From: jprocter <Jim Procter>
Date: Sun, 13 Aug 2006 13:58:29 +0000 (+0000)
Subject: fixed end-residue bug and subjob panel names bug
X-Git-Tag: Release_2_1~88
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c431a65bbe794a0dd27f3f806d3c5cf37c53279c;p=jalview.git

fixed end-residue bug and subjob panel names bug
---

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 231009a..a5c1094 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,196 +1,275 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import java.util.*;
-
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-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
-     */
-    public boolean updateSequence(SequenceI oldref, SequenceI newref) {
-      int found=Order.indexOf(oldref);
-      if (found>-1) {
-        Order.setElementAt(newref, found);
-      }
-      return found>-1;
-    }
-    /**
-     * 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
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+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
+     */
+    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.get(i)!=o.Order.get(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.get(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/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 0203383..816e531 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -420,12 +420,10 @@ public class SeqCigar
       seqs[i].setDatasetSequence(ref);
     }
     if (segments!=null) {
-      int delshift=0; // need to shift the segments to their absolute positions in the sequence cigar frame.
       for (int i=0; i<segments.length; i+=3) {
         //int start=shifts.shift(segments[i]-1)+1;
         //int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
-        colsel.hideColumns(delshift+segments[i], delshift+segments[i]+segments[i+2]-1);
-        delshift+=segments[i+2];
+        colsel.hideColumns(segments[i+1], segments[i+1]+segments[i+2]-1);
       }
     }
     return seqs;
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index b5d5199..dee67d3 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,714 +1,713 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.datamodel;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Sequence implements SequenceI
-{
-    SequenceI datasetSequence;
-    String name;
-    private String sequence;
-    String description;
-    int start;
-    int end;
-    Color color = Color.white;
-    Vector pdbIds;
-    String vamsasId;
-    DBRefEntry [] dbrefs;
-
-    /** This annotation is displayed below the alignment but the
-     * positions are tied to the residues of this sequence */
-    Vector annotation;
-
-    /** DOCUMENT ME!! */
-    public SequenceFeature [] sequenceFeatures;
-
-    /** This array holds hidden sequences
-     * of which this sequence is the representitive member of a group
-     */
-    SequenceGroup hiddenSequences;
-
-    /**
-     * Creates a new Sequence object.
-     *
-     * @param name DOCUMENT ME!
-     * @param sequence DOCUMENT ME!
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     */
-    public Sequence(String name, String sequence, int start, int end)
-    {
-      this.name = name;
-      this.sequence = sequence;
-      this.start = start;
-      this.end = end;
-
-      parseId();
-
-      checkValidRange();
-    }
-
-    com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
-                        "[/][0-9]{1,}[-][0-9]{1,}$");
-    com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
-                        "[0-9]{1,}$");
-
-    void parseId()
-    {
-        // Does sequence have the /start-end signiature?
-         if(limitrx.search(name))
-         {
-            name = limitrx.left();
-            endrx.search(limitrx.stringMatched());
-            setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));
-            setEnd(   Integer.parseInt( endrx.stringMatched() ));
-         }
-    }
-
-    void checkValidRange()
-    {
-      if (end < 1)
-      {
-        int endRes = 0;
-        char ch;
-        for (int j = 0; j < sequence.length(); j++)
-        {
-          ch = sequence.charAt(j);
-          if (!jalview.util.Comparison.isGap( (ch)))
-          {
-            endRes++;
-          }
-        }
-        if (endRes > 0)
-        {
-          endRes += start - 1;
-        }
-
-        this.end = endRes;
-      }
-
-    }
-
-    /**
-     * Creates a new Sequence object.
-     *
-     * @param name DOCUMENT ME!
-     * @param sequence DOCUMENT ME!
-     */
-    public Sequence(String name, String sequence)
-    {
-        this(name, sequence, 1, -1);
-    }
-
-    /**
-     * Creates a new Sequence object.
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public Sequence(SequenceI seq)
-    {
-        this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param v DOCUMENT ME!
-     */
-    public void setSequenceFeatures(SequenceFeature [] features)
-    {
-        sequenceFeatures = features;
-    }
-
-    public synchronized void addSequenceFeature(SequenceFeature sf)
-    {
-      if(sequenceFeatures==null)
-      {
-        sequenceFeatures = new SequenceFeature[0];
-      }
-
-      for(int i=0; i<sequenceFeatures.length; i++)
-      {
-        if(sequenceFeatures[i].equals(sf))
-        {
-          return;
-        }
-      }
-
-      SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
-      System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
-      temp[sequenceFeatures.length] = sf;
-
-      sequenceFeatures = temp;
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceFeature [] getSequenceFeatures()
-    {
-        return sequenceFeatures;
-    }
-
-    public void addPDBId(PDBEntry entry)
-    {
-      if(pdbIds == null)
-        pdbIds = new Vector();
-
-      pdbIds.addElement(entry);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param id DOCUMENT ME!
