-            endRes < startRes + av.getWrappedWidth())
-        {
-          out.println("<td colspan=\"" +
-                      (startRes + av.getWrappedWidth() - endRes) + "\">"
-                      + "&nbsp;&nbsp;</td>");
-        }
-
-        if (av.getScaleRightWrapped() && startPos < endPos)
-        {
-          out.println("<td nowrap>&nbsp;" + endPos +
-                      "&nbsp;&nbsp;</td>");
-        }
-
-        out.println("</tr>");
-      }
-
-      if (endRes < al.getWidth())
-      {
-        out.println("<tr><td height=\"5\"></td></tr>");
-      }
-    }
-
-    out.println("</table>");
-    out.println("</table>");
-  }
-
-  public static String getImageMapHTML()
-  {
-    return new String(
-        "<html>\n"
-        + "<head>\n"
-        + "<script language=\"JavaScript\">\n"
-        + "var ns4 = document.layers;\n"
-        + "var ns6 = document.getElementById && !document.all;\n"
-        + "var ie4 = document.all;\n"
-        + "offsetX = 0;\n"
-        + "offsetY = 20;\n"
-        + "var toolTipSTYLE=\"\";\n"
-        + "function initToolTips()\n"
-        + "{\n"
-        + "  if(ns4||ns6||ie4)\n"
-        + "  {\n"
-        + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
-        + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
-        + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
-        + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
-        + "    else\n"
-        + "    {\n"
-        + "      toolTipSTYLE.visibility = \"visible\";\n"
-        + "      toolTipSTYLE.display = \"none\";\n"
-        + "    }\n"
-        + "    document.onmousemove = moveToMouseLoc;\n"
-        + "  }\n"
-        + "}\n"
-        + "function toolTip(msg, fg, bg)\n"
-        + "{\n"
-        + "  if(toolTip.arguments.length < 1) // hide\n"
-        + "  {\n"
-        + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
-        + "    else toolTipSTYLE.display = \"none\";\n"
-        + "  }\n"
-        + "  else // show\n"
-        + "  {\n"
-        + "    if(!fg) fg = \"#555555\";\n"
-        + "    if(!bg) bg = \"#FFFFFF\";\n"
-        + "    var content =\n"
-        + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
-        + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
-        +
-        "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
-        + "    '\" size=\"-2\">&nbsp;' + msg +\n"
-        + "    '&nbsp;</font></td></table></td></table>';\n"
-        + "    if(ns4)\n"
-        + "    {\n"
-        + "      toolTipSTYLE.document.write(content);\n"
-        + "      toolTipSTYLE.document.close();\n"
-        + "      toolTipSTYLE.visibility = \"visible\";\n"
-        + "    }\n"
-        + "    if(ns6)\n"
-        + "    {\n"
-        +
-        "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
-        + "      toolTipSTYLE.display='block'\n"
-        + "    }\n"
-        + "    if(ie4)\n"
-        + "    {\n"
-        + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
-        + "      toolTipSTYLE.display='block'\n"
-        + "    }\n"
-        + "  }\n"
-        + "}\n"
-        + "function moveToMouseLoc(e)\n"
-        + "{\n"
-        + "  if(ns4||ns6)\n"
-        + "  {\n"
-        + "    x = e.pageX;\n"
-        + "    y = e.pageY;\n"
-        + "  }\n"
-        + "  else\n"
-        + "  {\n"
-        + "    x = event.x + document.body.scrollLeft;\n"
-        + "    y = event.y + document.body.scrollTop;\n"
-        + "  }\n"
-        + "  toolTipSTYLE.left = x + offsetX;\n"
-        + "  toolTipSTYLE.top = y + offsetY;\n"
-        + "  return true;\n"
-        + "}\n"
-        + "</script>\n"
-        + "</head>\n"
-        + "<body>\n"
-        + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
-        + "<script language=\"JavaScript\"><!--\n"
-        + "initToolTips(); //--></script>\n");
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+public class HTMLOutput
+{
+  AlignViewport av;
+  SequenceRenderer sr;
+  FeatureRenderer fr;
+  Color color;
+
+  public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr, FeatureRenderer fr1)
+  {
+    this.av = ap.av;
+    this.sr = sr;
+
+    fr = new FeatureRenderer(ap);
+    fr.transferSettings(fr1);
+
+    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();
+      }
+    }
+  }
+
+  void drawUnwrappedAlignment(PrintWriter out)
+  {
+    out.println("<table border=\"1\"><tr><td>\n");
+    out.println(
+        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");
+
+    //////////////
+    SequenceI seq;
+    AlignmentI alignment = av.getAlignment();
+
+    // 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);
+
+      String id = seq.getDisplayId(av.getShowJVSuffix());
+
+      out.println("<tr><td nowrap>" + id +
+                  "&nbsp;&nbsp;</td>");
+
+      for (int res = 0; res < seq.getLength(); res++)
+      {
+        if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+        {
+          color = sr.getResidueBoxColour(seq, res);
+
+          color = fr.findFeatureColour(color, seq, res);
+        }
+        else
+        {
+          color = Color.white;
+        }
+
+        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();
+    SequenceI seq;
+    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.getWrappedWidth())
+    {
+      int endRes = startRes + av.getWrappedWidth();
+
+      if (endRes > al.getWidth())
+      {
+        endRes = al.getWidth();
+      }
+
+      if (av.getScaleAboveWrapped())
+      {
+        out.println("<tr>");
+
+        if (av.getScaleLeftWrapped())
+        {
+          out.println("<td colspan=\"7\">&nbsp;</td>");
+        }
+        else
+        {
+          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("</tr>");
+      }
+
+      int startPos, endPos;
+      for (int s = 0; s < al.getHeight(); s++)
+      {
+        out.println("<tr>");
+        seq = al.getSequenceAt(s);
+
+        startPos = seq.findPosition(startRes);
+        endPos = seq.findPosition(endRes) - 1;
+
+        String id = seq.getDisplayId(av.getShowJVSuffix());
+
+        out.println("<td nowrap>" + id +
+                    "&nbsp;&nbsp;</td>");
+
+        if (av.getScaleLeftWrapped())
+        {
+          if (startPos > seq.getEnd() || endPos == 0)
+          {
+            out.println("<td nowrap>&nbsp;</td>");
+          }
+          else
+          {
+            out.println("<td nowrap>" + startPos +
+                        "&nbsp;&nbsp;</td>");
+          }
+        }
+
+        for (int res = startRes; res < endRes; res++)
+        {
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+          {
+            color = sr.getResidueBoxColour(seq, res);
+
+            color = fr.findFeatureColour(color, seq, res);
+          }
+          else
+          {
+            color = Color.white;
+          }
+
+          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>");
+          }
+
+        }
+
+        if (av.getScaleRightWrapped() &&
+            endRes < startRes + av.getWrappedWidth())
+        {
+          out.println("<td colspan=\"" +
+                      (startRes + av.getWrappedWidth() - endRes) + "\">"
+                      + "&nbsp;&nbsp;</td>");
+        }
+
+        if (av.getScaleRightWrapped() && startPos < endPos)
+        {
+          out.println("<td nowrap>&nbsp;" + endPos +
+                      "&nbsp;&nbsp;</td>");
+        }
+
+        out.println("</tr>");
+      }
+
+      if (endRes < al.getWidth())
+      {
+        out.println("<tr><td height=\"5\"></td></tr>");
+      }
+    }
+
+    out.println("</table>");
+    out.println("</table>");
+  }
+
+  public static String getImageMapHTML()
+  {
+    return new String(
+        "<html>\n"
+        + "<head>\n"
+        + "<script language=\"JavaScript\">\n"
+        + "var ns4 = document.layers;\n"
+        + "var ns6 = document.getElementById && !document.all;\n"
+        + "var ie4 = document.all;\n"
+        + "offsetX = 0;\n"
+        + "offsetY = 20;\n"
+        + "var toolTipSTYLE=\"\";\n"
+        + "function initToolTips()\n"
+        + "{\n"
+        + "  if(ns4||ns6||ie4)\n"
+        + "  {\n"
+        + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
+        + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
+        + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
+        + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
+        + "    else\n"
+        + "    {\n"
+        + "      toolTipSTYLE.visibility = \"visible\";\n"
+        + "      toolTipSTYLE.display = \"none\";\n"
+        + "    }\n"
+        + "    document.onmousemove = moveToMouseLoc;\n"
+        + "  }\n"
+        + "}\n"
+        + "function toolTip(msg, fg, bg)\n"
+        + "{\n"
+        + "  if(toolTip.arguments.length < 1) // hide\n"
+        + "  {\n"
+        + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
+        + "    else toolTipSTYLE.display = \"none\";\n"
+        + "  }\n"
+        + "  else // show\n"
+        + "  {\n"
+        + "    if(!fg) fg = \"#555555\";\n"
+        + "    if(!bg) bg = \"#FFFFFF\";\n"
+        + "    var content =\n"
+        + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
+        + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
+        +
+        "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
+        + "    '\" size=\"-2\">&nbsp;' + msg +\n"
+        + "    '&nbsp;</font></td></table></td></table>';\n"
+        + "    if(ns4)\n"
+        + "    {\n"
+        + "      toolTipSTYLE.document.write(content);\n"
+        + "      toolTipSTYLE.document.close();\n"
+        + "      toolTipSTYLE.visibility = \"visible\";\n"
+        + "    }\n"
+        + "    if(ns6)\n"
+        + "    {\n"
+        +
+        "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
+        + "      toolTipSTYLE.display='block'\n"
+        + "    }\n"
+        + "    if(ie4)\n"
+        + "    {\n"
+        + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
+        + "      toolTipSTYLE.display='block'\n"
+        + "    }\n"
+        + "  }\n"
+        + "}\n"
+        + "function moveToMouseLoc(e)\n"
+        + "{\n"
+        + "  if(ns4||ns6)\n"
+        + "  {\n"
+        + "    x = e.pageX;\n"
+        + "    y = e.pageY;\n"
+        + "  }\n"
+        + "  else\n"
+        + "  {\n"
+        + "    x = event.x + document.body.scrollLeft;\n"
+        + "    y = event.y + document.body.scrollTop;\n"
+        + "  }\n"
+        + "  toolTipSTYLE.left = x + offsetX;\n"
+        + "  toolTipSTYLE.top = y + offsetY;\n"
+        + "  return true;\n"
+        + "}\n"
+        + "</script>\n"
+        + "</head>\n"
+        + "<body>\n"
+        + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
+        + "<script language=\"JavaScript\"><!--\n"
+        + "initToolTips(); //--></script>\n");
+
+  }
+}
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 46899da..4deb858 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index dfe1ecf..7daee55 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
  */
-
 /**
  * PredFile.java
  * JalviewX / Vamsas Project
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 465b8a3..bc360ca 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 //////////////////////////////////////////////////////////////////
 package jalview.io;
 
diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index fd8bcd3..aa4f233 100755
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -1,172 +1,172 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import javax.swing.filechooser.FileFilter;
-
-public class JalviewFileFilter
-    extends FileFilter
-{
-  public static Hashtable suffixHash = new Hashtable();
-  private Hashtable filters = null;
-  private String description = "no description";
-  private String fullDescription = "full description";
-  private boolean useExtensionsInDescription = true;
-
-  public JalviewFileFilter(String extension, String description)
-  {
-    StringTokenizer st = new StringTokenizer(extension, ",");
-
-    while (st.hasMoreElements())
-    {
-      addExtension(st.nextToken().trim());
-    }
-
-    setDescription(description);
-  }
-
-  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]);
-    }
-
-    if (description != null)
-    {
-      setDescription(description);
-    }
-  }
-
-  public String getAcceptableExtension()
-  {
-    return filters.keys().nextElement().toString();
-  }
-
-  // takes account of the fact that database is a directory
-  public boolean accept(File f)
-  {
-    if (f != null)
-    {
-      String extension = getExtension(f);
-
-      if (f.isDirectory())
-      {
-        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());
-          }
-        }
-
-        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;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+import java.util.*;
+
+import javax.swing.filechooser.FileFilter;
+
+public class JalviewFileFilter
+    extends FileFilter
+{
+  public static Hashtable suffixHash = new Hashtable();
+  private Hashtable filters = null;
+  private String description = "no description";
+  private String fullDescription = "full description";
+  private boolean useExtensionsInDescription = true;
+
+  public JalviewFileFilter(String extension, String description)
+  {
+    StringTokenizer st = new StringTokenizer(extension, ",");
+
+    while (st.hasMoreElements())
+    {
+      addExtension(st.nextToken().trim());
+    }
+
+    setDescription(description);
+  }
+
+  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]);
+    }
+
+    if (description != null)
+    {
+      setDescription(description);
+    }
+  }
+
+  public String getAcceptableExtension()
+  {
+    return filters.keys().nextElement().toString();
+  }
+
+  // takes account of the fact that database is a directory
+  public boolean accept(File f)
+  {
+    if (f != null)
+    {
+      String extension = getExtension(f);
+
+      if (f.isDirectory())
+      {
+        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());
+          }
+        }
+
+        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 b32cbb6..e821ada 100755
--- a/src/jalview/io/JalviewFileView.java
+++ b/src/jalview/io/JalviewFileView.java
@@ -1,111 +1,111 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import javax.swing.*;
-import javax.swing.filechooser.*;
-
-public class JalviewFileView
-    extends FileView
-{
-  static Hashtable alignSuffix = new Hashtable();
-
-  static
-  {
-    alignSuffix.put("fasta", "Fasta file");
-    alignSuffix.put("fa", "Fasta file");
-    alignSuffix.put("fastq", "Fasta file");
-    alignSuffix.put("blc", "BLC file");
-    alignSuffix.put("msf", "MSF file");
-    alignSuffix.put("pfam", "PFAM file");
-    alignSuffix.put("aln", "Clustal file");
-    alignSuffix.put("pir", "PIR file");
-    alignSuffix.put("jar", "Jalview file");
-  }
-
-  public String getTypeDescription(File f)
-  {
-    String extension = getExtension(f);
-    String type = null;
-
-    if (extension != null)
-    {
-      if (alignSuffix.containsKey(extension))
-      {
-        type = alignSuffix.get(extension).toString();
-      }
-    }
-
-    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");
-      }
-    }
-
-    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;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.filechooser.*;
+
+public class JalviewFileView
+    extends FileView
+{
+  static Hashtable alignSuffix = new Hashtable();
+
+  static
+  {
+    alignSuffix.put("fasta", "Fasta file");
+    alignSuffix.put("fa", "Fasta file");
+    alignSuffix.put("fastq", "Fasta file");
+    alignSuffix.put("blc", "BLC file");
+    alignSuffix.put("msf", "MSF file");
+    alignSuffix.put("pfam", "PFAM file");
+    alignSuffix.put("aln", "Clustal file");
+    alignSuffix.put("pir", "PIR file");
+    alignSuffix.put("jar", "Jalview file");
+  }
+
+  public String getTypeDescription(File f)
+  {
+    String extension = getExtension(f);
+    String type = null;
+
+    if (extension != null)
+    {
+      if (alignSuffix.containsKey(extension))
+      {
+        type = alignSuffix.get(extension).toString();
+      }
+    }
+
+    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");
+      }
+    }
+
+    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/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 8d0f40b..7d09cce 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,21 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/package jalview.io;
+ */
+package jalview.io;
 
 import jalview.datamodel.*;
 
@@ -35,7 +36,7 @@ public class JnetAnnotationMaker
    * @param firstSeq int the index of the sequence to attach the annotation to (usually zero)
    * @param noMsa boolean
    * @param delMap mapping from columns in JPredFile prediction to residue number in al.getSequence(firstSeq)
-   */
+ */
   public static void add_annotation(JPredFile prediction, AlignmentI al,
                                     int firstSeq, boolean noMsa, int[] delMap)
       throws Exception
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index e2d3704..bb1ad7d 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/MatrixFile.java b/src/jalview/io/MatrixFile.java
index 5b9e79f..7b3bdab 100644
--- a/src/jalview/io/MatrixFile.java
+++ b/src/jalview/io/MatrixFile.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io;
 
 import java.io.IOException;
diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index fa6ef6d..91f7961 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -1,391 +1,391 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import jalview.datamodel.*;
-
-public class ModellerDescription
-{
-  /**
-   * Translates between a String containing a set of colon-separated values
-   * on a single line, and sequence start/end and other properties.
-   * See PIRFile IO for its use.
-   */
-  final String[] seqTypes =
-      {
-      "sequence", "structure", "structureX", "structureN"};
-  final String[] Fields =
-      {
-      "objectType", "objectId",
-      "startField", "startCode",
-      "endField", "endCode",
-      "description1", "description2",
-      "resolutionField", "tailField"};
-  final int TYPE = 0;
-  final int LOCALID = 1;
-  final int START = 2;
-  final int START_CHAIN = 3;
-  final int END = 4;
-  final int END_CHAIN = 5;
-  final int DESCRIPTION1 = 6;
-  final int DESCRIPTION2 = 7;
-  final int RESOLUTION = 8;
-  final int TAIL = 9;
-
-  /**
-   * 0 is free text or empty
-   * 1 is something that parses to an integer, or \@
-   */
-  final int Types[] =
-      {
-      0, 0, 1, 0, 1, 0, 0, 0, 0, 0
-  };
-  final char Padding[] =
-      {
-      ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.'
-  };
-
-  java.util.Hashtable fields = new java.util.Hashtable();
-  ModellerDescription()
-  {
-    fields.put(Fields[TAIL], "");
-  }
-
-  class resCode
-  {
-    Integer val;
-    String field;
-    resCode(String f, Integer v)
-    {
-      val = v;
-      field = f;
-    }
-
-    resCode(int v)
-    {
-      val = new Integer(v);
-      field = val.toString();
-    }
-  };
-
-  private resCode validResidueCode(String field)
-  {
-    Integer val = null;
-    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
-        "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
-
-    if (!r.search(field))
-    {
-      return null; // invalid
-    }
-    String value = r.stringMatched(3);
-    if (value == null)
-    {
-      value = r.stringMatched(1);
-    }
-    // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
-    //                             "'");
-    try
-    {
-      val = Integer.valueOf(value);
-      return new resCode(field, val); // successful numeric extraction
-    }
-    catch (Exception e)
-    {
-    }
-    return new resCode(field, null);
-  }
-
-  private java.util.Hashtable parseDescription(String desc)
-  {
-    java.util.Hashtable fields = new java.util.Hashtable();
-    java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":");
-    String field;
-    int type = -1;
-    if (st.countTokens() > 0)
-    {
-      // parse colon-fields
-      int i = 0;
-      field = st.nextToken(":");
-      do
-      {
-        if (seqTypes[i].equalsIgnoreCase(field))
-        {
-          break;
-        }
-      }
-      while (++i < seqTypes.length);
-
-      if (i < seqTypes.length)
-      {
-        // valid seqType for modeller
-        type = i;
-        i = 1; // continue parsing fields
-        while (i < TAIL && st.hasMoreTokens())
-        {
-          if ( (field = st.nextToken(":")) != null)
-          {
-            // validate residue field value
-            if (Types[i] == 1)
-            {
-              resCode val = validResidueCode(field);
-              if (val != null)
-              {
-                fields.put(new String(Fields[i] + "num"), val);
-              }
-              else
-              {
-                //      jalview.bin.Cache.log.debug(
-                //           "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
-                type = -1; /* invalid field! - throw the FieldSet away */
-              }
-              ;
-            }
-            fields.put(Fields[i++], field);
-          }
-        }
-        if (i == TAIL)
-        {
-          // slurp remaining fields
-          while (st.hasMoreTokens())
-          {
-            field += ":" + st.nextToken(":");
-          }
-          fields.put(Fields[TAIL], field);
-        }
-      }
-    }
-    if (type == -1)
-    {
-      // object is not a proper ModellerPIR object
-      fields = new java.util.Hashtable();
-      fields.put(Fields[TAIL], new String(desc));
-    }
-    else
-    {
-      fields.put(Fields[TYPE], seqTypes[type]);
-    }
-    return fields;
-  }
-
-  ModellerDescription(String desc)
-  {
-    if (desc == null)
-    {
-      desc = "";
-    }
-    fields = parseDescription(desc);
-  }
-
-  void setStartCode(int v)
-  {
-    resCode r;
-    fields.put(Fields[START] + "num", r = new resCode(v));
-    fields.put(Fields[START], r.field);
-  }
-
-  void setEndCode(int v)
-  {
-    resCode r;
-    fields.put(Fields[END] + "num", r = new resCode(v));
-    fields.put(Fields[END], r.field);
-  }
-
-  /**
-   * make a possibly updated modeller field line for the sequence object
-   * @param seq SequenceI
-   */
-  ModellerDescription(SequenceI seq)
-  {
-
-    if (seq.getDescription() != null)
-    {
-      fields = parseDescription(seq.getDescription());
-    }
-
-    if (isModellerFieldset())
-    {
-      // Set start and end before we update the type (in the case of a synthesized field set)
-      if (getStartNum() != seq.getStart() && getStartCode().val != null)
-      {
-        setStartCode(seq.getStart());
-      }
-
-      if (getEndNum() != seq.getEnd() && getStartCode().val != null)
-      {
-        setEndCode(seq.getEnd());
-      }
-    }
-    else
-    {
-      // synthesize fields
-      setStartCode(seq.getStart());
-      setEndCode(seq.getEnd());
-      fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten below...
-      // type - decide based on evidence of PDB database references - this also sets the local reference field
-      int t = 0; // sequence
-      if (seq.getDatasetSequence() != null &&
-          seq.getDatasetSequence().getDBRef() != null)
-      {
-        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
-        int i, j;
-        for (i = 0, j = dbr.length; i < j; i++)
-        {
-          if (dbr[i] != null)
-          {
-            // JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField
-            // JBPNote Need to get info from the user about whether the sequence is the one being modelled, or if it is a template.
-            if (dbr[i].getSource().equals(jalview.datamodel.DBRefSource.PDB))
-            {
-              fields.put(Fields[LOCALID], dbr[i].getAccessionId());
-              t = 2;
-              break;
-            }
-          }
-        }
-      }
-      fields.put(Fields[TYPE], seqTypes[t]);
-    }
-
-  }
-
-  /**
-   * Indicate if fields parsed to a modeller-like colon-separated value line
-   * @return boolean
-   */
-  boolean isModellerFieldset()
-  {
-    return (fields.containsKey(Fields[TYPE]));
-  }
-
-  String getDescriptionLine()
-  {
-    String desc = "";
-    int lastfield = Fields.length - 1;
-
-    if (isModellerFieldset())
-    {
-      String value;
-      // try to write a minimal modeller field set, so..
-
-      // find the last valid field in the entry
-
-      for (; lastfield > 6; lastfield--)
-      {
-        if (fields.containsKey(Fields[lastfield]))
-        {
-          break;
-        }
-      }
-
-      for (int i = 0; i < lastfield; i++)
-      {
-        value = (String) fields.get(Fields[i]);
-        if (value != null && value.length() > 0)
-        {
-          desc += ( (String) fields.get(Fields[i])) + ":";
-        }
-        else
-        {
-          desc += Padding[i] + ":";
-        }
-      }
-    }
-    // just return the last field if no others were defined.
-    if (fields.containsKey(Fields[lastfield]))
-    {
-      desc += (String) fields.get(Fields[lastfield]);
-    }
-    else
-    {
-      desc += ".";
-    }
-    return desc;
-  }
-
-  int getStartNum()
-  {
-    int start = 0;
-    resCode val = getStartCode();
-    if (val.val != null)
-    {
-      return val.val.intValue();
-    }
-    return start;
-  }
-
-  resCode getStartCode()
-  {
-    if (isModellerFieldset() && fields.containsKey(Fields[START] + "num"))
-    {
-      return (resCode) fields.get(Fields[START] + "num");
-    }
-    return null;
-  }
-
-  resCode getEndCode()
-  {
-    if (isModellerFieldset() && fields.containsKey(Fields[END] + "num"))
-    {
-      return (resCode) fields.get(Fields[END] + "num");
-    }
-    return null;
-  }
-
-  int getEndNum()
-  {
-    int end = 0;
-    resCode val = getEndCode();
-    if (val.val != null)
-    {
-      return val.val.intValue();
-    }
-    return end;
-  }
-
-  /**
-   * returns true if sequence object was modifed with a valid modellerField set
-   * @param newSeq SequenceI
-   * @return boolean
-   */
-  boolean updateSequenceI(SequenceI newSeq)
-  {
-    if (isModellerFieldset())
-    {
-      if (getStartCode().val != null)
-      {
-        newSeq.setStart(getStartNum());
-      }
-      else
-      {
-        newSeq.setStart(1);
-      }
-      if (getEndCode().val != null)
-      {
-        newSeq.setEnd(getEndNum());
-      }
-      else
-      {
-        newSeq.setEnd(newSeq.getStart() + newSeq.getLength());
-      }
-      return true;
-    }
-    return false;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import jalview.datamodel.*;
+
+public class ModellerDescription
+{
+  /**
+   * Translates between a String containing a set of colon-separated values
+   * on a single line, and sequence start/end and other properties.
+   * See PIRFile IO for its use.
+   */
+  final String[] seqTypes =
+      {
+      "sequence", "structure", "structureX", "structureN"};
+  final String[] Fields =
+      {
+      "objectType", "objectId",
+      "startField", "startCode",
+      "endField", "endCode",
+      "description1", "description2",
+      "resolutionField", "tailField"};
+  final int TYPE = 0;
+  final int LOCALID = 1;
+  final int START = 2;
+  final int START_CHAIN = 3;
+  final int END = 4;
+  final int END_CHAIN = 5;
+  final int DESCRIPTION1 = 6;
+  final int DESCRIPTION2 = 7;
+  final int RESOLUTION = 8;
+  final int TAIL = 9;
+
+  /**
+   * 0 is free text or empty
+   * 1 is something that parses to an integer, or \@
+   */
+  final int Types[] =
+      {
+      0, 0, 1, 0, 1, 0, 0, 0, 0, 0
+  };
+  final char Padding[] =
+      {
+      ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.'
+  };
+
+  java.util.Hashtable fields = new java.util.Hashtable();
+  ModellerDescription()
+  {
+    fields.put(Fields[TAIL], "");
+  }
+
+  class resCode
+  {
+    Integer val;
+    String field;
+    resCode(String f, Integer v)
+    {
+      val = v;
+      field = f;
+    }
+
+    resCode(int v)
+    {
+      val = new Integer(v);
+      field = val.toString();
+    }
+  };
+
+  private resCode validResidueCode(String field)
+  {
+    Integer val = null;
+    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
+        "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+
+    if (!r.search(field))
+    {
+      return null; // invalid
+    }
+    String value = r.stringMatched(3);
+    if (value == null)
+    {
+      value = r.stringMatched(1);
+    }
+    // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+    //                             "'");
+    try
+    {
+      val = Integer.valueOf(value);
+      return new resCode(field, val); // successful numeric extraction
+    }
+    catch (Exception e)
+    {
+    }
+    return new resCode(field, null);
+  }
+
+  private java.util.Hashtable parseDescription(String desc)
+  {
+    java.util.Hashtable fields = new java.util.Hashtable();
+    java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":");
+    String field;
+    int type = -1;
+    if (st.countTokens() > 0)
+    {
+      // parse colon-fields
+      int i = 0;
+      field = st.nextToken(":");
+      do
+      {
+        if (seqTypes[i].equalsIgnoreCase(field))
+        {
+          break;
+        }
+      }
+      while (++i < seqTypes.length);
+
+      if (i < seqTypes.length)
+      {
+        // valid seqType for modeller
+        type = i;
+        i = 1; // continue parsing fields
+        while (i < TAIL && st.hasMoreTokens())
+        {
+          if ( (field = st.nextToken(":")) != null)
+          {
+            // validate residue field value
+            if (Types[i] == 1)
+            {
+              resCode val = validResidueCode(field);
+              if (val != null)
+              {
+                fields.put(new String(Fields[i] + "num"), val);
+              }
+              else
+              {
+                //      jalview.bin.Cache.log.debug(
+                //           "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
+                type = -1; /* invalid field! - throw the FieldSet away */
+              }
+              ;
+            }
+            fields.put(Fields[i++], field);
+          }
+        }
+        if (i == TAIL)
+        {
+          // slurp remaining fields
+          while (st.hasMoreTokens())
+          {
+            field += ":" + st.nextToken(":");
+          }
+          fields.put(Fields[TAIL], field);
+        }
+      }
+    }
+    if (type == -1)
+    {
+      // object is not a proper ModellerPIR object
+      fields = new java.util.Hashtable();
+      fields.put(Fields[TAIL], new String(desc));
+    }
+    else
+    {
+      fields.put(Fields[TYPE], seqTypes[type]);
+    }
+    return fields;
+  }
+
+  ModellerDescription(String desc)
+  {
+    if (desc == null)
+    {
+      desc = "";
+    }
+    fields = parseDescription(desc);
+  }
+
+  void setStartCode(int v)
+  {
+    resCode r;
+    fields.put(Fields[START] + "num", r = new resCode(v));
+    fields.put(Fields[START], r.field);
+  }
+
+  void setEndCode(int v)
+  {
+    resCode r;
+    fields.put(Fields[END] + "num", r = new resCode(v));
+    fields.put(Fields[END], r.field);
+  }
+
+  /**
+   * make a possibly updated modeller field line for the sequence object
+   * @param seq SequenceI
+   */
+  ModellerDescription(SequenceI seq)
+  {
+
+    if (seq.getDescription() != null)
+    {
+      fields = parseDescription(seq.getDescription());
+    }
+
+    if (isModellerFieldset())
+    {
+      // Set start and end before we update the type (in the case of a synthesized field set)
+      if (getStartNum() != seq.getStart() && getStartCode().val != null)
+      {
+        setStartCode(seq.getStart());
+      }
+
+      if (getEndNum() != seq.getEnd() && getStartCode().val != null)
+      {
+        setEndCode(seq.getEnd());
+      }
+    }
+    else
+    {
+      // synthesize fields
+      setStartCode(seq.getStart());
+      setEndCode(seq.getEnd());
+      fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten below...
+      // type - decide based on evidence of PDB database references - this also sets the local reference field
+      int t = 0; // sequence
+      if (seq.getDatasetSequence() != null &&
+          seq.getDatasetSequence().getDBRef() != null)
+      {
+        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
+        int i, j;
+        for (i = 0, j = dbr.length; i < j; i++)
+        {
+          if (dbr[i] != null)
+          {
+            // JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField
+            // JBPNote Need to get info from the user about whether the sequence is the one being modelled, or if it is a template.
+            if (dbr[i].getSource().equals(jalview.datamodel.DBRefSource.PDB))
+            {
+              fields.put(Fields[LOCALID], dbr[i].getAccessionId());
+              t = 2;
+              break;
+            }
+          }
+        }
+      }
+      fields.put(Fields[TYPE], seqTypes[t]);
+    }
+
+  }
+
+  /**
+   * Indicate if fields parsed to a modeller-like colon-separated value line
+   * @return boolean
+   */
+  boolean isModellerFieldset()
+  {
+    return (fields.containsKey(Fields[TYPE]));
+  }
+
+  String getDescriptionLine()
+  {
+    String desc = "";
+    int lastfield = Fields.length - 1;
+
+    if (isModellerFieldset())
+    {
+      String value;
+      // try to write a minimal modeller field set, so..
+
+      // find the last valid field in the entry
+
+      for (; lastfield > 6; lastfield--)
+      {
+        if (fields.containsKey(Fields[lastfield]))
+        {
+          break;
+        }
+      }
+
+      for (int i = 0; i < lastfield; i++)
+      {
+        value = (String) fields.get(Fields[i]);
+        if (value != null && value.length() > 0)
+        {
+          desc += ( (String) fields.get(Fields[i])) + ":";
+        }
+        else
+        {
+          desc += Padding[i] + ":";
+        }
+      }
+    }
+    // just return the last field if no others were defined.
+    if (fields.containsKey(Fields[lastfield]))
+    {
+      desc += (String) fields.get(Fields[lastfield]);
+    }
+    else
+    {
+      desc += ".";
+    }
+    return desc;
+  }
+
+  int getStartNum()
+  {
+    int start = 0;
+    resCode val = getStartCode();
+    if (val.val != null)
+    {
+      return val.val.intValue();
+    }
+    return start;
+  }
+
+  resCode getStartCode()
+  {
+    if (isModellerFieldset() && fields.containsKey(Fields[START] + "num"))
+    {
+      return (resCode) fields.get(Fields[START] + "num");
+    }
+    return null;
+  }
+
+  resCode getEndCode()
+  {
+    if (isModellerFieldset() && fields.containsKey(Fields[END] + "num"))
+    {
+      return (resCode) fields.get(Fields[END] + "num");
+    }
+    return null;
+  }
+
+  int getEndNum()
+  {
+    int end = 0;
+    resCode val = getEndCode();
+    if (val.val != null)
+    {
+      return val.val.intValue();
+    }
+    return end;
+  }
+
+  /**
+   * returns true if sequence object was modifed with a valid modellerField set
+   * @param newSeq SequenceI
+   * @return boolean
+   */
+  boolean updateSequenceI(SequenceI newSeq)
+  {
+    if (isModellerFieldset())
+    {
+      if (getStartCode().val != null)
+      {
+        newSeq.setStart(getStartNum());
+      }
+      else
+      {
+        newSeq.setStart(1);
+      }
+      if (getEndCode().val != null)
+      {
+        newSeq.setEnd(getEndNum());
+      }
+      else
+      {
+        newSeq.setEnd(newSeq.getStart() + newSeq.getLength());
+      }
+      return true;
+    }
+    return false;
+  }
+}
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 9a7f6fb..7dd98c0 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
  */
-
 // NewickFile.java
 // Tree I/O
 // http://evolution.genetics.washington.edu/phylip/newick_doc.html
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index b18b8f4..3e5abd6 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 2b0bf13..07c660c 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index cd46541..e469b5f 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index ccbe818..4ba1851 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 1964c2f..e77355e 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.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
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.io;
 
 import jalview.bin.Cache;
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 1d42620..2a5f02f 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -1,303 +1,303 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.util.*;
-
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import uk.ac.ebi.www.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class WSWUBlastClient
-{
-  AlignmentPanel ap;
-  AlignmentI al;
-  CutAndPasteTransfer output = new CutAndPasteTransfer();
-  int jobsRunning = 0;
-
-  Vector suggestedIds = new Vector();
-  /**
-   * Creates a new WSWUBlastClient object.
-   *
-   * @param al DOCUMENT ME!
-   * @param ids DOCUMENT ME!
-   */
-  public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
-  {
-    this.ap = ap;
-    this.al = al;
-    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."
-        + "\n\nRunning WSWUBlast at EBI."
-        + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
-        +
-        "\nSOAP-based services provided by the European Bioinformatics Institute."
-        + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
-
-    Desktop.addInternalFrame(output,
-                             "BLASTing for unidentified sequences ", 800, 300);
-
-    for (int i = 0; i < ids.size(); i++)
-    {
-      Sequence sequence = (Sequence) ids.get(i);
-      System.out.println(sequence.getName());
-
-      BlastThread thread = new BlastThread(sequence);
-      thread.start();
-      jobsRunning++;
-    }
-
-    ImageTwirler thread = new ImageTwirler();
-    thread.start();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param id1 DOCUMENT ME!
-   * @param res DOCUMENT ME!
-   */
-  void parseResult(Sequence seq, String res)
-  {
-    StringTokenizer st = new StringTokenizer(res, "\n");
-    String data;
-    String id2;
-    int maxFound = 90;
-    StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
-
-    while (st.hasMoreTokens())
-    {
-      data = st.nextToken();
-
-      if (data.indexOf(">UNIPROT") > -1)
-      {
-        int index = data.indexOf(">UNIPROT") + 9;
-        id2 = data.substring(index, data.indexOf(" ", index));
-
-        boolean identitiesFound = false;
-        while (!identitiesFound)
-        {
-          data = st.nextToken();
-
-          if (data.indexOf("Identities") > -1)
-          {
-            identitiesFound = true;
-
-            int value = Integer.parseInt(data.substring(data.indexOf(
-                "(") + 1,
-                data.indexOf("%")));
-
-            if (value >= maxFound)
-            {
-              maxFound = value;
-              buffer.append(" " + id2 + " " + value + "%; ");
-              suggestedIds.addElement(new Object[]
-                                      {seq, id2});
-            }
-          }
-        }
-      }
-    }
-
-    output.appendText(buffer.toString());
-  }
-
-  void updateIds()
-  {
-    // This must be outside the run() body as java 1.5
-    // will not return any value from the OptionPane to the expired thread.
-    int reply = JOptionPane.showConfirmDialog(
-        Desktop.desktop, "Automatically update suggested ids?",
-        "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
-
-    if (reply == JOptionPane.YES_OPTION)
-    {
-      Enumeration keys = suggestedIds.elements();
-      while (keys.hasMoreElements())
-      {
-        Object[] object = (Object[]) keys.nextElement();
-
-        Sequence oldseq = (Sequence) object[0];
-
-        oldseq.setName(object[1].toString());
-
-        // Oldseq is actually in the dataset, we must find the
-        // Visible seq and change its name also.
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-          if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
-          {
-            al.getSequenceAt(i).setName(oldseq.getName());
-            break;
-          }
-        }
-
-        DBRefEntry[] entries = oldseq.getDBRef();
-        if (entries != null)
-        {
-          oldseq.addDBRef(new jalview.datamodel.
-                          DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,
-                                     "0",
-                                     entries[0].getAccessionId()));
-        }
-      }
-    }
-    ap.paintAlignment(true);
-
-  }
-
-  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)
-        {
-        }
-      }
-
-      if (jobsRunning == 0)
-      {
-        updateIds();
-      }
-    }
-  }
-
-  class BlastThread
-      extends Thread
-  {
-    Sequence sequence;
-    String jobid;
-    boolean jobComplete = false;
-
-    BlastThread(Sequence sequence)
-    {
-      System.out.println("blasting for: " + sequence.getName());
-      this.sequence = sequence;
-    }
-
-    public void run()
-    {
-      StartJob();
-
-      while (!jobComplete)
-      {
-        try
-        {
-          WSWUBlastService service = new WSWUBlastServiceLocator();
-          WSWUBlast wublast = service.getWSWUBlast();
-          WSFile[] results = wublast.getResults(jobid);
-
-          if (results != null)
-          {
-            String result = new String(wublast.poll(jobid, "tooloutput"));
-            parseResult(sequence, result);
-            jobComplete = true;
-            jobsRunning--;
-          }
-          else
-          {
-            Thread.sleep(10000);
-            System.out.println("WSWuBlastClient: I'm alive " +
-                               sequence.getName() + " " + jobid); // log.debug
-          }
-        }
-        catch (Exception ex)
-        {
-        }
-      }
-    }
-
-    void StartJob()
-    {
-      InputParams params = new InputParams();
-
-      params.setProgram("blastp");
-      params.setDatabase("uniprot");
-      params.setMatrix("pam10");
-
-      params.setNumal(5);
-      params.setSensitivity("low");
-      params.setSort("totalscore");
-      params.setOutformat("txt");
-      params.setAsync(true);
-
-      try
-      {
-        Data inputs[] = new Data[1];
-        Data input = new Data();
-        input.setType("sequence");
-        input.setContent(AlignSeq.extractGaps("-. ",
-                                              sequence.getSequenceAsString()));
-        inputs[0] = input;
-
-        WSWUBlastService service = new WSWUBlastServiceLocator();
-        WSWUBlast wublast = service.getWSWUBlast();
-        jobid = wublast.runWUBlast(params, inputs);
-      }
-      catch (Exception exp)
-      {
-        jobComplete = true;
-        jobsRunning--;
-        System.err.println("WSWUBlastClient error:\n" + exp.toString());
-        exp.printStackTrace();
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.util.*;
+
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import uk.ac.ebi.www.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class WSWUBlastClient
+{
+  AlignmentPanel ap;
+  AlignmentI al;
+  CutAndPasteTransfer output = new CutAndPasteTransfer();
+  int jobsRunning = 0;
+
+  Vector suggestedIds = new Vector();
+  /**
+   * Creates a new WSWUBlastClient object.
+   *
+   * @param al DOCUMENT ME!
+   * @param ids DOCUMENT ME!
+   */
+  public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
+  {
+    this.ap = ap;
+    this.al = al;
+    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."
+        + "\n\nRunning WSWUBlast at EBI."
+        + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
+        +
+        "\nSOAP-based services provided by the European Bioinformatics Institute."
+        + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
+
+    Desktop.addInternalFrame(output,
+                             "BLASTing for unidentified sequences ", 800, 300);
+
+    for (int i = 0; i < ids.size(); i++)
+    {
+      Sequence sequence = (Sequence) ids.get(i);
+      System.out.println(sequence.getName());
+
+      BlastThread thread = new BlastThread(sequence);
+      thread.start();
+      jobsRunning++;
+    }
+
+    ImageTwirler thread = new ImageTwirler();
+    thread.start();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param id1 DOCUMENT ME!
+   * @param res DOCUMENT ME!
+   */
+  void parseResult(Sequence seq, String res)
+  {
+    StringTokenizer st = new StringTokenizer(res, "\n");
+    String data;
+    String id2;
+    int maxFound = 90;
+    StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
+
+    while (st.hasMoreTokens())
+    {
+      data = st.nextToken();
+
+      if (data.indexOf(">UNIPROT") > -1)
+      {
+        int index = data.indexOf(">UNIPROT") + 9;
+        id2 = data.substring(index, data.indexOf(" ", index));
+
+        boolean identitiesFound = false;
+        while (!identitiesFound)
+        {
+          data = st.nextToken();
+
+          if (data.indexOf("Identities") > -1)
+          {
+            identitiesFound = true;
+
+            int value = Integer.parseInt(data.substring(data.indexOf(
+                "(") + 1,
+                data.indexOf("%")));
+
+            if (value >= maxFound)
+            {
+              maxFound = value;
+              buffer.append(" " + id2 + " " + value + "%; ");
+              suggestedIds.addElement(new Object[]
+                                      {seq, id2});
+            }
+          }
+        }
+      }
+    }
+
+    output.appendText(buffer.toString());
+  }
+
+  void updateIds()
+  {
+    // This must be outside the run() body as java 1.5
+    // will not return any value from the OptionPane to the expired thread.
+    int reply = JOptionPane.showConfirmDialog(
+        Desktop.desktop, "Automatically update suggested ids?",
+        "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
+
+    if (reply == JOptionPane.YES_OPTION)
+    {
+      Enumeration keys = suggestedIds.elements();
+      while (keys.hasMoreElements())
+      {
+        Object[] object = (Object[]) keys.nextElement();
+
+        Sequence oldseq = (Sequence) object[0];
+
+        oldseq.setName(object[1].toString());
+
+        // Oldseq is actually in the dataset, we must find the
+        // Visible seq and change its name also.
+        for (int i = 0; i < al.getHeight(); i++)
+        {
+          if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
+          {
+            al.getSequenceAt(i).setName(oldseq.getName());
+            break;
+          }
+        }
+
+        DBRefEntry[] entries = oldseq.getDBRef();
+        if (entries != null)
+        {
+          oldseq.addDBRef(new jalview.datamodel.
+                          DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,
+                                     "0",
+                                     entries[0].getAccessionId()));
+        }
+      }
+    }
+    ap.paintAlignment(true);
+
+  }
+
+  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)
+        {
+        }
+      }
+
+      if (jobsRunning == 0)
+      {
+        updateIds();
+      }
+    }
+  }
+
+  class BlastThread
+      extends Thread
+  {
+    Sequence sequence;
+    String jobid;
+    boolean jobComplete = false;
+
+    BlastThread(Sequence sequence)
+    {
+      System.out.println("blasting for: " + sequence.getName());
+      this.sequence = sequence;
+    }
+
+    public void run()
+    {
+      StartJob();
+
+      while (!jobComplete)
+      {
+        try
+        {
+          WSWUBlastService service = new WSWUBlastServiceLocator();
+          WSWUBlast wublast = service.getWSWUBlast();
+          WSFile[] results = wublast.getResults(jobid);
+
+          if (results != null)
+          {
+            String result = new String(wublast.poll(jobid, "tooloutput"));
+            parseResult(sequence, result);
+            jobComplete = true;
+            jobsRunning--;
+          }
+          else
+          {
+            Thread.sleep(10000);
+            System.out.println("WSWuBlastClient: I'm alive " +
+                               sequence.getName() + " " + jobid); // log.debug
+          }
+        }
+        catch (Exception ex)
+        {
+        }
+      }
+    }
+
+    void StartJob()
+    {
+      InputParams params = new InputParams();
+
+      params.setProgram("blastp");
+      params.setDatabase("uniprot");
+      params.setMatrix("pam10");
+
+      params.setNumal(5);
+      params.setSensitivity("low");
+      params.setSort("totalscore");
+      params.setOutformat("txt");
+      params.setAsync(true);
+
+      try
+      {
+        Data inputs[] = new Data[1];
+        Data input = new Data();
+        input.setType("sequence");
+        input.setContent(AlignSeq.extractGaps("-. ",
+                                              sequence.getSequenceAsString()));
+        inputs[0] = input;
+
+        WSWUBlastService service = new WSWUBlastServiceLocator();
+        WSWUBlast wublast = service.getWSWUBlast();
+        jobid = wublast.runWUBlast(params, inputs);
+      }
+      catch (Exception exp)
+      {
+        jobComplete = true;
+        jobsRunning--;
+        System.err.println("WSWUBlastClient error:\n" + exp.toString());
+        exp.printStackTrace();
+      }
+    }
+  }
+}
diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index 4cc540d..bcbcf38 100644
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import jalview.bin.Cache;
diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index c4d72c3..a26da89 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import jalview.datamodel.DBRefEntry;
diff --git a/src/jalview/io/vamsas/LocalDocSyncObject.java b/src/jalview/io/vamsas/LocalDocSyncObject.java
index bfc2123..99e72ab 100644
--- a/src/jalview/io/vamsas/LocalDocSyncObject.java
+++ b/src/jalview/io/vamsas/LocalDocSyncObject.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import uk.ac.vamsas.client.Vobject;
diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index b7e6f79..a475000 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 
@@ -267,4 +285,4 @@ public class Rangetype extends DatastoreItem
     }
   }
 