-     */
-    public void setPDBId(Vector id)
-    {
-        pdbIds = id;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getPDBId()
-    {
-        return pdbIds;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDisplayId(boolean jvsuffix)
-    {
-      StringBuffer result = new StringBuffer(name);
-      if (jvsuffix)
-      {
-        result.append("/" + start + "-" + end);
-      }
-
-      return result.toString();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     */
-    public void setName(String name)
-    {
-      this.name = name;
-      this.parseId();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName()
-    {
-       return this.name;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     */
-    public void setStart(int start)
-    {
-        this.start = start;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStart()
-    {
-        return this.start;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param end DOCUMENT ME!
-     */
-    public void setEnd(int end)
-    {
-        this.end = end;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEnd()
-    {
-        return this.end;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getLength()
-    {
-        return this.sequence.length();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setSequence(String seq)
-    {
-        this.sequence = seq;
-        checkValidRange();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getSequence()
-    {
-        return this.sequence;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getSequence(int start, int end)
-    {
-        // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
-        if (start >= sequence.length())
-        {
-            return "";
-        }
-
-        if (end >= sequence.length())
-        {
-            end = sequence.length();
-        }
-
-        return this.sequence.substring(start, end);
-    }
-    /**
-     * make a new Sequence object from start to end (including gaps) over this seqeunce
-     * @param start int
-     * @param end int
-     * @return SequenceI
-     */
-    public SequenceI getSubSequence(int start, int end) {
-      if (start<0)
-        start = 0;
-      String seq = getSequence(start, end);
-      if (seq=="")
-        return null;
-      start = findPosition(start);
-      end=findPosition(end);
-      // JBPNote - this is an incomplete copy.
-      SequenceI nseq = new Sequence(this.getName(), seq, start, end);
-      nseq.setDatasetSequence(getDatasetSequence());
-      return nseq;
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getCharAt(int i)
-    {
-        if (i < sequence.length())
-        {
-            return sequence.charAt(i);
-        }
-        else
-        {
-            return ' ';
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param desc DOCUMENT ME!
-     */
-    public void setDescription(String desc)
-    {
-        this.description = desc;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDescription()
-    {
-        return this.description;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param pos DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int findIndex(int pos)
-    {
-        // returns the alignment position for a residue
-        int j = start;
-        int i = 0;
-
-        while ((i < sequence.length()) && (j <= end) && (j <= pos))
-        {
-            if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
-            {
-                j++;
-            }
-
-            i++;
-        }
-
-        if ((j == end) && (j < pos))
-        {
-            return end + 1;
-        }
-        else
-        {
-            return i;
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int findPosition(int i)
-    {
-        // Returns the sequence position for an alignment position
-        int j = 0;
-        int pos = start;
-
-        while ((j < i) && (j < sequence.length()))
-        {
-            if (!jalview.util.Comparison.isGap((sequence.charAt(j))))
-            {
-                pos++;
-            }
-
-            j++;
-        }
-
-        return pos;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int[] gapMap()
-    {
-        // Returns an int array giving the position of each residue in the sequence in the alignment
-        String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);
-        int[] map = new int[seq.length()];
-        int j = 0;
-        int p = 0;
-
-        while (j < sequence.length())
-        {
-            if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
-            {
-                map[p++] = j;
-            }
-
-            j++;
-        }
-
-        return map;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void deleteCharAt(int i)
-    {
-        if (i >= sequence.length())
-        {
-            return;
-        }
-
-        sequence = sequence.substring(0, i) + sequence.substring(i + 1);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     */
-    public void deleteChars(int i, int j)
-    {
-        if (i >= sequence.length())
-        {
-            return;
-        }
-
-        if (j >= sequence.length())
-        {
-            sequence = sequence.substring(0, i);
-        }
-        else
-        {
-            sequence = sequence.substring(0, i) + sequence.substring(j);
-        }
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param c DOCUMENT ME!
-     * @param chop DOCUMENT ME!
-     */
-    public void insertCharAt(int i, char c)
-    {
-        String tmp = new String(sequence);
-
-        if (i < sequence.length())
-        {
-            sequence = tmp.substring(0, i) + String.valueOf(c) +
-                tmp.substring(i);
-        }
-        else
-        {
-            // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
-            char[] ch = new char[(1 + i) - sequence.length()];
-
-            for (int j = 0, k = ch.length; j < k; j++)
-                ch[j] = c;
-
-            sequence = tmp + String.valueOf(ch);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setColor(Color c)
-    {
-        this.color = c;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getColor()
-    {
-        return color;
-    }
-
-    public String getVamsasId()
-    {
-      return vamsasId;
-    }
-
-    public void setVamsasId(String id)
-    {
-      vamsasId = id;
-    }
-
-    public void setDBRef(DBRefEntry [] dbref)
-    {
-      dbrefs = dbref;
-    }
-
-    public DBRefEntry [] getDBRef()
-    {
-      return dbrefs;
-    }
-
-    public void addDBRef(DBRefEntry entry)