-}
\ No newline at end of file
+}
diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 8c73992..c37dfd3 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import java.util.Vector;
@@ -324,4 +342,4 @@ public class Sequencemapping extends Rangetype
       }
     }
     }
-}
\ No newline at end of file
+}
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index eb4af4a..663325c 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.io.vamsas;
 
 import java.io.IOException;
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 1bc0b72..675fc99 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index f8b91c4..b159e47 100755
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -1,108 +1,108 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.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));
-
-    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);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import javax.swing.*;
+import javax.swing.border.*;
+
+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));
+
+    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 c19db0e..5db9b74 100755
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -1,212 +1,212 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GCutAndPasteTransfer
-    extends JInternalFrame
-{
-  protected JTextArea textarea = new JTextArea();
-  protected JScrollPane scrollPane = new JScrollPane();
-  BorderLayout borderLayout1 = new BorderLayout();
-  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();
-  protected JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JMenuItem selectAll = new JMenuItem();
-  JMenu jMenu1 = new JMenu();
-  JMenuItem save = new JMenuItem();
-
-  /**
-   * Creates a new GCutAndPasteTransfer object.
-   */
-  public GCutAndPasteTransfer()
-  {
-    try
-    {
-      setJMenuBar(editMenubar);
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    scrollPane.setBorder(null);
-    ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    ok.setText("New Window");
-    ok.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setText("Close");
-    cancel.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    textarea.setBorder(null);
-
-    selectAll.setText("Select All");
-    selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    selectAll.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        selectAll_actionPerformed(e);
-      }
-    });
-    jMenu1.setText("File");
-    save.setText("Save");
-    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    save.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        save_actionPerformed(e);
-      }
-    });
-    copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    pasteMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    editMenubar.add(jMenu1);
-    editMenubar.add(editMenu);
-    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));
-    textarea.addMouseListener(new java.awt.event.MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        textarea_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(selectAll);
-    editMenu.add(copyItem);
-    editMenu.add(pasteMenu);
-    this.getContentPane().add(scrollPane, java.awt.BorderLayout.CENTER);
-    inputButtonPanel.add(ok);
-    inputButtonPanel.add(cancel);
-    jMenu1.add(save);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void textarea_mousePressed(MouseEvent e)
-  {
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void copyItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void pasteMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void ok_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void selectAll_actionPerformed(ActionEvent e)
-  {
-    textarea.selectAll();
-  }
-
-  public void save_actionPerformed(ActionEvent e)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GCutAndPasteTransfer
+    extends JInternalFrame
+{
+  protected JTextArea textarea = new JTextArea();
+  protected JScrollPane scrollPane = new JScrollPane();
+  BorderLayout borderLayout1 = new BorderLayout();
+  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();
+  protected JButton ok = new JButton();
+  JButton cancel = new JButton();
+  JMenuItem selectAll = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
+  JMenuItem save = new JMenuItem();
+
+  /**
+   * Creates a new GCutAndPasteTransfer object.
+   */
+  public GCutAndPasteTransfer()
+  {
+    try
+    {
+      setJMenuBar(editMenubar);
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    scrollPane.setBorder(null);
+    ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    ok.setText("New Window");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setText("Close");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    textarea.setBorder(null);
+
+    selectAll.setText("Select All");
+    selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    selectAll.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        selectAll_actionPerformed(e);
+      }
+    });
+    jMenu1.setText("File");
+    save.setText("Save");
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    save.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        save_actionPerformed(e);
+      }
+    });
+    copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    pasteMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    editMenubar.add(jMenu1);
+    editMenubar.add(editMenu);
+    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));
+    textarea.addMouseListener(new java.awt.event.MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        textarea_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(selectAll);
+    editMenu.add(copyItem);
+    editMenu.add(pasteMenu);
+    this.getContentPane().add(scrollPane, java.awt.BorderLayout.CENTER);
+    inputButtonPanel.add(ok);
+    inputButtonPanel.add(cancel);
+    jMenu1.add(save);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void textarea_mousePressed(MouseEvent e)
+  {
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void copyItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void pasteMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void selectAll_actionPerformed(ActionEvent e)
+  {
+    textarea.selectAll();
+  }
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GDasSourceBrowser.java b/src/jalview/jbgui/GDasSourceBrowser.java
index d4f6d1d..1e644a0 100755
--- a/src/jalview/jbgui/GDasSourceBrowser.java
+++ b/src/jalview/jbgui/GDasSourceBrowser.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index aa86809..4145be4 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 9d72d26..6f6e1e7 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/jbgui/GFontChooser.java b/src/jalview/jbgui/GFontChooser.java
index 6c04561..a620ebb 100755
--- a/src/jalview/jbgui/GFontChooser.java
+++ b/src/jalview/jbgui/GFontChooser.java
@@ -1,252 +1,252 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GFontChooser
-    extends JPanel
-{
-  JLabel jLabel1 = new JLabel();
-  protected JComboBox fontSize = new JComboBox();
-  protected JComboBox fontStyle = new JComboBox();
-  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();
-  protected JButton defaultButton = new JButton();
-  protected JCheckBox smoothFont = new JCheckBox();
-  BorderLayout borderLayout4 = new BorderLayout();
-  protected JCheckBox monospaced = new JCheckBox();
-  JPanel jPanel4 = new JPanel();
-
-  /**
-   * Creates a new GFontChooser object.
-   */
-  public GFontChooser()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));
-    jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
-    jLabel1.setText("Font: ");
-    jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
-    this.setLayout(null);
-    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.setBounds(new Rectangle(5, 6, 308, 23));
-    jPanel1.setLayout(borderLayout1);
-    jPanel2.setOpaque(false);
-    jPanel2.setBounds(new Rectangle(5, 37, 128, 21));
-    jPanel2.setLayout(borderLayout3);
-    jPanel3.setOpaque(false);
-    jPanel3.setBounds(new Rectangle(174, 38, 134, 21));
-    jPanel3.setLayout(borderLayout2);
-    defaultButton.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    defaultButton.setText("Set as Default");
-    defaultButton.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        defaultButton_actionPerformed(e);
-      }
-    });
-    smoothFont.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    smoothFont.setOpaque(false);
-    smoothFont.setText("Anti-alias Fonts (Slower to render)");
-    smoothFont.setBounds(new Rectangle(41, 65, 223, 23));
-    smoothFont.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        smoothFont_actionPerformed(e);
-      }
-    });
-    monospaced.setEnabled(false);
-    monospaced.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    monospaced.setOpaque(false);
-    monospaced.setToolTipText("Monospaced fonts are faster to render");
-    monospaced.setText("Monospaced");
-    jPanel4.setOpaque(false);
-    jPanel4.setBounds(new Rectangle(24, 92, 259, 35));
-    jPanel1.add(jLabel1, BorderLayout.WEST);
-    jPanel1.add(fontName, BorderLayout.CENTER);
-    jPanel1.add(monospaced, java.awt.BorderLayout.EAST);
-    this.add(jPanel3, null);
-    this.add(jPanel2, null);
-    jPanel2.add(fontSize, java.awt.BorderLayout.CENTER);
-    jPanel2.add(jLabel2, java.awt.BorderLayout.WEST);
-    jPanel4.add(defaultButton);
-    jPanel4.add(ok);
-    jPanel4.add(cancel);
-    this.add(smoothFont);
-    this.add(jPanel4);
-    jPanel3.add(jLabel3, java.awt.BorderLayout.WEST);
-    jPanel3.add(fontStyle, java.awt.BorderLayout.CENTER);
-    this.add(jPanel1, null);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void ok_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontName_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void fontStyle_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void defaultButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void smoothFont_actionPerformed(ActionEvent e)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GFontChooser
+    extends JPanel
+{
+  JLabel jLabel1 = new JLabel();
+  protected JComboBox fontSize = new JComboBox();
+  protected JComboBox fontStyle = new JComboBox();
+  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();
+  protected JButton defaultButton = new JButton();
+  protected JCheckBox smoothFont = new JCheckBox();
+  BorderLayout borderLayout4 = new BorderLayout();
+  protected JCheckBox monospaced = new JCheckBox();
+  JPanel jPanel4 = new JPanel();
+
+  /**
+   * Creates a new GFontChooser object.
+   */
+  public GFontChooser()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 11));
+    jLabel1.setHorizontalAlignment(SwingConstants.RIGHT);
+    jLabel1.setText("Font: ");
+    jLabel1.setVerticalTextPosition(javax.swing.SwingConstants.CENTER);
+    this.setLayout(null);
+    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.setBounds(new Rectangle(5, 6, 308, 23));
+    jPanel1.setLayout(borderLayout1);
+    jPanel2.setOpaque(false);
+    jPanel2.setBounds(new Rectangle(5, 37, 128, 21));
+    jPanel2.setLayout(borderLayout3);
+    jPanel3.setOpaque(false);
+    jPanel3.setBounds(new Rectangle(174, 38, 134, 21));
+    jPanel3.setLayout(borderLayout2);
+    defaultButton.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    defaultButton.setText("Set as Default");
+    defaultButton.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        defaultButton_actionPerformed(e);
+      }
+    });
+    smoothFont.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    smoothFont.setOpaque(false);
+    smoothFont.setText("Anti-alias Fonts (Slower to render)");
+    smoothFont.setBounds(new Rectangle(41, 65, 223, 23));
+    smoothFont.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        smoothFont_actionPerformed(e);
+      }
+    });
+    monospaced.setEnabled(false);
+    monospaced.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    monospaced.setOpaque(false);
+    monospaced.setToolTipText("Monospaced fonts are faster to render");
+    monospaced.setText("Monospaced");
+    jPanel4.setOpaque(false);
+    jPanel4.setBounds(new Rectangle(24, 92, 259, 35));
+    jPanel1.add(jLabel1, BorderLayout.WEST);
+    jPanel1.add(fontName, BorderLayout.CENTER);
+    jPanel1.add(monospaced, java.awt.BorderLayout.EAST);
+    this.add(jPanel3, null);
+    this.add(jPanel2, null);
+    jPanel2.add(fontSize, java.awt.BorderLayout.CENTER);
+    jPanel2.add(jLabel2, java.awt.BorderLayout.WEST);
+    jPanel4.add(defaultButton);
+    jPanel4.add(ok);
+    jPanel4.add(cancel);
+    this.add(smoothFont);
+    this.add(jPanel4);
+    jPanel3.add(jLabel3, java.awt.BorderLayout.WEST);
+    jPanel3.add(fontStyle, java.awt.BorderLayout.CENTER);
+    this.add(jPanel1, null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void ok_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void cancel_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fontName_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fontSize_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void fontStyle_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void defaultButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index 5c17ba7..82d78e3 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -1,255 +1,255 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-public class GPCAPanel
-    extends JInternalFrame
-{
-  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();
-  JMenuBar jMenuBar1 = new JMenuBar();
-  JMenu fileMenu = new JMenu();
-  JMenu saveMenu = new JMenu();
-  JMenuItem eps = new JMenuItem();
-  JMenuItem png = new JMenuItem();
-  JMenuItem print = new JMenuItem();
-  JMenuItem outputValues = new JMenuItem();
-  protected JMenu viewMenu = new JMenu();
-  protected JCheckBoxMenuItem showLabels = new JCheckBoxMenuItem();
-  JMenuItem bgcolour = new JMenuItem();
-  JMenuItem originalSeqData = new JMenuItem();
-  protected JMenu associateViewsMenu = new JMenu();
-
-  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);
-    }
-
-    setJMenuBar(jMenuBar1);
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    this.getContentPane().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);
-      }
-    });
-    fileMenu.setText("File");
-    saveMenu.setText("Save as");
-    eps.setText("EPS");
-    eps.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        eps_actionPerformed(e);
-      }
-    });
-    png.setText("PNG");
-    png.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        png_actionPerformed(e);
-      }
-    });
-    outputValues.setText("Output Values...");
-    outputValues.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        outputValues_actionPerformed(e);
-      }
-    });
-    print.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        print_actionPerformed(e);
-      }
-    });
-    viewMenu.setText("View");
-    viewMenu.addMenuListener(new MenuListener()
-    {
-      public void menuSelected(MenuEvent e)
-      {
-        viewMenu_menuSelected();
-      }
-
-      public void menuDeselected(MenuEvent e)
-      {
-      }
-
-      public void menuCanceled(MenuEvent e)
-      {
-      }
-    });
-    showLabels.setText("Show Labels");
-    showLabels.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        showLabels_actionPerformed(e);
-      }
-    });
-    print.setText("Print");
-    bgcolour.setText("Background Colour...");
-    bgcolour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        bgcolour_actionPerformed(e);
-      }
-    });
-    originalSeqData.setText("Input Data...");
-    originalSeqData.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        originalSeqData_actionPerformed(e);
-      }
-    });
-    associateViewsMenu.setText("Associate Nodes With");
-    this.getContentPane().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);
-    jMenuBar1.add(fileMenu);
-    jMenuBar1.add(viewMenu);
-    fileMenu.add(saveMenu);
-    fileMenu.add(outputValues);
-    fileMenu.add(print);
-    fileMenu.add(originalSeqData);
-    saveMenu.add(eps);
-    saveMenu.add(png);
-    viewMenu.add(showLabels);
-    viewMenu.add(bgcolour);
-    viewMenu.add(associateViewsMenu);
-  }
-
-  protected void xCombobox_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void yCombobox_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void zCombobox_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void eps_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void png_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void outputValues_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void print_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void showLabels_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void bgcolour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void originalSeqData_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void viewMenu_menuSelected()
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+public class GPCAPanel
+    extends JInternalFrame
+{
+  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();
+  JMenuBar jMenuBar1 = new JMenuBar();
+  JMenu fileMenu = new JMenu();
+  JMenu saveMenu = new JMenu();
+  JMenuItem eps = new JMenuItem();
+  JMenuItem png = new JMenuItem();
+  JMenuItem print = new JMenuItem();
+  JMenuItem outputValues = new JMenuItem();
+  protected JMenu viewMenu = new JMenu();
+  protected JCheckBoxMenuItem showLabels = new JCheckBoxMenuItem();
+  JMenuItem bgcolour = new JMenuItem();
+  JMenuItem originalSeqData = new JMenuItem();
+  protected JMenu associateViewsMenu = new JMenu();
+
+  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);
+    }
+
+    setJMenuBar(jMenuBar1);
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    this.getContentPane().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);
+      }
+    });
+    fileMenu.setText("File");
+    saveMenu.setText("Save as");
+    eps.setText("EPS");
+    eps.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        eps_actionPerformed(e);
+      }
+    });
+    png.setText("PNG");
+    png.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        png_actionPerformed(e);
+      }
+    });
+    outputValues.setText("Output Values...");
+    outputValues.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        outputValues_actionPerformed(e);
+      }
+    });
+    print.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        print_actionPerformed(e);
+      }
+    });
+    viewMenu.setText("View");
+    viewMenu.addMenuListener(new MenuListener()
+    {
+      public void menuSelected(MenuEvent e)
+      {
+        viewMenu_menuSelected();
+      }
+
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
+    showLabels.setText("Show Labels");
+    showLabels.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showLabels_actionPerformed(e);
+      }
+    });
+    print.setText("Print");
+    bgcolour.setText("Background Colour...");
+    bgcolour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        bgcolour_actionPerformed(e);
+      }
+    });
+    originalSeqData.setText("Input Data...");
+    originalSeqData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        originalSeqData_actionPerformed(e);
+      }
+    });
+    associateViewsMenu.setText("Associate Nodes With");
+    this.getContentPane().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);
+    jMenuBar1.add(fileMenu);
+    jMenuBar1.add(viewMenu);
+    fileMenu.add(saveMenu);
+    fileMenu.add(outputValues);
+    fileMenu.add(print);
+    fileMenu.add(originalSeqData);
+    saveMenu.add(eps);
+    saveMenu.add(png);
+    viewMenu.add(showLabels);
+    viewMenu.add(bgcolour);
+    viewMenu.add(associateViewsMenu);
+  }
+
+  protected void xCombobox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void yCombobox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void zCombobox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void eps_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void png_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void outputValues_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void print_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showLabels_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void bgcolour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void originalSeqData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void viewMenu_menuSelected()
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GPairwiseAlignPanel.java b/src/jalview/jbgui/GPairwiseAlignPanel.java
index f690a21..5e56bd9 100755
--- a/src/jalview/jbgui/GPairwiseAlignPanel.java
+++ b/src/jalview/jbgui/GPairwiseAlignPanel.java
@@ -1,90 +1,90 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GPairwiseAlignPanel
-    extends JPanel
-{
-  protected JScrollPane scrollPane = new JScrollPane();
-  protected JTextArea textarea = new JTextArea();
-  protected JButton viewInEditorButton = new JButton();
-  JPanel jPanel1 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  /**
-   * Creates a new GPairwiseAlignPanel object.
-   */
-  public GPairwiseAlignPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(borderLayout1);
-    textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
-    textarea.setText("");
-    textarea.setWrapStyleWord(false);
-    viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
-    viewInEditorButton.setText("View in alignment editor");
-    viewInEditorButton.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        viewInEditorButton_actionPerformed(e);
-      }
-    });
-    this.add(scrollPane, BorderLayout.CENTER);
-    scrollPane.getViewport().add(textarea, null);
-    this.add(jPanel1, BorderLayout.SOUTH);
-    jPanel1.add(viewInEditorButton, null);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GPairwiseAlignPanel
+    extends JPanel
+{
+  protected JScrollPane scrollPane = new JScrollPane();
+  protected JTextArea textarea = new JTextArea();
+  protected JButton viewInEditorButton = new JButton();
+  JPanel jPanel1 = new JPanel();
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  /**
+   * Creates a new GPairwiseAlignPanel object.
+   */
+  public GPairwiseAlignPanel()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
+    textarea.setText("");
+    textarea.setWrapStyleWord(false);
+    viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
+    viewInEditorButton.setText("View in alignment editor");
+    viewInEditorButton.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        viewInEditorButton_actionPerformed(e);
+      }
+    });
+    this.add(scrollPane, BorderLayout.CENTER);
+    scrollPane.getViewport().add(textarea, null);
+    this.add(jPanel1, BorderLayout.SOUTH);
+    jPanel1.add(viewInEditorButton, null);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void viewInEditorButton_actionPerformed(ActionEvent e)
+  {
+  }
+}
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 842ade9..fd142fc 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -1,565 +1,565 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.border.*;
-import javax.swing.event.*;
-import java.awt.Rectangle;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GPreferences
-    extends JPanel
-{
-  JTabbedPane tabbedPane = new JTabbedPane();
-
-  JButton ok = new JButton();
-  JButton cancel = new JButton();
-  JPanel okCancelPanel = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  protected JCheckBox quality = new JCheckBox();
-  JPanel visualTab = new JPanel();
-  protected JCheckBox fullScreen = new JCheckBox();
-  protected JCheckBox conservation = new JCheckBox();
-  protected JCheckBox identity = new JCheckBox();
-  protected JCheckBox annotations = new JCheckBox();
-  JLabel gapLabel = new JLabel();
-  protected JComboBox colour = new JComboBox();
-  JLabel colourLabel = new JLabel();
-  JLabel fontLabel = 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();
-  JPanel connectTab = new JPanel();
-  JLabel serverLabel = new JLabel();
-  protected JList linkURLList = new JList();
-  protected JTextField proxyServerTB = new JTextField();
-  protected JTextField proxyPortTB = new JTextField();
-  JLabel portLabel = new JLabel();
-  JLabel browserLabel = new JLabel();
-  protected JTextField defaultBrowser = new JTextField();
-  JButton newLink = new JButton();
-  JButton editLink = new JButton();
-  JButton deleteLink = new JButton();
-  JScrollPane linkScrollPane = new JScrollPane();
-  JPanel linkPanel = new JPanel();
-  BorderLayout borderLayout2 = new BorderLayout();
-  JPanel editLinkButtons = new JPanel();
-  GridLayout gridLayout1 = new GridLayout();
-  protected JList linkNameList = new JList();
-  JPanel linkPanel2 = new JPanel();
-  BorderLayout borderLayout3 = new BorderLayout();
-  protected JCheckBox useProxy = new JCheckBox();
-  JPanel jPanel1 = new JPanel();
-  TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
-  TitledBorder titledBorder2 = new TitledBorder("File Output");
-  GridBagLayout gridBagLayout2 = new GridBagLayout();
-  GridBagLayout gridBagLayout1 = new GridBagLayout();
-  GridBagLayout gridBagLayout3 = new GridBagLayout();
-  protected JComboBox sortby = new JComboBox();
-  JLabel sortLabel = new JLabel();
-  JPanel jPanel2 = new JPanel();
-  GridLayout gridLayout2 = new GridLayout();
-  JPanel jPanel3 = new JPanel();
-  JPanel exportTab = new JPanel();
-  JLabel epsLabel = new JLabel();
-  protected JComboBox epsRendering = new JComboBox();
-  JLabel jLabel1 = new JLabel();
-  protected JCheckBox blcjv = new JCheckBox();
-  protected JCheckBox pileupjv = new JCheckBox();
-  protected JCheckBox clustaljv = new JCheckBox();
-  protected JCheckBox msfjv = new JCheckBox();
-  protected JCheckBox fastajv = new JCheckBox();
-  protected JCheckBox pfamjv = new JCheckBox();
-  FlowLayout flowLayout1 = new FlowLayout();
-  protected JCheckBox pirjv = new JCheckBox();
-  JPanel jPanel11 = new JPanel();
-  Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
-  protected JCheckBox seqLimit = new JCheckBox();
-  GridLayout gridLayout3 = new GridLayout();
-  protected JCheckBox smoothFont = new JCheckBox();
-  JPanel calcTab = new JPanel();
-  protected JCheckBox autoCalculateConsCheck = new JCheckBox();
-  protected JCheckBox padGaps = new JCheckBox();
-  protected JCheckBox modellerOutput = new JCheckBox();
-  protected JPanel dasPanel = new JPanel();
-  BorderLayout borderLayout4 = new BorderLayout();
-  protected JCheckBox wrap = new JCheckBox();
-  protected JCheckBox rightAlign = new JCheckBox();
-  protected JCheckBox idItalics = new JCheckBox();
-  protected JCheckBox openoverv = new JCheckBox();
-  /**
-   * Creates a new GPreferences object.
-   */
-  public GPreferences()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(borderLayout1);
-    ok.setText("OK");
-    ok.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setText("Cancel");
-    cancel.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    quality.setEnabled(false);
-    quality.setFont(verdana11);
-    quality.setHorizontalAlignment(SwingConstants.RIGHT);
-    quality.setHorizontalTextPosition(SwingConstants.LEFT);
-    quality.setSelected(true);
-    quality.setText("Quality");
-    visualTab.setBorder(new TitledBorder("Open new alignment"));
-    visualTab.setLayout(null);
-    fullScreen.setFont(verdana11);
-    fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
-    fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
-    fullScreen.setText("Maximise Window");
-    conservation.setEnabled(false);
-    conservation.setFont(verdana11);
-    conservation.setHorizontalAlignment(SwingConstants.RIGHT);
-    conservation.setHorizontalTextPosition(SwingConstants.LEFT);
-    conservation.setSelected(true);
-    conservation.setText("Conservation");
-    identity.setEnabled(false);
-    identity.setFont(verdana11);
-    identity.setHorizontalAlignment(SwingConstants.RIGHT);
-    identity.setHorizontalTextPosition(SwingConstants.LEFT);
-    identity.setSelected(true);
-    identity.setText("Consensus");
-    annotations.setFont(verdana11);
-    annotations.setHorizontalAlignment(SwingConstants.RIGHT);
-    annotations.setHorizontalTextPosition(SwingConstants.LEFT);
-    annotations.setSelected(true);
-    annotations.setText("Show Annotations");
-    annotations.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        annotations_actionPerformed(e);
-      }
-    });
-    gapLabel.setFont(verdana11);
-    gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    gapLabel.setText("Gap Symbol ");
-    colour.setFont(verdana11);
-    colour.setBounds(new Rectangle(172, 225, 155, 21));
-    colourLabel.setFont(verdana11);
-    colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    colourLabel.setText("Colour ");
-    fontLabel.setFont(verdana11);
-    fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    fontLabel.setText("Font ");
-    fontSizeCB.setFont(verdana11);
-    fontSizeCB.setBounds(new Rectangle(319, 111, 49, 21));
-    fontStyleCB.setFont(verdana11);
-    fontStyleCB.setBounds(new Rectangle(367, 111, 70, 21));
-    fontNameCB.setFont(verdana11);
-    fontNameCB.setBounds(new Rectangle(172, 111, 147, 21));
-    gapSymbolCB.setFont(verdana11);
-    gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
-    startupCheckbox.setText("Open file");
-    startupCheckbox.setFont(verdana11);
-    startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
-    startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
-    startupCheckbox.setSelected(true);
-    startupFileTextfield.setFont(verdana11);
-    startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
-    startupFileTextfield.addMouseListener(new MouseAdapter()
-    {
-      public void mouseClicked(MouseEvent e)
-      {
-        if (e.getClickCount() > 1)
-        {
-          startupFileTextfield_mouseClicked();
-        }
-      }
-    });
-
-    connectTab.setLayout(gridBagLayout3);
-    serverLabel.setText("Address");
-    serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    serverLabel.setFont(verdana11);
-    proxyServerTB.setFont(verdana11);
-    proxyPortTB.setFont(verdana11);
-    portLabel.setFont(verdana11);
-    portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    portLabel.setText("Port");
-    browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
-    browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
-    browserLabel.setText("Default Browser (Unix)");
-    defaultBrowser.setFont(verdana11);
-    defaultBrowser.setText("");
-    newLink.setText("New");
-    newLink.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        newLink_actionPerformed(e);
-      }
-    });
-    editLink.setText("Edit");
-    editLink.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        editLink_actionPerformed(e);
-      }
-    });
-    deleteLink.setText("Delete");
-    deleteLink.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deleteLink_actionPerformed(e);
-      }
-    });
-
-    linkURLList.addListSelectionListener(new ListSelectionListener()
-    {
-      public void valueChanged(ListSelectionEvent e)
-      {
-        int index = linkURLList.getSelectedIndex();
-        linkNameList.setSelectedIndex(index);
-      }
-    });
-
-    linkNameList.addListSelectionListener(new ListSelectionListener()
-    {
-      public void valueChanged(ListSelectionEvent e)
-      {
-        int index = linkNameList.getSelectedIndex();
-        linkURLList.setSelectedIndex(index);
-      }
-    });
-
-    linkScrollPane.setBorder(null);
-    linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
-    linkPanel.setLayout(borderLayout2);
-    editLinkButtons.setLayout(gridLayout1);
-    gridLayout1.setRows(3);
-    linkNameList.setFont(verdana11);
-    linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-    linkPanel2.setLayout(borderLayout3);
-    linkURLList.setFont(verdana11);
-    linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
-    defaultBrowser.addMouseListener(new MouseAdapter()
-    {
-      public void mouseClicked(MouseEvent e)
-      {
-        if (e.getClickCount() > 1)
-        {
-          defaultBrowser_mouseClicked(e);
-        }
-      }
-    });
-    useProxy.setFont(verdana11);
-    useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
-    useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
-    useProxy.setText("Use a proxy server");
-    useProxy.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        useProxy_actionPerformed();
-      }
-    });
-    jPanel1.setBorder(titledBorder1);
-    jPanel1.setLayout(gridBagLayout1);
-    sortby.setFont(verdana11);
-    sortby.setBounds(new Rectangle(172, 249, 155, 21));
-    sortLabel.setFont(verdana11);
-    sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    sortLabel.setText("Sort by ");
-    jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
-    jPanel2.setLayout(gridLayout2);
-    gridLayout2.setRows(12);
-    jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
-    exportTab.setLayout(null);
-    epsLabel.setFont(verdana11);
-    epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    epsLabel.setText("EPS Rendering Style");
-    epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
-    epsRendering.setFont(verdana11);
-    epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
-    jLabel1.setFont(verdana11);
-    jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
-    jLabel1.setText("Append /start-end (/15-380)");
-    jLabel1.setFont(verdana11);
-    fastajv.setFont(verdana11);
-    fastajv.setHorizontalAlignment(SwingConstants.LEFT);
-    clustaljv.setText("Clustal     ");
-    blcjv.setText("BLC     ");
-    fastajv.setText("Fasta     ");
-    msfjv.setText("MSF     ");
-    pfamjv.setText("PFAM     ");
-    pileupjv.setText("Pileup     ");
-    msfjv.setFont(verdana11);
-    msfjv.setHorizontalAlignment(SwingConstants.LEFT);
-    pirjv.setText("PIR     ");
-    jPanel11.setFont(verdana11);
-    jPanel11.setBorder(titledBorder2);
-    jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
-    jPanel11.setLayout(gridLayout3);
-    blcjv.setFont(verdana11);
-    blcjv.setHorizontalAlignment(SwingConstants.LEFT);
-    clustaljv.setFont(verdana11);
-    clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
-    pfamjv.setFont(verdana11);
-    pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
-    pileupjv.setFont(verdana11);
-    pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
-    pirjv.setFont(verdana11);
-    pirjv.setHorizontalAlignment(SwingConstants.LEFT);
-    seqLimit.setFont(verdana11);
-    seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
-    seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
-    seqLimit.setText("Full Sequence Id");
-    gridLayout3.setRows(8);
-    smoothFont.setFont(verdana11);
-    smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
-    smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
-    smoothFont.setText("Smooth Font");
-    calcTab.setLayout(null);
-    autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    autoCalculateConsCheck.setText("AutoCalculate Consensus");
-    autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
-    padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    padGaps.setText("Pad gaps when editing");
-    padGaps.setBounds(new Rectangle(22, 94, 168, 23));
-    modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    modellerOutput.setText("Use Modeller Output");
-    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
-    dasPanel.setLayout(borderLayout4);
-    wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    wrap.setHorizontalAlignment(SwingConstants.TRAILING);
-    wrap.setHorizontalTextPosition(SwingConstants.LEADING);
-    wrap.setText("Wrap Alignment");
-    rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    rightAlign.setForeground(Color.black);
-    rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
-    rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
-    rightAlign.setText("Right Align Ids");
-    idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
-    idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
-    idItalics.setText("Sequence Name Italics");
-    openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    openoverv.setActionCommand("Open Overview");
-    openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
-    openoverv.setHorizontalTextPosition(SwingConstants.LEADING);
-    openoverv.setText("Open Overview Window");
-    openoverv.setBounds(new Rectangle(169, 17, 200, 23));
-    jPanel2.add(fullScreen);
-    jPanel2.add(annotations);
-    jPanel2.add(seqLimit);
-    jPanel2.add(rightAlign);
-    jPanel2.add(fontLabel);
-    jPanel2.add(idItalics);
-    jPanel2.add(smoothFont);
-    jPanel2.add(wrap);
-    jPanel2.add(gapLabel);
-    jPanel2.add(colourLabel);
-    jPanel2.add(sortLabel);
-    jPanel2.add(startupCheckbox);
-    visualTab.add(openoverv);
-    visualTab.add(startupFileTextfield);
-    visualTab.add(sortby);
-    visualTab.add(colour);
-    visualTab.add(gapSymbolCB);
-    visualTab.add(jPanel3);
-    visualTab.add(fontNameCB);
-    visualTab.add(fontSizeCB);
-    visualTab.add(fontStyleCB);
-    jPanel3.add(conservation);
-    jPanel3.add(identity);
-    jPanel3.add(quality);
-    visualTab.add(jPanel2);
-    linkPanel.add(editLinkButtons, BorderLayout.EAST);
-    editLinkButtons.add(newLink, null);
-    editLinkButtons.add(editLink, null);
-    editLinkButtons.add(deleteLink, null);
-    linkPanel.add(linkScrollPane, BorderLayout.CENTER);
-    linkScrollPane.getViewport().add(linkPanel2, null);
-    linkPanel2.add(linkURLList, BorderLayout.CENTER);
-    linkPanel2.add(linkNameList, BorderLayout.WEST);
-    okCancelPanel.add(ok);
-    okCancelPanel.add(cancel);
-    this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-
-    this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
-    jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.NONE,
-        new Insets(0, 2, 4, 0), 5, 0));
-    jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0
-                                                  , GridBagConstraints.WEST,
-                                                  GridBagConstraints.NONE,
-                                                  new Insets(0, 0, 4, 0), 11, 6));
-    connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0
-        , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
-        new Insets(16, 0, 0, 12), 359, -17));
-    connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
-        , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
-        new Insets(21, 0, 35, 12), 4, 6));
-    connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.NONE,
-        new Insets(16, 0, 0, 0), 5, 1));
-    jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
-        new Insets(0, 2, 4, 2), 54, 1));
-    jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
-        new Insets(0, 2, 4, 0), 263, 1));
-    connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
-        , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
-        new Insets(15, 0, 0, 15), 307, 1));
-
-    jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
-                                                 , GridBagConstraints.WEST,
-                                                 GridBagConstraints.NONE,
-                                                 new Insets(0, 2, 5, 185), 2,
-                                                 -4));
-    DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
-    dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
-    gapSymbolCB.setRenderer(dlcr);
-
-    tabbedPane.add(visualTab, "Visual");
-    tabbedPane.add(connectTab, "Connections");
-    tabbedPane.add(exportTab, "Output");
-    jPanel11.add(jLabel1);
-    jPanel11.add(blcjv);
-    jPanel11.add(clustaljv);
-    jPanel11.add(fastajv);
-    jPanel11.add(msfjv);
-    jPanel11.add(pfamjv);
-    jPanel11.add(pileupjv);
-    jPanel11.add(pirjv);
-    exportTab.add(modellerOutput);
-    tabbedPane.add(calcTab, "Editing");
-    calcTab.add(autoCalculateConsCheck);
-    calcTab.add(padGaps);
-    tabbedPane.add(dasPanel, "DAS Settings");
-
-    exportTab.add(epsLabel);
-    exportTab.add(epsRendering);
-    exportTab.add(jPanel11);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void ok_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void startupFileTextfield_mouseClicked()
-  {
-  }
-
-  public void newLink_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void editLink_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void deleteLink_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void defaultBrowser_mouseClicked(MouseEvent e)
-  {
-
-  }
-
-  public void linkURLList_keyTyped(KeyEvent e)
-  {
-
-  }
-
-  public void useProxy_actionPerformed()
-  {
-    proxyServerTB.setEnabled(useProxy.isSelected());
-    proxyPortTB.setEnabled(useProxy.isSelected());
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.event.*;
+import java.awt.Rectangle;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GPreferences
+    extends JPanel
+{
+  JTabbedPane tabbedPane = new JTabbedPane();
+
+  JButton ok = new JButton();
+  JButton cancel = new JButton();
+  JPanel okCancelPanel = new JPanel();
+  BorderLayout borderLayout1 = new BorderLayout();
+  protected JCheckBox quality = new JCheckBox();
+  JPanel visualTab = new JPanel();
+  protected JCheckBox fullScreen = new JCheckBox();
+  protected JCheckBox conservation = new JCheckBox();
+  protected JCheckBox identity = new JCheckBox();
+  protected JCheckBox annotations = new JCheckBox();
+  JLabel gapLabel = new JLabel();
+  protected JComboBox colour = new JComboBox();
+  JLabel colourLabel = new JLabel();
+  JLabel fontLabel = 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();
+  JPanel connectTab = new JPanel();
+  JLabel serverLabel = new JLabel();
+  protected JList linkURLList = new JList();
+  protected JTextField proxyServerTB = new JTextField();
+  protected JTextField proxyPortTB = new JTextField();
+  JLabel portLabel = new JLabel();
+  JLabel browserLabel = new JLabel();
+  protected JTextField defaultBrowser = new JTextField();
+  JButton newLink = new JButton();
+  JButton editLink = new JButton();
+  JButton deleteLink = new JButton();
+  JScrollPane linkScrollPane = new JScrollPane();
+  JPanel linkPanel = new JPanel();
+  BorderLayout borderLayout2 = new BorderLayout();
+  JPanel editLinkButtons = new JPanel();
+  GridLayout gridLayout1 = new GridLayout();
+  protected JList linkNameList = new JList();
+  JPanel linkPanel2 = new JPanel();
+  BorderLayout borderLayout3 = new BorderLayout();
+  protected JCheckBox useProxy = new JCheckBox();
+  JPanel jPanel1 = new JPanel();
+  TitledBorder titledBorder1 = new TitledBorder("Proxy Server");
+  TitledBorder titledBorder2 = new TitledBorder("File Output");
+  GridBagLayout gridBagLayout2 = new GridBagLayout();
+  GridBagLayout gridBagLayout1 = new GridBagLayout();
+  GridBagLayout gridBagLayout3 = new GridBagLayout();
+  protected JComboBox sortby = new JComboBox();
+  JLabel sortLabel = new JLabel();
+  JPanel jPanel2 = new JPanel();
+  GridLayout gridLayout2 = new GridLayout();
+  JPanel jPanel3 = new JPanel();
+  JPanel exportTab = new JPanel();
+  JLabel epsLabel = new JLabel();
+  protected JComboBox epsRendering = new JComboBox();
+  JLabel jLabel1 = new JLabel();
+  protected JCheckBox blcjv = new JCheckBox();
+  protected JCheckBox pileupjv = new JCheckBox();
+  protected JCheckBox clustaljv = new JCheckBox();
+  protected JCheckBox msfjv = new JCheckBox();
+  protected JCheckBox fastajv = new JCheckBox();
+  protected JCheckBox pfamjv = new JCheckBox();
+  FlowLayout flowLayout1 = new FlowLayout();
+  protected JCheckBox pirjv = new JCheckBox();
+  JPanel jPanel11 = new JPanel();
+  Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
+  protected JCheckBox seqLimit = new JCheckBox();
+  GridLayout gridLayout3 = new GridLayout();
+  protected JCheckBox smoothFont = new JCheckBox();
+  JPanel calcTab = new JPanel();
+  protected JCheckBox autoCalculateConsCheck = new JCheckBox();
+  protected JCheckBox padGaps = new JCheckBox();
+  protected JCheckBox modellerOutput = new JCheckBox();
+  protected JPanel dasPanel = new JPanel();
+  BorderLayout borderLayout4 = new BorderLayout();
+  protected JCheckBox wrap = new JCheckBox();
+  protected JCheckBox rightAlign = new JCheckBox();
+  protected JCheckBox idItalics = new JCheckBox();
+  protected JCheckBox openoverv = new JCheckBox();
+  /**
+   * Creates a new GPreferences object.
+   */
+  public GPreferences()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setText("Cancel");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    quality.setEnabled(false);
+    quality.setFont(verdana11);
+    quality.setHorizontalAlignment(SwingConstants.RIGHT);
+    quality.setHorizontalTextPosition(SwingConstants.LEFT);
+    quality.setSelected(true);
+    quality.setText("Quality");
+    visualTab.setBorder(new TitledBorder("Open new alignment"));
+    visualTab.setLayout(null);
+    fullScreen.setFont(verdana11);
+    fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
+    fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
+    fullScreen.setText("Maximise Window");
+    conservation.setEnabled(false);
+    conservation.setFont(verdana11);
+    conservation.setHorizontalAlignment(SwingConstants.RIGHT);
+    conservation.setHorizontalTextPosition(SwingConstants.LEFT);
+    conservation.setSelected(true);
+    conservation.setText("Conservation");
+    identity.setEnabled(false);
+    identity.setFont(verdana11);
+    identity.setHorizontalAlignment(SwingConstants.RIGHT);
+    identity.setHorizontalTextPosition(SwingConstants.LEFT);
+    identity.setSelected(true);
+    identity.setText("Consensus");
+    annotations.setFont(verdana11);
+    annotations.setHorizontalAlignment(SwingConstants.RIGHT);
+    annotations.setHorizontalTextPosition(SwingConstants.LEFT);
+    annotations.setSelected(true);
+    annotations.setText("Show Annotations");
+    annotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotations_actionPerformed(e);
+      }
+    });
+    gapLabel.setFont(verdana11);
+    gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    gapLabel.setText("Gap Symbol ");
+    colour.setFont(verdana11);
+    colour.setBounds(new Rectangle(172, 225, 155, 21));
+    colourLabel.setFont(verdana11);
+    colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    colourLabel.setText("Colour ");
+    fontLabel.setFont(verdana11);
+    fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    fontLabel.setText("Font ");
+    fontSizeCB.setFont(verdana11);
+    fontSizeCB.setBounds(new Rectangle(319, 111, 49, 21));
+    fontStyleCB.setFont(verdana11);
+    fontStyleCB.setBounds(new Rectangle(367, 111, 70, 21));
+    fontNameCB.setFont(verdana11);
+    fontNameCB.setBounds(new Rectangle(172, 111, 147, 21));
+    gapSymbolCB.setFont(verdana11);
+    gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
+    startupCheckbox.setText("Open file");
+    startupCheckbox.setFont(verdana11);
+    startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
+    startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
+    startupCheckbox.setSelected(true);
+    startupFileTextfield.setFont(verdana11);
+    startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));
+    startupFileTextfield.addMouseListener(new MouseAdapter()
+    {
+      public void mouseClicked(MouseEvent e)
+      {
+        if (e.getClickCount() > 1)
+        {
+          startupFileTextfield_mouseClicked();
+        }
+      }
+    });
+
+    connectTab.setLayout(gridBagLayout3);
+    serverLabel.setText("Address");
+    serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    serverLabel.setFont(verdana11);
+    proxyServerTB.setFont(verdana11);
+    proxyPortTB.setFont(verdana11);
+    portLabel.setFont(verdana11);
+    portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    portLabel.setText("Port");
+    browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+    browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
+    browserLabel.setText("Default Browser (Unix)");
+    defaultBrowser.setFont(verdana11);
+    defaultBrowser.setText("");
+    newLink.setText("New");
+    newLink.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        newLink_actionPerformed(e);
+      }
+    });
+    editLink.setText("Edit");
+    editLink.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        editLink_actionPerformed(e);
+      }
+    });
+    deleteLink.setText("Delete");
+    deleteLink.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        deleteLink_actionPerformed(e);
+      }
+    });
+
+    linkURLList.addListSelectionListener(new ListSelectionListener()
+    {
+      public void valueChanged(ListSelectionEvent e)
+      {
+        int index = linkURLList.getSelectedIndex();
+        linkNameList.setSelectedIndex(index);
+      }
+    });
+
+    linkNameList.addListSelectionListener(new ListSelectionListener()
+    {
+      public void valueChanged(ListSelectionEvent e)
+      {
+        int index = linkNameList.getSelectedIndex();
+        linkURLList.setSelectedIndex(index);
+      }
+    });
+
+    linkScrollPane.setBorder(null);
+    linkPanel.setBorder(new TitledBorder("URL link from Sequence ID"));
+    linkPanel.setLayout(borderLayout2);
+    editLinkButtons.setLayout(gridLayout1);
+    gridLayout1.setRows(3);
+    linkNameList.setFont(verdana11);
+    linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+    linkPanel2.setLayout(borderLayout3);
+    linkURLList.setFont(verdana11);
+    linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+    defaultBrowser.addMouseListener(new MouseAdapter()
+    {
+      public void mouseClicked(MouseEvent e)
+      {
+        if (e.getClickCount() > 1)
+        {
+          defaultBrowser_mouseClicked(e);
+        }
+      }
+    });
+    useProxy.setFont(verdana11);
+    useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
+    useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
+    useProxy.setText("Use a proxy server");
+    useProxy.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        useProxy_actionPerformed();
+      }
+    });
+    jPanel1.setBorder(titledBorder1);
+    jPanel1.setLayout(gridBagLayout1);
+    sortby.setFont(verdana11);
+    sortby.setBounds(new Rectangle(172, 249, 155, 21));
+    sortLabel.setFont(verdana11);
+    sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    sortLabel.setText("Sort by ");
+    jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
+    jPanel2.setLayout(gridLayout2);
+    gridLayout2.setRows(12);
+    jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
+    exportTab.setLayout(null);
+    epsLabel.setFont(verdana11);
+    epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    epsLabel.setText("EPS Rendering Style");
+    epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+    epsRendering.setFont(verdana11);
+    epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+    jLabel1.setFont(verdana11);
+    jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+    jLabel1.setText("Append /start-end (/15-380)");
+    jLabel1.setFont(verdana11);
+    fastajv.setFont(verdana11);
+    fastajv.setHorizontalAlignment(SwingConstants.LEFT);
+    clustaljv.setText("Clustal     ");
+    blcjv.setText("BLC     ");
+    fastajv.setText("Fasta     ");
+    msfjv.setText("MSF     ");
+    pfamjv.setText("PFAM     ");
+    pileupjv.setText("Pileup     ");
+    msfjv.setFont(verdana11);
+    msfjv.setHorizontalAlignment(SwingConstants.LEFT);
+    pirjv.setText("PIR     ");
+    jPanel11.setFont(verdana11);
+    jPanel11.setBorder(titledBorder2);
+    jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+    jPanel11.setLayout(gridLayout3);
+    blcjv.setFont(verdana11);
+    blcjv.setHorizontalAlignment(SwingConstants.LEFT);
+    clustaljv.setFont(verdana11);
+    clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
+    pfamjv.setFont(verdana11);
+    pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
+    pileupjv.setFont(verdana11);
+    pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
+    pirjv.setFont(verdana11);
+    pirjv.setHorizontalAlignment(SwingConstants.LEFT);
+    seqLimit.setFont(verdana11);
+    seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
+    seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
+    seqLimit.setText("Full Sequence Id");
+    gridLayout3.setRows(8);
+    smoothFont.setFont(verdana11);
+    smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
+    smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
+    smoothFont.setText("Smooth Font");
+    calcTab.setLayout(null);
+    autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    autoCalculateConsCheck.setText("AutoCalculate Consensus");
+    autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
+    padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    padGaps.setText("Pad gaps when editing");
+    padGaps.setBounds(new Rectangle(22, 94, 168, 23));
+    modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    modellerOutput.setText("Use Modeller Output");
+    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+    dasPanel.setLayout(borderLayout4);
+    wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    wrap.setHorizontalAlignment(SwingConstants.TRAILING);
+    wrap.setHorizontalTextPosition(SwingConstants.LEADING);
+    wrap.setText("Wrap Alignment");
+    rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    rightAlign.setForeground(Color.black);
+    rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
+    rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
+    rightAlign.setText("Right Align Ids");
+    idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
+    idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
+    idItalics.setText("Sequence Name Italics");
+    openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    openoverv.setActionCommand("Open Overview");
+    openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
+    openoverv.setHorizontalTextPosition(SwingConstants.LEADING);
+    openoverv.setText("Open Overview Window");
+    openoverv.setBounds(new Rectangle(169, 17, 200, 23));
+    jPanel2.add(fullScreen);
+    jPanel2.add(annotations);
+    jPanel2.add(seqLimit);
+    jPanel2.add(rightAlign);
+    jPanel2.add(fontLabel);
+    jPanel2.add(idItalics);
+    jPanel2.add(smoothFont);
+    jPanel2.add(wrap);
+    jPanel2.add(gapLabel);
+    jPanel2.add(colourLabel);
+    jPanel2.add(sortLabel);
+    jPanel2.add(startupCheckbox);
+    visualTab.add(openoverv);
+    visualTab.add(startupFileTextfield);
+    visualTab.add(sortby);
+    visualTab.add(colour);
+    visualTab.add(gapSymbolCB);
+    visualTab.add(jPanel3);
+    visualTab.add(fontNameCB);
+    visualTab.add(fontSizeCB);
+    visualTab.add(fontStyleCB);
+    jPanel3.add(conservation);
+    jPanel3.add(identity);
+    jPanel3.add(quality);
+    visualTab.add(jPanel2);
+    linkPanel.add(editLinkButtons, BorderLayout.EAST);
+    editLinkButtons.add(newLink, null);
+    editLinkButtons.add(editLink, null);
+    editLinkButtons.add(deleteLink, null);
+    linkPanel.add(linkScrollPane, BorderLayout.CENTER);
+    linkScrollPane.getViewport().add(linkPanel2, null);
+    linkPanel2.add(linkURLList, BorderLayout.CENTER);
+    linkPanel2.add(linkNameList, BorderLayout.WEST);
+    okCancelPanel.add(ok);
+    okCancelPanel.add(cancel);
+    this.add(tabbedPane, java.awt.BorderLayout.CENTER);
+
+    this.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
+    jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
+        , GridBagConstraints.WEST, GridBagConstraints.NONE,
+        new Insets(0, 2, 4, 0), 5, 0));
+    jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0
+                                                  , GridBagConstraints.WEST,
+                                                  GridBagConstraints.NONE,
+                                                  new Insets(0, 0, 4, 0), 11, 6));
+    connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0
+        , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+        new Insets(16, 0, 0, 12), 359, -17));
+    connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
+        , GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+        new Insets(21, 0, 35, 12), 4, 6));
+    connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0
+        , GridBagConstraints.WEST, GridBagConstraints.NONE,
+        new Insets(16, 0, 0, 0), 5, 1));
+    jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0
+        , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+        new Insets(0, 2, 4, 2), 54, 1));
+    jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
+        , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+        new Insets(0, 2, 4, 0), 263, 1));
+    connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
+        , GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+        new Insets(15, 0, 0, 15), 307, 1));
+
+    jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
+                                                 , GridBagConstraints.WEST,
+                                                 GridBagConstraints.NONE,
+                                                 new Insets(0, 2, 5, 185), 2,
+                                                 -4));
+    DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+    dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+    gapSymbolCB.setRenderer(dlcr);
+
+    tabbedPane.add(visualTab, "Visual");
+    tabbedPane.add(connectTab, "Connections");
+    tabbedPane.add(exportTab, "Output");
+    jPanel11.add(jLabel1);
+    jPanel11.add(blcjv);
+    jPanel11.add(clustaljv);
+    jPanel11.add(fastajv);
+    jPanel11.add(msfjv);
+    jPanel11.add(pfamjv);
+    jPanel11.add(pileupjv);
+    jPanel11.add(pirjv);
+    exportTab.add(modellerOutput);
+    tabbedPane.add(calcTab, "Editing");
+    calcTab.add(autoCalculateConsCheck);
+    calcTab.add(padGaps);
+    tabbedPane.add(dasPanel, "DAS Settings");
+
+    exportTab.add(epsLabel);
+    exportTab.add(epsRendering);
+    exportTab.add(jPanel11);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void annotations_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void startupFileTextfield_mouseClicked()
+  {
+  }
+
+  public void newLink_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void editLink_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void deleteLink_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void defaultBrowser_mouseClicked(MouseEvent e)
+  {
+
+  }
+
+  public void linkURLList_keyTyped(KeyEvent e)
+  {
+
+  }
+
+  public void useProxy_actionPerformed()
+  {
+    proxyServerTB.setEnabled(useProxy.isSelected());
+    proxyPortTB.setEnabled(useProxy.isSelected());
+  }
+
+}
diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java
index 40d00be..a5927f3 100755
--- a/src/jalview/jbgui/GSequenceLink.java
+++ b/src/jalview/jbgui/GSequenceLink.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/jbgui/GSliderPanel.java b/src/jalview/jbgui/GSliderPanel.java
index 568c66a..15058e1 100755
--- a/src/jalview/jbgui/GSliderPanel.java
+++ b/src/jalview/jbgui/GSliderPanel.java
@@ -1,194 +1,194 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GSliderPanel
-    extends JPanel
-{
-  // this is used for conservation colours, PID colours and redundancy threshold
-  protected JSlider slider = new JSlider();
-  protected JTextField valueField = new JTextField();
-  protected JLabel label = new JLabel();
-  protected JPanel southPanel = 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();
-  JPanel jPanel1 = new JPanel();
-  BorderLayout borderLayout2 = new BorderLayout();
-
-  /**
-   * Creates a new GSliderPanel object.
-   */
-  public GSliderPanel()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  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);
-    slider.addMouseListener(new MouseAdapter()
-    {
-      public void mouseReleased(MouseEvent e)
-      {
-        slider_mouseReleased(e);
-      }
-    });
-    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");
-    southPanel.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);
-    southPanel.setOpaque(false);
-    jPanel1.setLayout(borderLayout2);
-    jPanel1.setOpaque(false);
-    this.add(jPanel2, null);
-    jPanel2.add(label, null);
-    jPanel2.add(applyButton, null);
-    jPanel2.add(undoButton, null);
-    this.add(southPanel, null);
-    southPanel.add(jPanel1, java.awt.BorderLayout.EAST);
-    southPanel.add(slider, java.awt.BorderLayout.CENTER);
-    jPanel1.add(valueField, java.awt.BorderLayout.CENTER);
-    jPanel1.add(allGroupsCheck, java.awt.BorderLayout.EAST);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void valueField_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void undoButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void allGroupsCheck_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void slider_mouseReleased(MouseEvent e)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GSliderPanel
+    extends JPanel
+{
+  // this is used for conservation colours, PID colours and redundancy threshold
+  protected JSlider slider = new JSlider();
+  protected JTextField valueField = new JTextField();
+  protected JLabel label = new JLabel();
+  protected JPanel southPanel = 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();
+  JPanel jPanel1 = new JPanel();
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  /**
+   * Creates a new GSliderPanel object.
+   */
+  public GSliderPanel()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  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);
+    slider.addMouseListener(new MouseAdapter()
+    {
+      public void mouseReleased(MouseEvent e)
+      {
+        slider_mouseReleased(e);
+      }
+    });
+    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");
+    southPanel.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);
+    southPanel.setOpaque(false);
+    jPanel1.setLayout(borderLayout2);
+    jPanel1.setOpaque(false);
+    this.add(jPanel2, null);
+    jPanel2.add(label, null);
+    jPanel2.add(applyButton, null);
+    jPanel2.add(undoButton, null);
+    this.add(southPanel, null);
+    southPanel.add(jPanel1, java.awt.BorderLayout.EAST);
+    southPanel.add(slider, java.awt.BorderLayout.CENTER);
+    jPanel1.add(valueField, java.awt.BorderLayout.CENTER);
+    jPanel1.add(allGroupsCheck, java.awt.BorderLayout.EAST);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void valueField_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void applyButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void undoButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void allGroupsCheck_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void slider_mouseReleased(MouseEvent e)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 10e0b9b..395389b 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,322 +1,321 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.jbgui;
-
-import javax.swing.*;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
-
-public class GStructureViewer  extends JInternalFrame
-{
-  public GStructureViewer()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    this.setJMenuBar(menuBar);
-    fileMenu.setText("File");
-    savemenu.setActionCommand("Save Image");
-    savemenu.setText("Save As");
-    pdbFile.setText("PDB File");
-    pdbFile.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        pdbFile_actionPerformed(actionEvent);
-      }
-    });
-    png.setText("PNG");
-    png.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        png_actionPerformed(actionEvent);
-      }
-    });
-    eps.setText("EPS");
-    eps.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        eps_actionPerformed(actionEvent);
-      }
-    });
-    viewMapping.setText("View Mapping");
-    viewMapping.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        viewMapping_actionPerformed(actionEvent);
-      }
-    });
-    viewMenu.setText("View");
-    chainMenu.setText("Show Chain");
-    colourMenu.setText("Colours");
-    backGround.setText("Background Colour...");
-    backGround.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        backGround_actionPerformed(actionEvent);
-      }
-    });
-    seqColour.setSelected(true);
-    seqColour.setText("By Sequence");
-    seqColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        seqColour_actionPerformed(actionEvent);
-      }
-    });
-    chainColour.setText("By Chain");
-    chainColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        chainColour_actionPerformed(actionEvent);
-      }
-    });
-    chargeColour.setText("Charge & Cysteine");
-    chargeColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        chargeColour_actionPerformed(actionEvent);
-      }
-    });
-    zappoColour.setText("Zappo");
-    zappoColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        zappoColour_actionPerformed(actionEvent);
-      }
-    });
-    taylorColour.setText("Taylor");
-    taylorColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        taylorColour_actionPerformed(actionEvent);
-      }
-    });
-    hydroColour.setText("Hydro");
-    hydroColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        hydroColour_actionPerformed(actionEvent);
-      }
-    });
-    strandColour.setText("Strand");
-    strandColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        strandColour_actionPerformed(actionEvent);
-      }
-    });
-    helixColour.setText("Helix Propensity");
-    helixColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        helixColour_actionPerformed(actionEvent);
-      }
-    });
-    turnColour.setText("Turn Propensity");
-    turnColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        turnColour_actionPerformed(actionEvent);
-      }
-    });
-    buriedColour.setText("Buried Index");
-    buriedColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        buriedColour_actionPerformed(actionEvent);
-      }
-    });
-    userColour.setText("User Defined ...");
-    userColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        userColour_actionPerformed(actionEvent);
-      }
-    });
-    helpMenu.setText("Help");
-    jmolHelp.setText("Jmol Help");
-    jmolHelp.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        jmolHelp_actionPerformed(actionEvent);
-      }
-    });
-    menuBar.add(fileMenu);
-    menuBar.add(viewMenu);
-    menuBar.add(colourMenu);
-    menuBar.add(helpMenu);
-    fileMenu.add(savemenu);
-    fileMenu.add(viewMapping);
-    savemenu.add(pdbFile);
-    savemenu.add(png);
-    savemenu.add(eps);
-    viewMenu.add(chainMenu);
-    colourMenu.add(seqColour);
-    colourMenu.add(chainColour);
-    colourMenu.add(chargeColour);
-    colourMenu.add(zappoColour);
-    colourMenu.add(taylorColour);
-    colourMenu.add(hydroColour);
-    colourMenu.add(helixColour);
-    colourMenu.add(strandColour);
-    colourMenu.add(turnColour);
-    colourMenu.add(buriedColour);
-    colourMenu.add(userColour);
-    colourMenu.add(backGround);
-    helpMenu.add(jmolHelp);
-  }
-
-  JMenuBar menuBar = new JMenuBar();
-  JMenu fileMenu = new JMenu();
-  JMenu savemenu = new JMenu();
-  JMenuItem pdbFile = new JMenuItem();
-  JMenuItem png = new JMenuItem();
-  JMenuItem eps = new JMenuItem();
-  JMenuItem viewMapping = new JMenuItem();
-  JMenu viewMenu = new JMenu();
-  protected JMenu chainMenu = new JMenu();
-  JMenu jMenu1 = new JMenu();
-  JMenu colourMenu = new JMenu();
-  JMenuItem backGround = new JMenuItem();
-  protected JCheckBoxMenuItem seqColour = new JCheckBoxMenuItem();
-  JMenuItem chainColour = new JMenuItem();
-  JMenuItem chargeColour = new JMenuItem();
-  JMenuItem zappoColour = new JMenuItem();
-  JMenuItem taylorColour = new JMenuItem();
-  JMenuItem hydroColour = new JMenuItem();
-  JMenuItem strandColour = new JMenuItem();
-  JMenuItem helixColour = new JMenuItem();
-  JMenuItem turnColour = new JMenuItem();
-  JMenuItem buriedColour = new JMenuItem();
-  JMenuItem userColour = new JMenuItem();
-  JMenu helpMenu = new JMenu();
-  JMenuItem jmolHelp = new JMenuItem();
-  public void pdbFile_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void png_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void eps_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void viewMapping_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void seqColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void chainColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void chargeColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void zappoColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void taylorColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void hydroColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void helixColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void strandColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void turnColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void buriedColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void userColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void backGround_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import javax.swing.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+public class GStructureViewer  extends JInternalFrame
+{
+  public GStructureViewer()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    this.setJMenuBar(menuBar);
+    fileMenu.setText("File");
+    savemenu.setActionCommand("Save Image");
+    savemenu.setText("Save As");
+    pdbFile.setText("PDB File");
+    pdbFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        pdbFile_actionPerformed(actionEvent);
+      }
+    });
+    png.setText("PNG");
+    png.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        png_actionPerformed(actionEvent);
+      }
+    });
+    eps.setText("EPS");
+    eps.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        eps_actionPerformed(actionEvent);
+      }
+    });
+    viewMapping.setText("View Mapping");
+    viewMapping.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        viewMapping_actionPerformed(actionEvent);
+      }
+    });
+    viewMenu.setText("View");
+    chainMenu.setText("Show Chain");
+    colourMenu.setText("Colours");
+    backGround.setText("Background Colour...");
+    backGround.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        backGround_actionPerformed(actionEvent);
+      }
+    });
+    seqColour.setSelected(true);
+    seqColour.setText("By Sequence");
+    seqColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        seqColour_actionPerformed(actionEvent);
+      }
+    });
+    chainColour.setText("By Chain");
+    chainColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        chainColour_actionPerformed(actionEvent);
+      }
+    });
+    chargeColour.setText("Charge & Cysteine");
+    chargeColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        chargeColour_actionPerformed(actionEvent);
+      }
+    });
+    zappoColour.setText("Zappo");
+    zappoColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        zappoColour_actionPerformed(actionEvent);
+      }
+    });
+    taylorColour.setText("Taylor");
+    taylorColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        taylorColour_actionPerformed(actionEvent);
+      }
+    });
+    hydroColour.setText("Hydro");
+    hydroColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        hydroColour_actionPerformed(actionEvent);
+      }
+    });
+    strandColour.setText("Strand");
+    strandColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        strandColour_actionPerformed(actionEvent);
+      }
+    });
+    helixColour.setText("Helix Propensity");
+    helixColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        helixColour_actionPerformed(actionEvent);
+      }
+    });
+    turnColour.setText("Turn Propensity");
+    turnColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        turnColour_actionPerformed(actionEvent);
+      }
+    });
+    buriedColour.setText("Buried Index");
+    buriedColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        buriedColour_actionPerformed(actionEvent);
+      }
+    });
+    userColour.setText("User Defined ...");
+    userColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        userColour_actionPerformed(actionEvent);
+      }
+    });
+    helpMenu.setText("Help");
+    jmolHelp.setText("Jmol Help");
+    jmolHelp.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        jmolHelp_actionPerformed(actionEvent);
+      }
+    });
+    menuBar.add(fileMenu);
+    menuBar.add(viewMenu);
+    menuBar.add(colourMenu);
+    menuBar.add(helpMenu);
+    fileMenu.add(savemenu);
+    fileMenu.add(viewMapping);
+    savemenu.add(pdbFile);
+    savemenu.add(png);
+    savemenu.add(eps);
+    viewMenu.add(chainMenu);
+    colourMenu.add(seqColour);
+    colourMenu.add(chainColour);
+    colourMenu.add(chargeColour);
+    colourMenu.add(zappoColour);
+    colourMenu.add(taylorColour);
+    colourMenu.add(hydroColour);
+    colourMenu.add(helixColour);
+    colourMenu.add(strandColour);
+    colourMenu.add(turnColour);
+    colourMenu.add(buriedColour);
+    colourMenu.add(userColour);
+    colourMenu.add(backGround);
+    helpMenu.add(jmolHelp);
+  }
+
+  JMenuBar menuBar = new JMenuBar();
+  JMenu fileMenu = new JMenu();
+  JMenu savemenu = new JMenu();
+  JMenuItem pdbFile = new JMenuItem();
+  JMenuItem png = new JMenuItem();
+  JMenuItem eps = new JMenuItem();
+  JMenuItem viewMapping = new JMenuItem();
+  JMenu viewMenu = new JMenu();
+  protected JMenu chainMenu = new JMenu();
+  JMenu jMenu1 = new JMenu();
+  JMenu colourMenu = new JMenu();
+  JMenuItem backGround = new JMenuItem();
+  protected JCheckBoxMenuItem seqColour = new JCheckBoxMenuItem();
+  JMenuItem chainColour = new JMenuItem();
+  JMenuItem chargeColour = new JMenuItem();
+  JMenuItem zappoColour = new JMenuItem();
+  JMenuItem taylorColour = new JMenuItem();
+  JMenuItem hydroColour = new JMenuItem();
+  JMenuItem strandColour = new JMenuItem();
+  JMenuItem helixColour = new JMenuItem();
+  JMenuItem turnColour = new JMenuItem();
+  JMenuItem buriedColour = new JMenuItem();
+  JMenuItem userColour = new JMenuItem();
+  JMenu helpMenu = new JMenu();
+  JMenuItem jmolHelp = new JMenuItem();
+  public void pdbFile_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void png_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void eps_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void viewMapping_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void seqColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void chainColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void chargeColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void zappoColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void taylorColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void hydroColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void helixColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void strandColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void turnColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void buriedColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void userColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void backGround_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index 5d3b8b8..d2f5995 100755
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -1,248 +1,248 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-public class GTreePanel
-    extends JInternalFrame
-{
-  BorderLayout borderLayout1 = new BorderLayout();
-  public JScrollPane scrollPane = new JScrollPane();
-  JMenuBar jMenuBar1 = new JMenuBar();
-  JMenu fileMenu = new JMenu();
-  JMenuItem saveAsNewick = new JMenuItem();
-  JMenuItem printMenu = new JMenuItem();
-  protected JMenu viewMenu = new JMenu();
-  public JMenuItem font = new JMenuItem();
-  public JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
-  JMenuItem pngTree = new JMenuItem();
-  JMenuItem epsTree = new JMenuItem();
-  JMenu saveAsMenu = new JMenu();
-  JMenuItem textbox = new JMenuItem();
-  public JMenuItem originalSeqData = new JMenuItem();
-  protected JMenu associateLeavesMenu = new JMenu();
-  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);
-    fileMenu.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);
-      }
-    });
-    viewMenu.setText("View");
-    viewMenu.addMenuListener(new MenuListener()
-    {
-      public void menuSelected(MenuEvent e)
-      {
-        viewMenu_menuSelected();
-      }
-
-      public void menuDeselected(MenuEvent e)
-      {
-      }
-
-      public void menuCanceled(MenuEvent e)
-      {
-      }
-    });
-    font.setText("Font...");
-    font.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        font_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);
-      }
-    });
-    originalSeqData.setText("Input Data...");
-    originalSeqData.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        originalSeqData_actionPerformed(e);
-      }
-    });
-    associateLeavesMenu.setText("Associate Leaves With");
-    this.getContentPane().add(scrollPane, BorderLayout.CENTER);
-    jMenuBar1.add(fileMenu);
-    jMenuBar1.add(viewMenu);
-    fileMenu.add(saveAsMenu);
-    fileMenu.add(textbox);
-    fileMenu.add(printMenu);
-    fileMenu.add(originalSeqData);
-    viewMenu.add(fitToWindow);
-    viewMenu.add(font);
-    viewMenu.add(distanceMenu);
-    viewMenu.add(bootstrapMenu);
-    viewMenu.add(placeholdersMenu);
-    viewMenu.add(associateLeavesMenu);
-    saveAsMenu.add(saveAsNewick);
-    saveAsMenu.add(epsTree);
-    saveAsMenu.add(pngTree);
-  }
-
-  public void printMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void font_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void distanceMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void fitToWindow_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void pngTree_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void epsTree_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void saveAsNewick_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void placeholdersMenu_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void textbox_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void fullid_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void originalSeqData_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void viewMenu_menuSelected()
-  {
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+public class GTreePanel
+    extends JInternalFrame
+{
+  BorderLayout borderLayout1 = new BorderLayout();
+  public JScrollPane scrollPane = new JScrollPane();
+  JMenuBar jMenuBar1 = new JMenuBar();
+  JMenu fileMenu = new JMenu();
+  JMenuItem saveAsNewick = new JMenuItem();
+  JMenuItem printMenu = new JMenuItem();
+  protected JMenu viewMenu = new JMenu();
+  public JMenuItem font = new JMenuItem();
+  public JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
+  JMenuItem pngTree = new JMenuItem();
+  JMenuItem epsTree = new JMenuItem();
+  JMenu saveAsMenu = new JMenu();
+  JMenuItem textbox = new JMenuItem();
+  public JMenuItem originalSeqData = new JMenuItem();
+  protected JMenu associateLeavesMenu = new JMenu();
+  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);
+    fileMenu.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);
+      }
+    });
+    viewMenu.setText("View");
+    viewMenu.addMenuListener(new MenuListener()
+    {
+      public void menuSelected(MenuEvent e)
+      {
+        viewMenu_menuSelected();
+      }
+
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
+    font.setText("Font...");
+    font.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        font_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);
+      }
+    });
+    originalSeqData.setText("Input Data...");
+    originalSeqData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        originalSeqData_actionPerformed(e);
+      }
+    });
+    associateLeavesMenu.setText("Associate Leaves With");
+    this.getContentPane().add(scrollPane, BorderLayout.CENTER);
+    jMenuBar1.add(fileMenu);
+    jMenuBar1.add(viewMenu);
+    fileMenu.add(saveAsMenu);
+    fileMenu.add(textbox);
+    fileMenu.add(printMenu);
+    fileMenu.add(originalSeqData);
+    viewMenu.add(fitToWindow);
+    viewMenu.add(font);
+    viewMenu.add(distanceMenu);
+    viewMenu.add(bootstrapMenu);
+    viewMenu.add(placeholdersMenu);
+    viewMenu.add(associateLeavesMenu);
+    saveAsMenu.add(saveAsNewick);
+    saveAsMenu.add(epsTree);
+    saveAsMenu.add(pngTree);
+  }
+
+  public void printMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void font_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void distanceMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void bootstrapMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void fitToWindow_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void pngTree_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void epsTree_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void saveAsNewick_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void placeholdersMenu_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void textbox_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void fullid_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void originalSeqData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void viewMenu_menuSelected()
+  {
+  }
+}
diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 1801152..f974133 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -1,253 +1,253 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GUserDefinedColours
-    extends JPanel
-{
-  protected JColorChooser colorChooser = new JColorChooser();
-  protected JPanel buttonPanel = new JPanel();
-  protected GridLayout gridLayout = new GridLayout();
-  JPanel lowerPanel = 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();
-  JPanel namePanel = new JPanel();
-  JLabel jLabel1 = new JLabel();
-  protected JTextField schemeName = new JTextField();
-  BorderLayout borderLayout1 = new BorderLayout();
-  JPanel panel1 = new JPanel();
-  JPanel okCancelPanel = new JPanel();
-  JPanel saveLoadPanel = new JPanel();
-  BorderLayout borderLayout3 = new BorderLayout();
-  GridBagLayout gridBagLayout1 = new GridBagLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  FlowLayout flowLayout1 = new FlowLayout();
-  BorderLayout borderLayout4 = new BorderLayout();
-  JPanel jPanel4 = new JPanel();
-  BorderLayout borderLayout5 = new BorderLayout();
-  JLabel label = new JLabel();
-  protected JPanel casePanel = new JPanel();
-  protected JCheckBox caseSensitive = new JCheckBox();
-  protected JButton lcaseColour = new JButton();
-  /**
-   * Creates a new GUserDefinedColours object.
-   */
-  public GUserDefinedColours()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    this.setLayout(borderLayout4);
-    buttonPanel.setLayout(gridLayout);
-    gridLayout.setColumns(4);
-    gridLayout.setRows(5);
-    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));
-    lowerPanel.setOpaque(false);
-    lowerPanel.setLayout(borderLayout3);
-    colorChooser.setOpaque(false);
-    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    jLabel1.setText("Name");
-    namePanel.setMinimumSize(new Dimension(300, 31));
-    namePanel.setOpaque(false);
-    namePanel.setPreferredSize(new Dimension(240, 25));
-    namePanel.setLayout(borderLayout1);
-    schemeName.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    schemeName.setPreferredSize(new Dimension(105, 21));
-    schemeName.setText("");
-    schemeName.setHorizontalAlignment(SwingConstants.CENTER);
-    panel1.setLayout(flowLayout1);
-    panel1.setOpaque(false);
-    okCancelPanel.setOpaque(false);
-    saveLoadPanel.setOpaque(false);
-    jPanel4.setLayout(borderLayout5);
-    label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
-    label.setOpaque(false);
-    label.setPreferredSize(new Dimension(260, 34));
-    label.setText(
-        "<html>Save your colour scheme with a unique name and it will be added " +
-        "to the Colour menu.</html>");
-    caseSensitive.setText("Case Sensitive");
-    caseSensitive.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        caseSensitive_actionPerformed(e);
-      }
-    });
-    lcaseColour.setText("Lower Case Colour");
-    lcaseColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        lcaseColour_actionPerformed(e);
-      }
-    });
-
-    saveLoadPanel.add(savebutton);
-    saveLoadPanel.add(loadbutton);
-    okCancelPanel.add(applyButton);
-    okCancelPanel.add(okButton);
-    okCancelPanel.add(cancelButton);
-    lowerPanel.add(saveLoadPanel, java.awt.BorderLayout.NORTH);
-    lowerPanel.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
-
-    namePanel.add(schemeName, java.awt.BorderLayout.CENTER);
-    namePanel.add(jLabel1, java.awt.BorderLayout.WEST);
-    panel1.add(namePanel, null);
-    panel1.add(buttonPanel, null);
-    panel1.add(casePanel);
-    casePanel.add(caseSensitive);
-    casePanel.add(lcaseColour);
-    panel1.add(lowerPanel, null);
-    panel1.add(label);
-
-    jPanel4.add(panel1, java.awt.BorderLayout.CENTER);
-    this.add(jPanel4, java.awt.BorderLayout.CENTER);
-    this.add(colorChooser, java.awt.BorderLayout.EAST);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void okButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void applyButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void loadbutton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void savebutton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void cancelButton_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void caseSensitive_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void lcaseColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GUserDefinedColours
+    extends JPanel
+{
+  protected JColorChooser colorChooser = new JColorChooser();
+  protected JPanel buttonPanel = new JPanel();
+  protected GridLayout gridLayout = new GridLayout();
+  JPanel lowerPanel = 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();
+  JPanel namePanel = new JPanel();
+  JLabel jLabel1 = new JLabel();
+  protected JTextField schemeName = new JTextField();
+  BorderLayout borderLayout1 = new BorderLayout();
+  JPanel panel1 = new JPanel();
+  JPanel okCancelPanel = new JPanel();
+  JPanel saveLoadPanel = new JPanel();
+  BorderLayout borderLayout3 = new BorderLayout();
+  GridBagLayout gridBagLayout1 = new GridBagLayout();
+  BorderLayout borderLayout2 = new BorderLayout();
+  FlowLayout flowLayout1 = new FlowLayout();
+  BorderLayout borderLayout4 = new BorderLayout();
+  JPanel jPanel4 = new JPanel();
+  BorderLayout borderLayout5 = new BorderLayout();
+  JLabel label = new JLabel();
+  protected JPanel casePanel = new JPanel();
+  protected JCheckBox caseSensitive = new JCheckBox();
+  protected JButton lcaseColour = new JButton();
+  /**
+   * Creates a new GUserDefinedColours object.
+   */
+  public GUserDefinedColours()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout4);
+    buttonPanel.setLayout(gridLayout);
+    gridLayout.setColumns(4);
+    gridLayout.setRows(5);
+    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));
+    lowerPanel.setOpaque(false);
+    lowerPanel.setLayout(borderLayout3);
+    colorChooser.setOpaque(false);
+    jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    jLabel1.setText("Name");
+    namePanel.setMinimumSize(new Dimension(300, 31));
+    namePanel.setOpaque(false);
+    namePanel.setPreferredSize(new Dimension(240, 25));
+    namePanel.setLayout(borderLayout1);
+    schemeName.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    schemeName.setPreferredSize(new Dimension(105, 21));
+    schemeName.setText("");
+    schemeName.setHorizontalAlignment(SwingConstants.CENTER);
+    panel1.setLayout(flowLayout1);
+    panel1.setOpaque(false);
+    okCancelPanel.setOpaque(false);
+    saveLoadPanel.setOpaque(false);
+    jPanel4.setLayout(borderLayout5);
+    label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
+    label.setOpaque(false);
+    label.setPreferredSize(new Dimension(260, 34));
+    label.setText(
+        "<html>Save your colour scheme with a unique name and it will be added " +
+        "to the Colour menu.</html>");
+    caseSensitive.setText("Case Sensitive");
+    caseSensitive.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        caseSensitive_actionPerformed(e);
+      }
+    });
+    lcaseColour.setText("Lower Case Colour");
+    lcaseColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        lcaseColour_actionPerformed(e);
+      }
+    });
+
+    saveLoadPanel.add(savebutton);
+    saveLoadPanel.add(loadbutton);
+    okCancelPanel.add(applyButton);
+    okCancelPanel.add(okButton);
+    okCancelPanel.add(cancelButton);
+    lowerPanel.add(saveLoadPanel, java.awt.BorderLayout.NORTH);
+    lowerPanel.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
+
+    namePanel.add(schemeName, java.awt.BorderLayout.CENTER);
+    namePanel.add(jLabel1, java.awt.BorderLayout.WEST);
+    panel1.add(namePanel, null);
+    panel1.add(buttonPanel, null);
+    panel1.add(casePanel);
+    casePanel.add(caseSensitive);
+    casePanel.add(lcaseColour);
+    panel1.add(lowerPanel, null);
+    panel1.add(label);
+
+    jPanel4.add(panel1, java.awt.BorderLayout.CENTER);
+    this.add(jPanel4, java.awt.BorderLayout.CENTER);
+    this.add(colorChooser, java.awt.BorderLayout.EAST);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void okButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void applyButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void loadbutton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void savebutton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void cancelButton_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void caseSensitive_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void lcaseColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+}
diff --git a/src/jalview/jbgui/GWebserviceInfo.java b/src/jalview/jbgui/GWebserviceInfo.java
index ca68115..7aadd77 100755
--- a/src/jalview/jbgui/GWebserviceInfo.java
+++ b/src/jalview/jbgui/GWebserviceInfo.java
@@ -1,115 +1,115 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GWebserviceInfo
-    extends JPanel
-{
-  protected JTextArea infoText = new JTextArea();
-  JScrollPane jScrollPane1 = new JScrollPane();
-  JPanel jPanel1 = new JPanel();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  protected JPanel titlePanel = new JPanel();
-  BorderLayout borderLayout3 = new BorderLayout();
-  protected JPanel buttonPanel = new JPanel();
-  public JButton cancel = new JButton();
-  public JButton showResultsNewFrame = new JButton();
-  public JButton mergeResults = new JButton();
-  GridBagLayout gridBagLayout1 = new GridBagLayout();
-  /**
-   * Creates a new GWebserviceInfo object.
-   */
-  public GWebserviceInfo()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
-   */
-  private void jbInit()
-      throws Exception
-  {
-    infoText.setFont(new java.awt.Font("Verdana", 0, 10));
-    infoText.setBorder(null);
-    infoText.setEditable(false);
-    infoText.setText("");
-    infoText.setLineWrap(true);
-    infoText.setWrapStyleWord(true);
-    this.setLayout(borderLayout1);
-    jPanel1.setLayout(borderLayout2);
-    titlePanel.setBackground(Color.white);
-    titlePanel.setPreferredSize(new Dimension(0, 60));
-    titlePanel.setLayout(borderLayout3);
-    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);
-      }
-    });
-    buttonPanel.setLayout(gridBagLayout1);
-    buttonPanel.setOpaque(false);
-    showResultsNewFrame.setText("New Window");
-    mergeResults.setText("Merge Results");
-    this.setBackground(Color.white);
-    this.add(jPanel1, BorderLayout.NORTH);
-    jPanel1.add(jScrollPane1, BorderLayout.CENTER);
-    jScrollPane1.getViewport().add(infoText, null);
-    jPanel1.add(titlePanel, BorderLayout.NORTH);
-    titlePanel.add(buttonPanel, BorderLayout.EAST);
-    buttonPanel.add(cancel, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0
-        , GridBagConstraints.CENTER,
-        GridBagConstraints.NONE,
-        new Insets(19, 6, 16, 4), 0, 0));
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
-   */
-  protected void cancel_actionPerformed(ActionEvent e)
-  {
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class GWebserviceInfo
+    extends JPanel
+{
+  protected JTextArea infoText = new JTextArea();
+  JScrollPane jScrollPane1 = new JScrollPane();
+  JPanel jPanel1 = new JPanel();
+  BorderLayout borderLayout1 = new BorderLayout();
+  BorderLayout borderLayout2 = new BorderLayout();
+  protected JPanel titlePanel = new JPanel();
+  BorderLayout borderLayout3 = new BorderLayout();
+  protected JPanel buttonPanel = new JPanel();
+  public JButton cancel = new JButton();
+  public JButton showResultsNewFrame = new JButton();
+  public JButton mergeResults = new JButton();
+  GridBagLayout gridBagLayout1 = new GridBagLayout();
+  /**
+   * Creates a new GWebserviceInfo object.
+   */
+  public GWebserviceInfo()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @throws Exception DOCUMENT ME!
+   */
+  private void jbInit()
+      throws Exception
+  {
+    infoText.setFont(new java.awt.Font("Verdana", 0, 10));
+    infoText.setBorder(null);
+    infoText.setEditable(false);
+    infoText.setText("");
+    infoText.setLineWrap(true);
+    infoText.setWrapStyleWord(true);
+    this.setLayout(borderLayout1);
+    jPanel1.setLayout(borderLayout2);
+    titlePanel.setBackground(Color.white);
+    titlePanel.setPreferredSize(new Dimension(0, 60));
+    titlePanel.setLayout(borderLayout3);
+    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);
+      }
+    });
+    buttonPanel.setLayout(gridBagLayout1);
+    buttonPanel.setOpaque(false);
+    showResultsNewFrame.setText("New Window");
+    mergeResults.setText("Merge Results");
+    this.setBackground(Color.white);
+    this.add(jPanel1, BorderLayout.NORTH);
+    jPanel1.add(jScrollPane1, BorderLayout.CENTER);
+    jScrollPane1.getViewport().add(infoText, null);
+    jPanel1.add(titlePanel, BorderLayout.NORTH);
+    titlePanel.add(buttonPanel, BorderLayout.EAST);
+    buttonPanel.add(cancel, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0
+        , GridBagConstraints.CENTER,
+        GridBagConstraints.NONE,
+        new Insets(19, 6, 16, 4), 0, 0));
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  protected void cancel_actionPerformed(ActionEvent e)
+  {
+  }
+}
diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 2f79875..673854a 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -1,851 +1,851 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.math;
-
-import java.io.*;
-
-import jalview.util.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Matrix
-{
-  /**
-   * SMJSPUBLIC
-   */
-  public double[][] value;
-
-  /** DOCUMENT ME!! */
-  public int rows;
-
-  /** DOCUMENT ME!! */
-  public int cols;
-
-  /** DOCUMENT ME!! */
-  public double[] d; // Diagonal
-
-  /** DOCUMENT ME!! */
-  public double[] e; // off diagonal
-
-  /**
-   * Creates a new Matrix object.
-   *
-   * @param value DOCUMENT ME!
-   * @param rows DOCUMENT ME!
-   * @param cols DOCUMENT ME!
-   */
-  public Matrix(double[][] value, int rows, int cols)
-  {
-    this.rows = rows;
-    this.cols = cols;
-    this.value = value;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Matrix transpose()
-  {
-    double[][] out = new double[cols][rows];
-
-    for (int i = 0; i < cols; i++)
-    {
-      for (int j = 0; j < rows; j++)
-      {
-        out[i][j] = value[j][i];
-      }
-    }
-
-    return new Matrix(out, cols, rows);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ps DOCUMENT ME!
-   */
-  public void print(PrintStream ps)
-  {
-    for (int i = 0; i < rows; i++)
-    {
-      for (int j = 0; j < cols; j++)
-      {
-        Format.print(ps, "%8.2f", value[i][j]);
-      }
-
-      ps.println();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param in DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Matrix preMultiply(Matrix in)
-  {
-    double[][] tmp = new double[in.rows][this.cols];
-
-    for (int i = 0; i < in.rows; i++)
-    {
-      for (int j = 0; j < this.cols; j++)
-      {
-        tmp[i][j] = 0.0;
-
-        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);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param in DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public double[] vectorPostMultiply(double[] in)
-  {
-    double[] out = new double[in.length];
-
-    for (int i = 0; i < in.length; i++)
-    {
-      out[i] = 0.0;
-
-      for (int k = 0; k < in.length; k++)
-      {
-        out[i] += (value[i][k] * in[k]);
-      }
-    }
-
-    return out;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param in DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Matrix postMultiply(Matrix in)
-  {
-    double[][] out = new double[this.rows][in.cols];
-
-    for (int i = 0; i < this.rows; i++)
-    {
-      for (int j = 0; j < in.cols; j++)
-      {
-        out[i][j] = 0.0;
-
-        for (int k = 0; k < rows; k++)
-        {
-          out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
-        }
-      }
-    }
-
-    return new Matrix(out, this.cols, in.rows);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Matrix copy()
-  {
-    double[][] newmat = new double[rows][cols];
-
-    for (int i = 0; i < rows; i++)
-    {
-      for (int j = 0; j < cols; j++)
-      {
-        newmat[i][j] = value[i][j];
-      }
-    }
-
-    return new Matrix(newmat, rows, cols);
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  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;
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  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);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  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;
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  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);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param a DOCUMENT ME!
-   * @param b DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public double sign(double a, double b)
-  {
-    if (b < 0)
-    {
-      return -Math.abs(a);
-    }
-    else
-    {
-      return Math.abs(a);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public double[] getColumn(int n)
-  {
-    double[] out = new double[rows];
-
-    for (int i = 0; i < rows; i++)
-    {
-      out[i] = value[i][n];
-    }
-
-    return out;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ps DOCUMENT ME!
-   */
-  public void printD(PrintStream ps)
-  {
-    for (int j = 0; j < rows; j++)
-    {
-      Format.print(ps, "%15.4e", d[j]);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ps DOCUMENT ME!
-   */
-  public void printE(PrintStream ps)
-  {
-    for (int j = 0; j < rows; j++)
-    {
-      Format.print(ps, "%15.4e", e[j]);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param args DOCUMENT ME!
-   */
-  public static void main(String[] args)
-  {
-    int n = Integer.parseInt(args[0]);
-    double[][] in = new double[n][n];
-
-    for (int i = 0; i < n; i++)
-    {
-      for (int j = 0; j < n; j++)
-      {
-        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();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.math;
+
+import java.io.*;
+
+import jalview.util.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Matrix
+{
+  /**
+   * SMJSPUBLIC
+   */
+  public double[][] value;
+
+  /** DOCUMENT ME!! */
+  public int rows;
+
+  /** DOCUMENT ME!! */
+  public int cols;
+
+  /** DOCUMENT ME!! */
+  public double[] d; // Diagonal
+
+  /** DOCUMENT ME!! */
+  public double[] e; // off diagonal
+
+  /**
+   * Creates a new Matrix object.
+   *
+   * @param value DOCUMENT ME!
+   * @param rows DOCUMENT ME!
+   * @param cols DOCUMENT ME!
+   */
+  public Matrix(double[][] value, int rows, int cols)
+  {
+    this.rows = rows;
+    this.cols = cols;
+    this.value = value;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Matrix transpose()
+  {
+    double[][] out = new double[cols][rows];
+
+    for (int i = 0; i < cols; i++)
+    {
+      for (int j = 0; j < rows; j++)
+      {
+        out[i][j] = value[j][i];
+      }
+    }
+
+    return new Matrix(out, cols, rows);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ps DOCUMENT ME!
+   */
+  public void print(PrintStream ps)
+  {
+    for (int i = 0; i < rows; i++)
+    {
+      for (int j = 0; j < cols; j++)
+      {
+        Format.print(ps, "%8.2f", value[i][j]);
+      }
+
+      ps.println();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param in DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Matrix preMultiply(Matrix in)
+  {
+    double[][] tmp = new double[in.rows][this.cols];
+
+    for (int i = 0; i < in.rows; i++)
+    {
+      for (int j = 0; j < this.cols; j++)
+      {
+        tmp[i][j] = 0.0;
+
+        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);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param in DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public double[] vectorPostMultiply(double[] in)
+  {
+    double[] out = new double[in.length];
+
+    for (int i = 0; i < in.length; i++)
+    {
+      out[i] = 0.0;
+
+      for (int k = 0; k < in.length; k++)
+      {
+        out[i] += (value[i][k] * in[k]);
+      }
+    }
+
+    return out;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param in DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Matrix postMultiply(Matrix in)
+  {
+    double[][] out = new double[this.rows][in.cols];
+
+    for (int i = 0; i < this.rows; i++)
+    {
+      for (int j = 0; j < in.cols; j++)
+      {
+        out[i][j] = 0.0;
+
+        for (int k = 0; k < rows; k++)
+        {
+          out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
+        }
+      }
+    }
+
+    return new Matrix(out, this.cols, in.rows);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Matrix copy()
+  {
+    double[][] newmat = new double[rows][cols];
+
+    for (int i = 0; i < rows; i++)
+    {
+      for (int j = 0; j < cols; j++)
+      {
+        newmat[i][j] = value[i][j];
+      }
+    }
+
+    return new Matrix(newmat, rows, cols);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  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;
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  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);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  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;
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  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);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param a DOCUMENT ME!
+   * @param b DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public double sign(double a, double b)
+  {
+    if (b < 0)
+    {
+      return -Math.abs(a);
+    }
+    else
+    {
+      return Math.abs(a);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public double[] getColumn(int n)
+  {
+    double[] out = new double[rows];
+
+    for (int i = 0; i < rows; i++)
+    {
+      out[i] = value[i][n];
+    }
+
+    return out;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ps DOCUMENT ME!
+   */
+  public void printD(PrintStream ps)
+  {
+    for (int j = 0; j < rows; j++)
+    {
+      Format.print(ps, "%15.4e", d[j]);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ps DOCUMENT ME!
+   */
+  public void printE(PrintStream ps)
+  {
+    for (int j = 0; j < rows; j++)
+    {
+      Format.print(ps, "%15.4e", e[j]);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param args DOCUMENT ME!
+   */
+  public static void main(String[] args)
+  {
+    int n = Integer.parseInt(args[0]);
+    double[][] in = new double[n][n];
+
+    for (int i = 0; i < n; i++)
+    {
+      for (int j = 0; j < n; j++)
+      {
+        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 eff8dea..e752618 100755
--- a/src/jalview/math/RotatableMatrix.java
+++ b/src/jalview/math/RotatableMatrix.java
@@ -1,331 +1,331 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.math;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class RotatableMatrix
-{
-  float[][] matrix;
-  float[] temp;
-  float[][] rot;
-
-  /**
-   * Creates a new RotatableMatrix object.
-   *
-   * @param rows DOCUMENT ME!
-   * @param cols DOCUMENT ME!
-   */
-  public RotatableMatrix(int rows, int cols)
-  {
-    matrix = new float[rows][cols];
-
-    temp = new float[3];
-
-    rot = new float[3][3];
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   * @param value DOCUMENT ME!
-   */
-  public void addElement(int i, int j, float value)
-  {
-    matrix[i][j] = value;
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  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]);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param degrees DOCUMENT ME!
-   * @param axis DOCUMENT ME!
-   */
-  public void rotate(float degrees, char axis)
-  {
-    float costheta = (float) Math.cos( (degrees * Math.PI) / (float) 180.0);
-
-    float sintheta = (float) Math.sin( (degrees * Math.PI) / (float) 180.0);
-
-    if (axis == 'z')
-    {
-      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);
-    }
-
-    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);
-    }
-
-    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);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param vect DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public float[] vectorMultiply(float[] vect)
-  {
-    temp[0] = vect[0];
-
-    temp[1] = vect[1];
-
-    temp[2] = vect[2];
-
-    for (int i = 0; i < 3; i++)
-    {
-      temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) +
-          (matrix[i][2] * vect[2]);
-    }
-
-    vect[0] = temp[0];
-
-    vect[1] = temp[1];
-
-    vect[2] = temp[2];
-
-    return vect;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param mat DOCUMENT ME!
-   */
-  public void preMultiply(float[][] mat)
-  {
-    float[][] tmp = new float[3][3];
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        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];
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param mat DOCUMENT ME!
-   */
-  public void postMultiply(float[][] mat)
-  {
-    float[][] tmp = new float[3][3];
-
-    for (int i = 0; i < 3; i++)
-    {
-      for (int j = 0; j < 3; j++)
-      {
-        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];
-      }
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param args DOCUMENT ME!
-   */
-  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);
-
-    n.addElement(1, 2, 1);
-
-    n.addElement(2, 0, 2);
-
-    n.addElement(2, 1, 1);
-
-    n.addElement(2, 2, 1);
-
-    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;
-
-    vect[2] = 6;
-
-    vect = m.vectorMultiply(vect);
-
-    System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void setIdentity()
-  {
-    matrix[0][0] = (float) 1.0;
-
-    matrix[1][1] = (float) 1.0;
-
-    matrix[2][2] = (float) 1.0;
-
-    matrix[0][1] = (float) 0.0;
-
-    matrix[0][2] = (float) 0.0;
-
-    matrix[1][0] = (float) 0.0;
-
-    matrix[1][2] = (float) 0.0;
-
-    matrix[2][0] = (float) 0.0;
-
-    matrix[2][1] = (float) 0.0;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.math;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class RotatableMatrix
+{
+  float[][] matrix;
+  float[] temp;
+  float[][] rot;
+
+  /**
+   * Creates a new RotatableMatrix object.
+   *
+   * @param rows DOCUMENT ME!
+   * @param cols DOCUMENT ME!
+   */
+  public RotatableMatrix(int rows, int cols)
+  {
+    matrix = new float[rows][cols];
+
+    temp = new float[3];
+
+    rot = new float[3][3];
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   * @param value DOCUMENT ME!
+   */
+  public void addElement(int i, int j, float value)
+  {
+    matrix[i][j] = value;
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  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]);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param degrees DOCUMENT ME!
+   * @param axis DOCUMENT ME!
+   */
+  public void rotate(float degrees, char axis)
+  {
+    float costheta = (float) Math.cos( (degrees * Math.PI) / (float) 180.0);
+
+    float sintheta = (float) Math.sin( (degrees * Math.PI) / (float) 180.0);
+
+    if (axis == 'z')
+    {
+      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);
+    }
+
+    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);
+    }
+
+    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);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param vect DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float[] vectorMultiply(float[] vect)
+  {
+    temp[0] = vect[0];
+
+    temp[1] = vect[1];
+
+    temp[2] = vect[2];
+
+    for (int i = 0; i < 3; i++)
+    {
+      temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1]) +
+          (matrix[i][2] * vect[2]);
+    }
+
+    vect[0] = temp[0];
+
+    vect[1] = temp[1];
+
+    vect[2] = temp[2];
+
+    return vect;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param mat DOCUMENT ME!
+   */
+  public void preMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        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];
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param mat DOCUMENT ME!
+   */
+  public void postMultiply(float[][] mat)
+  {
+    float[][] tmp = new float[3][3];
+
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        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];
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param args DOCUMENT ME!
+   */
+  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);
+
+    n.addElement(1, 2, 1);
+
+    n.addElement(2, 0, 2);
+
+    n.addElement(2, 1, 1);
+
+    n.addElement(2, 2, 1);
+
+    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;
+
+    vect[2] = 6;
+
+    vect = m.vectorMultiply(vect);
+
+    System.out.println(vect[0] + " " + vect[1] + " " + vect[2]);
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void setIdentity()
+  {
+    matrix[0][0] = (float) 1.0;
+
+    matrix[1][1] = (float) 1.0;
+
+    matrix[2][2] = (float) 1.0;
+
+    matrix[0][1] = (float) 0.0;
+
+    matrix[0][2] = (float) 0.0;
+
+    matrix[1][0] = (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/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java
index f43acd6..70f1c8f 100644
--- a/src/jalview/schemabinding/version2/AlcodMap.java
+++ b/src/jalview/schemabinding/version2/AlcodMap.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Alcodon.java b/src/jalview/schemabinding/version2/Alcodon.java
index cffbd9a..2e8cf54 100644
--- a/src/jalview/schemabinding/version2/Alcodon.java
+++ b/src/jalview/schemabinding/version2/Alcodon.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java
index b8b2a41..c368681 100644
--- a/src/jalview/schemabinding/version2/AlcodonFrame.java
+++ b/src/jalview/schemabinding/version2/AlcodonFrame.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 9ee76e3..8e4d632 100755
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java
index 36f9f93..047817a 100755
--- a/src/jalview/schemabinding/version2/AnnotationColours.java
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java
index eca3e6a..52a6a44 100755
--- a/src/jalview/schemabinding/version2/AnnotationElement.java
+++ b/src/jalview/schemabinding/version2/AnnotationElement.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java
index 54d64ff..c14411a 100755
--- a/src/jalview/schemabinding/version2/Colour.java
+++ b/src/jalview/schemabinding/version2/Colour.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java
index 4d67250..3c4146e 100644
--- a/src/jalview/schemabinding/version2/DBRef.java
+++ b/src/jalview/schemabinding/version2/DBRef.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java
index 109ec6e..bda2674 100755
--- a/src/jalview/schemabinding/version2/Feature.java
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java
index 5ce4054..0f0922e 100755
--- a/src/jalview/schemabinding/version2/FeatureSettings.java
+++ b/src/jalview/schemabinding/version2/FeatureSettings.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java
index 47b28a3..b7b5728 100755
--- a/src/jalview/schemabinding/version2/Features.java
+++ b/src/jalview/schemabinding/version2/Features.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Group.java b/src/jalview/schemabinding/version2/Group.java
index 826667e..8f4f37f 100644
--- a/src/jalview/schemabinding/version2/Group.java
+++ b/src/jalview/schemabinding/version2/Group.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java
index 716bfbc..5765abd 100644
--- a/src/jalview/schemabinding/version2/HiddenColumns.java
+++ b/src/jalview/schemabinding/version2/HiddenColumns.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index ca77ed2..b69f9fc 100755
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index a5dc2f7..d07b686 100755
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java
index f7e049a..c2f8601 100755
--- a/src/jalview/schemabinding/version2/JalviewModel.java
+++ b/src/jalview/schemabinding/version2/JalviewModel.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index cb66b37..85fbf6f 100755
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java
index 7c059da..6daaf33 100755
--- a/src/jalview/schemabinding/version2/JalviewUserColours.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColours.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/MapListFrom.java b/src/jalview/schemabinding/version2/MapListFrom.java
index acfe18e..cc987e7 100644
--- a/src/jalview/schemabinding/version2/MapListFrom.java
+++ b/src/jalview/schemabinding/version2/MapListFrom.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/MapListTo.java b/src/jalview/schemabinding/version2/MapListTo.java
index 8c3a7e0..7362b73 100644
--- a/src/jalview/schemabinding/version2/MapListTo.java
+++ b/src/jalview/schemabinding/version2/MapListTo.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java
index 21d56e7..e808a6c 100644
--- a/src/jalview/schemabinding/version2/MapListType.java
+++ b/src/jalview/schemabinding/version2/MapListType.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Mapping.java b/src/jalview/schemabinding/version2/Mapping.java
index 8dbc12f..bf89ce6 100644
--- a/src/jalview/schemabinding/version2/Mapping.java
+++ b/src/jalview/schemabinding/version2/Mapping.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/MappingChoice.java b/src/jalview/schemabinding/version2/MappingChoice.java
index 5f1930d..952234f 100644
--- a/src/jalview/schemabinding/version2/MappingChoice.java
+++ b/src/jalview/schemabinding/version2/MappingChoice.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java
index 94a5566..2a62c88 100644
--- a/src/jalview/schemabinding/version2/OtherData.java
+++ b/src/jalview/schemabinding/version2/OtherData.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java
index 6ff1819..d06ffb9 100755
--- a/src/jalview/schemabinding/version2/Pdbentry.java
+++ b/src/jalview/schemabinding/version2/Pdbentry.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java
index 3dbc99c..c9881c9 100755
--- a/src/jalview/schemabinding/version2/PdbentryItem.java
+++ b/src/jalview/schemabinding/version2/PdbentryItem.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
 /**
diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
index 04685b9..cc32063 100755
--- a/src/jalview/schemabinding/version2/Pdbids.java
+++ b/src/jalview/schemabinding/version2/Pdbids.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java
index bfc4dde..3476fb2 100755
--- a/src/jalview/schemabinding/version2/Property.java
+++ b/src/jalview/schemabinding/version2/Property.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
index e606eeb..5a8fce9 100755
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 481c37f..890da6d 100755
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/SequenceSetProperties.java b/src/jalview/schemabinding/version2/SequenceSetProperties.java
index a078c78..5dc9880 100644
--- a/src/jalview/schemabinding/version2/SequenceSetProperties.java
+++ b/src/jalview/schemabinding/version2/SequenceSetProperties.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java
index 0d07812..41a75f7 100755
--- a/src/jalview/schemabinding/version2/SequenceType.java
+++ b/src/jalview/schemabinding/version2/SequenceType.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java
index 5cd78bd..57c375c 100755
--- a/src/jalview/schemabinding/version2/Setting.java
+++ b/src/jalview/schemabinding/version2/Setting.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 968a559..ce76b38 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java
index 4e3f124..b3c2207 100755
--- a/src/jalview/schemabinding/version2/ThresholdLine.java
+++ b/src/jalview/schemabinding/version2/ThresholdLine.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java
index 3bbc231..3e844f0 100755
--- a/src/jalview/schemabinding/version2/Tree.java
+++ b/src/jalview/schemabinding/version2/Tree.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java
index 3cb65e0..d1b0045 100755
--- a/src/jalview/schemabinding/version2/UserColourScheme.java
+++ b/src/jalview/schemabinding/version2/UserColourScheme.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java
index 062024f..8304664 100755
--- a/src/jalview/schemabinding/version2/UserColours.java
+++ b/src/jalview/schemabinding/version2/UserColours.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index ae8e17f..0d23a50 100755
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java
index 26814dc..bbb13d9 100755
--- a/src/jalview/schemabinding/version2/VamsasModel.java
+++ b/src/jalview/schemabinding/version2/VamsasModel.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index aa97a95..84383ff 100755
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
index fbc56a3..23e7ce7 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
index cd87309..f8688f2 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
index 5341376..f7941c2 100644
--- a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
index 3d32ff6..7751b64 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
index 44576ee..b2c9b26 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
index 61221a1..aceaa70 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
index bdd9739..ac4c781 100644
--- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
index 1a55978..4d03443 100644
--- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
index 92c919e..ae22bf6 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
index 930aac9..fd56535 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
index 380d46e..eda2f2d 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
index 417dbbb..bda2658 100644
--- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
index f307ee4..f90651a 100644
--- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
index 21b3b67..553e571 100644
--- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
index 427702d..5c6393c 100644
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
index 9aad95c..9825926 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
index d6fd0ba..977ce86 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
index dd155dd..77247fd 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
index f39b18f..4660bc3 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
index 4de1738..655fa14 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
index 7dc7bc5..6ccd7c0 100644
--- a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
index 63543d7..8d0dec6 100644
--- a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
index 95e1a87..6d66576 100644
--- a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
index 46f6682..84040b4 100644
--- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
index dbf0c3a..58108ec 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
index 693ad61..1ffbb1e 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
index 2547f1d..79499fc 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
index 15f2e37..78bbbed 100644
--- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
index 4dfd168..5777dd7 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
index aa0c798..177c4c4 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
index 9c3c578..a46e119 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
index fa73621..a7198ad 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
index 23783bb..c89f9f5 100644
--- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
index 8584429..b23af9f 100644
--- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
index 951e7ca..98226fa 100644
--- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
index 9d508a4..36d300c 100644
--- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
index be7012a..2215d02 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
index bda1c5e..f21230b 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
index 375f435..8528c16 100644
--- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
index bc14cfd..b235ab2 100644
--- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
index 4faa6c1..580f17c 100644
--- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.schemabinding.version2.descriptors;
 