-    {
-      if(dbrefs == null)
-        dbrefs = new DBRefEntry[0];
-
-      DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1];
-      System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
-
-      temp[temp.length-1] = entry;
-
-      dbrefs = temp;
-    }
-
-    public void setDatasetSequence(SequenceI seq)
-    {
-      datasetSequence = seq;
-    }
-
-    public SequenceI getDatasetSequence()
-    {
-      return datasetSequence;
-    }
-
-    public AlignmentAnnotation [] getAnnotation()
-    {
-      if(annotation==null)
-        return null;
-
-      AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];
-      for(int r = 0; r<ret.length; r++)
-        ret[r] = (AlignmentAnnotation)annotation.elementAt(r);
-
-      return ret;
-    }
-
-    public void addAlignmentAnnotation(AlignmentAnnotation annotation)
-    {
-      if(this.annotation==null)
-        this.annotation = new Vector();
-
-      this.annotation.addElement( annotation );
-    }
-
-    public SequenceGroup getHiddenSequences()
-    {
-      return hiddenSequences;
-    }
-
-    public void addHiddenSequence(SequenceI seq)
-    {
-      if(hiddenSequences==null)
-      {
-        hiddenSequences = new SequenceGroup();
-      }
-      hiddenSequences.addSequence(seq, false);
-    }
-
-    public void showHiddenSequence(SequenceI seq)
-    {
-      hiddenSequences.deleteSequence(seq, false);
-      if (hiddenSequences.getSize(false) < 1)
-      {
-        hiddenSequences = null;
-      }
-    }
-
-    public void changeCase(boolean toUpper, int start, int end)
-    {
-      StringBuffer newSeq = new StringBuffer();
-
-      if(end>sequence.length())
-        end = sequence.length();
-
-      if (start > 0)
-      {
-        newSeq.append(sequence.substring(0, start));
-      }
-
-      if (toUpper)
-        newSeq.append(sequence.substring(start, end).toUpperCase());
-      else
-        newSeq.append(sequence.substring(start, end).toLowerCase());
-
-      if (end < sequence.length())
-        newSeq.append(sequence.substring(end));
-
-      sequence = newSeq.toString();
-    }
-
-    public void toggleCase(int start, int end)
-    {
-      StringBuffer newSeq = new StringBuffer();
-
-     if(end>sequence.length())
-       end = sequence.length();
-
-     if (start > 0)
-     {
-       newSeq.append(sequence.substring(0, start));
-     }
-
-     char nextChar;
-     for(int c=start; c<end; c++)
-     {
-       nextChar = sequence.charAt(c);
-       if(Character.isLetter(nextChar))
-       {
-         if(Character.isUpperCase(nextChar))
-           nextChar = Character.toLowerCase(nextChar);
-         else
-           nextChar = Character.toUpperCase(nextChar);
-       }
-
-
-       newSeq.append(nextChar);
-     }
-
-     if (end < sequence.length())
-       newSeq.append(sequence.substring(end));
-
-     sequence = newSeq.toString();
-    }
-
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package jalview.datamodel;
+
+import java.awt.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence implements SequenceI
+{
+    SequenceI datasetSequence;
+    String name;
+    private String sequence;
+    String description;
+    int start;
+    int end;
+    Color color = Color.white;
+    Vector pdbIds;
+    String vamsasId;
+    DBRefEntry [] dbrefs;
+
+    /** This annotation is displayed below the alignment but the
+     * positions are tied to the residues of this sequence */
+    Vector annotation;
+
+    /** DOCUMENT ME!! */
+    public SequenceFeature [] sequenceFeatures;
+
+    /** This array holds hidden sequences
+     * of which this sequence is the representitive member of a group
+     */
+    SequenceGroup hiddenSequences;
+
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param name DOCUMENT ME!
+     * @param sequence DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public Sequence(String name, String sequence, int start, int end)
+    {
+      this.name = name;
+      this.sequence = sequence;
+      this.start = start;
+      this.end = end;
+
+      parseId();
+
+      checkValidRange();
+    }
+
+    com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
+                        "[/][0-9]{1,}[-][0-9]{1,}$");
+    com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
+                        "[0-9]{1,}$");
+
+    void parseId()
+    {
+        // Does sequence have the /start-end signiature?
+         if(limitrx.search(name))
+         {
+            name = limitrx.left();
+            endrx.search(limitrx.stringMatched());
+            setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));
+            setEnd(   Integer.parseInt( endrx.stringMatched() ));
+         }
+    }
+
+    void checkValidRange()
+    {
+      if (end < 1)
+      {
+        int endRes = 0;
+        char ch;
+        for (int j = 0; j < sequence.length(); j++)
+        {
+          ch = sequence.charAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
+        }
+        if (endRes > 0)
+        {
+          endRes += start - 1;
+        }
+
+        this.end = endRes;
+      }
+
+    }
+
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param name DOCUMENT ME!
+     * @param sequence DOCUMENT ME!
+     */
+    public Sequence(String name, String sequence)
+    {
+        this(name, sequence, 1, -1);
+    }
+
+    /**
+     * Creates a new Sequence object.
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public Sequence(SequenceI seq)
+    {
+        this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     */
+    public void setSequenceFeatures(SequenceFeature [] features)
+    {
+        sequenceFeatures = features;
+    }
+
+    public synchronized void addSequenceFeature(SequenceFeature sf)
+    {
+      if(sequenceFeatures==null)
+      {
+        sequenceFeatures = new SequenceFeature[0];
+      }
+
+      for(int i=0; i<sequenceFeatures.length; i++)
+      {
+        if(sequenceFeatures[i].equals(sf))
+        {
+          return;
+        }
+      }
+
+      SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
+      System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
+      temp[sequenceFeatures.length] = sf;
+
+      sequenceFeatures = temp;
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceFeature [] getSequenceFeatures()
+    {
+        return sequenceFeatures;
+    }
+
+    public void addPDBId(PDBEntry entry)
+    {
+      if(pdbIds == null)
+        pdbIds = new Vector();
+
+      pdbIds.addElement(entry);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id DOCUMENT ME!