   //---------------------------------/
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 6a7a3cf..d4baa86 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,230 +1,230 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationColourGradient
-    extends ResidueColourScheme
-{
-  public static int NO_THRESHOLD = -1;
-  public static int BELOW_THRESHOLD = 0;
-  public static int ABOVE_THRESHOLD = 1;
-
-  public AlignmentAnnotation annotation;
-  int aboveAnnotationThreshold = -1;
-  public boolean thresholdIsMinMax = false;
-
-  GraphLine annotationThreshold;
-
-  float r1, g1, b1, rr, gg, bb, dr, dg, db;
-
-  ColourSchemeI colourScheme;
-
-  public boolean predefinedColours = false;
-
-  /**
-   * Creates a new AnnotationColourGradient object.
-   */
-  public AnnotationColourGradient(AlignmentAnnotation annotation,
-                                  ColourSchemeI originalColour,
-                                  int aboveThreshold)
-  {
-    if (originalColour instanceof AnnotationColourGradient)
-    {
-      colourScheme = ( (AnnotationColourGradient) originalColour).colourScheme;
-    }
-    else
-    {
-      colourScheme = originalColour;
-    }
-
-    this.annotation = annotation;
-
-    aboveAnnotationThreshold = aboveThreshold;
-
-    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
-    {
-      annotationThreshold = annotation.threshold;
-    }
-  }
-
-  /**
-   * Creates a new AnnotationColourGradient object.
-   */
-  public AnnotationColourGradient(AlignmentAnnotation annotation,
-                                  Color minColour, Color maxColour,
-                                  int aboveThreshold)
-  {
-    this.annotation = annotation;
-
-    aboveAnnotationThreshold = aboveThreshold;
-
-    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
-    {
-      annotationThreshold = annotation.threshold;
-    }
-
-    r1 = minColour.getRed();
-    g1 = minColour.getGreen();
-    b1 = minColour.getBlue();
-
-    rr = maxColour.getRed() - r1;
-    gg = maxColour.getGreen() - g1;
-    bb = maxColour.getBlue() - b1;
-  }
-
-  public String getAnnotation()
-  {
-    return annotation.label;
-  }
-
-  public int getAboveThreshold()
-  {
-    return aboveAnnotationThreshold;
-  }
-
-  public float getAnnotationThreshold()
-  {
-    if (annotationThreshold == null)
-    {
-      return 0;
-    }
-    else
-    {
-      return annotationThreshold.value;
-    }
-  }
-
-  public ColourSchemeI getBaseColour()
-  {
-    return colourScheme;
-  }
-
-  public Color getMinColour()
-  {
-    return new Color( (int) r1, (int) g1, (int) b1);
-  }
-
-  public Color getMaxColour()
-  {
-    return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c)
-  {
-    return Color.red;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c, int j)
-  {
-    Color currentColour = Color.white;
-
-    if ( (threshold == 0) || aboveThreshold(c, j))
-    {
-      if (j < annotation.annotations.length
-          && annotation.annotations[j] != null
-          && !jalview.util.Comparison.isGap(c))
-      {
-
-       if (predefinedColours)
-        {
-          if(annotation.annotations[j].colour != null)
-              return annotation.annotations[j].colour;
-          else
-            return currentColour;
-        }
-
-        if (aboveAnnotationThreshold == NO_THRESHOLD
-            ||
-            (annotationThreshold != null && aboveAnnotationThreshold == ABOVE_THRESHOLD &&
-             annotation.annotations[j].value >= annotationThreshold.value)
-            ||
-            (annotationThreshold != null && aboveAnnotationThreshold == BELOW_THRESHOLD &&
-             annotation.annotations[j].value <= annotationThreshold.value))
-        {
-
-          float range=1f;
-          if (thresholdIsMinMax
-              && annotation.threshold != null
-              && aboveAnnotationThreshold == ABOVE_THRESHOLD
-              && annotation.annotations[j].value>annotation.threshold.value)
-          {
-            range =
-                (annotation.annotations[j].value - annotation.threshold.value) /
-                (annotation.graphMax - annotation.threshold.value);
-          }
-          else if (thresholdIsMinMax
-                   && annotation.threshold != null
-                   && aboveAnnotationThreshold == BELOW_THRESHOLD
-              &&  annotation.annotations[j].value > annotation.graphMin)
-          {
-            range =
-                ( annotation.annotations[j].value - annotation.graphMin ) /
-                (annotation.threshold.value - annotation.graphMin );
-          }
-          else
-          {
-            range = (annotation.annotations[j].value -
-                     annotation.graphMin) /
-                (annotation.graphMax - annotation.graphMin);
-          }
-
-
-          if (colourScheme != null)
-          {
-            currentColour = colourScheme.findColour(c, j);
-          }
-          else if (range != 0)
-          {
-            dr = rr * range   + r1;
-            dg = gg * range   + g1;
-            db = bb * range   + b1;
-
-            currentColour = new Color( (int) dr, (int) dg, (int) db);
-          }
-        }
-      }
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class AnnotationColourGradient
+    extends ResidueColourScheme
+{
+  public static int NO_THRESHOLD = -1;
+  public static int BELOW_THRESHOLD = 0;
+  public static int ABOVE_THRESHOLD = 1;
+
+  public AlignmentAnnotation annotation;
+  int aboveAnnotationThreshold = -1;
+  public boolean thresholdIsMinMax = false;
+
+  GraphLine annotationThreshold;
+
+  float r1, g1, b1, rr, gg, bb, dr, dg, db;
+
+  ColourSchemeI colourScheme;
+
+  public boolean predefinedColours = false;
+
+  /**
+   * Creates a new AnnotationColourGradient object.
+   */
+  public AnnotationColourGradient(AlignmentAnnotation annotation,
+                                  ColourSchemeI originalColour,
+                                  int aboveThreshold)
+  {
+    if (originalColour instanceof AnnotationColourGradient)
+    {
+      colourScheme = ( (AnnotationColourGradient) originalColour).colourScheme;
+    }
+    else
+    {
+      colourScheme = originalColour;
+    }
+
+    this.annotation = annotation;
+
+    aboveAnnotationThreshold = aboveThreshold;
+
+    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+    {
+      annotationThreshold = annotation.threshold;
+    }
+  }
+
+  /**
+   * Creates a new AnnotationColourGradient object.
+   */
+  public AnnotationColourGradient(AlignmentAnnotation annotation,
+                                  Color minColour, Color maxColour,
+                                  int aboveThreshold)
+  {
+    this.annotation = annotation;
+
+    aboveAnnotationThreshold = aboveThreshold;
+
+    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+    {
+      annotationThreshold = annotation.threshold;
+    }
+
+    r1 = minColour.getRed();
+    g1 = minColour.getGreen();
+    b1 = minColour.getBlue();
+
+    rr = maxColour.getRed() - r1;
+    gg = maxColour.getGreen() - g1;
+    bb = maxColour.getBlue() - b1;
+  }
+
+  public String getAnnotation()
+  {
+    return annotation.label;
+  }
+
+  public int getAboveThreshold()
+  {
+    return aboveAnnotationThreshold;
+  }
+
+  public float getAnnotationThreshold()
+  {
+    if (annotationThreshold == null)
+    {
+      return 0;
+    }
+    else
+    {
+      return annotationThreshold.value;
+    }
+  }
+
+  public ColourSchemeI getBaseColour()
+  {
+    return colourScheme;
+  }
+
+  public Color getMinColour()
+  {
+    return new Color( (int) r1, (int) g1, (int) b1);
+  }
+
+  public Color getMaxColour()
+  {
+    return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c)
+  {
+    return Color.red;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    Color currentColour = Color.white;
+
+    if ( (threshold == 0) || aboveThreshold(c, j))
+    {
+      if (j < annotation.annotations.length
+          && annotation.annotations[j] != null
+          && !jalview.util.Comparison.isGap(c))
+      {
+
+       if (predefinedColours)
+        {
+          if(annotation.annotations[j].colour != null)
+              return annotation.annotations[j].colour;
+          else
+            return currentColour;
+        }
+
+        if (aboveAnnotationThreshold == NO_THRESHOLD
+            ||
+            (annotationThreshold != null && aboveAnnotationThreshold == ABOVE_THRESHOLD &&
+             annotation.annotations[j].value >= annotationThreshold.value)
+            ||
+            (annotationThreshold != null && aboveAnnotationThreshold == BELOW_THRESHOLD &&
+             annotation.annotations[j].value <= annotationThreshold.value))
+        {
+
+          float range=1f;
+          if (thresholdIsMinMax
+              && annotation.threshold != null
+              && aboveAnnotationThreshold == ABOVE_THRESHOLD
+              && annotation.annotations[j].value>annotation.threshold.value)
+          {
+            range =
+                (annotation.annotations[j].value - annotation.threshold.value) /
+                (annotation.graphMax - annotation.threshold.value);
+          }
+          else if (thresholdIsMinMax
+                   && annotation.threshold != null
+                   && aboveAnnotationThreshold == BELOW_THRESHOLD
+              &&  annotation.annotations[j].value > annotation.graphMin)
+          {
+            range =
+                ( annotation.annotations[j].value - annotation.graphMin ) /
+                (annotation.threshold.value - annotation.graphMin );
+          }
+          else
+          {
+            range = (annotation.annotations[j].value -
+                     annotation.graphMin) /
+                (annotation.graphMax - annotation.graphMin);
+          }
+
+
+          if (colourScheme != null)
+          {
+            currentColour = colourScheme.findColour(c, j);
+          }
+          else if (range != 0)
+          {
+            dr = rr * range   + r1;
+            dg = gg * range   + g1;
+            db = bb * range   + b1;
+
+            currentColour = new Color( (int) dr, (int) dg, (int) db);
+          }
+        }
+      }
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+}
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 0db55c0..afca132 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,94 +1,94 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-
-public class Blosum62ColourScheme
-    extends ResidueColourScheme
-{
-  public Blosum62ColourScheme()
-  {
-    super();
-  }
-
-  public Color findColour(char res, int j)
-  {
-    if ('a' <= res && res <= 'z')
-    {
-      // TO UPPERCASE !!!
-      res -= ('a' - 'A');
-    }
-
-    if (consensus == null ||
-        j >= consensus.length ||
-        consensus[j] == null ||
-        (threshold != 0 && !aboveThreshold(res, j)))
-    {
-      return Color.white;
-    }
-
-    Color currentColour;
-
-    if (!jalview.util.Comparison.isGap(res))
-    {
-      String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
-
-      if (max.indexOf(res) > -1)
-      {
-        currentColour = new Color(154, 154, 255);
-      }
-      else
-      {
-        int c = 0;
-        int max_aa = 0;
-        int n = max.length();
-
-        do
-        {
-          c += ResidueProperties.getBLOSUM62(
-              max.charAt(max_aa), res);
-        }
-        while (++max_aa < n);
-
-        if (c > 0)
-        {
-          currentColour = new Color(204, 204, 255);
-        }
-        else
-        {
-          currentColour = Color.white;
-        }
-      }
-
-      if (conservationColouring)
-      {
-        currentColour = applyConservation(currentColour, j);
-      }
-    }
-    else
-    {
-      return Color.white;
-    }
-
-    return currentColour;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+
+public class Blosum62ColourScheme
+    extends ResidueColourScheme
+{
+  public Blosum62ColourScheme()
+  {
+    super();
+  }
+
+  public Color findColour(char res, int j)
+  {
+    if ('a' <= res && res <= 'z')
+    {
+      // TO UPPERCASE !!!
+      res -= ('a' - 'A');
+    }
+
+    if (consensus == null ||
+        j >= consensus.length ||
+        consensus[j] == null ||
+        (threshold != 0 && !aboveThreshold(res, j)))
+    {
+      return Color.white;
+    }
+
+    Color currentColour;
+
+    if (!jalview.util.Comparison.isGap(res))
+    {
+      String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
+
+      if (max.indexOf(res) > -1)
+      {
+        currentColour = new Color(154, 154, 255);
+      }
+      else
+      {
+        int c = 0;
+        int max_aa = 0;
+        int n = max.length();
+
+        do
+        {
+          c += ResidueProperties.getBLOSUM62(
+              max.charAt(max_aa), res);
+        }
+        while (++max_aa < n);
+
+        if (c > 0)
+        {
+          currentColour = new Color(204, 204, 255);
+        }
+        else
+        {
+          currentColour = Color.white;
+        }
+      }
+
+      if (conservationColouring)
+      {
+        currentColour = applyConservation(currentColour, j);
+      }
+    }
+    else
+    {
+      return Color.white;
+    }
+
+    return currentColour;
+  }
+}
diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index c973035..a1b3ba4 100755
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -1,52 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class BuriedColourScheme
-    extends ScoreColourScheme
-{
-  /**
-   * Creates a new BuriedColourScheme object.
-   */
-  public BuriedColourScheme()
-  {
-    super(ResidueProperties.buried, ResidueProperties.buriedmin,
-          ResidueProperties.buriedmax);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(0, (float) (1.0 - c), c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BuriedColourScheme
+    extends ScoreColourScheme
+{
+  /**
+   * Creates a new BuriedColourScheme object.
+   */
+  public BuriedColourScheme()
+  {
+    super(ResidueProperties.buried, ResidueProperties.buriedmin,
+          ResidueProperties.buriedmax);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(0, (float) (1.0 - c), c);
+  }
+}
diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index bc2f9ea..5e7ebb8 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 96699c6..8deb556 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,43 +1,43 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-public interface ColourSchemeI
-{
-  public Color findColour(char c);
-
-  public Color findColour(char c, int j);
-
-  public void setConsensus(java.util.Hashtable[] h);
-
-  public void setConservation(jalview.analysis.Conservation c);
-
-  public boolean conservationApplied();
-
-  public void setConservationInc(int i);
-
-  public int getConservationInc();
-
-  public int getThreshold();
-
-  public void setThreshold(int ct, boolean ignoreGaps);
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+public interface ColourSchemeI
+{
+  public Color findColour(char c);
+
+  public Color findColour(char c, int j);
+
+  public void setConsensus(java.util.Hashtable[] h);
+
+  public void setConservation(jalview.analysis.Conservation c);
+
+  public boolean conservationApplied();
+
+  public void setConservationInc(int i);
+
+  public int getConservationInc();
+
+  public int getThreshold();
+
+  public void setThreshold(int ct, boolean ignoreGaps);
+
+}
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 2f81d13..9acadda 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index 5cd7b52..5d34eff 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java
index 7894965..c6ecd28 100755
--- a/src/jalview/schemes/HelixColourScheme.java
+++ b/src/jalview/schemes/HelixColourScheme.java
@@ -1,36 +1,36 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-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);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+public class HelixColourScheme
+    extends ScoreColourScheme
+{
+  public HelixColourScheme()
+  {
+    super(ResidueProperties.helix, ResidueProperties.helixmin,
+          ResidueProperties.helixmax);
+  }
+
+  public 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 9af174d..548b176 100755
--- a/src/jalview/schemes/HydrophobicColourScheme.java
+++ b/src/jalview/schemes/HydrophobicColourScheme.java
@@ -1,52 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class HydrophobicColourScheme
-    extends ScoreColourScheme
-{
-  /**
-   * Creates a new HydrophobicColourScheme object.
-   */
-  public HydrophobicColourScheme()
-  {
-    super(ResidueProperties.hyd, ResidueProperties.hydmin,
-          ResidueProperties.hydmax);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(c, (float) 0.0, (float) 1.0 - c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class HydrophobicColourScheme
+    extends ScoreColourScheme
+{
+  /**
+   * Creates a new HydrophobicColourScheme object.
+   */
+  public HydrophobicColourScheme()
+  {
+    super(ResidueProperties.hyd, ResidueProperties.hydmin,
+          ResidueProperties.hydmax);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(c, (float) 0.0, (float) 1.0 - c);
+  }
+}
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 4e14202..d83d913 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,87 +1,87 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class NucleotideColourScheme
-    extends ResidueColourScheme
-{
-  /**
-   * Creates a new NucleotideColourScheme object.
-   */
-  public NucleotideColourScheme()
-  {
-    super(ResidueProperties.nucleotide, 0);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c)
-  {
-    // System.out.println("called"); log.debug
-    return colors[ResidueProperties.nucleotideIndex[c]];
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param n DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c, int j)
-  {
-    Color currentColour;
-    if ( (threshold == 0) || aboveThreshold(c, j))
-    {
-      try
-      {
-        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
-      }
-      catch (Exception ex)
-      {
-        return Color.white;
-      }
-    }
-    else
-    {
-      return Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme
+    extends ResidueColourScheme
+{
+  /**
+   * Creates a new NucleotideColourScheme object.
+   */
+  public NucleotideColourScheme()
+  {
+    super(ResidueProperties.nucleotide, 0);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c)
+  {
+    // System.out.println("called"); log.debug
+    return colors[ResidueProperties.nucleotideIndex[c]];
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param n DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    Color currentColour;
+    if ( (threshold == 0) || aboveThreshold(c, j))
+    {
+      try
+      {
+        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+      }
+      catch (Exception ex)
+      {
+        return Color.white;
+      }
+    }
+    else
+    {
+      return Color.white;
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+}
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e1dbf46..0ab66e6 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,94 +1,94 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-public class PIDColourScheme
-    extends ResidueColourScheme
-{
-  public Color[] pidColours;
-  public float[] thresholds;
-  SequenceGroup group;
-
-  public PIDColourScheme()
-  {
-    this.pidColours = ResidueProperties.pidColours;
-    this.thresholds = ResidueProperties.pidThresholds;
-  }
-
-  public Color findColour(char c, int j)
-  {
-    if ('a' <= c && c <= 'z')
-    {
-      c -= ('a' - 'A');
-    }
-
-    if (consensus == null
-        || j >= consensus.length
-        || consensus[j] == null)
-    {
-      return Color.white;
-    }
-
-    if ( (threshold != 0) && !aboveThreshold(c, j))
-    {
-      return Color.white;
-    }
-
-    Color currentColour = Color.white;
-
-    double sc = 0;
-
-    if (consensus.length <= j)
-    {
-      return Color.white;
-    }
-
-    if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) !=
-          -1) &&
-        consensus[j].contains(String.valueOf(c)))
-    {
-      sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
-
-      if (!jalview.util.Comparison.isGap(c))
-      {
-        for (int i = 0; i < thresholds.length; i++)
-        {
-          if (sc > thresholds[i])
-          {
-            currentColour = pidColours[i];
-
-            break;
-          }
-        }
-      }
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+
+public class PIDColourScheme
+    extends ResidueColourScheme
+{
+  public Color[] pidColours;
+  public float[] thresholds;
+  SequenceGroup group;
+
+  public PIDColourScheme()
+  {
+    this.pidColours = ResidueProperties.pidColours;
+    this.thresholds = ResidueProperties.pidThresholds;
+  }
+
+  public Color findColour(char c, int j)
+  {
+    if ('a' <= c && c <= 'z')
+    {
+      c -= ('a' - 'A');
+    }
+
+    if (consensus == null
+        || j >= consensus.length
+        || consensus[j] == null)
+    {
+      return Color.white;
+    }
+
+    if ( (threshold != 0) && !aboveThreshold(c, j))
+    {
+      return Color.white;
+    }
+
+    Color currentColour = Color.white;
+
+    double sc = 0;
+
+    if (consensus.length <= j)
+    {
+      return Color.white;
+    }
+
+    if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) !=
+          -1) &&
+        consensus[j].contains(String.valueOf(c)))
+    {
+      sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
+
+      if (!jalview.util.Comparison.isGap(c))
+      {
+        for (int i = 0; i < thresholds.length; i++)
+        {
+          if (sc > thresholds[i])
+          {
+            currentColour = pidColours[i];
+
+            break;
+          }
+        }
+      }
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+}
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index f43aa02..417e31c 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,271 +1,271 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class ResidueColourScheme
-    implements ColourSchemeI
-{
-
-  boolean conservationColouring = false;
-
-  Color[] colors;
-  int threshold = 0;
-
-  /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
-  protected String ignoreGaps = AAFrequency.PID_GAPS;
-
-  /** Consenus as a hashtable array */
-  Hashtable[] consensus;
-
-  /** Conservation string as a char array */
-  char[] conservation;
-  int conservationLength=0;
-
-  /** DOCUMENT ME!! */
-  int inc = 30;
-
-  /**
-   * Creates a new ResidueColourScheme object.
-   *
-   * @param colors DOCUMENT ME!
-   * @param threshold DOCUMENT ME!
-   */
-  public ResidueColourScheme(Color[] colours, int threshold)
-  {
-    this.colors = colours;
-    this.threshold = threshold;
-  }
-
-  /**
-   * Creates a new ResidueColourScheme object.
-   */
-  public ResidueColourScheme()
-  {
-  }
-
-  /**
-   * Find a colour without an index in a sequence
-   */
-  public Color findColour(char c)
-  {
-    return colors[ResidueProperties.aaIndex[c]];
-  }
-
-  public Color findColour(char c, int j)
-  {
-    Color currentColour;
-
-    if ( (threshold == 0) || aboveThreshold(c, j))
-    {
-      currentColour = colors[ResidueProperties.aaIndex[c]];
-    }
-    else
-    {
-      currentColour = Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-
-  /**
-   * Get the percentage threshold for this colour scheme
-   *
-   * @return Returns the percentage threshold
-   */
-  public int getThreshold()
-  {
-    return threshold;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ct DOCUMENT ME!
-   */
-  public void setThreshold(int ct, boolean ignoreGaps)
-  {
-    threshold = ct;
-    if (ignoreGaps)
-    {
-      this.ignoreGaps = AAFrequency.PID_NOGAPS;
-    }
-    else
-    {
-      this.ignoreGaps = AAFrequency.PID_GAPS;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public boolean aboveThreshold(char c, int j)
-  {
-    if ('a' <= c && c <= 'z')
-    {
-      // TO UPPERCASE !!!
-      //Faster than toUpperCase
-      c -= ('a' - 'A');
-    }
-
-    if (consensus == null || consensus.length<j || consensus[j] == null)
-    {
-      return false;
-    }
-
-    if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
-        consensus[j].contains(String.valueOf(c)))
-    {
-      if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
-      {
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  public boolean conservationApplied()
-  {
-    return conservationColouring;
-  }
-
-  public void setConservationInc(int i)
-  {
-    inc = i;
-  }
-
-  public int getConservationInc()
-  {
-    return inc;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param consensus DOCUMENT ME!
-   */
-  public void setConsensus(Hashtable[] consensus)
-  {
-    if (consensus == null)
-    {
-      return;
-    }
-
-    this.consensus = consensus;
-  }
-
-  public void setConservation(Conservation cons)
-  {
-    if (cons == null)
-    {
-      conservationColouring = false;
-      conservation = null;
-    }
-    else
-    {
-      conservationColouring = true;
-      int i, iSize = cons.getConsSequence().getLength();
-      conservation = new char[iSize];
-      for (i = 0; i < iSize; i++)
-      {
-        conservation[i] = cons.getConsSequence().getCharAt(i);
-      }
-      conservationLength = conservation.length;
-    }
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param i DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-
-  Color applyConservation(Color currentColour, int i)
-  {
-
-    if ((conservationLength>i) && (conservation[i] != '*') && (conservation[i] != '+'))
-    {
-      if ( jalview.util.Comparison.isGap(conservation[i]))
-      {
-        currentColour = Color.white;
-      }
-      else
-      {
-        float t = 11 - (conservation[i] - '0');
-        if (t == 0)
-        {
-          return Color.white;
-        }
-
-        int red = currentColour.getRed();
-        int green = currentColour.getGreen();
-        int blue = currentColour.getBlue();
-
-        int dr = 255 - red;
-        int dg = 255 - green;
-        int db = 255 - blue;
-
-        dr *= t / 10f;
-        dg *= t / 10f;
-        db *= t / 10f;
-
-        red += (inc / 20f) * dr;
-        green += (inc / 20f) * dg;
-        blue += (inc / 20f) * db;
-
-        if (red > 255 || green > 255 || blue > 255)
-        {
-          currentColour = Color.white;
-        }
-        else
-        {
-          currentColour = new Color(red, green, blue);
-        }
-      }
-    }
-    return currentColour;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme
+    implements ColourSchemeI
+{
+
+  boolean conservationColouring = false;
+
+  Color[] colors;
+  int threshold = 0;
+
+  /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
+  protected String ignoreGaps = AAFrequency.PID_GAPS;
+
+  /** Consenus as a hashtable array */
+  Hashtable[] consensus;
+
+  /** Conservation string as a char array */
+  char[] conservation;
+  int conservationLength=0;
+
+  /** DOCUMENT ME!! */
+  int inc = 30;
+
+  /**
+   * Creates a new ResidueColourScheme object.
+   *
+   * @param colors DOCUMENT ME!
+   * @param threshold DOCUMENT ME!
+   */
+  public ResidueColourScheme(Color[] colours, int threshold)
+  {
+    this.colors = colours;
+    this.threshold = threshold;
+  }
+
+  /**
+   * Creates a new ResidueColourScheme object.
+   */
+  public ResidueColourScheme()
+  {
+  }
+
+  /**
+   * Find a colour without an index in a sequence
+   */
+  public Color findColour(char c)
+  {
+    return colors[ResidueProperties.aaIndex[c]];
+  }
+
+  public Color findColour(char c, int j)
+  {
+    Color currentColour;
+
+    if ( (threshold == 0) || aboveThreshold(c, j))
+    {
+      currentColour = colors[ResidueProperties.aaIndex[c]];
+    }
+    else
+    {
+      currentColour = Color.white;
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+
+  /**
+   * Get the percentage threshold for this colour scheme
+   *
+   * @return Returns the percentage threshold
+   */
+  public int getThreshold()
+  {
+    return threshold;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ct DOCUMENT ME!
+   */
+  public void setThreshold(int ct, boolean ignoreGaps)
+  {
+    threshold = ct;
+    if (ignoreGaps)
+    {
+      this.ignoreGaps = AAFrequency.PID_NOGAPS;
+    }
+    else
+    {
+      this.ignoreGaps = AAFrequency.PID_GAPS;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean aboveThreshold(char c, int j)
+  {
+    if ('a' <= c && c <= 'z')
+    {
+      // TO UPPERCASE !!!
+      //Faster than toUpperCase
+      c -= ('a' - 'A');
+    }
+
+    if (consensus == null || consensus.length<j || consensus[j] == null)
+    {
+      return false;
+    }
+
+    if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
+        consensus[j].contains(String.valueOf(c)))
+    {
+      if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+      {
+        return true;
+      }
+    }
+
+    return false;
+  }
+
+  public boolean conservationApplied()
+  {
+    return conservationColouring;
+  }
+
+  public void setConservationInc(int i)
+  {
+    inc = i;
+  }
+
+  public int getConservationInc()
+  {
+    return inc;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param consensus DOCUMENT ME!
+   */
+  public void setConsensus(Hashtable[] consensus)
+  {
+    if (consensus == null)
+    {
+      return;
+    }
+
+    this.consensus = consensus;
+  }
+
+  public void setConservation(Conservation cons)
+  {
+    if (cons == null)
+    {
+      conservationColouring = false;
+      conservation = null;
+    }
+    else
+    {
+      conservationColouring = true;
+      int i, iSize = cons.getConsSequence().getLength();
+      conservation = new char[iSize];
+      for (i = 0; i < iSize; i++)
+      {
+        conservation[i] = cons.getConsSequence().getCharAt(i);
+      }
+      conservationLength = conservation.length;
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param i DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+
+  Color applyConservation(Color currentColour, int i)
+  {
+
+    if ((conservationLength>i) && (conservation[i] != '*') && (conservation[i] != '+'))
+    {
+      if ( jalview.util.Comparison.isGap(conservation[i]))
+      {
+        currentColour = Color.white;
+      }
+      else
+      {
+        float t = 11 - (conservation[i] - '0');
+        if (t == 0)
+        {
+          return Color.white;
+        }
+
+        int red = currentColour.getRed();
+        int green = currentColour.getGreen();
+        int blue = currentColour.getBlue();
+
+        int dr = 255 - red;
+        int dg = 255 - green;
+        int db = 255 - blue;
+
+        dr *= t / 10f;
+        dg *= t / 10f;
+        db *= t / 10f;
+
+        red += (inc / 20f) * dr;
+        green += (inc / 20f) * dg;
+        blue += (inc / 20f) * db;
+
+        if (red > 255 || green > 255 || blue > 255)
+        {
+          currentColour = Color.white;
+        }
+        else
+        {
+          currentColour = new Color(red, green, blue);
+        }
+      }
+    }
+    return currentColour;
+  }
+
+}
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 98868d2..421e1cd 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 134ed4c..b55189b 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,121 +1,121 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class ScoreColourScheme
-    extends ResidueColourScheme
-{
-  /** DOCUMENT ME!! */
-  public double min;
-
-  /** DOCUMENT ME!! */
-  public double max;
-
-  /** DOCUMENT ME!! */
-  public double[] scores;
-
-  /**
-   * Creates a new ScoreColourScheme object.
-   *
-   * @param scores DOCUMENT ME!
-   * @param min DOCUMENT ME!
-   * @param max DOCUMENT ME!
-   */
-  public ScoreColourScheme(double[] scores, double min, double max)
-  {
-    super();
-
-    this.scores = scores;
-    this.min = min;
-    this.max = max;
-
-    // Make colours in constructor
-    // Why wasn't this done earlier?
-    int i, iSize = scores.length;
-    colors = new Color[scores.length];
-    for (i = 0; i < iSize; i++)
-    {
-      float red = (float) (scores[i] - (float) min) / (float) (max - min);
-
-      if (red > 1.0f)
-      {
-        red = 1.0f;
-      }
-
-      if (red < 0.0f)
-      {
-        red = 0.0f;
-      }
-      colors[i] = makeColour(red);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color findColour(char c, int j)
-  {
-    if (threshold > 0)
-    {
-      if (!aboveThreshold(c, j))
-      {
-        return Color.white;
-      }
-    }
-
-    if (jalview.util.Comparison.isGap(c))
-    {
-      return Color.white;
-    }
-
-    Color currentColour = colors[ResidueProperties.aaIndex[c]];
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(c, (float) 0.0, (float) 1.0 - c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme
+    extends ResidueColourScheme
+{
+  /** DOCUMENT ME!! */
+  public double min;
+
+  /** DOCUMENT ME!! */
+  public double max;
+
+  /** DOCUMENT ME!! */
+  public double[] scores;
+
+  /**
+   * Creates a new ScoreColourScheme object.
+   *
+   * @param scores DOCUMENT ME!
+   * @param min DOCUMENT ME!
+   * @param max DOCUMENT ME!
+   */
+  public ScoreColourScheme(double[] scores, double min, double max)
+  {
+    super();
+
+    this.scores = scores;
+    this.min = min;
+    this.max = max;
+
+    // Make colours in constructor
+    // Why wasn't this done earlier?
+    int i, iSize = scores.length;
+    colors = new Color[scores.length];
+    for (i = 0; i < iSize; i++)
+    {
+      float red = (float) (scores[i] - (float) min) / (float) (max - min);
+
+      if (red > 1.0f)
+      {
+        red = 1.0f;
+      }
+
+      if (red < 0.0f)
+      {
+        red = 0.0f;
+      }
+      colors[i] = makeColour(red);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    if (threshold > 0)
+    {
+      if (!aboveThreshold(c, j))
+      {
+        return Color.white;
+      }
+    }
+
+    if (jalview.util.Comparison.isGap(c))
+    {
+      return Color.white;
+    }
+
+    Color currentColour = colors[ResidueProperties.aaIndex[c]];
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(c, (float) 0.0, (float) 1.0 - c);
+  }
+}
diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 69a0922..0a976ea 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.schemes;
 