+     */
+    public void setPDBId(Vector id)
+    {
+        pdbIds = id;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getPDBId()
+    {
+        return pdbIds;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDisplayId(boolean jvsuffix)
+    {
+      StringBuffer result = new StringBuffer(name);
+      if (jvsuffix)
+      {
+        result.append("/" + start + "-" + end);
+      }
+
+      return result.toString();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
+      this.name = name;
+      this.parseId();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
+       return this.name;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     */
+    public void setStart(int start)
+    {
+        this.start = start;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStart()
+    {
+        return this.start;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param end DOCUMENT ME!
+     */
+    public void setEnd(int end)
+    {
+        this.end = end;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEnd()
+    {
+        return this.end;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getLength()
+    {
+        return this.sequence.length();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setSequence(String seq)
+    {
+        this.sequence = seq;
+        checkValidRange();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence()
+    {
+        return this.sequence;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getSequence(int start, int end)
+    {
+        // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
+        if (start >= sequence.length())
+        {
+            return "";
+        }
+
+        if (end >= sequence.length())
+        {
+            end = sequence.length();
+        }
+
+        return this.sequence.substring(start, end);
+    }
+    /**
+     * make a new Sequence object from start to end (including gaps) over this seqeunce
+     * @param start int
+     * @param end int
+     * @return SequenceI
+     */
+    public SequenceI getSubSequence(int start, int end) {
+      if (start<0)
+        start = 0;
+      String seq = getSequence(start, end);
+      if (seq=="")
+        return null;
+      int nstart = findPosition(start);
+      int nend=findPosition(end-1)-1;
+      // JBPNote - this is an incomplete copy.
+      SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
+      nseq.setDatasetSequence(getDatasetSequence());
+      return nseq;
+    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getCharAt(int i)
+    {
+        if (i < sequence.length())
+        {
+            return sequence.charAt(i);
+        }
+        else
+        {
+            return ' ';
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param desc DOCUMENT ME!
+     */
+    public void setDescription(String desc)
+    {
+        this.description = desc;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDescription()
+    {
+        return this.description;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param pos DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findIndex(int pos)
+    {
+        // returns the alignment position for a residue
+        int j = start;
+        int i = 0;
+
+        while ((i < sequence.length()) && (j <= end) && (j <= pos))
+        {
+            if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
+            {
+                j++;
+            }
+
+            i++;
+        }
+
+        if ((j == end) && (j < pos))
+        {
+            return end + 1;
+        }
+        else
+        {
+            return i;
+        }
+    }
+
+    /**
+     * Returns the sequence position for an alignment position
+     *
+     * @param i column index in alignment (from 1)
+     *
+     * @return residue number for residue (left of and) nearest ith column
+     */
+    public int findPosition(int i)
+    {
+        int j = 0;
+        int pos = start;
+        int seqlen=sequence.length();
+        while ((j < i) && (j < seqlen))
+        {
+            if (!jalview.util.Comparison.isGap((sequence.charAt(j))))
+            {
+                pos++;
+            }
+
+            j++;
+        }
+
+        return pos;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] gapMap()
+    {
+        // Returns an int array giving the position of each residue in the sequence in the alignment
+        String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);
+        int[] map = new int[seq.length()];
+        int j = 0;
+        int p = 0;
+
+        while (j < sequence.length())
+        {
+            if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
+            {
+                map[p++] = j;
+            }
+
+            j++;
+        }
+
+        return map;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void deleteCharAt(int i)
+    {
+        if (i >= sequence.length())
+        {
+            return;
+        }
+
+        sequence = sequence.substring(0, i) + sequence.substring(i + 1);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     */
+    public void deleteChars(int i, int j)
+    {
+        if (i >= sequence.length())
+        {
+            return;
+        }
+
+        if (j >= sequence.length())
+        {
+            sequence = sequence.substring(0, i);
+        }
+        else
+        {
+            sequence = sequence.substring(0, i) + sequence.substring(j);
+        }
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param c DOCUMENT ME!
+     * @param chop DOCUMENT ME!