 public class ScoreMatrix
diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java
index ec57d50..c64af1b 100755
--- a/src/jalview/schemes/StrandColourScheme.java
+++ b/src/jalview/schemes/StrandColourScheme.java
@@ -1,52 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class StrandColourScheme
-    extends ScoreColourScheme
-{
-  /**
-   * Creates a new StrandColourScheme object.
-   */
-  public StrandColourScheme()
-  {
-    super(ResidueProperties.strand, ResidueProperties.strandmin,
-          ResidueProperties.strandmax);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(c, c, (float) 1.0 - c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class StrandColourScheme
+    extends ScoreColourScheme
+{
+  /**
+   * Creates a new StrandColourScheme object.
+   */
+  public StrandColourScheme()
+  {
+    super(ResidueProperties.strand, ResidueProperties.strandmin,
+          ResidueProperties.strandmax);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(c, c, (float) 1.0 - c);
+  }
+}
diff --git a/src/jalview/schemes/TaylorColourScheme.java b/src/jalview/schemes/TaylorColourScheme.java
index 3a5c4da..f3ac31e 100755
--- a/src/jalview/schemes/TaylorColourScheme.java
+++ b/src/jalview/schemes/TaylorColourScheme.java
@@ -1,28 +1,28 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-public class TaylorColourScheme
-    extends ResidueColourScheme
-{
-  public TaylorColourScheme()
-  {
-    super(ResidueProperties.taylor, 0);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+public class TaylorColourScheme
+    extends ResidueColourScheme
+{
+  public TaylorColourScheme()
+  {
+    super(ResidueProperties.taylor, 0);
+  }
+}
diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java
index 2bd779b..c2f06fd 100755
--- a/src/jalview/schemes/TurnColourScheme.java
+++ b/src/jalview/schemes/TurnColourScheme.java
@@ -1,52 +1,52 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class TurnColourScheme
-    extends ScoreColourScheme
-{
-  /**
-   * Creates a new TurnColourScheme object.
-   */
-  public TurnColourScheme()
-  {
-    super(ResidueProperties.turn, ResidueProperties.turnmin,
-          ResidueProperties.turnmax);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Color makeColour(float c)
-  {
-    return new Color(c, 1 - c, 1 - c);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TurnColourScheme
+    extends ScoreColourScheme
+{
+  /**
+   * Creates a new TurnColourScheme object.
+   */
+  public TurnColourScheme()
+  {
+    super(ResidueProperties.turn, ResidueProperties.turnmin,
+          ResidueProperties.turnmax);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Color makeColour(float c)
+  {
+    return new Color(c, 1 - c, 1 - c);
+  }
+}
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index ab9ad2f..140b06e 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java
index f674a51..327f9e2 100755
--- a/src/jalview/schemes/ZappoColourScheme.java
+++ b/src/jalview/schemes/ZappoColourScheme.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/structure/SequenceListener.java b/src/jalview/structure/SequenceListener.java
index 5370e12..7021f95 100644
--- a/src/jalview/structure/SequenceListener.java
+++ b/src/jalview/structure/SequenceListener.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
index 5436eae..15225d7 100644
--- a/src/jalview/structure/StructureListener.java
+++ b/src/jalview/structure/StructureListener.java
@@ -1,32 +1,32 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.structure;
-
-public interface StructureListener
-{
-  public String getPdbFile();
-
-  public void mouseOverStructure(int atomIndex, String strInfo);
-
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbId);
-
-  public void updateColours(Object source);
-
-  public java.awt.Color getColour(int atomIndex, int pdbResNum, String chain, String pdbId);
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.structure;
+
+public interface StructureListener
+{
+  public String getPdbFile();
+
+  public void mouseOverStructure(int atomIndex, String strInfo);
+
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbId);
+
+  public void updateColours(Object source);
+
+  public java.awt.Color getColour(int atomIndex, int pdbResNum, String chain, String pdbId);
+}
diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 06e6bc3..9a238b4 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,100 +1,99 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.structure;
-
-import jalview.datamodel.*;
-
-public class StructureMapping
-{
-  String mappingDetails;
-  SequenceI sequence;
-  String pdbfile;
-  String pdbid;
-  String pdbchain;
-
-  //Mapping index 0 is resNum, index 1 is atomNo
-  int[][] mapping;
-
-  public StructureMapping(SequenceI seq,
-                          String pdbfile,
-                          String pdbid,
-                          String chain,
-                          int[][] mapping,
-                          String mappingDetails)
-  {
-    sequence = seq;
-    this.pdbfile = pdbfile;
-    this.pdbid = pdbid;
-    this.pdbchain = chain;
-    this.mapping = mapping;
-    this.mappingDetails = mappingDetails;
-  }
-
-  public SequenceI getSequence()
-  {
-    return sequence;
-  }
-
-  public String getChain()
-  {
-    return pdbchain;
-  }
-
-  public String getPdbId()
-  {
-    return pdbid;
-  }
-
-  public int getAtomNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][1];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getPDBResNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][0];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getSeqPos(int pdbResNum)
-  {
-    for (int i = 0; i < mapping.length; i++)
-    {
-      if (mapping[i][0] == pdbResNum)
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.structure;
+
+import jalview.datamodel.*;
+
+public class StructureMapping
+{
+  String mappingDetails;
+  SequenceI sequence;
+  String pdbfile;
+  String pdbid;
+  String pdbchain;
+
+  //Mapping index 0 is resNum, index 1 is atomNo
+  int[][] mapping;
+
+  public StructureMapping(SequenceI seq,
+                          String pdbfile,
+                          String pdbid,
+                          String chain,
+                          int[][] mapping,
+                          String mappingDetails)
+  {
+    sequence = seq;
+    this.pdbfile = pdbfile;
+    this.pdbid = pdbid;
+    this.pdbchain = chain;
+    this.mapping = mapping;
+    this.mappingDetails = mappingDetails;
+  }
+
+  public SequenceI getSequence()
+  {
+    return sequence;
+  }
+
+  public String getChain()
+  {
+    return pdbchain;
+  }
+
+  public String getPdbId()
+  {
+    return pdbid;
+  }
+
+  public int getAtomNum(int seqpos)
+  {
+    if (mapping.length > seqpos)
+    {
+      return mapping[seqpos][1];
+    }
+    else
+    {
+      return 0;
+    }
+  }
+
+  public int getPDBResNum(int seqpos)
+  {
+    if (mapping.length > seqpos)
+    {
+      return mapping[seqpos][0];
+    }
+    else
+    {
+      return 0;
+    }
+  }
+
+  public int getSeqPos(int pdbResNum)
+  {
+    for (int i = 0; i < mapping.length; i++)
+    {
+      if (mapping[i][0] == pdbResNum)
+      {
+        return i;
+      }
+    }
+    return -1;
+  }
+}
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index e12e3ab..52195a3 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/structure/VamsasListener.java b/src/jalview/structure/VamsasListener.java
index 1bf3931..962c928 100644
--- a/src/jalview/structure/VamsasListener.java
+++ b/src/jalview/structure/VamsasListener.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.structure;
 
 import jalview.datamodel.SequenceI;
diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index 2b8a4bd..05f2fc3 100755
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -1,931 +1,931 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.util;
-
-import java.io.*;
-import java.lang.reflect.*;
-
-/**
- * BrowserLauncher is a class that provides one static method, openURL, which opens the default
- * web browser for the current user of the system to the given URL.  It may support other
- * protocols depending on the system -- mailto, ftp, etc. -- but that has not been rigorously
- * tested and is not guaranteed to work.
- * <p>
- * Yes, this is platform-specific code, and yes, it may rely on classes on certain platforms
- * that are not part of the standard JDK.  What we're trying to do, though, is to take something
- * that's frequently desirable but inherently platform-specific -- opening a default browser --
- * and allow programmers (you, for example) to do so without worrying about dropping into native
- * code or doing anything else similarly evil.
- * <p>
- * Anyway, this code is completely in Java and will run on all JDK 1.1-compliant systems without
- * modification or a need for additional libraries.  All classes that are required on certain
- * platforms to allow this to run are dynamically loaded at runtime via reflection and, if not
- * found, will not cause this to do anything other than returning an error when opening the
- * browser.
- * <p>
- * There are certain system requirements for this class, as it's running through Runtime.exec(),
- * which is Java's way of making a native system call.  Currently, this requires that a Macintosh
- * have a Finder which supports the GURL event, which is true for Mac OS 8.0 and 8.1 systems that
- * have the Internet Scripting AppleScript dictionary installed in the Scripting Additions folder
- * in the Extensions folder (which is installed by default as far as I know under Mac OS 8.0 and
- * 8.1), and for all Mac OS 8.5 and later systems.  On Windows, it only runs under Win32 systems
- * (Windows 95, 98, and NT 4.0, as well as later versions of all).  On other systems, this drops
- * back from the inherently platform-sensitive concept of a default browser and simply attempts
- * to launch Netscape via a shell command.
- * <p>
- * This code is Copyright 1999-2001 by Eric Albert (ejalbert\@cs.stanford.edu) and may be
- * redistributed or modified in any form without restrictions as long as the portion of this
- * comment from this paragraph through the end of the comment is not removed.  The author
- * requests that he be notified of any application, applet, or other binary that makes use of
- * this code, but that's more out of curiosity than anything and is not required.  This software
- * includes no warranty.  The author is not repsonsible for any loss of data or functionality
- * or any adverse or unexpected effects of using this software.
- * <p>
- * Credits:
- * <br>Steven Spencer, JavaWorld magazine (<a href="http://www.javaworld.com/javaworld/javatips/jw-javatip66.html">Java Tip 66</a>)
- * <br>Thanks also to Ron B. Yeh, Eric Shapiro, Ben Engber, Paul Teitlebaum, Andrea Cantatore,
- * Larry Barowski, Trevor Bedzek, Frank Miedrich, and Ron Rabakukk
- *
- * @author Eric Albert (<a href="mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
- * @version 1.4b1 (Released June 20, 2001)
- */
-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";
-
-  /**
-   * 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.    s 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)
-            {
-              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.getDefault("DEFAULT_BROWSER", "firefox");
-
-        break;
-    }
-
-    return browser;
-  }
-
-  /**
-   * used to ensure that browser is up-to-date after a configuration
-   * change (Unix DEFAULT_BROWSER property change).
-   */
-  public static void resetBrowser()
-  {
-    browser = null;
-  }
-
-  /**
-   * 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);
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import java.io.*;
+import java.lang.reflect.*;
+
+/**
+ * BrowserLauncher is a class that provides one static method, openURL, which opens the default
+ * web browser for the current user of the system to the given URL.  It may support other
+ * protocols depending on the system -- mailto, ftp, etc. -- but that has not been rigorously
+ * tested and is not guaranteed to work.
+ * <p>
+ * Yes, this is platform-specific code, and yes, it may rely on classes on certain platforms
+ * that are not part of the standard JDK.  What we're trying to do, though, is to take something
+ * that's frequently desirable but inherently platform-specific -- opening a default browser --
+ * and allow programmers (you, for example) to do so without worrying about dropping into native
+ * code or doing anything else similarly evil.
+ * <p>
+ * Anyway, this code is completely in Java and will run on all JDK 1.1-compliant systems without
+ * modification or a need for additional libraries.  All classes that are required on certain
+ * platforms to allow this to run are dynamically loaded at runtime via reflection and, if not
+ * found, will not cause this to do anything other than returning an error when opening the
+ * browser.
+ * <p>
+ * There are certain system requirements for this class, as it's running through Runtime.exec(),
+ * which is Java's way of making a native system call.  Currently, this requires that a Macintosh
+ * have a Finder which supports the GURL event, which is true for Mac OS 8.0 and 8.1 systems that
+ * have the Internet Scripting AppleScript dictionary installed in the Scripting Additions folder
+ * in the Extensions folder (which is installed by default as far as I know under Mac OS 8.0 and
+ * 8.1), and for all Mac OS 8.5 and later systems.  On Windows, it only runs under Win32 systems
+ * (Windows 95, 98, and NT 4.0, as well as later versions of all).  On other systems, this drops
+ * back from the inherently platform-sensitive concept of a default browser and simply attempts
+ * to launch Netscape via a shell command.
+ * <p>
+ * This code is Copyright 1999-2001 by Eric Albert (ejalbert\@cs.stanford.edu) and may be
+ * redistributed or modified in any form without restrictions as long as the portion of this
+ * comment from this paragraph through the end of the comment is not removed.  The author
+ * requests that he be notified of any application, applet, or other binary that makes use of
+ * this code, but that's more out of curiosity than anything and is not required.  This software
+ * includes no warranty.  The author is not repsonsible for any loss of data or functionality
+ * or any adverse or unexpected effects of using this software.
+ * <p>
+ * Credits:
+ * <br>Steven Spencer, JavaWorld magazine (<a href="http://www.javaworld.com/javaworld/javatips/jw-javatip66.html">Java Tip 66</a>)
+ * <br>Thanks also to Ron B. Yeh, Eric Shapiro, Ben Engber, Paul Teitlebaum, Andrea Cantatore,
+ * Larry Barowski, Trevor Bedzek, Frank Miedrich, and Ron Rabakukk
+ *
+ * @author Eric Albert (<a href="mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
+ * @version 1.4b1 (Released June 20, 2001)
+ */
+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";
+
+  /**
+   * 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.    s 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)
+            {
+              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.getDefault("DEFAULT_BROWSER", "firefox");
+
+        break;
+    }
+
+    return browser;
+  }
+
+  /**
+   * used to ensure that browser is up-to-date after a configuration
+   * change (Unix DEFAULT_BROWSER property change).
+   */
+  public static void resetBrowser()
+  {
+    browser = null;
+  }
+
+  /**
+   * 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 67a668a..aad9667 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,226 +1,226 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.util;
-
-import jalview.datamodel.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Comparison
-{
-  /** DOCUMENT ME!! */
-  public static final String GapChars = " .-";
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param ii DOCUMENT ME!
-   * @param jj DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public static final 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.getSequenceAsString();
-    String sj = jj.getSequenceAsString();
-
-    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 final static float PID(String seq1, String seq2)
-  {
-    return PID(seq1, seq2, 0, seq1.length());
-  }
-
-  static final int caseShift = 'a' - 'A';
-
-  // Another pid with region specification
-  public final static float PID(String seq1, String seq2, int start, int end)
-  {
-
-    int s1len = seq1.length();
-    int s2len = seq2.length();
-
-    int len = Math.min(s1len, s2len);
-
-    if (end < len)
-    {
-      len = end;
-    }
-
-    if (len < start)
-    {
-      start = len - 1; // we just use a single residue for the difference
-    }
-
-    int bad = 0;
-    char chr1;
-    char chr2;
-
-    for (int i = start; i < len; i++)
-    {
-      chr1 = seq1.charAt(i);
-
-      chr2 = seq2.charAt(i);
-
-      if ('a' <= chr1 && chr1 <= 'z')
-      {
-        // TO UPPERCASE !!!
-        //Faster than toUpperCase
-        chr1 -= caseShift;
-      }
-      if ('a' <= chr2 && chr2 <= 'z')
-      {
-        // TO UPPERCASE !!!
-        //Faster than toUpperCase
-        chr2 -= caseShift;
-      }
-
-      if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2))
-      {
-        bad++;
-      }
-    }
-
-    return ( (float) 100 * (len - bad)) / len;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public static final boolean isGap(char c)
-  {
-    return (c == '-' || c == '.' || c == ' ') ? true : false;
-  }
-
-  public static final boolean isNucleotide(SequenceI[] seqs)
-  {
-    int i = 0, iSize = seqs.length, j, jSize;
-    float nt = 0, aa = 0;
-    char c;
-    while (i < iSize)
-    {
-      jSize = seqs[i].getLength();
-      for (j = 0; j < jSize; j++)
-      {
-        c = seqs[i].getCharAt(j);
-        if ('a' <= c && c <= 'z')
-        {
-          c -= ('a' - 'A');
-        }
-
-        if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
-        {
-          nt++;
-        }
-        else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j)))
-        {
-          aa++;
-        }
-      }
-      i++;
-    }
-
-    if ( (nt / (nt + aa)) > 0.85f)
-    {
-      return true;
-    }
-    else
-    {
-      return false;
-    }
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Comparison
+{
+  /** DOCUMENT ME!! */
+  public static final String GapChars = " .-";
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ii DOCUMENT ME!
+   * @param jj DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static final 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.getSequenceAsString();
+    String sj = jj.getSequenceAsString();
+
+    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 final static float PID(String seq1, String seq2)
+  {
+    return PID(seq1, seq2, 0, seq1.length());
+  }
+
+  static final int caseShift = 'a' - 'A';
+
+  // Another pid with region specification
+  public final static float PID(String seq1, String seq2, int start, int end)
+  {
+
+    int s1len = seq1.length();
+    int s2len = seq2.length();
+
+    int len = Math.min(s1len, s2len);
+
+    if (end < len)
+    {
+      len = end;
+    }
+
+    if (len < start)
+    {
+      start = len - 1; // we just use a single residue for the difference
+    }
+
+    int bad = 0;
+    char chr1;
+    char chr2;
+
+    for (int i = start; i < len; i++)
+    {
+      chr1 = seq1.charAt(i);
+
+      chr2 = seq2.charAt(i);
+
+      if ('a' <= chr1 && chr1 <= 'z')
+      {
+        // TO UPPERCASE !!!
+        //Faster than toUpperCase
+        chr1 -= caseShift;
+      }
+      if ('a' <= chr2 && chr2 <= 'z')
+      {
+        // TO UPPERCASE !!!
+        //Faster than toUpperCase
+        chr2 -= caseShift;
+      }
+
+      if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2))
+      {
+        bad++;
+      }
+    }
+
+    return ( (float) 100 * (len - bad)) / len;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static final boolean isGap(char c)
+  {
+    return (c == '-' || c == '.' || c == ' ') ? true : false;
+  }
+
+  public static final boolean isNucleotide(SequenceI[] seqs)
+  {
+    int i = 0, iSize = seqs.length, j, jSize;
+    float nt = 0, aa = 0;
+    char c;
+    while (i < iSize)
+    {
+      jSize = seqs[i].getLength();
+      for (j = 0; j < jSize; j++)
+      {
+        c = seqs[i].getCharAt(j);
+        if ('a' <= c && c <= 'z')
+        {
+          c -= ('a' - 'A');
+        }
+
+        if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
+        {
+          nt++;
+        }
+        else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j)))
+        {
+          aa++;
+        }
+      }
+      i++;
+    }
+
+    if ( (nt / (nt + aa)) > 0.85f)
+    {
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+
+  }
+}
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 7592748..0208453 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java
index 7c9b585..5786ed2 100755
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -1,867 +1,864 @@
-/*
- * Cay S. Horstmann & Gary Cornell, Core Java
- * Published By Sun Microsystems Press/Prentice-Hall
- * Copyright (C) 1997 Sun Microsystems Inc.
- * All Rights Reserved.
- *
- * Permission to use, copy, modify, and distribute this
- * software and its documentation for NON-COMMERCIAL purposes
- * and without fee is hereby granted provided that this
- * copyright notice appears in all copies.
- *
- * THE AUTHORS AND PUBLISHER MAKE NO REPRESENTATIONS OR
- * WARRANTIES ABOUT THE SUITABILITY OF THE SOFTWARE, EITHER
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
- * PARTICULAR PURPOSE, OR NON-INFRINGEMENT. THE AUTHORS
- * AND PUBLISHER SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED
- * BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING
- * THIS SOFTWARE OR ITS DERIVATIVES.
- */
-
-/**
- * A class for formatting numbers that follows printf conventions.
- * Also implements C-like atoi and atof functions
- * @version 1.03 25 Oct 1997
- * @author Cay Horstmann
- */
-package jalview.util;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-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
-
-  /**
-   * Creates a new Format object.
-   *
-   * @param s DOCUMENT ME!
-   */
-  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 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
-   * Use multiple Format objects to format more than one number
-   * @param s the format string following printf conventions
-   * The string has a prefix, a format code and a suffix. The prefix and suffix
-   * become part of the formatted output. The format code directs the
-   * formatting of the (single) parameter to be formatted. The code has the
-   * following structure
-   * <ul>
-   * <li> a % (required)
-   * <li> a modifier (optional)
-   * <dl>
-   * <dt> + <dd> forces display of + for positive numbers
-   * <dt> 0 <dd> show leading zeroes
-   * <dt> - <dd> align left in the field
-   * <dt> space <dd> prepend a space in front of positive numbers
-   * <dt> # <dd> use "alternate" format. Add 0 or 0x for octal or hexadecimal numbers. Don't suppress trailing zeroes in general floating point format.
-   * </dl>
-   * <li> an integer denoting field width (optional)
-   * <li> a period followed by an integer denoting precision (optional)
-   * <li> a format descriptor (required)
-   * <dl>
-   * <dt>f <dd> floating point number in fixed format
-   * <dt>e, E <dd> floating point number in exponential notation (scientific format). The E format results in an uppercase E for the exponent (1.14130E+003), the e format in a lowercase e.
-   * <dt>g, G <dd> floating point number in general format (fixed format for small numbers, exponential format for large numbers). Trailing zeroes are suppressed. The G format results in an uppercase E for the exponent (if any), the g format in a lowercase e.
-   * <dt>d, i <dd> integer in decimal
-   * <dt>x <dd> integer in hexadecimal
-   * <dt>o <dd> integer in octal
-   * <dt>s <dd> string
-   * <dt>c <dd> character
-   * </dl>
-   * </ul>
-   * @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;
-    }
-
-    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;
-  }
-
-  /**
-   * 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);
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param base DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private static long parseLong(String s, int base)
-  {
-    int i = 0;
-    int sign = 1;
-    long r = 0;
-
-    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;
-  }
-
-  /**
-   * 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;
-  }
-
-  /**
-   * 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));
-  }
-
-  /**
-   * 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);
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
-   * @param n DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private static String repeat(char c, int n)
-  {
-    if (n <= 0)
-    {
-      return "";
-    }
-
-    StringBuffer s = new StringBuffer(n);
-
-    for (int i = 0; i < n; i++)
-    {
-      s.append(c);
-    }
-
-    return s.toString();
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param x DOCUMENT ME!
-   * @param n DOCUMENT ME!
-   * @param m DOCUMENT ME!
-   * @param d DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private static String convert(long x, int n, int m, String d)
-  {
-    if (x == 0)
-    {
-      return "0";
-    }
-
-    String r = "";
-
-    while (x != 0)
-    {
-      r = d.charAt( (int) (x & m)) + r;
-      x = x >>> n;
-    }
-
-    return r;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param r DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  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;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param r DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private String sign(int s, String r)
-  {
-    String p = "";
-
-    if (s < 0)
-    {
-      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;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param d DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private String fixed_format(double d)
-  {
-    boolean removeTrailing = ( (fmt == 'G') || (fmt == 'g')) && !alternate;
-
-    // remove trailing zeroes and decimal point
-    if (d > 0x7FFFFFFFFFFFFFFFL)
-    {
-      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;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param d DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  private String exp_format(double d)
-  {
-    String f = "";
-    int e = 0;
-    double dd = d;
-    double factor = 1;
-
-    if (d != 0)
-    {
-      while (dd > 10)
-      {
-        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());
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
+ */
+/**
+ * A class for formatting numbers that follows printf conventions.
+ * Also implements C-like atoi and atof functions
+ * @version 1.03 25 Oct 1997
+ * @author Cay Horstmann
+ */
+package jalview.util;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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
+
+  /**
+   * Creates a new Format object.
+   *
+   * @param s DOCUMENT ME!
+   */
+  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 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
+   * Use multiple Format objects to format more than one number
+   * @param s the format string following printf conventions
+   * The string has a prefix, a format code and a suffix. The prefix and suffix
+   * become part of the formatted output. The format code directs the
+   * formatting of the (single) parameter to be formatted. The code has the
+   * following structure
+   * <ul>
+   * <li> a % (required)
+   * <li> a modifier (optional)
+   * <dl>
+   * <dt> + <dd> forces display of + for positive numbers
+   * <dt> 0 <dd> show leading zeroes
+   * <dt> - <dd> align left in the field
+   * <dt> space <dd> prepend a space in front of positive numbers
+   * <dt> # <dd> use "alternate" format. Add 0 or 0x for octal or hexadecimal numbers. Don't suppress trailing zeroes in general floating point format.
+   * </dl>
+   * <li> an integer denoting field width (optional)
+   * <li> a period followed by an integer denoting precision (optional)
+   * <li> a format descriptor (required)
+   * <dl>
+   * <dt>f <dd> floating point number in fixed format
+   * <dt>e, E <dd> floating point number in exponential notation (scientific format). The E format results in an uppercase E for the exponent (1.14130E+003), the e format in a lowercase e.
+   * <dt>g, G <dd> floating point number in general format (fixed format for small numbers, exponential format for large numbers). Trailing zeroes are suppressed. The G format results in an uppercase E for the exponent (if any), the g format in a lowercase e.
+   * <dt>d, i <dd> integer in decimal
+   * <dt>x <dd> integer in hexadecimal
+   * <dt>o <dd> integer in octal
+   * <dt>s <dd> string
+   * <dt>c <dd> character
+   * </dl>
+   * </ul>
+   * @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;
+    }
+
+    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;
+  }
+
+  /**
+   * 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);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param base DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private static long parseLong(String s, int base)
+  {
+    int i = 0;
+    int sign = 1;
+    long r = 0;
+
+    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;
+  }
+
+  /**
+   * 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;
+  }
+
+  /**
+   * 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));
+  }
+
+  /**
+   * 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);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private static String repeat(char c, int n)
+  {
+    if (n <= 0)
+    {
+      return "";
+    }
+
+    StringBuffer s = new StringBuffer(n);
+
+    for (int i = 0; i < n; i++)
+    {
+      s.append(c);
+    }
+
+    return s.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param x DOCUMENT ME!
+   * @param n DOCUMENT ME!
+   * @param m DOCUMENT ME!
+   * @param d DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private static String convert(long x, int n, int m, String d)
+  {
+    if (x == 0)
+    {
+      return "0";
+    }
+
+    String r = "";
+
+    while (x != 0)
+    {
+      r = d.charAt( (int) (x & m)) + r;
+      x = x >>> n;
+    }
+
+    return r;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param r DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  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;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param r DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private String sign(int s, String r)
+  {
+    String p = "";
+
+    if (s < 0)
+    {
+      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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param d DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private String fixed_format(double d)
+  {
+    boolean removeTrailing = ( (fmt == 'G') || (fmt == 'g')) && !alternate;
+
+    // remove trailing zeroes and decimal point
+    if (d > 0x7FFFFFFFFFFFFFFFL)
+    {
+      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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param d DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  private String exp_format(double d)
+  {
+    String f = "";
+    int e = 0;
+    double dd = d;
+    double factor = 1;
+
+    if (d != 0)
+    {
+      while (dd > 10)
+      {
+        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/ImageMaker.java b/src/jalview/util/ImageMaker.java
index 632c2ad..cec6cc3 100755
--- a/src/jalview/util/ImageMaker.java
+++ b/src/jalview/util/ImageMaker.java
@@ -1,190 +1,190 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.util;
-
-import java.io.*;
-import javax.imageio.*;
-
-import java.awt.*;
-import java.awt.image.*;
-
-import org.jibble.epsgraphics.*;
-import jalview.gui.*;
-import jalview.io.*;
-
-public class ImageMaker
-{
-  public static final int EPS = 0;
-  public static final int PNG = 1;
-  int type = -1;
-
-  EpsGraphics2D pg;
-  Graphics graphics;
-  FileOutputStream out;
-  BufferedImage bi;
-
-  public ImageMaker(Component parent, int type, String title,
-                    int width, int height, File file, String EPStitle)
-  {
-    this.type = type;
-
-    if (file == null)
-    {
-      JalviewFileChooser chooser;
-      chooser = type == EPS ? getEPSChooser() : getPNGChooser();
-
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(title);
-      chooser.setToolTipText("Save");
-
-      int value = chooser.showSaveDialog(parent);
-
-      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
-      {
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                      chooser.getSelectedFile().getParent());
-
-        file = chooser.getSelectedFile();
-      }
-    }
-
-    if (file != null)
-    {
-      try
-      {
-        out = new FileOutputStream(file);
-
-        if (type == EPS)
-        {
-          setupEPS(width, height, EPStitle);
-        }
-        else
-        {
-          setupPNG(width, height);
-        }
-      }
-      catch (Exception ex)
-      {
-        System.out.println("Error creating " + (type == EPS ? "EPS" : "PNG") +
-                           " file.");
-      }
-    }
-  }
-
-  public Graphics getGraphics()
-  {
-    return graphics;
-  }
-
-  void setupPNG(int width, int height)
-  {
-    bi = new BufferedImage(width, height,
-                           BufferedImage.TYPE_INT_RGB);
-    graphics = bi.getGraphics();
-    Graphics2D ig2 = (Graphics2D) graphics;
-    ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                         RenderingHints.VALUE_ANTIALIAS_ON);
-  }
-
-  public void writeImage()
-  {
-    try
-    {
-      switch (type)
-      {
-        case EPS:
-          pg.flush();
-          pg.close();
-          break;
-        case PNG:
-          ImageIO.write(bi, "png", out);
-          out.close();
-          break;
-      }
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  void setupEPS(int width, int height, String title)
-  {
-    boolean accurateText = true;
-
-    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
-        "Prompt each time");
-
-    // If we need to prompt, and if the GUI is visible then
-    // Prompt for EPS rendering style
-    if (renderStyle.equalsIgnoreCase("Prompt each time")
-        && !
-        (System.getProperty("java.awt.headless") != null
-         && System.getProperty("java.awt.headless").equals("true")))
-    {
-      EPSOptions eps = new EPSOptions();
-      renderStyle = eps.getValue();
-
-      if (renderStyle == null || eps.cancelled)
-      {
-        return;
-      }
-    }
-
-    if (renderStyle.equalsIgnoreCase("text"))
-    {
-      accurateText = false;
-    }
-
-    try
-    {
-      pg = new EpsGraphics2D(title, out, 0, 0, width,
-                             height);
-      Graphics2D ig2 = (Graphics2D) pg;
-      ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                           RenderingHints.VALUE_ANTIALIAS_ON);
-
-      pg.setAccurateTextMode(accurateText);
-
-      graphics = pg;
-    }
-    catch (Exception ex)
-    {}
-  }
-
-  JalviewFileChooser getPNGChooser()
-  {
-    return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-        "LAST_DIRECTORY"), new String[]
-                                             {"png"},
-                                             new String[]
-                                             {"Portable network graphics"},
-                                             "Portable network graphics");
-  }
-
-  JalviewFileChooser getEPSChooser()
-  {
-    return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-        "LAST_DIRECTORY"), new String[]
-                                             {"eps"},
-                                             new String[]
-                                             {"Encapsulated Postscript"},
-                                             "Encapsulated Postscript");
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import java.io.*;
+import javax.imageio.*;
+
+import java.awt.*;
+import java.awt.image.*;
+
+import org.jibble.epsgraphics.*;
+import jalview.gui.*;
+import jalview.io.*;
+
+public class ImageMaker
+{
+  public static final int EPS = 0;
+  public static final int PNG = 1;
+  int type = -1;
+
+  EpsGraphics2D pg;
+  Graphics graphics;
+  FileOutputStream out;
+  BufferedImage bi;
+
+  public ImageMaker(Component parent, int type, String title,
+                    int width, int height, File file, String EPStitle)
+  {
+    this.type = type;
+
+    if (file == null)
+    {
+      JalviewFileChooser chooser;
+      chooser = type == EPS ? getEPSChooser() : getPNGChooser();
+
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle(title);
+      chooser.setToolTipText("Save");
+
+      int value = chooser.showSaveDialog(parent);
+
+      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      {
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                      chooser.getSelectedFile().getParent());
+
+        file = chooser.getSelectedFile();
+      }
+    }
+
+    if (file != null)
+    {
+      try
+      {
+        out = new FileOutputStream(file);
+
+        if (type == EPS)
+        {
+          setupEPS(width, height, EPStitle);
+        }
+        else
+        {
+          setupPNG(width, height);
+        }
+      }
+      catch (Exception ex)
+      {
+        System.out.println("Error creating " + (type == EPS ? "EPS" : "PNG") +
+                           " file.");
+      }
+    }
+  }
+
+  public Graphics getGraphics()
+  {
+    return graphics;
+  }
+
+  void setupPNG(int width, int height)
+  {
+    bi = new BufferedImage(width, height,
+                           BufferedImage.TYPE_INT_RGB);
+    graphics = bi.getGraphics();
+    Graphics2D ig2 = (Graphics2D) graphics;
+    ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                         RenderingHints.VALUE_ANTIALIAS_ON);
+  }
+
+  public void writeImage()
+  {
+    try
+    {
+      switch (type)
+      {
+        case EPS:
+          pg.flush();
+          pg.close();
+          break;
+        case PNG:
+          ImageIO.write(bi, "png", out);
+          out.close();
+          break;
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  void setupEPS(int width, int height, String title)
+  {
+    boolean accurateText = true;
+
+    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+        "Prompt each time");
+
+    // If we need to prompt, and if the GUI is visible then
+    // Prompt for EPS rendering style
+    if (renderStyle.equalsIgnoreCase("Prompt each time")
+        && !
+        (System.getProperty("java.awt.headless") != null
+         && System.getProperty("java.awt.headless").equals("true")))
+    {
+      EPSOptions eps = new EPSOptions();
+      renderStyle = eps.getValue();
+
+      if (renderStyle == null || eps.cancelled)
+      {
+        return;
+      }
+    }
+
+    if (renderStyle.equalsIgnoreCase("text"))
+    {
+      accurateText = false;
+    }
+
+    try
+    {
+      pg = new EpsGraphics2D(title, out, 0, 0, width,
+                             height);
+      Graphics2D ig2 = (Graphics2D) pg;
+      ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                           RenderingHints.VALUE_ANTIALIAS_ON);
+
+      pg.setAccurateTextMode(accurateText);
+
+      graphics = pg;
+    }
+    catch (Exception ex)
+    {}
+  }
+
+  JalviewFileChooser getPNGChooser()
+  {
+    return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+        "LAST_DIRECTORY"), new String[]
+                                             {"png"},
+                                             new String[]
+                                             {"Portable network graphics"},
+                                             "Portable network graphics");
+  }
+
+  JalviewFileChooser getEPSChooser()
+  {
+    return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+        "LAST_DIRECTORY"), new String[]
+                                             {"eps"},
+                                             new String[]
+                                             {"Encapsulated Postscript"},
+                                             "Encapsulated Postscript");
+  }
+}
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 90dfc8c..31c02e8 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index 71ad6f7..b68dd40 100644
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.util;
 