+     */
+    public void insertCharAt(int i, char c)
+    {
+        String tmp = new String(sequence);
+
+        if (i < sequence.length())
+        {
+            sequence = tmp.substring(0, i) + String.valueOf(c) +
+                tmp.substring(i);
+        }
+        else
+        {
+            // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
+            char[] ch = new char[(1 + i) - sequence.length()];
+
+            for (int j = 0, k = ch.length; j < k; j++)
+                ch[j] = c;
+
+            sequence = tmp + String.valueOf(ch);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setColor(Color c)
+    {
+        this.color = c;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color getColor()
+    {
+        return color;
+    }
+
+    public String getVamsasId()
+    {
+      return vamsasId;
+    }
+
+    public void setVamsasId(String id)
+    {
+      vamsasId = id;
+    }
+
+    public void setDBRef(DBRefEntry [] dbref)
+    {
+      dbrefs = dbref;
+    }
+
+    public DBRefEntry [] getDBRef()
+    {
+      return dbrefs;
+    }
+
+    public void addDBRef(DBRefEntry entry)
+    {
+      if(dbrefs == null)
+        dbrefs = new DBRefEntry[0];
+
+      DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1];
+      System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+
+      temp[temp.length-1] = entry;
+
+      dbrefs = temp;
+    }
+
+    public void setDatasetSequence(SequenceI seq)
+    {
+      datasetSequence = seq;
+    }
+
+    public SequenceI getDatasetSequence()
+    {
+      return datasetSequence;
+    }
+
+    public AlignmentAnnotation [] getAnnotation()
+    {
+      if(annotation==null)
+        return null;
+
+      AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];
+      for(int r = 0; r<ret.length; r++)
+        ret[r] = (AlignmentAnnotation)annotation.elementAt(r);
+
+      return ret;
+    }
+
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+    {
+      if(this.annotation==null)
+        this.annotation = new Vector();
+
+      this.annotation.addElement( annotation );
+    }
+
+    public SequenceGroup getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
+
+    public void addHiddenSequence(SequenceI seq)
+    {
+      if(hiddenSequences==null)
+      {
+        hiddenSequences = new SequenceGroup();
+      }
+      hiddenSequences.addSequence(seq, false);
+    }
+
+    public void showHiddenSequence(SequenceI seq)
+    {
+      hiddenSequences.deleteSequence(seq, false);
+      if (hiddenSequences.getSize(false) < 1)
+      {
+        hiddenSequences = null;
+      }
+    }
+
+    public void changeCase(boolean toUpper, int start, int end)
+    {
+      StringBuffer newSeq = new StringBuffer();
+
+      if(end>sequence.length())
+        end = sequence.length();
+
+      if (start > 0)
+      {
+        newSeq.append(sequence.substring(0, start));
+      }
+
+      if (toUpper)
+        newSeq.append(sequence.substring(start, end).toUpperCase());
+      else
+        newSeq.append(sequence.substring(start, end).toLowerCase());
+
+      if (end < sequence.length())
+        newSeq.append(sequence.substring(end));
+
+      sequence = newSeq.toString();
+    }
+
+    public void toggleCase(int start, int end)
+    {
+      StringBuffer newSeq = new StringBuffer();
+
+     if(end>sequence.length())
+       end = sequence.length();
+
+     if (start > 0)
+     {
+       newSeq.append(sequence.substring(0, start));
+     }
+
+     char nextChar;
+     for(int c=start; c<end; c++)
+     {
+       nextChar = sequence.charAt(c);
+       if(Character.isLetter(nextChar))
+       {
+         if(Character.isUpperCase(nextChar))
+           nextChar = Character.toLowerCase(nextChar);
+         else
+           nextChar = Character.toUpperCase(nextChar);
+       }
+
+
+       newSeq.append(nextChar);
+     }
+
+     if (end < sequence.length())
+       newSeq.append(sequence.substring(end));
+
+     sequence = newSeq.toString();
+    }
+
+}
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 63ef9f0..c8beeb1 100755
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -1,468 +1,472 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import jalview.jbgui.*;
-
-
-/**
- * Base class for web service client thread and gui
- *
- * @author $author$
- * @version $Revision$
- */
-public class WebserviceInfo extends GWebserviceInfo
-{
-
-    /** Job is Queued */
-    public static final int STATE_QUEUING = 0;
-
-    /** Job is Running */
-    public static final int STATE_RUNNING = 1;
-
-    /** Job has finished with no errors */
-    public static final int STATE_STOPPED_OK = 2;
-
-    /** Job has been cancelled with no errors */
-    public static final int STATE_CANCELLED_OK = 3;
-
-    /** job has stopped because of some error */
-    public static final int STATE_STOPPED_ERROR = 4;
-
-    /** job has failed because of some unavoidable service interruption */
-    public static final int STATE_STOPPED_SERVERERROR = 5;
-    int currentStatus = STATE_QUEUING;
-    Image image;
-    int angle = 0;
-    String title = "";
-    jalview.ws.WSClientI thisService;
-    boolean serviceIsCancellable;
-    JInternalFrame frame;
-    JTabbedPane subjobs=null;
-    java.util.Vector jobPanes = null;
-    // tabbed or not
-    public synchronized int addJobPane() {
-      JScrollPane jobpane = new JScrollPane();
-      JTextArea progressText = new JTextArea();
-      progressText.setFont(new java.awt.Font("Verdana", 0, 10));
-      progressText.setBorder(null);
-      progressText.setEditable(false);
-      progressText.setText("WS Job");
-      progressText.setLineWrap(true);
-      progressText.setWrapStyleWord(true);
-      jobpane.setName("JobPane");
-      jobpane.getViewport().add(progressText, null);
-      jobpane.setBorder(null);
-      if (jobPanes==null) {
-        jobPanes = new Vector();
-      }
-      int newpane = jobPanes.size();
-      jobPanes.add(jobpane);
-
-      if (newpane==0) {
-        this.add(jobpane, BorderLayout.CENTER);
-      } else {
-        if (newpane==1) {
-        // revert to a tabbed pane.