 /**
diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index 017921f..8c3b933 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/util/ShiftList.java b/src/jalview/util/ShiftList.java
index 8885e2c..9e14172 100644
--- a/src/jalview/util/ShiftList.java
+++ b/src/jalview/util/ShiftList.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/util/TableSorter.java b/src/jalview/util/TableSorter.java
index 469bd7f..f51417f 100755
--- a/src/jalview/util/TableSorter.java
+++ b/src/jalview/util/TableSorter.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 21dee38..ac70ae2 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.util;
 
 import java.util.Vector;
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 82b411a..a67599b 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index e3f7478..815ecda 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java
index 61b8ba1..5508eef 100755
--- a/src/jalview/ws/Discoverer.java
+++ b/src/jalview/ws/Discoverer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index e14816c..49a7567 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 106bb53..418e45e 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws;
 
 import java.util.*;
diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 63e60d7..a461abb 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 8d373ac..9706c18 100644
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -1,721 +1,721 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws;
-
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.datamodel.Alignment;
-import jalview.gui.*;
-import vamsas.objects.simple.MsaResult;
-
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
-class MsaWSThread
-    extends WSThread implements WSClientI
-{
-  boolean submitGaps = false; // pass sequences including gaps to alignment
-
-  // service
-
-  boolean preserveOrder = true; // and always store and recover sequence
-
-  // order
-
-  class MsaWSJob
-      extends WSThread.WSJob
-  {
-    // hold special input for this
-    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
-        SequenceSet();
-
-    /**
-     * MsaWSJob
-     *
-     * @param jobNum
-     *            int
-     * @param jobId
-     *            String
-     */
-    public MsaWSJob(int jobNum, SequenceI[] inSeqs)
-    {
-      this.jobnum = jobNum;
-      if (!prepareInput(inSeqs, 2))
-      {
-        submitted = true;
-        subjobComplete = true;
-        result = new MsaResult();
-        result.setFinished(true);
-        result.setStatus("Job never ran - input returned to user.");
-      }
-
-    }
-
-    Hashtable SeqNames = new Hashtable();
-    Vector emptySeqs = new Vector();
-    /**
-     * prepare input sequences for MsaWS service
-     * @param seqs jalview sequences to be prepared
-     * @param minlen minimum number of residues required for this MsaWS service
-     * @return true if seqs contains sequences to be submitted to service.
-     */
-    private boolean prepareInput(SequenceI[] seqs, int minlen)
-    {
-      int nseqs = 0;
-      if (minlen < 0)
-      {
-        throw new Error("Implementation error: minlen must be zero or more.");
-      }
-      for (int i = 0; i < seqs.length; i++)
-      {
-        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          nseqs++;
-        }
-      }
-      boolean valid = nseqs > 1; // need at least two seqs
-      vamsas.objects.simple.Sequence[] seqarray =
-          (valid)
-          ? new vamsas.objects.simple.Sequence[nseqs]
-          : null;
-      for (int i = 0, n = 0; i < seqs.length; i++)
-      {
-
-        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
-        // for
-        // any
-        // subjob
-        SeqNames.put(newname, jalview.analysis.SeqsetUtils
-                     .SeqCharacterHash(seqs[i]));
-        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          seqarray[n] = new vamsas.objects.simple.Sequence();
-          seqarray[n].setId(newname);
-          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
-                               : AlignSeq.extractGaps(
-                                   jalview.util.Comparison.GapChars, seqs[i]
-                                   .getSequenceAsString()));
-        }
-        else
-        {
-          String empty = null;
-          if (seqs[i].getEnd() >= seqs[i].getStart())
-          {
-            empty = (submitGaps) ? seqs[i].getSequenceAsString()
-                : AlignSeq.extractGaps(
-                    jalview.util.Comparison.GapChars, seqs[i]
-                    .getSequenceAsString());
-          }
-          emptySeqs.add(new String[]
-                        {newname, empty});
-        }
-      }
-      this.seqs = new vamsas.objects.simple.SequenceSet();
-      this.seqs.setSeqs(seqarray);
-      return valid;
-    }
-
-    /**
-     *
-     * @return true if getAlignment will return a valid alignment result.
-     */
-    public boolean hasResults()
-    {
-      if (subjobComplete && result != null && result.isFinished()
-          && ( (MsaResult) result).getMsa() != null &&
-          ( (MsaResult) result).getMsa().getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-
-    public Object[] getAlignment()
-    {
-
-      if (result != null && result.isFinished())
-      {
-        SequenceI[] alseqs = null;
-        char alseq_gapchar = '-';
-        int alseq_l = 0;
-        if ( ( (MsaResult) result).getMsa() != null)
-        {
-          alseqs = getVamsasAlignment( ( (MsaResult) result).getMsa());
-          alseq_gapchar = ( (MsaResult) result).getMsa().getGapchar().charAt(0);
-          alseq_l = alseqs.length;
-        }
-        if (emptySeqs.size() > 0)
-        {
-          SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
-          // get width
-          int i, w = 0;
-          if (alseq_l > 0)
-          {
-            for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
-            {
-              if (w < alseqs[i].getLength())
-              {
-                w = alseqs[i].getLength();
-              }
-              t_alseqs[i] = alseqs[i];
-              alseqs[i] = null;
-            }
-          }
-          // check that aligned width is at least as wide as emptySeqs width.
-          int ow = w, nw = w;
-          for (i = 0, w = emptySeqs.size(); i < w; i++)
-          {
-            String[] es = (String[]) emptySeqs.get(i);
-            if (es != null && es[1] != null)
-            {
-              int sw = es[1].length();
-              if (nw < sw)
-              {
-                nw = sw;
-              }
-            }
-          }
-          // make a gapped string.
-          StringBuffer insbuff = new StringBuffer(w);
-          for (i = 0; i < nw; i++)
-          {
-            insbuff.append(alseq_gapchar);
-          }
-          if (ow < nw)
-          {
-            for (i = 0; i < alseq_l; i++)
-            {
-              int sw = t_alseqs[i].getLength();
-              if (nw > sw)
-              {
-                // pad at end
-                alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() +
-                                      insbuff.substring(0, sw - nw));
-              }
-            }
-          }
-          for (i = 0, w = emptySeqs.size(); i < w; i++)
-          {
-            String[] es = (String[]) emptySeqs.get(i);
-            if (es[1] == null)
-            {
-              t_alseqs[i +
-                  alseq_l] = new jalview.datamodel.Sequence(es[0],
-                  insbuff.toString(), 1, 0);
-            }
-            else
-            {
-              if (es[1].length() < nw)
-              {
-                t_alseqs[i +
-                    alseq_l] = new jalview.datamodel.Sequence(es[0],
-                    es[1] + insbuff.substring(0, nw - es[1].length()), 1,
-                    1 + es[1].length());
-              }
-              else
-              {
-                t_alseqs[i +
-                    alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);
-              }
-            }
-          }
-          alseqs = t_alseqs;
-        }
-        AlignmentOrder msaorder = new AlignmentOrder(alseqs);
-        // always recover the order - makes parseResult()'s life easier.
-        jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
-        // account for any missing sequences
-        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
-        return new Object[]
-            {
-            alseqs, msaorder};
-      }
-      return null;
-    }
-
-    /**
-     * mark subjob as cancelled and set result object appropriatly
-     */
-    void cancel()
-    {
-      cancelled = true;
-      subjobComplete = true;
-      result = null;
-    }
-
-    /**
-     *
-     * @return boolean true if job can be submitted.
-     */
-    boolean hasValidInput()
-    {
-      if (seqs.getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-  }
-
-  String alTitle; // name which will be used to form new alignment window.
-  Alignment dataset; // dataset to which the new alignment will be
-
-  // associated.
-
-  ext.vamsas.MuscleWS server = null;
-  /**
-   * set basic options for this (group) of Msa jobs
-   *
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   */
-  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              AlignmentView alview,
-              String wsname, boolean subgaps, boolean presorder)
-  {
-    super(alFrame, wsinfo, alview, wsname, wsUrl);
-    this.server = server;
-    this.submitGaps = subgaps;
-    this.preserveOrder = presorder;
-  }
-
-  /**
-   * create one or more Msa jobs to align visible seuqences in _msa
-   *
-   * @param title
-   *            String
-   * @param _msa
-   *            AlignmentView
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   * @param seqset
-   *            Alignment
-   */
-  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              String wsname, String title, AlignmentView _msa, boolean subgaps,
-              boolean presorder, Alignment seqset)
-  {
-    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
-    OutputHeader = wsInfo.getProgressText();
-    alTitle = title;
-    dataset = seqset;
-
-    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
-    if (conmsa != null)
-    {
-      int njobs = conmsa.length;
-      jobs = new MsaWSJob[njobs];
-      for (int j = 0; j < njobs; j++)
-      {
-        if (j != 0)
-        {
-          jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
-        }
-        else
-        {
-          jobs[j] = new MsaWSJob(0, conmsa[j]);
-        }
-        if (njobs > 0)
-        {
-          wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
-        }
-        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
-      }
-    }
-  }
-
-  public boolean isCancellable()
-  {
-    return true;
-  }
-
-  public void cancelJob()
-  {
-    if (!jobComplete && jobs != null)
-    {
-      boolean cancelled = true;
-      for (int job = 0; job < jobs.length; job++)
-      {
-        if (jobs[job].submitted && !jobs[job].subjobComplete)
-        {
-          String cancelledMessage = "";
-          try
-          {
-            vamsas.objects.simple.WsJobId cancelledJob = server
-                .cancel(jobs[job].jobId);
-            if (cancelledJob.getStatus() == 2)
-            {
-              // CANCELLED_JOB
-              cancelledMessage = "Job cancelled.";
-              ( (MsaWSJob) jobs[job]).cancel();
-              wsInfo.setStatus(jobs[job].jobnum,
-                               WebserviceInfo.STATE_CANCELLED_OK);
-            }
-            else if (cancelledJob.getStatus() == 3)
-            {
-              // VALID UNSTOPPABLE JOB
-              cancelledMessage +=
-                  "Server cannot cancel this job. just close the window.\n";
-              cancelled = false;
-              // wsInfo.setStatus(jobs[job].jobnum,
-              //                 WebserviceInfo.STATE_RUNNING);
-            }
-
-            if (cancelledJob.getJobId() != null)
-            {
-              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
-            }
-
-            cancelledMessage += "\n";
-          }
-          catch (Exception exc)
-          {
-            cancelledMessage +=
-                ("\nProblems cancelling the job : Exception received...\n"
-                 + exc + "\n");
-            Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
-                           exc);
-          }
-          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
-                                 + cancelledMessage + "\n");
-        }
-      }
-      if (cancelled)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
-        jobComplete = true;
-      }
-      this.interrupt(); // kick thread to update job states.
-    }
-    else
-    {
-      if (!jobComplete)
-      {
-        wsInfo
-            .setProgressText(OutputHeader
-                             + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
-      }
-    }
-  }
-
-  void pollJob(WSJob job)
-      throws Exception
-  {
-    ( (MsaWSJob) job).result = server.getResult( ( (MsaWSJob) job).jobId);
-  }
-
-  void StartJob(WSJob job)
-  {
-    if (! (job instanceof MsaWSJob))
-    {
-      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
-                      job.getClass());
-    }
-    MsaWSJob j = (MsaWSJob) job;
-    if (j.submitted)
-    {
-      if (Cache.log.isDebugEnabled())
-      {
-        Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
-      }
-      return;
-    }
-    if (j.seqs.getSeqs() == null)
-    {
-      // special case - selection consisted entirely of empty sequences...
-      j.submitted = true;
-      j.result = new MsaResult();
-      j.result.setFinished(true);
-      j.result.setStatus("Empty Alignment Job");
-      ( (MsaResult) j.result).setMsa(null);
-    }
-    try
-    {
-      vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
-
-      if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
-      {
-        j.jobId = jobsubmit.getJobId();
-        j.submitted = true;
-        j.subjobComplete = false;
-        // 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 (probably a server side problem)\n"
-                   + "When contacting Server:" + WsUrl + "\n"
-                   + e.toString() + "\n");
-      j.allowedServerExceptions = 0;
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo
-          .appendProgressText(
-              j.jobnum,
-              "Failed to submit sequences for alignment.\n"
-              + "It is most likely that there is a problem with the server.\n"
-              + "Just close the window\n");
-
-      // e.printStackTrace(); // TODO: JBPNote DEBUG
-    }
-  }
-
-  private jalview.datamodel.Sequence[] getVamsasAlignment(
-      vamsas.objects.simple.Alignment valign)
-  {
-    // TODO: refactor to helper class for vamsas.objects.simple objects
-    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()
-  {
-    int results = 0; // number of result sets received
-    JobStateSummary finalState = new JobStateSummary();
-    try
-    {
-      for (int j = 0; j < jobs.length; j++)
-      {
-        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
-        {
-          results++;
-          vamsas.objects.simple.Alignment valign = ( (MsaResult) jobs[j].result).
-              getMsa();
-          if (valign != null)
-          {
-            wsInfo.appendProgressText(jobs[j].jobnum,
-                                      "\nAlignment Object Method Notes\n");
-            String[] lines = valign.getMethod();
-            for (int line = 0; line < lines.length; line++)
-            {
-              wsInfo.appendProgressText(jobs[j].jobnum, 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
-          }
-        }
-      }
-    }
-    catch (Exception ex)
-    {
-
-      Cache.log.error("Unexpected exception when processing results for " +
-                      alTitle, ex);
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-    }
-    if (results > 0)
-    {
-      wsInfo.showResultsNewFrame
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(true);
-        }
-      });
-      wsInfo.mergeResults
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(false);
-        }
-      });
-      wsInfo.setResultsReady();
-    }
-    else
-    {
-      wsInfo.setFinishedNoResults();
-    }
-  }
-
-  void displayResults(boolean newFrame)
-  {
-    // view input or result data for each block
-    Vector alorders = new Vector();
-    SequenceI[][] results = new SequenceI[jobs.length][];
-    AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
-    for (int j = 0; j < jobs.length; j++)
-    {
-      if (jobs[j].hasResults())
-      {
-        Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();
-        alorders.add(res[1]);
-        results[j] = (SequenceI[]) res[0];
-        orders[j] = (AlignmentOrder) res[1];
-         
-//    SequenceI[] alignment = input.getUpdated
-      }
-      else
-      {
-        results[j] = null;
-      }
-    }
-    Object[] newview = input.getUpdatedView(results, orders, getGapChar());
-    // trash references to original result data
-    for (int j = 0; j < jobs.length; j++)
-    {
-      results[j] = null;
-      orders[j] = null;
-    }
-    SequenceI[] alignment = (SequenceI[]) newview[0];
-    ColumnSelection columnselection = (ColumnSelection) newview[1];
-    Alignment al = new Alignment(alignment);
-    // TODO: add 'provenance' property to alignment from the method notes accompanying each subjob
-    if (dataset != null)
-    {
-      al.setDataset(dataset);
-    }
-
-    propagateDatasetMappings(al);
-    // JBNote- TODO: warn user if a block is input rather than aligned data ?
-
-    if (newFrame)
-    {
-      AlignFrame af = new AlignFrame(al, columnselection,
-                                     AlignFrame.DEFAULT_WIDTH,
-                                     AlignFrame.DEFAULT_HEIGHT);
-
-      // initialise with same renderer settings as in parent alignframe.
-      af.getFeatureRenderer().transferSettings(
-          this.featureSettings);
-      // update orders
-      if (alorders.size() > 0)
-      {
-        if (alorders.size() == 1)
-        {
-          af.addSortByOrderMenuItem(WebServiceName + " Ordering",
-                                    (AlignmentOrder) alorders.get(0));
-        }
-        else
-        {
-          // construct a non-redundant ordering set
-          Vector names = new Vector();
-          for (int i = 0, l = alorders.size(); i < l; i++)
-          {
-            String orderName = new String(" Region " + i);
-            int j = i + 1;
-
-            while (j < l)
-            {
-              if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (
-                  AlignmentOrder) alorders.get(j))))
-              {
-                alorders.remove(j);
-                l--;
-                orderName += "," + j;
-              }
-              else
-              {
-                j++;
-              }
-            }
-
-            if (i == 0 && j == 1)
-            {
-              names.add(new String(""));
-            }
-            else
-            {
-              names.add(orderName);
-            }
-          }
-          for (int i = 0, l = alorders.size(); i < l; i++)
-          {
-            af.addSortByOrderMenuItem(WebServiceName
-                                      + ( (String) names.get(i)) +
-                                      " Ordering",
-                                      (AlignmentOrder) alorders.get(i));
-          }
-        }
-      }
-
-      Desktop.addInternalFrame(af, alTitle,
-                               AlignFrame.DEFAULT_WIDTH,
-                               AlignFrame.DEFAULT_HEIGHT);
-
-    }
-    else
-    {
-      System.out.println("MERGE WITH OLD FRAME");
-      // TODO: modify alignment in original frame, replacing old for new alignment using the commands.EditCommand model to ensure the update can be undone
-    }
-  }
-
-  public boolean canMergeResults()
-  {
-    return false;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.gui.*;
+import vamsas.objects.simple.MsaResult;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ *
+ * <p>
+ * Description:
+ * </p>
+ *
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ *
+ * <p>
+ * Company: Dundee University
+ * </p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+class MsaWSThread
+    extends WSThread implements WSClientI
+{
+  boolean submitGaps = false; // pass sequences including gaps to alignment
+
+  // service
+
+  boolean preserveOrder = true; // and always store and recover sequence
+
+  // order
+
+  class MsaWSJob
+      extends WSThread.WSJob
+  {
+    // hold special input for this
+    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
+        SequenceSet();
+
+    /**
+     * MsaWSJob
+     *
+     * @param jobNum
+     *            int
+     * @param jobId
+     *            String
+     */
+    public MsaWSJob(int jobNum, SequenceI[] inSeqs)
+    {
+      this.jobnum = jobNum;
+      if (!prepareInput(inSeqs, 2))
+      {
+        submitted = true;
+        subjobComplete = true;
+        result = new MsaResult();
+        result.setFinished(true);
+        result.setStatus("Job never ran - input returned to user.");
+      }
+
+    }
+
+    Hashtable SeqNames = new Hashtable();
+    Vector emptySeqs = new Vector();
+    /**
+     * prepare input sequences for MsaWS service
+     * @param seqs jalview sequences to be prepared
+     * @param minlen minimum number of residues required for this MsaWS service
+     * @return true if seqs contains sequences to be submitted to service.
+     */
+    private boolean prepareInput(SequenceI[] seqs, int minlen)
+    {
+      int nseqs = 0;
+      if (minlen < 0)
+      {
+        throw new Error("Implementation error: minlen must be zero or more.");
+      }
+      for (int i = 0; i < seqs.length; i++)
+      {
+        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          nseqs++;
+        }
+      }
+      boolean valid = nseqs > 1; // need at least two seqs
+      vamsas.objects.simple.Sequence[] seqarray =
+          (valid)
+          ? new vamsas.objects.simple.Sequence[nseqs]
+          : null;
+      for (int i = 0, n = 0; i < seqs.length; i++)
+      {
+
+        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+        // for
+        // any
+        // subjob
+        SeqNames.put(newname, jalview.analysis.SeqsetUtils
+                     .SeqCharacterHash(seqs[i]));
+        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          seqarray[n] = new vamsas.objects.simple.Sequence();
+          seqarray[n].setId(newname);
+          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
+                               : AlignSeq.extractGaps(
+                                   jalview.util.Comparison.GapChars, seqs[i]
+                                   .getSequenceAsString()));
+        }
+        else
+        {
+          String empty = null;
+          if (seqs[i].getEnd() >= seqs[i].getStart())
+          {
+            empty = (submitGaps) ? seqs[i].getSequenceAsString()
+                : AlignSeq.extractGaps(
+                    jalview.util.Comparison.GapChars, seqs[i]
+                    .getSequenceAsString());
+          }
+          emptySeqs.add(new String[]
+                        {newname, empty});
+        }
+      }
+      this.seqs = new vamsas.objects.simple.SequenceSet();
+      this.seqs.setSeqs(seqarray);
+      return valid;
+    }
+
+    /**
+     *
+     * @return true if getAlignment will return a valid alignment result.
+     */
+    public boolean hasResults()
+    {
+      if (subjobComplete && result != null && result.isFinished()
+          && ( (MsaResult) result).getMsa() != null &&
+          ( (MsaResult) result).getMsa().getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+
+    public Object[] getAlignment()
+    {
+
+      if (result != null && result.isFinished())
+      {
+        SequenceI[] alseqs = null;
+        char alseq_gapchar = '-';
+        int alseq_l = 0;
+        if ( ( (MsaResult) result).getMsa() != null)
+        {
+          alseqs = getVamsasAlignment( ( (MsaResult) result).getMsa());
+          alseq_gapchar = ( (MsaResult) result).getMsa().getGapchar().charAt(0);
+          alseq_l = alseqs.length;
+        }
+        if (emptySeqs.size() > 0)
+        {
+          SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
+          // get width
+          int i, w = 0;
+          if (alseq_l > 0)
+          {
+            for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
+            {
+              if (w < alseqs[i].getLength())
+              {
+                w = alseqs[i].getLength();
+              }
+              t_alseqs[i] = alseqs[i];
+              alseqs[i] = null;
+            }
+          }
+          // check that aligned width is at least as wide as emptySeqs width.
+          int ow = w, nw = w;
+          for (i = 0, w = emptySeqs.size(); i < w; i++)
+          {
+            String[] es = (String[]) emptySeqs.get(i);
+            if (es != null && es[1] != null)
+            {
+              int sw = es[1].length();
+              if (nw < sw)
+              {
+                nw = sw;
+              }
+            }
+          }
+          // make a gapped string.
+          StringBuffer insbuff = new StringBuffer(w);
+          for (i = 0; i < nw; i++)
+          {
+            insbuff.append(alseq_gapchar);
+          }
+          if (ow < nw)
+          {
+            for (i = 0; i < alseq_l; i++)
+            {
+              int sw = t_alseqs[i].getLength();
+              if (nw > sw)
+              {
+                // pad at end
+                alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() +
+                                      insbuff.substring(0, sw - nw));
+              }
+            }
+          }
+          for (i = 0, w = emptySeqs.size(); i < w; i++)
+          {
+            String[] es = (String[]) emptySeqs.get(i);
+            if (es[1] == null)
+            {
+              t_alseqs[i +
+                  alseq_l] = new jalview.datamodel.Sequence(es[0],
+                  insbuff.toString(), 1, 0);
+            }
+            else
+            {
+              if (es[1].length() < nw)
+              {
+                t_alseqs[i +
+                    alseq_l] = new jalview.datamodel.Sequence(es[0],
+                    es[1] + insbuff.substring(0, nw - es[1].length()), 1,
+                    1 + es[1].length());
+              }
+              else
+              {
+                t_alseqs[i +
+                    alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);
+              }
+            }
+          }
+          alseqs = t_alseqs;
+        }
+        AlignmentOrder msaorder = new AlignmentOrder(alseqs);
+        // always recover the order - makes parseResult()'s life easier.
+        jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
+        // account for any missing sequences
+        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
+        return new Object[]
+            {
+            alseqs, msaorder};
+      }
+      return null;
+    }
+
+    /**
+     * mark subjob as cancelled and set result object appropriatly
+     */
+    void cancel()
+    {
+      cancelled = true;
+      subjobComplete = true;
+      result = null;
+    }
+
+    /**
+     *
+     * @return boolean true if job can be submitted.
+     */
+    boolean hasValidInput()
+    {
+      if (seqs.getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+  }
+
+  String alTitle; // name which will be used to form new alignment window.
+  Alignment dataset; // dataset to which the new alignment will be
+
+  // associated.
+
+  ext.vamsas.MuscleWS server = null;
+  /**
+   * set basic options for this (group) of Msa jobs
+   *
+   * @param subgaps
+   *            boolean
+   * @param presorder
+   *            boolean
+   */
+  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
+              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+              AlignmentView alview,
+              String wsname, boolean subgaps, boolean presorder)
+  {
+    super(alFrame, wsinfo, alview, wsname, wsUrl);
+    this.server = server;
+    this.submitGaps = subgaps;
+    this.preserveOrder = presorder;
+  }
+
+  /**
+   * create one or more Msa jobs to align visible seuqences in _msa
+   *
+   * @param title
+   *            String
+   * @param _msa
+   *            AlignmentView
+   * @param subgaps
+   *            boolean
+   * @param presorder
+   *            boolean
+   * @param seqset
+   *            Alignment
+   */
+  MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
+              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+              String wsname, String title, AlignmentView _msa, boolean subgaps,
+              boolean presorder, Alignment seqset)
+  {
+    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
+    OutputHeader = wsInfo.getProgressText();
+    alTitle = title;
+    dataset = seqset;
+
+    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+    if (conmsa != null)
+    {
+      int njobs = conmsa.length;
+      jobs = new MsaWSJob[njobs];
+      for (int j = 0; j < njobs; j++)
+      {
+        if (j != 0)
+        {
+          jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
+        }
+        else
+        {
+          jobs[j] = new MsaWSJob(0, conmsa[j]);
+        }
+        if (njobs > 0)
+        {
+          wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
+        }
+        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
+      }
+    }
+  }
+
+  public boolean isCancellable()
+  {
+    return true;
+  }
+
+  public void cancelJob()
+  {
+    if (!jobComplete && jobs != null)
+    {
+      boolean cancelled = true;
+      for (int job = 0; job < jobs.length; job++)
+      {
+        if (jobs[job].submitted && !jobs[job].subjobComplete)
+        {
+          String cancelledMessage = "";
+          try
+          {
+            vamsas.objects.simple.WsJobId cancelledJob = server
+                .cancel(jobs[job].jobId);
+            if (cancelledJob.getStatus() == 2)
+            {
+              // CANCELLED_JOB
+              cancelledMessage = "Job cancelled.";
+              ( (MsaWSJob) jobs[job]).cancel();
+              wsInfo.setStatus(jobs[job].jobnum,
+                               WebserviceInfo.STATE_CANCELLED_OK);
+            }
+            else if (cancelledJob.getStatus() == 3)
+            {
+              // VALID UNSTOPPABLE JOB
+              cancelledMessage +=
+                  "Server cannot cancel this job. just close the window.\n";
+              cancelled = false;
+              // wsInfo.setStatus(jobs[job].jobnum,
+              //                 WebserviceInfo.STATE_RUNNING);
+            }
+
+            if (cancelledJob.getJobId() != null)
+            {
+              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
+            }
+
+            cancelledMessage += "\n";
+          }
+          catch (Exception exc)
+          {
+            cancelledMessage +=
+                ("\nProblems cancelling the job : Exception received...\n"
+                 + exc + "\n");
+            Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
+                           exc);
+          }
+          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
+                                 + cancelledMessage + "\n");
+        }
+      }
+      if (cancelled)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+        jobComplete = true;
+      }
+      this.interrupt(); // kick thread to update job states.
+    }
+    else
+    {
+      if (!jobComplete)
+      {
+        wsInfo
+            .setProgressText(OutputHeader
+                             + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+      }
+    }
+  }
+
+  void pollJob(WSJob job)
+      throws Exception
+  {
+    ( (MsaWSJob) job).result = server.getResult( ( (MsaWSJob) job).jobId);
+  }
+
+  void StartJob(WSJob job)
+  {
+    if (! (job instanceof MsaWSJob))
+    {
+      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
+                      job.getClass());
+    }
+    MsaWSJob j = (MsaWSJob) job;
+    if (j.submitted)
+    {
+      if (Cache.log.isDebugEnabled())
+      {
+        Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
+      }
+      return;
+    }
+    if (j.seqs.getSeqs() == null)
+    {
+      // special case - selection consisted entirely of empty sequences...
+      j.submitted = true;
+      j.result = new MsaResult();
+      j.result.setFinished(true);
+      j.result.setStatus("Empty Alignment Job");
+      ( (MsaResult) j.result).setMsa(null);
+    }
+    try
+    {
+      vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
+
+      if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
+      {
+        j.jobId = jobsubmit.getJobId();
+        j.submitted = true;
+        j.subjobComplete = false;
+        // 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 (probably a server side problem)\n"
+                   + "When contacting Server:" + WsUrl + "\n"
+                   + e.toString() + "\n");
+      j.allowedServerExceptions = 0;
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo
+          .appendProgressText(
+              j.jobnum,
+              "Failed to submit sequences for alignment.\n"
+              + "It is most likely that there is a problem with the server.\n"
+              + "Just close the window\n");
+
+      // e.printStackTrace(); // TODO: JBPNote DEBUG
+    }
+  }
+
+  private jalview.datamodel.Sequence[] getVamsasAlignment(
+      vamsas.objects.simple.Alignment valign)
+  {
+    // TODO: refactor to helper class for vamsas.objects.simple objects
+    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()
+  {
+    int results = 0; // number of result sets received
+    JobStateSummary finalState = new JobStateSummary();
+    try
+    {
+      for (int j = 0; j < jobs.length; j++)
+      {
+        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
+        {
+          results++;
+          vamsas.objects.simple.Alignment valign = ( (MsaResult) jobs[j].result).
+              getMsa();
+          if (valign != null)
+          {
+            wsInfo.appendProgressText(jobs[j].jobnum,
+                                      "\nAlignment Object Method Notes\n");
+            String[] lines = valign.getMethod();
+            for (int line = 0; line < lines.length; line++)
+            {
+              wsInfo.appendProgressText(jobs[j].jobnum, 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
+          }
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+
+      Cache.log.error("Unexpected exception when processing results for " +
+                      alTitle, ex);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+    }
+    if (results > 0)
+    {
+      wsInfo.showResultsNewFrame
+          .addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(
+            java.awt.event.ActionEvent evt)
+        {
+          displayResults(true);
+        }
+      });
+      wsInfo.mergeResults
+          .addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(
+            java.awt.event.ActionEvent evt)
+        {
+          displayResults(false);
+        }
+      });
+      wsInfo.setResultsReady();
+    }
+    else
+    {
+      wsInfo.setFinishedNoResults();
+    }
+  }
+
+  void displayResults(boolean newFrame)
+  {
+    // view input or result data for each block
+    Vector alorders = new Vector();
+    SequenceI[][] results = new SequenceI[jobs.length][];
+    AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
+    for (int j = 0; j < jobs.length; j++)
+    {
+      if (jobs[j].hasResults())
+      {
+        Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();
+        alorders.add(res[1]);
+        results[j] = (SequenceI[]) res[0];
+        orders[j] = (AlignmentOrder) res[1];
+         
+//    SequenceI[] alignment = input.getUpdated
+      }
+      else
+      {
+        results[j] = null;
+      }
+    }
+    Object[] newview = input.getUpdatedView(results, orders, getGapChar());
+    // trash references to original result data
+    for (int j = 0; j < jobs.length; j++)
+    {
+      results[j] = null;
+      orders[j] = null;
+    }
+    SequenceI[] alignment = (SequenceI[]) newview[0];
+    ColumnSelection columnselection = (ColumnSelection) newview[1];
+    Alignment al = new Alignment(alignment);
+    // TODO: add 'provenance' property to alignment from the method notes accompanying each subjob
+    if (dataset != null)
+    {
+      al.setDataset(dataset);
+    }
+
+    propagateDatasetMappings(al);
+    // JBNote- TODO: warn user if a block is input rather than aligned data ?
+
+    if (newFrame)
+    {
+      AlignFrame af = new AlignFrame(al, columnselection,
+                                     AlignFrame.DEFAULT_WIDTH,
+                                     AlignFrame.DEFAULT_HEIGHT);
+
+      // initialise with same renderer settings as in parent alignframe.
+      af.getFeatureRenderer().transferSettings(
+          this.featureSettings);
+      // update orders
+      if (alorders.size() > 0)
+      {
+        if (alorders.size() == 1)
+        {
+          af.addSortByOrderMenuItem(WebServiceName + " Ordering",
+                                    (AlignmentOrder) alorders.get(0));
+        }
+        else
+        {
+          // construct a non-redundant ordering set
+          Vector names = new Vector();
+          for (int i = 0, l = alorders.size(); i < l; i++)
+          {
+            String orderName = new String(" Region " + i);
+            int j = i + 1;
+
+            while (j < l)
+            {
+              if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (
+                  AlignmentOrder) alorders.get(j))))
+              {
+                alorders.remove(j);
+                l--;
+                orderName += "," + j;
+              }
+              else
+              {
+                j++;
+              }
+            }
+
+            if (i == 0 && j == 1)
+            {
+              names.add(new String(""));
+            }
+            else
+            {
+              names.add(orderName);
+            }
+          }
+          for (int i = 0, l = alorders.size(); i < l; i++)
+          {
+            af.addSortByOrderMenuItem(WebServiceName
+                                      + ( (String) names.get(i)) +
+                                      " Ordering",
+                                      (AlignmentOrder) alorders.get(i));
+          }
+        }
+      }
+
+      Desktop.addInternalFrame(af, alTitle,
+                               AlignFrame.DEFAULT_WIDTH,
+                               AlignFrame.DEFAULT_HEIGHT);
+
+    }
+    else
+    {
+      System.out.println("MERGE WITH OLD FRAME");
+      // TODO: modify alignment in original frame, replacing old for new alignment using the commands.EditCommand model to ensure the update can be undone
+    }
+  }
+
+  public boolean canMergeResults()
+  {
+    return false;
+  }
+}
diff --git a/src/jalview/ws/SeqSearchWSClient.java b/src/jalview/ws/SeqSearchWSClient.java
index e52cefd..6da2ebb 100644
--- a/src/jalview/ws/SeqSearchWSClient.java
+++ b/src/jalview/ws/SeqSearchWSClient.java
@@ -1,294 +1,294 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws;
-
-import java.awt.Component;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.*;
-
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SeqSearchWSClient
-    extends WSClient
-{
-  /**
-   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
-   */
-  ext.vamsas.SeqSearchI server;
-  AlignFrame alignFrame;
-
-  /**
-   * Creates a new MsaWSClient object that uses a service
-   * given by an externally retrieved ServiceHandle
-   *
-   * @param sh service handle of type AbstractName(MsaWS)
-   * @param altitle DOCUMENT ME!
-   * @param msa DOCUMENT ME!
-   * @param submitGaps DOCUMENT ME!
-   * @param preserveOrder DOCUMENT ME!
-   */
-
-  public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
-                     jalview.datamodel.AlignmentView msa, String db,
-                     Alignment seqdataset,
-                     AlignFrame _alignFrame)
-  {
-    super();
-    alignFrame = _alignFrame;
-    // can generalise the two errors below for metadata mapping from interface name to service client name
-    if (!sh.getAbstractName().equals(this.getServiceActionKey()))
-    {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-                                    "The Service called \n" + sh.getName() +
-                                    "\nis not a \nSequence Search Service !",
-                                    "Internal Jalview Error",
-                                    JOptionPane.WARNING_MESSAGE);
-
-      return;
-    }
-
-    if ( (wsInfo = setWebService(sh)) == null)
-    {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-                                    "The Sequence Search Service named " +
-                                    sh.getName() +
-                                    " is unknown", "Internal Jalview Error",
-                                    JOptionPane.WARNING_MESSAGE);
-
-      return;
-    }
-    startSeqSearchClient(altitle, msa, db, seqdataset);
-
-  }
-  /**
- * non-process web service interaction - use this for calling HEADLESS synchronous service methods
- * @param sh
- */
-  public SeqSearchWSClient(ServiceHandle sh)
-  {
-    setWebService(sh, true);
-  }
-
-  public SeqSearchWSClient()
-  {
-
-    super();
-    // add a class reference to the list
-  }
-  private void startSeqSearchClient(String altitle, AlignmentView msa,
-                                String db,
-                                Alignment seqdataset)
-  {
-    if (!locateWebService())
-    {
-      return;
-    }
-    String visdb = (db==null || db == "") ? "default" : db; // need a visible name for a sequence db
-    boolean profileSearch = msa.getSequences().length>2 ? true : false;
-    // single sequence or profile from alignment view
-    wsInfo.setProgressText( "Searching "+visdb+(!profileSearch ? " with sequence "+msa.getSequences()[0].getRefSeq().getName()
-              : " with profile") +
-                           " from " + altitle + "\nJob details\n");
-    
-    String jobtitle = WebServiceName+((WebServiceName.indexOf("earch")>-1) ? " " : " search ")+" of "+visdb+(!profileSearch ? " with sequence "+msa.getSequences()[0].getRefSeq().getName()
-            : " with profile") +
-            " from " + altitle;
-    SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL, wsInfo, alignFrame,
-                                            WebServiceName,
-                                            jobtitle,
-                                            msa,
-                                            db,
-                                            seqdataset);
-    wsInfo.setthisService(ssthread);
-    ssthread.start();
-  }
-
-  /**
-   * Initializes the server field with a valid service implementation.
-   *
-   * @return true if service was located.
-   */
-  private boolean locateWebService()
-  {
-    // this can be abstracted using reflection
-    // TODO: MuscleWS transmuted to generic MsaWS client
-    SeqSearchServiceLocator loc = new SeqSearchServiceLocator(); // Default
-
-    try
-    {
-      this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(WsURL));
-      ( (SeqSearchServiceSoapBindingStub)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(WebserviceInfo.ERROR);
-      ex.printStackTrace();
-
-      return false;
-    }
-
-    loc.getEngine().setOption("axis", "1");
-
-    return true;
-  }
-
-  protected String getServiceActionKey()
-  {
-    return "SeqSearch";
-  }
-
-  protected String getServiceActionDescription()
-  {
-    return "Sequence Database Search";
-  }
-  // simple caching of db parameters for each service endpoint
-  private static Hashtable dbParamsForEndpoint;
-  static { 
-    dbParamsForEndpoint = new Hashtable();
-  }
-  public String[] getSupportedDatabases() throws Exception
-  {
-    
-    // check that we haven't already been to this service endpoint
-    if (dbParamsForEndpoint.containsKey(WsURL))
-    {
-      return (String[]) dbParamsForEndpoint.get(WsURL);
-    }
-    if (!locateWebService())
-    {
-      throw new Exception("Cannot contact service endpoint at "+WsURL); 
-    }
-    String database = server.getDatabase();
-    if (database==null)
-    {
-      dbParamsForEndpoint.put(WsURL, new String[] {});
-      return null;
-    }
-    StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
-    String[] dbs = new String[en.countTokens()];
-    for (int i=0; i<dbs.length; i++)
-    {
-      dbs[i++] = en.nextToken().trim();
-    }
-    dbParamsForEndpoint.put(WsURL, dbs);
-    return dbs;
-  }
-  public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
-          final AlignFrame af)
-  {
-    // look for existing database service submenus on wsmenu
-    Hashtable dbsrchs = new Hashtable();
-    Vector newdbsrch = new Vector();
-    Component entries[] =  wsmenu.getComponents();
-    for (int i = 0; entries!=null && i<entries.length; i++)
-    {
-      if (entries[i] instanceof JMenu)
-      {
-        dbsrchs.put(entries[i].getName(), entries[i]);
-      }
-    }
-    JMenu defmenu=(JMenu) dbsrchs.get("Default Database");
-    if (defmenu==null)
-    {
-      dbsrchs.put("Default Database", defmenu = new JMenu("Default Database"));
-      newdbsrch.addElement(defmenu);
-    }
-      
-      String dbs[] = null;
-      try {
-        dbs = new jalview.ws.SeqSearchWSClient(sh).getSupportedDatabases();
-      } catch (Exception e)
-      {
-        jalview.bin.Cache.log.warn("Database list request failed, so disabling SeqSearch Service client "+sh.getName()+" at "+sh.getEndpointURL(), e);
-        return;
-      }
-      JMenuItem method;
-      // do default entry
-      defmenu.add(method = new JMenuItem(sh.getName()));
-      method.setToolTipText(sh.getEndpointURL());
-      method.addActionListener(new ActionListener()
-      {
-        public void actionPerformed(ActionEvent e)
-        {
-          // use same input gatherer as for secondary structure prediction
-          // we could actually parameterise the gatherer method here...
-          AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
-          new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, null, 
-                  af.getViewport().getAlignment().getDataset(),
-                  af);
-          }
-        }
-      );
-      // add entry for each database the service supports
-      for (int db=0; dbs!=null && db<dbs.length; db++)
-      {
-        JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);
-        if (dbmenu==null)
-        {
-          dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));
-          newdbsrch.addElement(dbmenu);
-        }
-        // add the client handler code for this service
-        dbmenu.add(method = new JMenuItem(sh.getName()));
-        method.setToolTipText(sh.getEndpointURL());
-        final String searchdb = dbs[db];
-        method.addActionListener(new ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
-            new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, searchdb, 
-                      af.getViewport().getAlignment().getDataset(),
-                      af);
-          }
-        });
-      }
-    // add the databases onto the seqsearch menu
-    Enumeration e = newdbsrch.elements();
-    while (e.hasMoreElements())
-    {
-      Object el = e.nextElement();
-      if (el instanceof JMenu)
-      {
-        wsmenu.add((JMenu) el);
-      } else {
-        wsmenu.add((JMenuItem) el);
-      }
-    }
-    
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqSearchWSClient
+    extends WSClient
+{
+  /**
+   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+   */
+  ext.vamsas.SeqSearchI server;
+  AlignFrame alignFrame;
+
+  /**
+   * Creates a new MsaWSClient object that uses a service
+   * given by an externally retrieved ServiceHandle
+   *
+   * @param sh service handle of type AbstractName(MsaWS)
+   * @param altitle DOCUMENT ME!
+   * @param msa DOCUMENT ME!
+   * @param submitGaps DOCUMENT ME!
+   * @param preserveOrder DOCUMENT ME!
+   */
+
+  public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+                     jalview.datamodel.AlignmentView msa, String db,
+                     Alignment seqdataset,
+                     AlignFrame _alignFrame)
+  {
+    super();
+    alignFrame = _alignFrame;
+    // can generalise the two errors below for metadata mapping from interface name to service client name
+    if (!sh.getAbstractName().equals(this.getServiceActionKey()))
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+                                    "The Service called \n" + sh.getName() +
+                                    "\nis not a \nSequence Search Service !",
+                                    "Internal Jalview Error",
+                                    JOptionPane.WARNING_MESSAGE);
+
+      return;
+    }
+
+    if ( (wsInfo = setWebService(sh)) == null)
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+                                    "The Sequence Search Service named " +
+                                    sh.getName() +
+                                    " is unknown", "Internal Jalview Error",
+                                    JOptionPane.WARNING_MESSAGE);
+
+      return;
+    }
+    startSeqSearchClient(altitle, msa, db, seqdataset);
+
+  }
+  /**
+ * non-process web service interaction - use this for calling HEADLESS synchronous service methods
+ * @param sh
+ */
+  public SeqSearchWSClient(ServiceHandle sh)
+  {
+    setWebService(sh, true);
+  }
+
+  public SeqSearchWSClient()
+  {
+
+    super();
+    // add a class reference to the list
+  }
+  private void startSeqSearchClient(String altitle, AlignmentView msa,
+                                String db,
+                                Alignment seqdataset)
+  {
+    if (!locateWebService())
+    {
+      return;
+    }
+    String visdb = (db==null || db == "") ? "default" : db; // need a visible name for a sequence db
+    boolean profileSearch = msa.getSequences().length>2 ? true : false;
+    // single sequence or profile from alignment view
+    wsInfo.setProgressText( "Searching "+visdb+(!profileSearch ? " with sequence "+msa.getSequences()[0].getRefSeq().getName()
+              : " with profile") +
+                           " from " + altitle + "\nJob details\n");
+    
+    String jobtitle = WebServiceName+((WebServiceName.indexOf("earch")>-1) ? " " : " search ")+" of "+visdb+(!profileSearch ? " with sequence "+msa.getSequences()[0].getRefSeq().getName()
+            : " with profile") +
+            " from " + altitle;
+    SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL, wsInfo, alignFrame,
+                                            WebServiceName,
+                                            jobtitle,
+                                            msa,
+                                            db,
+                                            seqdataset);
+    wsInfo.setthisService(ssthread);
+    ssthread.start();
+  }
+
+  /**
+   * Initializes the server field with a valid service implementation.
+   *
+   * @return true if service was located.
+   */
+  private boolean locateWebService()
+  {
+    // this can be abstracted using reflection
+    // TODO: MuscleWS transmuted to generic MsaWS client
+    SeqSearchServiceLocator loc = new SeqSearchServiceLocator(); // Default
+
+    try
+    {
+      this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(WsURL));
+      ( (SeqSearchServiceSoapBindingStub)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(WebserviceInfo.ERROR);
+      ex.printStackTrace();
+
+      return false;
+    }
+
+    loc.getEngine().setOption("axis", "1");
+
+    return true;
+  }
+
+  protected String getServiceActionKey()
+  {
+    return "SeqSearch";
+  }
+
+  protected String getServiceActionDescription()
+  {
+    return "Sequence Database Search";
+  }
+  // simple caching of db parameters for each service endpoint
+  private static Hashtable dbParamsForEndpoint;
+  static { 
+    dbParamsForEndpoint = new Hashtable();
+  }
+  public String[] getSupportedDatabases() throws Exception
+  {
+    
+    // check that we haven't already been to this service endpoint
+    if (dbParamsForEndpoint.containsKey(WsURL))
+    {
+      return (String[]) dbParamsForEndpoint.get(WsURL);
+    }
+    if (!locateWebService())
+    {
+      throw new Exception("Cannot contact service endpoint at "+WsURL); 
+    }
+    String database = server.getDatabase();
+    if (database==null)
+    {
+      dbParamsForEndpoint.put(WsURL, new String[] {});
+      return null;
+    }
+    StringTokenizer en = new StringTokenizer(database.trim(), ",| ");
+    String[] dbs = new String[en.countTokens()];
+    for (int i=0; i<dbs.length; i++)
+    {
+      dbs[i++] = en.nextToken().trim();
+    }
+    dbParamsForEndpoint.put(WsURL, dbs);
+    return dbs;
+  }
+  public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
+          final AlignFrame af)
+  {
+    // look for existing database service submenus on wsmenu
+    Hashtable dbsrchs = new Hashtable();
+    Vector newdbsrch = new Vector();
+    Component entries[] =  wsmenu.getComponents();
+    for (int i = 0; entries!=null && i<entries.length; i++)
+    {
+      if (entries[i] instanceof JMenu)
+      {
+        dbsrchs.put(entries[i].getName(), entries[i]);
+      }
+    }
+    JMenu defmenu=(JMenu) dbsrchs.get("Default Database");
+    if (defmenu==null)
+    {
+      dbsrchs.put("Default Database", defmenu = new JMenu("Default Database"));
+      newdbsrch.addElement(defmenu);
+    }
+      
+      String dbs[] = null;
+      try {
+        dbs = new jalview.ws.SeqSearchWSClient(sh).getSupportedDatabases();
+      } catch (Exception e)
+      {
+        jalview.bin.Cache.log.warn("Database list request failed, so disabling SeqSearch Service client "+sh.getName()+" at "+sh.getEndpointURL(), e);
+        return;
+      }
+      JMenuItem method;
+      // do default entry
+      defmenu.add(method = new JMenuItem(sh.getName()));
+      method.setToolTipText(sh.getEndpointURL());
+      method.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          // use same input gatherer as for secondary structure prediction
+          // we could actually parameterise the gatherer method here...
+          AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
+          new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, null, 
+                  af.getViewport().getAlignment().getDataset(),
+                  af);
+          }
+        }
+      );
+      // add entry for each database the service supports
+      for (int db=0; dbs!=null && db<dbs.length; db++)
+      {
+        JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);
+        if (dbmenu==null)
+        {
+          dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));
+          newdbsrch.addElement(dbmenu);
+        }
+        // add the client handler code for this service
+        dbmenu.add(method = new JMenuItem(sh.getName()));
+        method.setToolTipText(sh.getEndpointURL());
+        final String searchdb = dbs[db];
+        method.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
+            new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, searchdb, 
+                      af.getViewport().getAlignment().getDataset(),
+                      af);
+          }
+        });
+      }
+    // add the databases onto the seqsearch menu
+    Enumeration e = newdbsrch.elements();
+    while (e.hasMoreElements())
+    {
+      Object el = e.nextElement();
+      if (el instanceof JMenu)
+      {
+        wsmenu.add((JMenu) el);
+      } else {
+        wsmenu.add((JMenuItem) el);
+      }
+    }
+    
+  }
+}
diff --git a/src/jalview/ws/SeqSearchWSThread.java b/src/jalview/ws/SeqSearchWSThread.java
index 07686fe..36e4bc0 100644
--- a/src/jalview/ws/SeqSearchWSThread.java
+++ b/src/jalview/ws/SeqSearchWSThread.java
@@ -1,667 +1,667 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws;
-
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.NewickFile;
-import vamsas.objects.simple.MsaResult;
-import vamsas.objects.simple.SeqSearchResult;
-
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
-class SeqSearchWSThread
-    extends WSThread implements WSClientI
-{
-  String dbs=null;
-  boolean profile=false;
-
-  class SeqSearchWSJob
-      extends WSThread.WSJob
-  {
-    // hold special input for this
-    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
-        SequenceSet();
-
-    /**
-     * MsaWSJob
-     *
-     * @param jobNum
-     *            int
-     * @param jobId
-     *            String
-     */
-    public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)
-    {
-      this.jobnum = jobNum;
-      if (!prepareInput(inSeqs, 2))
-      {
-        submitted = true;
-        subjobComplete = true;
-        result = new MsaResult();
-        result.setFinished(true);
-        result.setStatus("Job never ran - input returned to user.");
-      }
-
-    }
-
-    Hashtable SeqNames = new Hashtable();
-    Vector emptySeqs = new Vector();
-    /**
-     * prepare input sequences for service
-     * @param seqs jalview sequences to be prepared
-     * @param minlen minimum number of residues required for this MsaWS service
-     * @return true if seqs contains sequences to be submitted to service.
-     */
-    private boolean prepareInput(SequenceI[] seqs, int minlen)
-    {
-      int nseqs = 0;
-      if (minlen < 0)
-      {
-        throw new Error("Implementation error: minlen must be zero or more.");
-      }
-      for (int i = 0; i < seqs.length; i++)
-      {
-        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          nseqs++;
-        }
-      }
-      boolean valid = nseqs >= 1; // need at least one sequence for valid input TODO: generalise
-      vamsas.objects.simple.Sequence[] seqarray =
-          (valid)
-          ? new vamsas.objects.simple.Sequence[nseqs]
-          : null;
-      boolean submitGaps = (nseqs==1) ? false : true; // profile is submitted with gaps  
-      for (int i = 0, n = 0; i < seqs.length; i++)
-      {
-
-        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
-        // for
-        // any
-        // subjob
-        SeqNames.put(newname, jalview.analysis.SeqsetUtils
-                     .SeqCharacterHash(seqs[i]));
-        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
-        {
-          seqarray[n] = new vamsas.objects.simple.Sequence();
-          seqarray[n].setId(newname);
-          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
-                               : AlignSeq.extractGaps(
-                                   jalview.util.Comparison.GapChars, seqs[i]
-                                   .getSequenceAsString()));
-        }
-        else
-        {
-          String empty = null;
-          if (seqs[i].getEnd() >= seqs[i].getStart())
-          {
-            empty = (submitGaps) ? seqs[i].getSequenceAsString()
-                : AlignSeq.extractGaps(
-                    jalview.util.Comparison.GapChars, seqs[i]
-                    .getSequenceAsString());
-          }
-          emptySeqs.add(new String[]
-                        {newname, empty});
-        }
-      }
-      if (submitGaps)
-      {
-        // almost certainly have to remove gapped columns here
-      }
-      this.seqs = new vamsas.objects.simple.SequenceSet();
-      this.seqs.setSeqs(seqarray);
-      return valid;
-    }
-
-    /**
-     *
-     * @return true if getAlignment will return a valid alignment result.
-     */
-    public boolean hasResults()
-    {
-      if (subjobComplete && result != null && result.isFinished()
-          && ( (SeqSearchResult) result).getAlignment() != null &&
-          ( (SeqSearchResult) result).getAlignment().getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-
-    /**
-     * return sequence search results for display
-     * @return null or { Alignment(+features and annotation), NewickFile)}
-     */
-    public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
-    {
-
-      if (result != null && result.isFinished())
-      {
-        SequenceI[] alseqs = null;
-        //char alseq_gapchar = '-';
-        //int alseq_l = 0;
-        if ( ( (SeqSearchResult) result).getAlignment() != null)
-        {
-          alseqs = getVamsasAlignment( ( (SeqSearchResult) result).getAlignment());
-          //alseq_gapchar = ( (SeqSearchResult) result).getAlignment().getGapchar().charAt(0);
-          //alseq_l = alseqs.length;
-        }
-        /**
-         * what has to be done. 1 - annotate returned alignment with annotation file and sequence features file, and associate any tree-nodes.
-         * 2. connect alignment back to any associated dataset: 2.a. deuniquify recovers sequence information - but additionally, 
-         * relocations must be made from the returned aligned sequence back to the dataset.
-         */
-        // construct annotated alignment as it would be done by the jalview applet
-        jalview.datamodel.Alignment al = new Alignment(alseqs);
-        // al.setDataset(dataset);
-        // make dataset
-        String inFile=null;
-        try {
-          inFile = ((SeqSearchResult) result).getAnnotation();
-          if (inFile!=null && inFile.length()>0)
-          {
-            new jalview.io.AnnotationFile().readAnnotationFile(al, inFile, jalview.io.AppletFormatAdapter.PASTE);
-          }
-          }
-        catch (Exception e)
-        {
-          System.err.println("Failed to parse the annotation file associated with the alignment.");
-          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
-          e.printStackTrace(System.err);
-        }
-        
-        try {
-          inFile = ((SeqSearchResult) result).getFeatures();
-          if (inFile!=null && inFile.length()>0)
-          {
-            jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(inFile, jalview.io.AppletFormatAdapter.PASTE);
-            ff.parse(al, featureColours, false);
-          }
-        }
-        catch (Exception e)
-        {
-          System.err.println("Failed to parse the Features file associated with the alignment.");
-          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
-          e.printStackTrace(System.err);
-        }
-        jalview.io.NewickFile nf=null;
-        try {
-          inFile = ((SeqSearchResult) result).getNewickTree();
-          if (inFile!=null && inFile.length()>0)
-          {
-            nf = new jalview.io.NewickFile(inFile, jalview.io.AppletFormatAdapter.PASTE);
-            if (!nf.isValid()) {
-              nf.close();
-              nf = null;
-            }
-          }
-        }
-        catch (Exception e)
-        {
-          System.err.println("Failed to parse the treeFile associated with the alignment.");
-          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
-          e.printStackTrace(System.err);
-        }
-        
-        /* TODO: housekeeping w.r.t. recovery of dataset and annotation references for input sequences, and then dataset sequence creation for new sequences retrieved from service
-         * // finally, attempt to de-uniquify to recover input sequence identity, and try to map back onto dataset
-        Note: this
-        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true);
-        will NOT WORK - the returned alignment may contain multiple versions of the input sequence, each being a subsequence of the original.
-        deuniquify also removes existing annotation and features added in the previous step...
-        al.setDataset(dataset);
-        // add in new sequences retrieved from sequence search which are not already in dataset.
-        // trigger a 'fetchDBids' to annotate sequences with database ids...
-        */
-
-        return new Object[]
-            {
-            al, nf};
-      }
-      return null;
-    }
-
-    /**
-     * mark subjob as cancelled and set result object appropriatly
-     */
-    void cancel()
-    {
-      cancelled = true;
-      subjobComplete = true;
-      result = null;
-    }
-
-    /**
-     *
-     * @return boolean true if job can be submitted.
-     */
-    boolean hasValidInput()
-    {
-      if (seqs.getSeqs() != null)
-      {
-        return true;
-      }
-      return false;
-    }
-  }
-
-  String alTitle; // name which will be used to form new alignment window.
-  Alignment dataset; // dataset to which the new alignment will be
-
-  // associated.
-
-  ext.vamsas.SeqSearchI server = null;
-
-  private String dbArg;
-  /**
-   * set basic options for this (group) of Msa jobs
-   *
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   */
-  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              AlignmentView alview,
-              String wsname, String db)
-  {
-    super(alFrame, wsinfo, alview, wsname, wsUrl);
-    this.server = server;
-    this.dbArg = db;
-  }
-
-  /**
-   * create one or more Msa jobs to align visible seuqences in _msa
-   *
-   * @param title
-   *            String
-   * @param _msa
-   *            AlignmentView
-   * @param subgaps
-   *            boolean
-   * @param presorder
-   *            boolean
-   * @param seqset
-   *            Alignment
-   */
-  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
-              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-              String wsname, String title, AlignmentView _msa, String db, Alignment seqset)
-  {
-    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
-    OutputHeader = wsInfo.getProgressText();
-    alTitle = title;
-    dataset = seqset;
-
-    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
-    if (conmsa != null)
-    {
-      int njobs = conmsa.length;
-      jobs = new SeqSearchWSJob[njobs];
-      for (int j = 0; j < njobs; j++)
-      {
-        if (j != 0)
-        {
-          jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);
-        }
-        else
-        {
-          jobs[j] = new SeqSearchWSJob(0, conmsa[j]);
-        }
-        if (njobs > 0)
-        {
-          wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
-        }
-        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
-      }
-    }
-  }
-
-  public boolean isCancellable()
-  {
-    return true;
-  }
-
-  public void cancelJob()
-  {
-    if (!jobComplete && jobs != null)
-    {
-      boolean cancelled = true;
-      for (int job = 0; job < jobs.length; job++)
-      {
-        if (jobs[job].submitted && !jobs[job].subjobComplete)
-        {
-          String cancelledMessage = "";
-          try
-          {
-            vamsas.objects.simple.WsJobId cancelledJob = server
-                .cancel(jobs[job].jobId);
-            if (cancelledJob.getStatus() == 2)
-            {
-              // CANCELLED_JOB
-              cancelledMessage = "Job cancelled.";
-              ( (SeqSearchWSJob) jobs[job]).cancel();
-              wsInfo.setStatus(jobs[job].jobnum,
-                               WebserviceInfo.STATE_CANCELLED_OK);
-            }
-            else if (cancelledJob.getStatus() == 3)
-            {
-              // VALID UNSTOPPABLE JOB
-              cancelledMessage +=
-                  "Server cannot cancel this job. just close the window.\n";
-              cancelled = false;
-              // wsInfo.setStatus(jobs[job].jobnum,
-              //                 WebserviceInfo.STATE_RUNNING);
-            }
-
-            if (cancelledJob.getJobId() != null)
-            {
-              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
-            }
-
-            cancelledMessage += "\n";
-          }
-          catch (Exception exc)
-          {
-            cancelledMessage +=
-                ("\nProblems cancelling the job : Exception received...\n"
-                 + exc + "\n");
-            Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
-                           exc);
-          }
-          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
-                                 + cancelledMessage + "\n");
-        }
-      }
-      if (cancelled)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
-        jobComplete = true;
-      }
-      this.interrupt(); // kick thread to update job states.
-    }
-    else
-    {
-      if (!jobComplete)
-      {
-        wsInfo
-            .setProgressText(OutputHeader
-                             + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
-      }
-    }
-  }
-
-  void pollJob(WSJob job)
-      throws Exception
-  {
-    ( (SeqSearchWSJob) job).result = server.getResult( ( (SeqSearchWSJob) job).jobId);
-  }
-
-  void StartJob(WSJob job)
-  {
-    if (! (job instanceof SeqSearchWSJob))
-    {
-      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
-                      job.getClass());
-    }
-    SeqSearchWSJob j = (SeqSearchWSJob) job;
-    if (j.submitted)
-    {
-      if (Cache.log.isDebugEnabled())
-      {
-        Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
-      }
-      return;
-    }
-    if (j.seqs.getSeqs() == null)
-    {
-      // special case - selection consisted entirely of empty sequences...
-      j.submitted = true;
-      j.result = new MsaResult();
-      j.result.setFinished(true);
-      j.result.setStatus("Empty Alignment Job");
-      ( (MsaResult) j.result).setMsa(null);
-    }
-    try
-    {
-      vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs.getSeqs()[0], dbArg);
-
-      if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
-      {
-        j.jobId = jobsubmit.getJobId();
-        j.submitted = true;
-        j.subjobComplete = false;
-        // 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 (probably a server side problem)\n"
-                   + "When contacting Server:" + WsUrl + "\n"
-                   + e.toString() + "\n");
-      j.allowedServerExceptions = 0;
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      wsInfo
-          .appendProgressText(
-              j.jobnum,
-              "Failed to submit sequences for alignment.\n"
-              + "It is most likely that there is a problem with the server.\n"
-              + "Just close the window\n");
-
-      // e.printStackTrace(); // TODO: JBPNote DEBUG
-    }
-  }
-
-  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()
-  {
-    int results = 0; // number of result sets received
-    JobStateSummary finalState = new JobStateSummary();
-    try
-    {
-      for (int j = 0; j < jobs.length; j++)
-      {
-        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
-        {
-          results++;
-          vamsas.objects.simple.Alignment valign = ( (SeqSearchResult) jobs[j].result).
-              getAlignment();
-          if (valign != null)
-          {
-            wsInfo.appendProgressText(jobs[j].jobnum,
-                                      "\nAlignment Object Method Notes\n");
-            String[] lines = valign.getMethod();
-            for (int line = 0; line < lines.length; line++)
-            {
-              wsInfo.appendProgressText(jobs[j].jobnum, 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
-          }
-        }
-      }
-    }
-    catch (Exception ex)
-    {
-
-      Cache.log.error("Unexpected exception when processing results for " +
-                      alTitle, ex);
-      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-    }
-    if (results > 0)
-    {
-      wsInfo.showResultsNewFrame
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(true);
-        }
-      });
-      wsInfo.mergeResults
-          .addActionListener(new java.awt.event.ActionListener()
-      {
-        public void actionPerformed(
-            java.awt.event.ActionEvent evt)
-        {
-          displayResults(false);
-        }
-      });
-      wsInfo.setResultsReady();
-    }
-    else
-    {
-      wsInfo.setFinishedNoResults();
-    }
-  }
-
-  void displayResults(boolean newFrame)
-  {
-    if (!newFrame)
-    {
-      System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
-      return;
-    }
-    // each subjob is an independent alignment for the moment
-    //Alignment al[] = new Alignment[jobs.length];
-    //NewickFile nf[] = new NewickFile[jobs.length];
-    for (int j = 0; j < jobs.length; j++)
-    {
-      Hashtable featureColours = new Hashtable();
-      Alignment al=null;
-      NewickFile nf = null;
-      if (jobs[j].hasResults())
-      {
-        Object[] res = ( (SeqSearchWSJob) jobs[j]).getAlignment(dataset, featureColours);
-        if (res==null) { continue; };
-        al = (Alignment) res[0];
-        nf = (NewickFile) res[1];
-      }
-      else
-      {
-        al = null;
-        nf = null;
-        continue;
-      }
-    /*
-     * We can't map new alignment back with insertions from input's hidden regions until dataset mapping is sorted out...
-     * but basically it goes like this:
-     1. Merge each domain hit back onto the visible segments in the same way as a Jnet prediction is mapped back
-     
-     Object[] newview = input.getUpdatedView(results, orders, getGapChar());
-    // trash references to original result data
-    for (int j = 0; j < jobs.length; j++)
-    {
-      results[j] = null;
-      orders[j] = null;
-    }
-    SequenceI[] alignment = (SequenceI[]) newview[0];
-    ColumnSelection columnselection = (ColumnSelection) newview[1];
-    Alignment al = new Alignment(alignment);
-
-    if (dataset != null)
-    {
-      al.setDataset(dataset);
-    }
-
-    propagateDatasetMappings(al);
-    }
-    */
-      
-      AlignFrame af = new AlignFrame(al,//  columnselection,
-              AlignFrame.DEFAULT_WIDTH,
-              AlignFrame.DEFAULT_HEIGHT);
-      if (nf!=null)
-      {
-        af.ShowNewickTree(nf, "Tree from "+this.alTitle);
-      }
-      // initialise with same renderer settings as in parent alignframe.
-      af.getFeatureRenderer().transferSettings(
-              this.featureSettings);
-      Desktop.addInternalFrame(af, alTitle,
-              AlignFrame.DEFAULT_WIDTH,
-              AlignFrame.DEFAULT_HEIGHT);
-    }
-  }
-
-  public boolean canMergeResults()
-  {
-    return false;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import java.util.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.io.NewickFile;
+import vamsas.objects.simple.MsaResult;
+import vamsas.objects.simple.SeqSearchResult;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ *
+ * <p>
+ * Description:
+ * </p>
+ *
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ *
+ * <p>
+ * Company: Dundee University
+ * </p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+class SeqSearchWSThread
+    extends WSThread implements WSClientI
+{
+  String dbs=null;
+  boolean profile=false;
+
+  class SeqSearchWSJob
+      extends WSThread.WSJob
+  {
+    // hold special input for this
+    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
+        SequenceSet();
+
+    /**
+     * MsaWSJob
+     *
+     * @param jobNum
+     *            int
+     * @param jobId
+     *            String
+     */
+    public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)
+    {
+      this.jobnum = jobNum;
+      if (!prepareInput(inSeqs, 2))
+      {
+        submitted = true;
+        subjobComplete = true;
+        result = new MsaResult();
+        result.setFinished(true);
+        result.setStatus("Job never ran - input returned to user.");
+      }
+
+    }
+
+    Hashtable SeqNames = new Hashtable();
+    Vector emptySeqs = new Vector();
+    /**
+     * prepare input sequences for service
+     * @param seqs jalview sequences to be prepared
+     * @param minlen minimum number of residues required for this MsaWS service
+     * @return true if seqs contains sequences to be submitted to service.
+     */
+    private boolean prepareInput(SequenceI[] seqs, int minlen)
+    {
+      int nseqs = 0;
+      if (minlen < 0)
+      {
+        throw new Error("Implementation error: minlen must be zero or more.");
+      }
+      for (int i = 0; i < seqs.length; i++)
+      {
+        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          nseqs++;
+        }
+      }
+      boolean valid = nseqs >= 1; // need at least one sequence for valid input TODO: generalise
+      vamsas.objects.simple.Sequence[] seqarray =
+          (valid)
+          ? new vamsas.objects.simple.Sequence[nseqs]
+          : null;
+      boolean submitGaps = (nseqs==1) ? false : true; // profile is submitted with gaps  
+      for (int i = 0, n = 0; i < seqs.length; i++)
+      {
+
+        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+        // for
+        // any
+        // subjob
+        SeqNames.put(newname, jalview.analysis.SeqsetUtils
+                     .SeqCharacterHash(seqs[i]));
+        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          seqarray[n] = new vamsas.objects.simple.Sequence();
+          seqarray[n].setId(newname);
+          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
+                               : AlignSeq.extractGaps(
+                                   jalview.util.Comparison.GapChars, seqs[i]
+                                   .getSequenceAsString()));
+        }
+        else
+        {
+          String empty = null;
+          if (seqs[i].getEnd() >= seqs[i].getStart())
+          {
+            empty = (submitGaps) ? seqs[i].getSequenceAsString()
+                : AlignSeq.extractGaps(
+                    jalview.util.Comparison.GapChars, seqs[i]
+                    .getSequenceAsString());
+          }
+          emptySeqs.add(new String[]
+                        {newname, empty});
+        }
+      }
+      if (submitGaps)
+      {
+        // almost certainly have to remove gapped columns here
+      }
+      this.seqs = new vamsas.objects.simple.SequenceSet();
+      this.seqs.setSeqs(seqarray);
+      return valid;
+    }
+
+    /**
+     *
+     * @return true if getAlignment will return a valid alignment result.
+     */
+    public boolean hasResults()
+    {
+      if (subjobComplete && result != null && result.isFinished()
+          && ( (SeqSearchResult) result).getAlignment() != null &&
+          ( (SeqSearchResult) result).getAlignment().getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+
+    /**
+     * return sequence search results for display
+     * @return null or { Alignment(+features and annotation), NewickFile)}
+     */
+    public Object[] getAlignment(Alignment dataset, Hashtable featureColours)
+    {
+
+      if (result != null && result.isFinished())
+      {
+        SequenceI[] alseqs = null;
+        //char alseq_gapchar = '-';
+        //int alseq_l = 0;
+        if ( ( (SeqSearchResult) result).getAlignment() != null)
+        {
+          alseqs = getVamsasAlignment( ( (SeqSearchResult) result).getAlignment());
+          //alseq_gapchar = ( (SeqSearchResult) result).getAlignment().getGapchar().charAt(0);
+          //alseq_l = alseqs.length;
+        }
+        /**
+         * what has to be done. 1 - annotate returned alignment with annotation file and sequence features file, and associate any tree-nodes.
+         * 2. connect alignment back to any associated dataset: 2.a. deuniquify recovers sequence information - but additionally, 
+         * relocations must be made from the returned aligned sequence back to the dataset.
+         */
+        // construct annotated alignment as it would be done by the jalview applet
+        jalview.datamodel.Alignment al = new Alignment(alseqs);
+        // al.setDataset(dataset);
+        // make dataset
+        String inFile=null;
+        try {
+          inFile = ((SeqSearchResult) result).getAnnotation();
+          if (inFile!=null && inFile.length()>0)
+          {
+            new jalview.io.AnnotationFile().readAnnotationFile(al, inFile, jalview.io.AppletFormatAdapter.PASTE);
+          }
+          }
+        catch (Exception e)
+        {
+          System.err.println("Failed to parse the annotation file associated with the alignment.");
+          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
+          e.printStackTrace(System.err);
+        }
+        
+        try {
+          inFile = ((SeqSearchResult) result).getFeatures();
+          if (inFile!=null && inFile.length()>0)
+          {
+            jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(inFile, jalview.io.AppletFormatAdapter.PASTE);
+            ff.parse(al, featureColours, false);
+          }
+        }
+        catch (Exception e)
+        {
+          System.err.println("Failed to parse the Features file associated with the alignment.");
+          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
+          e.printStackTrace(System.err);
+        }
+        jalview.io.NewickFile nf=null;
+        try {
+          inFile = ((SeqSearchResult) result).getNewickTree();
+          if (inFile!=null && inFile.length()>0)
+          {
+            nf = new jalview.io.NewickFile(inFile, jalview.io.AppletFormatAdapter.PASTE);
+            if (!nf.isValid()) {
+              nf.close();
+              nf = null;
+            }
+          }
+        }
+        catch (Exception e)
+        {
+          System.err.println("Failed to parse the treeFile associated with the alignment.");
+          System.err.println(">>>EOF"+inFile+"\n<<<EOF\n");
+          e.printStackTrace(System.err);
+        }
+        
+        /* TODO: housekeeping w.r.t. recovery of dataset and annotation references for input sequences, and then dataset sequence creation for new sequences retrieved from service
+         * // finally, attempt to de-uniquify to recover input sequence identity, and try to map back onto dataset
+        Note: this
+        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true);
+        will NOT WORK - the returned alignment may contain multiple versions of the input sequence, each being a subsequence of the original.
+        deuniquify also removes existing annotation and features added in the previous step...
+        al.setDataset(dataset);
+        // add in new sequences retrieved from sequence search which are not already in dataset.
+        // trigger a 'fetchDBids' to annotate sequences with database ids...
+        */
+
+        return new Object[]
+            {
+            al, nf};
+      }
+      return null;
+    }
+
+    /**
+     * mark subjob as cancelled and set result object appropriatly
+     */
+    void cancel()
+    {
+      cancelled = true;
+      subjobComplete = true;
+      result = null;
+    }
+
+    /**
+     *
+     * @return boolean true if job can be submitted.
+     */
+    boolean hasValidInput()
+    {
+      if (seqs.getSeqs() != null)
+      {
+        return true;
+      }
+      return false;
+    }
+  }
+
+  String alTitle; // name which will be used to form new alignment window.
+  Alignment dataset; // dataset to which the new alignment will be
+
+  // associated.
+
+  ext.vamsas.SeqSearchI server = null;
+
+  private String dbArg;
+  /**
+   * set basic options for this (group) of Msa jobs
+   *
+   * @param subgaps
+   *            boolean
+   * @param presorder
+   *            boolean
+   */
+  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+              AlignmentView alview,
+              String wsname, String db)
+  {
+    super(alFrame, wsinfo, alview, wsname, wsUrl);
+    this.server = server;
+    this.dbArg = db;
+  }
+
+  /**
+   * create one or more Msa jobs to align visible seuqences in _msa
+   *
+   * @param title
+   *            String
+   * @param _msa
+   *            AlignmentView
+   * @param subgaps
+   *            boolean
+   * @param presorder
+   *            boolean
+   * @param seqset
+   *            Alignment
+   */
+  SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
+              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+              String wsname, String title, AlignmentView _msa, String db, Alignment seqset)
+  {
+    this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
+    OutputHeader = wsInfo.getProgressText();
+    alTitle = title;
+    dataset = seqset;
+
+    SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+    if (conmsa != null)
+    {
+      int njobs = conmsa.length;
+      jobs = new SeqSearchWSJob[njobs];
+      for (int j = 0; j < njobs; j++)
+      {
+        if (j != 0)
+        {
+          jobs[j] = new SeqSearchWSJob(wsinfo.addJobPane(), conmsa[j]);
+        }
+        else
+        {
+          jobs[j] = new SeqSearchWSJob(0, conmsa[j]);
+        }
+        if (njobs > 0)
+        {
+          wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
+        }
+        wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
+      }
+    }
+  }
+
+  public boolean isCancellable()
+  {
+    return true;
+  }
+
+  public void cancelJob()
+  {
+    if (!jobComplete && jobs != null)
+    {
+      boolean cancelled = true;
+      for (int job = 0; job < jobs.length; job++)
+      {
+        if (jobs[job].submitted && !jobs[job].subjobComplete)
+        {
+          String cancelledMessage = "";
+          try
+          {
+            vamsas.objects.simple.WsJobId cancelledJob = server
+                .cancel(jobs[job].jobId);
+            if (cancelledJob.getStatus() == 2)
+            {
+              // CANCELLED_JOB
+              cancelledMessage = "Job cancelled.";
+              ( (SeqSearchWSJob) jobs[job]).cancel();
+              wsInfo.setStatus(jobs[job].jobnum,
+                               WebserviceInfo.STATE_CANCELLED_OK);
+            }
+            else if (cancelledJob.getStatus() == 3)
+            {
+              // VALID UNSTOPPABLE JOB
+              cancelledMessage +=
+                  "Server cannot cancel this job. just close the window.\n";
+              cancelled = false;
+              // wsInfo.setStatus(jobs[job].jobnum,
+              //                 WebserviceInfo.STATE_RUNNING);
+            }
+
+            if (cancelledJob.getJobId() != null)
+            {
+              cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
+            }
+
+            cancelledMessage += "\n";
+          }
+          catch (Exception exc)
+          {
+            cancelledMessage +=
+                ("\nProblems cancelling the job : Exception received...\n"
+                 + exc + "\n");
+            Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
+                           exc);
+          }
+          wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
+                                 + cancelledMessage + "\n");
+        }
+      }
+      if (cancelled)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
+        jobComplete = true;
+      }
+      this.interrupt(); // kick thread to update job states.
+    }
+    else
+    {
+      if (!jobComplete)
+      {
+        wsInfo
+            .setProgressText(OutputHeader
+                             + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+      }
+    }
+  }
+
+  void pollJob(WSJob job)
+      throws Exception
+  {
+    ( (SeqSearchWSJob) job).result = server.getResult( ( (SeqSearchWSJob) job).jobId);
+  }
+
+  void StartJob(WSJob job)
+  {
+    if (! (job instanceof SeqSearchWSJob))
+    {
+      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
+                      job.getClass());
+    }
+    SeqSearchWSJob j = (SeqSearchWSJob) job;
+    if (j.submitted)
+    {
+      if (Cache.log.isDebugEnabled())
+      {
+        Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
+      }
+      return;
+    }
+    if (j.seqs.getSeqs() == null)
+    {
+      // special case - selection consisted entirely of empty sequences...
+      j.submitted = true;
+      j.result = new MsaResult();
+      j.result.setFinished(true);
+      j.result.setStatus("Empty Alignment Job");
+      ( (MsaResult) j.result).setMsa(null);
+    }
+    try
+    {
+      vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs.getSeqs()[0], dbArg);
+
+      if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
+      {
+        j.jobId = jobsubmit.getJobId();
+        j.submitted = true;
+        j.subjobComplete = false;
+        // 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 (probably a server side problem)\n"
+                   + "When contacting Server:" + WsUrl + "\n"
+                   + e.toString() + "\n");
+      j.allowedServerExceptions = 0;
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo
+          .appendProgressText(
+              j.jobnum,
+              "Failed to submit sequences for alignment.\n"
+              + "It is most likely that there is a problem with the server.\n"
+              + "Just close the window\n");
+
+      // e.printStackTrace(); // TODO: JBPNote DEBUG
+    }
+  }
+
+  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()
+  {
+    int results = 0; // number of result sets received
+    JobStateSummary finalState = new JobStateSummary();
+    try
+    {
+      for (int j = 0; j < jobs.length; j++)
+      {
+        finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
+        {
+          results++;
+          vamsas.objects.simple.Alignment valign = ( (SeqSearchResult) jobs[j].result).
+              getAlignment();
+          if (valign != null)
+          {
+            wsInfo.appendProgressText(jobs[j].jobnum,
+                                      "\nAlignment Object Method Notes\n");
+            String[] lines = valign.getMethod();
+            for (int line = 0; line < lines.length; line++)
+            {
+              wsInfo.appendProgressText(jobs[j].jobnum, 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
+          }
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+
+      Cache.log.error("Unexpected exception when processing results for " +
+                      alTitle, ex);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+    }
+    if (results > 0)
+    {
+      wsInfo.showResultsNewFrame
+          .addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(
+            java.awt.event.ActionEvent evt)
+        {
+          displayResults(true);
+        }
+      });
+      wsInfo.mergeResults
+          .addActionListener(new java.awt.event.ActionListener()
+      {
+        public void actionPerformed(
+            java.awt.event.ActionEvent evt)
+        {
+          displayResults(false);
+        }
+      });
+      wsInfo.setResultsReady();
+    }
+    else
+    {
+      wsInfo.setFinishedNoResults();
+    }
+  }
+
+  void displayResults(boolean newFrame)
+  {
+    if (!newFrame)
+    {
+      System.err.println("MERGE WITH OLD FRAME NOT IMPLEMENTED");
+      return;
+    }
+    // each subjob is an independent alignment for the moment
+    //Alignment al[] = new Alignment[jobs.length];
+    //NewickFile nf[] = new NewickFile[jobs.length];
+    for (int j = 0; j < jobs.length; j++)
+    {
+      Hashtable featureColours = new Hashtable();
+      Alignment al=null;
+      NewickFile nf = null;
+      if (jobs[j].hasResults())
+      {
+        Object[] res = ( (SeqSearchWSJob) jobs[j]).getAlignment(dataset, featureColours);
+        if (res==null) { continue; };
+        al = (Alignment) res[0];
+        nf = (NewickFile) res[1];
+      }
+      else
+      {
+        al = null;
+        nf = null;
+        continue;
+      }
+    /*
+     * We can't map new alignment back with insertions from input's hidden regions until dataset mapping is sorted out...
+     * but basically it goes like this:
+     1. Merge each domain hit back onto the visible segments in the same way as a Jnet prediction is mapped back
+     
+     Object[] newview = input.getUpdatedView(results, orders, getGapChar());
+    // trash references to original result data
+    for (int j = 0; j < jobs.length; j++)
+    {
+      results[j] = null;
+      orders[j] = null;
+    }
+    SequenceI[] alignment = (SequenceI[]) newview[0];
+    ColumnSelection columnselection = (ColumnSelection) newview[1];
+    Alignment al = new Alignment(alignment);
+
+    if (dataset != null)
+    {
+      al.setDataset(dataset);
+    }
+
+    propagateDatasetMappings(al);
+    }
+    */
+      
+      AlignFrame af = new AlignFrame(al,//  columnselection,
+              AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
+      if (nf!=null)
+      {
+        af.ShowNewickTree(nf, "Tree from "+this.alTitle);
+      }
+      // initialise with same renderer settings as in parent alignframe.
+      af.getFeatureRenderer().transferSettings(
+              this.featureSettings);
+      Desktop.addInternalFrame(af, alTitle,
+              AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
+    }
+  }
+
+  public boolean canMergeResults()
+  {
+    return false;
+  }
+}
diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 0d93cb8..8bd8423 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws;
 