-        JScrollPane firstpane;
-        this.remove(firstpane=(JScrollPane) jobPanes.get(0));
-        subjobs=new JTabbedPane();
-          this.add(subjobs, BorderLayout.CENTER);
-          subjobs.add(firstpane);
-          subjobs.setTitleAt(0, firstpane.getName());
-        }
-        subjobs.add(jobpane);
-      }
-      return newpane; // index for accessor methods below
-    }
-    /**
-     * Creates a new WebserviceInfo object.
-     *
-     * @param title short name and job type
-     * @param info reference or other human readable description
-     */
-    public WebserviceInfo(String title, String info)
-    {
-        init(title, info, 520, 500);
-    }
-
-    /**
-     * Creates a new WebserviceInfo object.
-     *
-     * @param title DOCUMENT ME!
-     * @param info DOCUMENT ME!
-     * @param width DOCUMENT ME!
-     * @param height DOCUMENT ME!
-     */
-    public WebserviceInfo(String title, String info, int width, int height)
-    {
-        init(title, info, width, height);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public jalview.ws.WSClientI getthisService()
-    {
-        return thisService;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param newservice DOCUMENT ME!
-     */
-    public void setthisService(jalview.ws.WSClientI newservice)
-    {
-        thisService = newservice;
-        serviceIsCancellable = newservice.isCancellable();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param title DOCUMENT ME!
-     * @param info DOCUMENT ME!
-     * @param width DOCUMENT ME!
-     * @param height DOCUMENT ME!
-     */
-    void init(String title, String info, int width, int height)
-    {
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, title, width, height);
-        frame.setClosable(false);
-
-        this.title = title;
-        setInfoText(info);
-
-        java.net.URL url = getClass().getResource("/images/logo.gif");
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-
-        try
-        {
-            mt.waitForID(0);
-        }
-        catch (Exception ex)
-        {
-        }
-
-        AnimatedPanel ap = new AnimatedPanel();
-        titlePanel.add(ap, BorderLayout.CENTER);
-
-        Thread thread = new Thread(ap);
-        thread.start();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param status integer status from state constants
-     */
-    public void setStatus(int status)
-    {
-        currentStatus = status;
-    }
-    /**
-     * subjob status indicator
-     * @param jobpane
-     * @param status
-     */
-    public void setStatus(int jobpane, int status) {
-      if (jobpane<0 || jobpane>=jobPanes.size()) {
-        throw new Error("setStatus called for non-existent job pane."+jobpane);
-      }
-      switch (status) {
-      case STATE_QUEUING:
-        setProgressText(jobpane, "QUEUED");
-        break;
-      case STATE_RUNNING:
-        setProgressText(jobpane, "RUNNING");
-        break;
-      case STATE_STOPPED_OK:
-        setProgressText(jobpane, "FINISHED");
-      break;
-      case STATE_CANCELLED_OK:
-        setProgressText(jobpane, "CANCELLED");
-        break;
-      case STATE_STOPPED_ERROR:
-        setProgressText(jobpane, "BROKEN");
-        break;
-      case STATE_STOPPED_SERVERERROR:
-        setProgressText(jobpane, "ALERT");
-        break;
-        default:
-          setProgressText(jobpane, "UNKNOWN STATE");
-      }
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getInfoText()
-    {
-        return infoText.getText();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void setInfoText(String text)
-    {
-        infoText.setText(text);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void appendInfoText(String text)
-    {
-        infoText.append(text);
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getProgressText(int which)
-    {
-      if (jobPanes == null)
-        addJobPane();
-      return ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
-              getComponent(0)).getText();
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void setProgressText(int which, String text)
-    {
-      if (jobPanes == null)
-        addJobPane();
-      ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
-       getComponent(0)).setText(text);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param text DOCUMENT ME!
-     */
-    public void appendProgressText(int which, String text)
-    {
-      if (jobPanes == null)
-        addJobPane();
-      ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
-       getComponent(0)).append(text);
-    }
-    /**
-     * setProgressText(0, text)
-     */
-    public void setProgressText(String text)
-    {
-      setProgressText(0, text);
-    }
-    /**
-     * appendProgressText(0, text)
-     */
-    public void appendProgressText(String text)
-    {
-      appendProgressText(0, text);
-    }
-    /**
-     * getProgressText(0)
-     */
-    public String getProgressText()
-    {
-      return getProgressText(0);
-    }
-    /**
-     * get the tab title for a subjob
-     * @param which int
-     * @return String
-     */
-    public String getProgressName(int which) {
-      if (jobPanes==null)
-        addJobPane();
-      if (subjobs!=null)
-        return subjobs.getTitleAt(which);
-      else
-        return ((JScrollPane) jobPanes.get(which)).getViewport().getComponent(0).getName();
-    }
-    /**
-     * set the tab title for a subjob
-     * @param name String
-     * @param which int
-     */
-    public void setProgressName(String name, int which) {
-      if (subjobs!=null)
-        subjobs.setTitleAt(which, name);
-      else
-        ((JScrollPane) jobPanes.get(which)).getViewport().getComponent(0).setName(name);
-    }
-
-    /**
-     * Gui action for cancelling the current job, if possible.