 import java.util.ArrayList;
diff --git a/src/jalview/ws/WSClient.java b/src/jalview/ws/WSClient.java
index 91fd4b0..df52803 100755
--- a/src/jalview/ws/WSClient.java
+++ b/src/jalview/ws/WSClient.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/ws/WSClientI.java b/src/jalview/ws/WSClientI.java
index 92b7bb3..8fa4ecb 100755
--- a/src/jalview/ws/WSClientI.java
+++ b/src/jalview/ws/WSClientI.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
diff --git a/src/jalview/ws/WSThread.java b/src/jalview/ws/WSThread.java
index a9e9b0b..3ad9690 100644
--- a/src/jalview/ws/WSThread.java
+++ b/src/jalview/ws/WSThread.java
@@ -1,449 +1,449 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws;
-
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.gui.FeatureRenderer.FeatureRendererSettings;
-
-public abstract class WSThread
-    extends Thread
-{
-  /**
-   * Generic properties for Web Service Client threads.
-   */
-  /**
-   * view that this job was associated with
-   */
-  AlignmentI currentView = null;
-  /**
-   * feature settings from view that job was associated with
-   */
-  FeatureRendererSettings featureSettings = null;
-  /**
-   * metadata about this web service
-   */
-  WebserviceInfo wsInfo = null;
-  /**
-   * original input data for this job
-   */
-  AlignmentView input = null;
-  /**
-   * dataset sequence relationships to be propagated onto new results
-   */
-  AlignedCodonFrame[] codonframe = null;
-  /**
-   * are there jobs still running in this thread.
-   */
-  boolean jobComplete = false;
-  
-  abstract class WSJob
-  {
-    /**
-     * Generic properties for an individual job within a Web Service Client thread
-     */
-    int jobnum = 0; // WebServiceInfo pane for this job
-    String jobId; // ws job ticket
-    /**
-     * has job been cancelled
-     */
-    boolean cancelled = false;
-    /**
-     * number of exceptions left before job dies
-     */
-    int allowedServerExceptions = 3;
-    /**
-     * has job been submitted
-     */
-    boolean submitted = false;
-    /**
-     * are all sub-jobs complete
-     */
-    boolean subjobComplete = false;
-    /**
-     *
-     * @return true if job has completed and valid results are available
-     */
-    abstract boolean hasResults();
-
-    /**
-     *
-     * @return boolean true if job can be submitted.
-     */
-    abstract boolean hasValidInput();
-
-    /**
-     * The last result object returned by the service.
-     */
-    vamsas.objects.simple.Result result;
-  }
-
-  class JobStateSummary
-  {
-    /**
-     * number of jobs running
-     */
-    int running = 0;
-    /**
-     * number of jobs queued
-     */
-    int queuing = 0;
-    /**
-     * number of jobs finished
-     */
-    int finished = 0;
-    /**
-     * number of jobs failed
-     */
-    int error = 0;
-    /**
-     * number of jobs stopped due to server error
-     */
-    int serror = 0;
-    /**
-     * number of jobs cancelled
-     */
-    int cancelled = 0;
-    /**
-     * number of jobs finished with results
-     */
-    int results = 0;
-    /**
-     * processes WSJob and updates job status counters and WebService status displays
-     * @param wsInfo
-     * @param OutputHeader
-     * @param j
-     */
-    void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
-                             WSJob j)
-    {
-      if (j.result != null)
-      {
-        String progheader = "";
-        // Parse state of job[j]
-        if (j.result.isRunning())
-        {
-          running++;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
-        }
-        else if (j.result.isQueued())
-        {
-          queuing++;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
-        }
-        else if (j.result.isFinished())
-        {
-          finished++;
-          j.subjobComplete = true;
-          if (j.hasResults())
-          {
-            results++;
-          }
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else if (j.result.isFailed())
-        {
-          progheader += "Job failed.\n";
-          j.subjobComplete = true;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
-          error++;
-        }
-        else if (j.result.isServerError())
-        {
-          serror++;
-          j.subjobComplete = true;
-          wsInfo.setStatus(j.jobnum,
-                           WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        }
-        else if (j.result.isBroken() || j.result.isFailed())
-        {
-          error++;
-          j.subjobComplete = true;
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
-        }
-        // and pass on any sub-job messages to the user
-        wsInfo.setProgressText(j.jobnum, OutputHeader);
-        wsInfo.appendProgressText(j.jobnum, progheader);
-        if (j.result.getStatus() != null)
-        {
-          wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
-        }
-      }
-      else
-      {
-        if (j.submitted && j.subjobComplete)
-        {
-          if (j.allowedServerExceptions == 0)
-          {
-            serror++;
-          }
-          else if (j.result == null)
-          {
-            error++;
-          }
-        }
-      }
-    }
-  }
-  /**
-   * one or more jobs being managed by this thread.
-   */
-  WSJob jobs[] = null;
-  /**
-   * full name of service
-   */
-  String WebServiceName = null;
-  String OutputHeader;
-  String WsUrl = null;
-  /**
-   * query web service for status of job.
-   * on return, job.result must not be null - if it is then it will be
-   * assumed that the job status query timed out and a server exception
-   * will be logged.
-   * @param job
-   * @throws Exception will be logged as a server exception for this job
-   */
-  abstract void pollJob(WSJob job)
-      throws Exception;
-
-  public void run()
-  {
-    JobStateSummary jstate = null;
-    if (jobs == null)
-    {
-      jobComplete = true;
-    }
-    while (!jobComplete)
-    {
-      jstate = new JobStateSummary();
-      for (int j = 0; j < jobs.length; j++)
-      {
-
-        if (!jobs[j].submitted && jobs[j].hasValidInput())
-        {
-          StartJob(jobs[j]);
-        }
-
-        if (jobs[j].submitted && !jobs[j].subjobComplete)
-        {
-          try
-          {
-            pollJob(jobs[j]);
-            if (jobs[j].result == null)
-            {
-              throw (new Exception(
-                  "Timed out when communicating with server\nTry again later.\n"));
-            }
-            jalview.bin.Cache.log.debug("Job " + j + " Result state " +
-                                        jobs[j].result.getState()
-                                        + "(ServerError=" +
-                                        jobs[j].result.isServerError() + ")");
-          }
-          catch (Exception ex)
-          {
-            // Deal with Transaction exceptions
-            wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
-                                      + " Server exception!\n" + ex.getMessage());
-            Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
-                           + ") Server exception: " + ex.getMessage());
-
-            if (jobs[j].allowedServerExceptions > 0)
-            {
-              jobs[j].allowedServerExceptions--;
-              Cache.log.debug("Sleeping after a server exception.");
-              try
-              {
-                Thread.sleep(5000);
-              }
-              catch (InterruptedException ex1)
-              {
-              }
-            }
-            else
-            {
-              Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
-              jobs[j].subjobComplete = true;
-              wsInfo.setStatus(jobs[j].jobnum,
-                               WebserviceInfo.STATE_STOPPED_SERVERERROR);
-            }
-          }
-          catch (OutOfMemoryError er)
-          {
-            jobComplete = true;
-            jobs[j].subjobComplete = true;
-            jobs[j].result = null; // may contain out of date result object
-            wsInfo.setStatus(jobs[j].jobnum,
-                             WebserviceInfo.STATE_STOPPED_ERROR);
-            JOptionPane
-                .showInternalMessageDialog(
-                    Desktop.desktop,
-                    "Out of memory handling result for job !!"
-                    +
-                    "\nSee help files for increasing Java Virtual Machine memory.",
-                    "Out of memory", JOptionPane.WARNING_MESSAGE);
-            Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
-                            WsUrl + "/" + jobs[j].jobId, er);
-            System.gc();
-          }
-        }
-        jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-      }
-      // Decide on overall state based on collected jobs[] states
-      if (jstate.running > 0)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-      }
-      else if (jstate.queuing > 0)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
-      }
-      else
-      {
-        jobComplete = true;
-        if (jstate.finished > 0)
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else if (jstate.error > 0)
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-        }
-        else if (jstate.serror > 0)
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        }
-      }
-      if (!jobComplete)
-      {
-        try
-        {
-          Thread.sleep(5000);
-        }
-        catch (InterruptedException e)
-        {
-          Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
-        }
-        // System.out.println("I'm alive "+alTitle);
-      }
-    }
-    if (jobComplete && jobs != null)
-    {
-      parseResult(); // tidy up and make results available to user
-    }
-    else
-    {
-      Cache.log.debug("WebServiceJob poll loop finished with no jobs created.");
-      wsInfo.setFinishedNoResults();
-    }
-  }
-
-  /**
-   * submit job to web service
-   * @param job
-   */
-  abstract void StartJob(WSJob job);
-
-  /**
-   * process the set of WSJob objects into a set of results, and tidy up.
-   */
-  abstract void parseResult();
-
-  /**
-   * helper function to conserve dataset references to sequence objects returned from web services
-   * 1. Propagates AlCodonFrame data from <code>codonframe</code> to <code>al</code>
-   * @param al
-   */
-  protected void propagateDatasetMappings(Alignment al)
-  {
-    if (codonframe!=null)
-    {
-      SequenceI[] alignment = al.getSequencesArray();
-      for (int sq = 0; sq<alignment.length; sq++)
-      {
-        for (int i=0; i<codonframe.length; i++)
-        {
-          if (codonframe[i]!=null &&
-                  codonframe[i].involvesSequence(alignment[sq]))
-          {
-            al.addCodonFrame(codonframe[i]);
-            codonframe[i] = null;
-            break;
-          }
-        }
-      }
-    }
-  }
-
-  /**
-   * 
-   * @param alignFrame reference for copying mappings across
-   * @param wsInfo gui attachment point
-   * @param input input data for the calculation
-   * @param webServiceName name of service
-   * @param wsUrl  url of the service being invoked
-   */
-  public WSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
-          AlignmentView input, String webServiceName,
-          String wsUrl)
-  {
-    this(alignFrame, wsinfo, input, wsUrl);
-    WebServiceName = webServiceName;
-  }
-  char defGapChar = '-';
-  /**
-   * 
-   * @return gap character to use for any alignment generation
-   */
-  public char getGapChar()
-  {
-    return defGapChar;
-  }
-
-  /**
-   * 
-   * @param alframe - reference for copying mappings and display styles across
-   * @param wsinfo2 - gui attachment point
-   * @param alview - input data for the calculation
-   * @param wsurl2 - url of the service being invoked
-   */
-  public WSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
-          AlignmentView alview, String wsurl2)
-  {
-    super();
-    // this.alignFrame = alframe;
-    currentView = alframe.getCurrentView().getAlignment();
-    featureSettings = alframe.getFeatureRenderer().getSettings();
-    defGapChar = alframe.getViewport().getGapCharacter();
-    this.wsInfo = wsinfo2;
-    this.input = alview;
-    WsUrl = wsurl2;
-    if (alframe!=null)
-    {
-      AlignedCodonFrame[] cf = alframe.getViewport().getAlignment().getCodonFrames();
-      if (cf!=null)
-      {
-        codonframe = new AlignedCodonFrame[cf.length];
-        System.arraycopy(cf, 0, codonframe, 0, cf.length);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import javax.swing.*;
+
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+
+public abstract class WSThread
+    extends Thread
+{
+  /**
+   * Generic properties for Web Service Client threads.
+   */
+  /**
+   * view that this job was associated with
+   */
+  AlignmentI currentView = null;
+  /**
+   * feature settings from view that job was associated with
+   */
+  FeatureRendererSettings featureSettings = null;
+  /**
+   * metadata about this web service
+   */
+  WebserviceInfo wsInfo = null;
+  /**
+   * original input data for this job
+   */
+  AlignmentView input = null;
+  /**
+   * dataset sequence relationships to be propagated onto new results
+   */
+  AlignedCodonFrame[] codonframe = null;
+  /**
+   * are there jobs still running in this thread.
+   */
+  boolean jobComplete = false;
+  
+  abstract class WSJob
+  {
+    /**
+     * Generic properties for an individual job within a Web Service Client thread
+     */
+    int jobnum = 0; // WebServiceInfo pane for this job
+    String jobId; // ws job ticket
+    /**
+     * has job been cancelled
+     */
+    boolean cancelled = false;
+    /**
+     * number of exceptions left before job dies
+     */
+    int allowedServerExceptions = 3;
+    /**
+     * has job been submitted
+     */
+    boolean submitted = false;
+    /**
+     * are all sub-jobs complete
+     */
+    boolean subjobComplete = false;
+    /**
+     *
+     * @return true if job has completed and valid results are available
+     */
+    abstract boolean hasResults();
+
+    /**
+     *
+     * @return boolean true if job can be submitted.
+     */
+    abstract boolean hasValidInput();
+
+    /**
+     * The last result object returned by the service.
+     */
+    vamsas.objects.simple.Result result;
+  }
+
+  class JobStateSummary
+  {
+    /**
+     * number of jobs running
+     */
+    int running = 0;
+    /**
+     * number of jobs queued
+     */
+    int queuing = 0;
+    /**
+     * number of jobs finished
+     */
+    int finished = 0;
+    /**
+     * number of jobs failed
+     */
+    int error = 0;
+    /**
+     * number of jobs stopped due to server error
+     */
+    int serror = 0;
+    /**
+     * number of jobs cancelled
+     */
+    int cancelled = 0;
+    /**
+     * number of jobs finished with results
+     */
+    int results = 0;
+    /**
+     * processes WSJob and updates job status counters and WebService status displays
+     * @param wsInfo
+     * @param OutputHeader
+     * @param j
+     */
+    void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,
+                             WSJob j)
+    {
+      if (j.result != null)
+      {
+        String progheader = "";
+        // Parse state of job[j]
+        if (j.result.isRunning())
+        {
+          running++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
+        }
+        else if (j.result.isQueued())
+        {
+          queuing++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
+        }
+        else if (j.result.isFinished())
+        {
+          finished++;
+          j.subjobComplete = true;
+          if (j.hasResults())
+          {
+            results++;
+          }
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else if (j.result.isFailed())
+        {
+          progheader += "Job failed.\n";
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+          error++;
+        }
+        else if (j.result.isServerError())
+        {
+          serror++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum,
+                           WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        }
+        else if (j.result.isBroken() || j.result.isFailed())
+        {
+          error++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+        }
+        // and pass on any sub-job messages to the user
+        wsInfo.setProgressText(j.jobnum, OutputHeader);
+        wsInfo.appendProgressText(j.jobnum, progheader);
+        if (j.result.getStatus() != null)
+        {
+          wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
+        }
+      }
+      else
+      {
+        if (j.submitted && j.subjobComplete)
+        {
+          if (j.allowedServerExceptions == 0)
+          {
+            serror++;
+          }
+          else if (j.result == null)
+          {
+            error++;
+          }
+        }
+      }
+    }
+  }
+  /**
+   * one or more jobs being managed by this thread.
+   */
+  WSJob jobs[] = null;
+  /**
+   * full name of service
+   */
+  String WebServiceName = null;
+  String OutputHeader;
+  String WsUrl = null;
+  /**
+   * query web service for status of job.
+   * on return, job.result must not be null - if it is then it will be
+   * assumed that the job status query timed out and a server exception
+   * will be logged.
+   * @param job
+   * @throws Exception will be logged as a server exception for this job
+   */
+  abstract void pollJob(WSJob job)
+      throws Exception;
+
+  public void run()
+  {
+    JobStateSummary jstate = null;
+    if (jobs == null)
+    {
+      jobComplete = true;
+    }
+    while (!jobComplete)
+    {
+      jstate = new JobStateSummary();
+      for (int j = 0; j < jobs.length; j++)
+      {
+
+        if (!jobs[j].submitted && jobs[j].hasValidInput())
+        {
+          StartJob(jobs[j]);
+        }
+
+        if (jobs[j].submitted && !jobs[j].subjobComplete)
+        {
+          try
+          {
+            pollJob(jobs[j]);
+            if (jobs[j].result == null)
+            {
+              throw (new Exception(
+                  "Timed out when communicating with server\nTry again later.\n"));
+            }
+            jalview.bin.Cache.log.debug("Job " + j + " Result state " +
+                                        jobs[j].result.getState()
+                                        + "(ServerError=" +
+                                        jobs[j].result.isServerError() + ")");
+          }
+          catch (Exception ex)
+          {
+            // Deal with Transaction exceptions
+            wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
+                                      + " Server exception!\n" + ex.getMessage());
+            Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+                           + ") Server exception: " + ex.getMessage());
+
+            if (jobs[j].allowedServerExceptions > 0)
+            {
+              jobs[j].allowedServerExceptions--;
+              Cache.log.debug("Sleeping after a server exception.");
+              try
+              {
+                Thread.sleep(5000);
+              }
+              catch (InterruptedException ex1)
+              {
+              }
+            }
+            else
+            {
+              Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+              jobs[j].subjobComplete = true;
+              wsInfo.setStatus(jobs[j].jobnum,
+                               WebserviceInfo.STATE_STOPPED_SERVERERROR);
+            }
+          }
+          catch (OutOfMemoryError er)
+          {
+            jobComplete = true;
+            jobs[j].subjobComplete = true;
+            jobs[j].result = null; // may contain out of date result object
+            wsInfo.setStatus(jobs[j].jobnum,
+                             WebserviceInfo.STATE_STOPPED_ERROR);
+            JOptionPane
+                .showInternalMessageDialog(
+                    Desktop.desktop,
+                    "Out of memory handling result for job !!"
+                    +
+                    "\nSee help files for increasing Java Virtual Machine memory.",
+                    "Out of memory", JOptionPane.WARNING_MESSAGE);
+            Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
+                            WsUrl + "/" + jobs[j].jobId, er);
+            System.gc();
+          }
+        }
+        jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+      }
+      // Decide on overall state based on collected jobs[] states
+      if (jstate.running > 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+      }
+      else if (jstate.queuing > 0)
+      {
+        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+      }
+      else
+      {
+        jobComplete = true;
+        if (jstate.finished > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else if (jstate.error > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+        }
+        else if (jstate.serror > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        }
+      }
+      if (!jobComplete)
+      {
+        try
+        {
+          Thread.sleep(5000);
+        }
+        catch (InterruptedException e)
+        {
+          Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
+        }
+        // System.out.println("I'm alive "+alTitle);
+      }
+    }
+    if (jobComplete && jobs != null)
+    {
+      parseResult(); // tidy up and make results available to user
+    }
+    else
+    {
+      Cache.log.debug("WebServiceJob poll loop finished with no jobs created.");
+      wsInfo.setFinishedNoResults();
+    }
+  }
+
+  /**
+   * submit job to web service
+   * @param job
+   */
+  abstract void StartJob(WSJob job);
+
+  /**
+   * process the set of WSJob objects into a set of results, and tidy up.
+   */
+  abstract void parseResult();
+
+  /**
+   * helper function to conserve dataset references to sequence objects returned from web services
+   * 1. Propagates AlCodonFrame data from <code>codonframe</code> to <code>al</code>
+   * @param al
+   */
+  protected void propagateDatasetMappings(Alignment al)
+  {
+    if (codonframe!=null)
+    {
+      SequenceI[] alignment = al.getSequencesArray();
+      for (int sq = 0; sq<alignment.length; sq++)
+      {
+        for (int i=0; i<codonframe.length; i++)
+        {
+          if (codonframe[i]!=null &&
+                  codonframe[i].involvesSequence(alignment[sq]))
+          {
+            al.addCodonFrame(codonframe[i]);
+            codonframe[i] = null;
+            break;
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * 
+   * @param alignFrame reference for copying mappings across
+   * @param wsInfo gui attachment point
+   * @param input input data for the calculation
+   * @param webServiceName name of service
+   * @param wsUrl  url of the service being invoked
+   */
+  public WSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
+          AlignmentView input, String webServiceName,
+          String wsUrl)
+  {
+    this(alignFrame, wsinfo, input, wsUrl);
+    WebServiceName = webServiceName;
+  }
+  char defGapChar = '-';
+  /**
+   * 
+   * @return gap character to use for any alignment generation
+   */
+  public char getGapChar()
+  {
+    return defGapChar;
+  }
+
+  /**
+   * 
+   * @param alframe - reference for copying mappings and display styles across
+   * @param wsinfo2 - gui attachment point
+   * @param alview - input data for the calculation
+   * @param wsurl2 - url of the service being invoked
+   */
+  public WSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
+          AlignmentView alview, String wsurl2)
+  {
+    super();
+    // this.alignFrame = alframe;
+    currentView = alframe.getCurrentView().getAlignment();
+    featureSettings = alframe.getFeatureRenderer().getSettings();
+    defGapChar = alframe.getViewport().getGapCharacter();
+    this.wsInfo = wsinfo2;
+    this.input = alview;
+    WsUrl = wsurl2;
+    if (alframe!=null)
+    {
+      AlignedCodonFrame[] cf = alframe.getViewport().getAlignment().getCodonFrames();
+      if (cf!=null)
+      {
+        codonframe = new AlignedCodonFrame[cf.length];
+        System.arraycopy(cf, 0, codonframe, 0, cf.length);
+      }
+    }
+  }
+}
diff --git a/src/jalview/ws/dbsources/DasSequenceSource.java b/src/jalview/ws/dbsources/DasSequenceSource.java
index accb0b9..2576d74 100644
--- a/src/jalview/ws/dbsources/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/DasSequenceSource.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 import java.util.Hashtable;
diff --git a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
index dc73e74..c80a99a 100644
--- a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
+++ b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 import java.io.BufferedReader;
diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 65b4e21..86d18ce 100644
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 import java.util.Hashtable;
diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 2858c23..ec0546d 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 68a2424..a98e7e2 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 import jalview.datamodel.Alignment;
@@ -107,4 +125,4 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     return al;
   }
 
-}
\ No newline at end of file
+}
diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index 7cea532..7fcbdbd 100644
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index e6d46da..2b629b8 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 4136e62..2075a0b 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index 3d3ab53..cd9400a 100644
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index e0e2b4f..2797a82 100644
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index f29a555..1140a1b 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.ws.dbsources;
 
diff --git a/src/jalview/ws/dbsources/UnprotName.java b/src/jalview/ws/dbsources/UnprotName.java
index 4fbbe97..7513a79 100644
--- a/src/jalview/ws/dbsources/UnprotName.java
+++ b/src/jalview/ws/dbsources/UnprotName.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 /**
diff --git a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java b/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
index fa961f0..68e110d 100644
--- a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
+++ b/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources.das;
 
 import jalview.datamodel.AlignmentI;
diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index e9aff35..683f465 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -1,235 +1,235 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws.ebi;
-
-import java.io.*;
-import java.util.*;
-import javax.xml.namespace.*;
-import javax.xml.rpc.*;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.axis.encoding.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class EBIFetchClient
-{
-  Call call;
-  String format = "default";
-  String style = "raw";
-
-  /**
-   * Creates a new EBIFetchClient object.
-   */
-  public EBIFetchClient()
-  {
-    try
-    {
-      call = (Call)new Service().createCall();
-      call.setTargetEndpointAddress(new java.net.URL(
-          "http://www.ebi.ac.uk/ws/services/Dbfetch"));
-    }
-    catch (Exception ex)
-    {
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String[] getSupportedDBs()
-  {
-    try
-    {
-      call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
-      call.setReturnType(XMLType.SOAP_ARRAY);
-
-      return (String[]) call.invoke(new Object[]
-                                    {});
-    }
-    catch (Exception ex)
-    {
-      return null;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String[] getSupportedFormats()
-  {
-    try
-    {
-      call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
-      call.setReturnType(XMLType.SOAP_ARRAY);
-
-      return (String[]) call.invoke(new Object[]
-                                    {});
-    }
-    catch (Exception ex)
-    {
-      return null;
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String[] getSupportedStyles()
-  {
-    try
-    {
-      call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
-      call.setReturnType(XMLType.SOAP_ARRAY);
-
-      return (String[]) call.invoke(new Object[]
-                                    {});
-    }
-    catch (Exception ex)
-    {
-      return null;
-    }
-  }
-
-
-  public File fetchDataAsFile(String ids, String f, String s)
-  {
-    String[] data = fetchData(ids, f, s);
-    File outFile = null;
-    try
-    {
-      outFile = File.createTempFile("jalview", ".xml");
-      outFile.deleteOnExit();
-      PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
-      int index = 0;
-      while (index < data.length)
-      {
-        out.println(data[index]);
-        index++;
-      }
-      out.close();
-    }
-    catch (Exception ex)
-    {}
-    return outFile;
-  }
-
-  /**
-   * Single DB multiple record retrieval
-   *
-   * @param ids db:query1;query2;query3
-   * @param f raw/xml
-   * @param s ?
-   *
-   * @return Raw string array result of query set
-   */
-  public String[] fetchData(String ids, String f, String s)
-  {
-    // Need to split
-    // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
-    StringTokenizer queries = new StringTokenizer(ids, ";");
-    String db = null;
-    StringBuffer querystring = null;
-    while (queries.hasMoreTokens())
-    {
-      String query = queries.nextToken();
-      int p;
-      if ( (p = query.indexOf(':')) > -1)
-      {
-        db = query.substring(0, p);
-        query = query.substring(p + 1);
-      }
-      if (querystring == null)
-      {
-        querystring = new StringBuffer(query);
-      }
-      else
-      {
-        querystring.append("," + query);
-      }
-    }
-    if (db == null)
-    {
-      System.err.println("Invalid Query string : '" + ids +
-                         "'\nShould be of form 'dbname:q1;q2;q3;q4'");
-    }
-    return fetchBatch(querystring.toString(), db, f, s);
-  }
-
-  public String[] fetchBatch(String ids, String db, String f, String s)
-  {
-    // max 50 ids can be added at one time
-    try
-    {
-      //call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
-      call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
-      call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
-      call.addParameter("db", 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;
-      }
-
-      try
-      {
-        return (String[]) call.invoke(new Object[]
-                                      {ids.toLowerCase(), db.toLowerCase(),
-                                      format, style});
-      }
-      catch (OutOfMemoryError er)
-      {
-        System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db + ":\n" +
-                           ids);
-      }
-      return null;
-    }
-    catch (Exception ex)
-    {
-      if (ex.getMessage().startsWith(
-          "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
-      {
-        return null;
-      }
-      System.err.println("Unexpected exception when retrieving from " + db +
-                         "\nQuery was : '" + ids + "'");
-      ex.printStackTrace(System.err);
-      return null;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws.ebi;
+
+import java.io.*;
+import java.util.*;
+import javax.xml.namespace.*;
+import javax.xml.rpc.*;
+
+import org.apache.axis.client.Call;
+import org.apache.axis.client.Service;
+import org.apache.axis.encoding.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class EBIFetchClient
+{
+  Call call;
+  String format = "default";
+  String style = "raw";
+
+  /**
+   * Creates a new EBIFetchClient object.
+   */
+  public EBIFetchClient()
+  {
+    try
+    {
+      call = (Call)new Service().createCall();
+      call.setTargetEndpointAddress(new java.net.URL(
+          "http://www.ebi.ac.uk/ws/services/Dbfetch"));
+    }
+    catch (Exception ex)
+    {
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedDBs()
+  {
+    try
+    {
+      call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
+      call.setReturnType(XMLType.SOAP_ARRAY);
+
+      return (String[]) call.invoke(new Object[]
+                                    {});
+    }
+    catch (Exception ex)
+    {
+      return null;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedFormats()
+  {
+    try
+    {
+      call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
+      call.setReturnType(XMLType.SOAP_ARRAY);
+
+      return (String[]) call.invoke(new Object[]
+                                    {});
+    }
+    catch (Exception ex)
+    {
+      return null;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String[] getSupportedStyles()
+  {
+    try
+    {
+      call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
+      call.setReturnType(XMLType.SOAP_ARRAY);
+
+      return (String[]) call.invoke(new Object[]
+                                    {});
+    }
+    catch (Exception ex)
+    {
+      return null;
+    }
+  }
+
+
+  public File fetchDataAsFile(String ids, String f, String s)
+  {
+    String[] data = fetchData(ids, f, s);
+    File outFile = null;
+    try
+    {
+      outFile = File.createTempFile("jalview", ".xml");
+      outFile.deleteOnExit();
+      PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+      int index = 0;
+      while (index < data.length)
+      {
+        out.println(data[index]);
+        index++;
+      }
+      out.close();
+    }
+    catch (Exception ex)
+    {}
+    return outFile;
+  }
+
+  /**
+   * Single DB multiple record retrieval
+   *
+   * @param ids db:query1;query2;query3
+   * @param f raw/xml
+   * @param s ?
+   *
+   * @return Raw string array result of query set
+   */
+  public String[] fetchData(String ids, String f, String s)
+  {
+    // Need to split
+    // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
+    StringTokenizer queries = new StringTokenizer(ids, ";");
+    String db = null;
+    StringBuffer querystring = null;
+    while (queries.hasMoreTokens())
+    {
+      String query = queries.nextToken();
+      int p;
+      if ( (p = query.indexOf(':')) > -1)
+      {
+        db = query.substring(0, p);
+        query = query.substring(p + 1);
+      }
+      if (querystring == null)
+      {
+        querystring = new StringBuffer(query);
+      }
+      else
+      {
+        querystring.append("," + query);
+      }
+    }
+    if (db == null)
+    {
+      System.err.println("Invalid Query string : '" + ids +
+                         "'\nShould be of form 'dbname:q1;q2;q3;q4'");
+    }
+    return fetchBatch(querystring.toString(), db, f, s);
+  }
+
+  public String[] fetchBatch(String ids, String db, String f, String s)
+  {
+    // max 50 ids can be added at one time
+    try
+    {
+      //call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
+      call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
+      call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
+      call.addParameter("db", 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;
+      }
+
+      try
+      {
+        return (String[]) call.invoke(new Object[]
+                                      {ids.toLowerCase(), db.toLowerCase(),
+                                      format, style});
+      }
+      catch (OutOfMemoryError er)
+      {
+        System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db + ":\n" +
+                           ids);
+      }
+      return null;
+    }
+    catch (Exception ex)
+    {
+      if (ex.getMessage().startsWith(
+          "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
+      {
+        return null;
+      }
+      System.err.println("Unexpected exception when retrieving from " + db +
+                         "\nQuery was : '" + ids + "'");
+      ex.printStackTrace(System.err);
+      return null;
+    }
+  }
+}
diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 0785ea2..3a167e5 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.seqfetcher;
 
 import jalview.datamodel.AlignmentI;
@@ -275,4 +293,4 @@ public class ASequenceFetcher
     return false;
   }
 
-}
\ No newline at end of file
+}
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index f0e81fa..1b347f3 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.seqfetcher;
 
 import jalview.datamodel.AlignmentI;
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index 21272be..ad05073 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.seqfetcher;
 
 import jalview.datamodel.Alignment;
diff --git a/src/vamsas/IMsaWS.java b/src/vamsas/IMsaWS.java
index 7d02a94..b245155 100755
--- a/src/vamsas/IMsaWS.java
+++ b/src/vamsas/IMsaWS.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 vamsas;
 
 import vamsas.objects.simple.*;
diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 18fa20c..41c3308 100755
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -1,10 +1,21 @@
-/**
- * Alignment.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Alignment  extends vamsas.objects.simple.Object  implements java.io.Serializable {
diff --git a/src/vamsas/objects/simple/Alignment_Helper.java b/src/vamsas/objects/simple/Alignment_Helper.java
index 5a54fe0..b8d76c4 100755
--- a/src/vamsas/objects/simple/Alignment_Helper.java
+++ b/src/vamsas/objects/simple/Alignment_Helper.java
@@ -1,10 +1,21 @@
-/**
- * Alignment_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Alignment_Helper {
diff --git a/src/vamsas/objects/simple/JpredResult.java b/src/vamsas/objects/simple/JpredResult.java
index 26eb6b7..3f815fd 100755
--- a/src/vamsas/objects/simple/JpredResult.java
+++ b/src/vamsas/objects/simple/JpredResult.java
@@ -1,10 +1,21 @@
-/**
- * JpredResult.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class JpredResult
diff --git a/src/vamsas/objects/simple/JpredResult_Helper.java b/src/vamsas/objects/simple/JpredResult_Helper.java
index 12dff09..61e8e28 100755
--- a/src/vamsas/objects/simple/JpredResult_Helper.java
+++ b/src/vamsas/objects/simple/JpredResult_Helper.java
@@ -1,10 +1,21 @@
-/**
- * JpredResult_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class JpredResult_Helper
diff --git a/src/vamsas/objects/simple/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java
index c8327dd..8229475 100755
--- a/src/vamsas/objects/simple/MsaResult.java
+++ b/src/vamsas/objects/simple/MsaResult.java
@@ -1,119 +1,130 @@
-/**
- * MsaResult.java
- *
- * 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package 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;
-  }
-
-  /**
-   * 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;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package 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;
+  }
+
+  /**
+   * 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 b43e05b..f9d0924 100755
--- a/src/vamsas/objects/simple/MsaResult_Helper.java
+++ b/src/vamsas/objects/simple/MsaResult_Helper.java
@@ -1,78 +1,89 @@
-/**
- * MsaResult_Helper.java
- *
- * 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package 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;
-  }
-
-  /**
-   * 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);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package 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;
+  }
+
+  /**
+   * 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);
+  }
+}
diff --git a/src/vamsas/objects/simple/Msfalignment.java b/src/vamsas/objects/simple/Msfalignment.java
index 242b14f..58c5f87 100755
--- a/src/vamsas/objects/simple/Msfalignment.java
+++ b/src/vamsas/objects/simple/Msfalignment.java
@@ -1,10 +1,21 @@
-/**
- * Msfalignment.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Msfalignment
diff --git a/src/vamsas/objects/simple/Msfalignment_Helper.java b/src/vamsas/objects/simple/Msfalignment_Helper.java
index 9b9288d..5c7483d 100755
--- a/src/vamsas/objects/simple/Msfalignment_Helper.java
+++ b/src/vamsas/objects/simple/Msfalignment_Helper.java
@@ -1,10 +1,21 @@
-/**
- * Msfalignment_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Msfalignment_Helper
diff --git a/src/vamsas/objects/simple/Object.java b/src/vamsas/objects/simple/Object.java
index 4bf69bd..7757079 100755
--- a/src/vamsas/objects/simple/Object.java
+++ b/src/vamsas/objects/simple/Object.java
@@ -1,10 +1,21 @@
-/**
- * Object.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public abstract class Object  implements java.io.Serializable {
diff --git a/src/vamsas/objects/simple/Object_Helper.java b/src/vamsas/objects/simple/Object_Helper.java
index a1b944c..42a6066 100755
--- a/src/vamsas/objects/simple/Object_Helper.java
+++ b/src/vamsas/objects/simple/Object_Helper.java
@@ -1,10 +1,21 @@
-/**
- * Object_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Object_Helper {
diff --git a/src/vamsas/objects/simple/Result.java b/src/vamsas/objects/simple/Result.java
index b349019..f761c5a 100755
--- a/src/vamsas/objects/simple/Result.java
+++ b/src/vamsas/objects/simple/Result.java
@@ -1,10 +1,21 @@
-/**
- * Result.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Result  implements java.io.Serializable {
diff --git a/src/vamsas/objects/simple/Result_Helper.java b/src/vamsas/objects/simple/Result_Helper.java
index 14ed2b5..966c0bf 100755
--- a/src/vamsas/objects/simple/Result_Helper.java
+++ b/src/vamsas/objects/simple/Result_Helper.java
@@ -1,10 +1,21 @@
-/**
- * Result_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Result_Helper {
diff --git a/src/vamsas/objects/simple/Secstructpred.java b/src/vamsas/objects/simple/Secstructpred.java
index 8b334f4..f3b7e45 100755
--- a/src/vamsas/objects/simple/Secstructpred.java
+++ b/src/vamsas/objects/simple/Secstructpred.java
@@ -1,10 +1,21 @@
-/**
- * Secstructpred.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Secstructpred
diff --git a/src/vamsas/objects/simple/Secstructpred_Helper.java b/src/vamsas/objects/simple/Secstructpred_Helper.java
index 7e2ef3d..2ce035c 100755
--- a/src/vamsas/objects/simple/Secstructpred_Helper.java
+++ b/src/vamsas/objects/simple/Secstructpred_Helper.java
@@ -1,10 +1,21 @@
-/**
- * Secstructpred_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Secstructpred_Helper
diff --git a/src/vamsas/objects/simple/SeqSearchResult.java b/src/vamsas/objects/simple/SeqSearchResult.java
index 4d75aad..2f2a956 100644
--- a/src/vamsas/objects/simple/SeqSearchResult.java
+++ b/src/vamsas/objects/simple/SeqSearchResult.java
@@ -1,10 +1,21 @@
-/**
- * SeqSearchResult.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class SeqSearchResult  extends vamsas.objects.simple.Result  implements java.io.Serializable {
diff --git a/src/vamsas/objects/simple/SeqSearchResult_Helper.java b/src/vamsas/objects/simple/SeqSearchResult_Helper.java
index 3f6e30d..abb877a 100644
--- a/src/vamsas/objects/simple/SeqSearchResult_Helper.java
+++ b/src/vamsas/objects/simple/SeqSearchResult_Helper.java
@@ -1,10 +1,21 @@
-/**
- * SeqSearchResult_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class SeqSearchResult_Helper {
diff --git a/src/vamsas/objects/simple/Sequence.java b/src/vamsas/objects/simple/Sequence.java
index d2eccb0..2fa032e 100755
--- a/src/vamsas/objects/simple/Sequence.java
+++ b/src/vamsas/objects/simple/Sequence.java
@@ -1,10 +1,21 @@
-/**
- * Sequence.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Sequence  implements java.io.Serializable {
diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java
index 62e58b4..7e9ea5b 100755
--- a/src/vamsas/objects/simple/SequenceSet.java
+++ b/src/vamsas/objects/simple/SequenceSet.java
@@ -1,10 +1,21 @@
-/**
- * SequenceSet.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class SequenceSet  implements java.io.Serializable {
diff --git a/src/vamsas/objects/simple/SequenceSet_Helper.java b/src/vamsas/objects/simple/SequenceSet_Helper.java
index 77586ba..5e8a99f 100755
--- a/src/vamsas/objects/simple/SequenceSet_Helper.java
+++ b/src/vamsas/objects/simple/SequenceSet_Helper.java
@@ -1,10 +1,21 @@
-/**
- * SequenceSet_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class SequenceSet_Helper {
diff --git a/src/vamsas/objects/simple/Sequence_Helper.java b/src/vamsas/objects/simple/Sequence_Helper.java
index f675384..a74115a 100755
--- a/src/vamsas/objects/simple/Sequence_Helper.java
+++ b/src/vamsas/objects/simple/Sequence_Helper.java
@@ -1,10 +1,21 @@
-/**
- * Sequence_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class Sequence_Helper {
diff --git a/src/vamsas/objects/simple/WsJobId.java b/src/vamsas/objects/simple/WsJobId.java
index 4bc1f2e..a40f29e 100755
--- a/src/vamsas/objects/simple/WsJobId.java
+++ b/src/vamsas/objects/simple/WsJobId.java
@@ -1,10 +1,21 @@
-/**
- * WsJobId.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class WsJobId  implements java.io.Serializable {
diff --git a/src/vamsas/objects/simple/WsJobId_Helper.java b/src/vamsas/objects/simple/WsJobId_Helper.java
index 3988ce9..23fa516 100755
--- a/src/vamsas/objects/simple/WsJobId_Helper.java
+++ b/src/vamsas/objects/simple/WsJobId_Helper.java
@@ -1,10 +1,21 @@
-/**
- * WsJobId_Helper.java
- *
- * 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 (Version 2.4)
+ * Copyright (C) 2008 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 vamsas.objects.simple;
 
 public class WsJobId_Helper {
diff --git a/utils/help2Website.java b/utils/help2Website.java
index 7a666ad..6bb4dfc 100755
--- a/utils/help2Website.java
+++ b/utils/help2Website.java
@@ -1,95 +1,113 @@
-import java.io.*;
-import java.util.*;
-
-public class help2Website
-{
-
-	public static void main(String [] args)
-	{
-		String line = "";
-		try{
-			Hashtable targets = new Hashtable();
-
-			File toc = new File("helpTOC.xml");
-			File jhm = new File("help.jhm");
-
-			BufferedReader in = new BufferedReader(new FileReader(jhm));
-
-			PrintWriter out = new PrintWriter(new FileWriter("helpTOC.html"));
-			out.println("<html><head><title>Jalview - Help </title></head>\n"
-			+"<body bgcolor=#F1F1F1>\n"
-			+"<p><center><strong>Contents</strong></center></p>\n");
-
-
-			StringTokenizer st;
-			StringBuffer indent = new StringBuffer();
-			String target, url, text;
-			while( (line = in.readLine()) != null)
-			{
-				if(line.indexOf("target")==-1)
-					continue;
-
-
-				st = new StringTokenizer(line, "\"");
-				st.nextToken(); //<mapID target="
-
-				target = st.nextToken();
-				st.nextToken(); //" url="
-
-				url = st.nextToken();
-				targets.put(target, url);
-			}
-
-			in = new BufferedReader(new FileReader(toc));
-			while( (line = in.readLine()) != null)
-			{
-				if(line.indexOf("</tocitem>")!=-1)
-					indent.setLength(indent.length()-18);
-
-				if(line.indexOf("<tocitem")==-1)
-					continue;
-
-				st = new StringTokenizer(line, "\"");
-				st.nextToken();
-
-				text = st.nextToken();
-				st.nextToken();
-
-				target = st.nextToken();
-
-				if(targets.get(target)!=null)
-					out.println("<br>"+indent+"<a href=\""
-							+ targets.get(target)
-							+"\" target=bodyframe>"
-							+text
-							+"</a>");
-				else
-					out.println("<br>"+indent+text);
-
-
-				if(line.indexOf("/>")==-1)
-					indent.append("&nbsp;&nbsp;&nbsp;");
-
-			}
-
-			out.println("</body>\n</html>");
-
-
-			out.close();
-
-		}
-
-		catch(Exception ex)
-		{
-
-			ex.printStackTrace();
-
-			System.out.println("\n"+line+"\n");
-
-			System.out.println("Usage: move to Help directory. help2Website will read"
-			+"\nhelpTOC.xml and help.jhm producing output helpTOC.html");
-		}
-	}
-
-
-}
\ No newline at end of file
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
+ */
+import java.io.*;
+import java.util.*;
+
+public class help2Website
+{
+
+	public static void main(String [] args)
+	{
+		String line = "";
+		try{
+			Hashtable targets = new Hashtable();
+
+			File toc = new File("helpTOC.xml");
+			File jhm = new File("help.jhm");
+
+			BufferedReader in = new BufferedReader(new FileReader(jhm));
+
+			PrintWriter out = new PrintWriter(new FileWriter("helpTOC.html"));
+			out.println("<html><head><title>Jalview - Help </title></head>\n"
+			+"<body bgcolor=#F1F1F1>\n"
+			+"<p><center><strong>Contents</strong></center></p>\n");
+
+
+			StringTokenizer st;
+			StringBuffer indent = new StringBuffer();
+			String target, url, text;
+			while( (line = in.readLine()) != null)
+			{
+				if(line.indexOf("target")==-1)
+					continue;
+
+
+				st = new StringTokenizer(line, "\"");
+				st.nextToken(); //<mapID target="
+
+				target = st.nextToken();
+				st.nextToken(); //" url="
+
+				url = st.nextToken();
+				targets.put(target, url);
+			}
+
+			in = new BufferedReader(new FileReader(toc));
+			while( (line = in.readLine()) != null)
+			{
+				if(line.indexOf("</tocitem>")!=-1)
+					indent.setLength(indent.length()-18);
+
+				if(line.indexOf("<tocitem")==-1)
+					continue;
+
+				st = new StringTokenizer(line, "\"");
+				st.nextToken();
+
+				text = st.nextToken();
+				st.nextToken();
+
+				target = st.nextToken();
+
+				if(targets.get(target)!=null)
+					out.println("<br>"+indent+"<a href=\""
+							+ targets.get(target)
+							+"\" target=bodyframe>"
+							+text
+							+"</a>");
+				else
+					out.println("<br>"+indent+text);
+
+
+				if(line.indexOf("/>")==-1)
+					indent.append("&nbsp;&nbsp;&nbsp;");
+
+			}
+
+			out.println("</body>\n</html>");
+
+
+			out.close();
+
+		}
+
+		catch(Exception ex)
+		{
+
+			ex.printStackTrace();
+
+			System.out.println("\n"+line+"\n");
+
+			System.out.println("Usage: move to Help directory. help2Website will read"
+			+"\nhelpTOC.xml and help.jhm producing output helpTOC.html");
+		}
+	}
+
+
+}