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void cancel_actionPerformed(ActionEvent e)
-    {
-        if (!serviceIsCancellable)
-        {
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                "This job cannot be cancelled.\nJust close the window.", "Cancel job",
-                JOptionPane.WARNING_MESSAGE);
-        }
-        else
-        {
-            frame.setClosable(true);
-            thisService.cancelJob();
-        }
-    }
-
-    public void setResultsReady()
-    {
-      frame.setClosable(true);
-      buttonPanel.remove(cancel);
-      buttonPanel.add(showResultsNewFrame);
-      buttonPanel.add(mergeResults);
-      buttonPanel.setLayout(new GridLayout(2,1,5,5));
-      buttonPanel.validate();
-      validate();
-    }
-
-
-  class AnimatedPanel extends JPanel implements Runnable
-    {
-        long startTime = 0;
-        BufferedImage offscreen;
-
-        public void run()
-        {
-            startTime = System.currentTimeMillis();
-            Graphics2D g = null;
-
-            while (currentStatus < STATE_STOPPED_OK)
-            {
-                try
-                {
-                    Thread.sleep(50);
-
-                    int units = (int) ( (System.currentTimeMillis() - startTime) /
-                                       10f);
-                    angle += units;
-                    angle %= 360;
-                    startTime = System.currentTimeMillis();
-
-                    if (offscreen == null || offscreen.getWidth(this) != getWidth()
-                        || offscreen.getHeight(this) != getHeight())
-                    {
-                      offscreen = new BufferedImage(getWidth(), getHeight(),
-                                                    BufferedImage.TYPE_INT_ARGB);
-                      g = (Graphics2D) offscreen.getGraphics();
-                    }
-
-                    g.setColor(Color.white);
-                    g.fillRect(0, 0, getWidth(), getHeight());
-
-                    g.setFont(new Font("Arial", Font.BOLD, 12));
-                    g.setColor(Color.black);
-
-                    switch (currentStatus)
-                    {
-                      case STATE_QUEUING:
-                        g.drawString(title.concat(" - queuing"), 60, 30);
-
-                        break;
-
-                      case STATE_RUNNING:
-                        g.drawString(title.concat(" - running"), 60, 30);
-
-                        break;
-
-                      case STATE_STOPPED_OK:
-                        g.drawString(title.concat(" - complete"), 60, 30);
-
-                        break;
-
-                      case STATE_CANCELLED_OK:
-                        g.drawString(title.concat(" - job cancelled!"), 60, 30);
-
-                        break;
-
-                      case STATE_STOPPED_ERROR:
-                        g.drawString(title.concat(" - job error!"), 60, 30);
-
-                        break;
-
-                      case STATE_STOPPED_SERVERERROR:
-                        g.drawString(title.concat(" - Server Error! (try later)"),
-                                     60,
-                                     30);
-
-                        break;
-                    }
-
-
-                    if (currentStatus >= STATE_STOPPED_OK)
-                      angle = 0;
-
-                    if (image != null)
-                    {
-                      g.rotate(Math.toRadians(angle), 28, 28);
-                      g.drawImage(image, 10, 10, this);
-                      g.rotate( -Math.toRadians(angle), 28, 28);
-                    }
-
-
-                    repaint();
-                }
-                catch (Exception ex)
-                {
-                }
-            }
-
-            cancel.setEnabled(false);
-        }
-
-        public void paintComponent(Graphics g1)
-        {
-            g1.drawImage(offscreen, 0,0,this);
-        }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+import jalview.jbgui.*;
+
+
+/**
+ * Base class for web service client thread and gui
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class WebserviceInfo extends GWebserviceInfo
+{
+
+    /** Job is Queued */
+    public static final int STATE_QUEUING = 0;
+
+    /** Job is Running */
+    public static final int STATE_RUNNING = 1;
+
+    /** Job has finished with no errors */
+    public static final int STATE_STOPPED_OK = 2;
+
+    /** Job has been cancelled with no errors */
+    public static final int STATE_CANCELLED_OK = 3;
+
+    /** job has stopped because of some error */
+    public static final int STATE_STOPPED_ERROR = 4;
+
+    /** job has failed because of some unavoidable service interruption */
+    public static final int STATE_STOPPED_SERVERERROR = 5;
+    int currentStatus = STATE_QUEUING;
+    Image image;
+    int angle = 0;
+    String title = "";
+    jalview.ws.WSClientI thisService;
+    boolean serviceIsCancellable;
+    JInternalFrame frame;
+    JTabbedPane subjobs=null;
+    java.util.Vector jobPanes = null;
+    // tabbed or not
+    public synchronized int addJobPane() {
+      JScrollPane jobpane = new JScrollPane();
+      JTextArea progressText = new JTextArea();
+      progressText.setFont(new java.awt.Font("Verdana", 0, 10));
+      progressText.setBorder(null);
+      progressText.setEditable(false);
+      progressText.setText("WS Job");
+      progressText.setLineWrap(true);
+      progressText.setWrapStyleWord(true);
+      jobpane.setName("JobPane");
+      jobpane.getViewport().add(progressText, null);
+      jobpane.setBorder(null);
+      if (jobPanes==null) {
+        jobPanes = new Vector();
+      }
+      int newpane = jobPanes.size();
+      jobPanes.add(jobpane);
+
+      if (newpane==0) {
+        this.add(jobpane, BorderLayout.CENTER);
+      } else {
+        if (newpane==1) {
+        // revert to a tabbed pane.
+        JScrollPane firstpane;
+        this.remove(firstpane=(JScrollPane) jobPanes.get(0));
+        subjobs=new JTabbedPane();
+          this.add(subjobs, BorderLayout.CENTER);
+          subjobs.add(firstpane);
+          subjobs.setTitleAt(0, firstpane.getName());
+        }
+        subjobs.add(jobpane);
+      }
+      return newpane; // index for accessor methods below
+    }
+    /**
+     * Creates a new WebserviceInfo object.
+     *
+     * @param title short name and job type
+     * @param info reference or other human readable description
+     */
+    public WebserviceInfo(String title, String info)
+    {
+        init(title, info, 520, 500);
+    }
+
+    /**
+     * Creates a new WebserviceInfo object.
+     *
+     * @param title DOCUMENT ME!
+     * @param info DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    public WebserviceInfo(String title, String info, int width, int height)
+    {
+        init(title, info, width, height);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public jalview.ws.WSClientI getthisService()
+    {
+        return thisService;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param newservice DOCUMENT ME!
+     */
+    public void setthisService(jalview.ws.WSClientI newservice)
+    {
+        thisService = newservice;
+        serviceIsCancellable = newservice.isCancellable();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param title DOCUMENT ME!
+     * @param info DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param height DOCUMENT ME!
+     */
+    void init(String title, String info, int width, int height)
+    {
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, title, width, height);
+        frame.setClosable(false);
+
+        this.title = title;
+        setInfoText(info);
+
+        java.net.URL url = getClass().getResource("/images/logo.gif");
+        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+
+        MediaTracker mt = new MediaTracker(this);
+        mt.addImage(image, 0);
+
+        try
+        {
+            mt.waitForID(0);
+        }
+        catch (Exception ex)
+        {
+        }
+
+        AnimatedPanel ap = new AnimatedPanel();
+        titlePanel.add(ap, BorderLayout.CENTER);
+
+        Thread thread = new Thread(ap);
+        thread.start();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param status integer status from state constants
+     */
+    public void setStatus(int status)
+    {
+        currentStatus = status;
+    }
+    /**
+     * subjob status indicator
+     * @param jobpane
+     * @param status
+     */
+    public void setStatus(int jobpane, int status) {
+      if (jobpane<0 || jobpane>=jobPanes.size()) {
+        throw new Error("setStatus called for non-existent job pane."+jobpane);
+      }
+      switch (status) {
+      case STATE_QUEUING:
+        setProgressName(jobpane+" - QUEUED", jobpane);
+        break;
+      case STATE_RUNNING:
+        setProgressName(jobpane+" - RUNNING", jobpane);
+        break;
+      case STATE_STOPPED_OK:
+        setProgressName(jobpane+" - FINISHED", jobpane);
+      break;
+      case STATE_CANCELLED_OK:
+        setProgressName(jobpane+" - CANCELLED", jobpane);
+        break;
+      case STATE_STOPPED_ERROR:
+        setProgressName(jobpane+" - BROKEN",jobpane);
+        break;
+      case STATE_STOPPED_SERVERERROR:
+        setProgressName(jobpane+" - ALERT", jobpane);
+        break;
+        default:
+          setProgressName(jobpane+" - UNKNOWN STATE", jobpane);
+      }
+    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getInfoText()
+    {
+        return infoText.getText();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param text DOCUMENT ME!
+     */
+    public void setInfoText(String text)
+    {
+        infoText.setText(text);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param text DOCUMENT ME!
+     */
+    public void appendInfoText(String text)
+    {
+        infoText.append(text);
+    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getProgressText(int which)
+    {
+      if (jobPanes == null)
+        addJobPane();
+      return ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
+              getComponent(0)).getText();
+    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param text DOCUMENT ME!
+     */
+    public void setProgressText(int which, String text)
+    {
+      if (jobPanes == null)
+        addJobPane();
+      ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
+       getComponent(0)).setText(text);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param text DOCUMENT ME!
+     */
+    public void appendProgressText(int which, String text)
+    {
+      if (jobPanes == null)
+        addJobPane();
+      ( (JTextArea) ( (JScrollPane) jobPanes.get(which)).getViewport().
+       getComponent(0)).append(text);
+    }
+    /**
+     * setProgressText(0, text)
+     */
+    public void setProgressText(String text)
+    {
+      setProgressText(0, text);
+    }
+    /**
+     * appendProgressText(0, text)
+     */
+    public void appendProgressText(String text)
+    {
+      appendProgressText(0, text);
+    }
+    /**
+     * getProgressText(0)
+     */
+    public String getProgressText()
+    {
+      return getProgressText(0);
+    }
+    /**
+     * get the tab title for a subjob
+     * @param which int
+     * @return String
+     */
+    public String getProgressName(int which) {
+      if (jobPanes==null)
+        addJobPane();
+      if (subjobs!=null)
+        return subjobs.getTitleAt(which);
+      else
+        return ((JScrollPane) jobPanes.get(which)).getViewport().getComponent(0).getName();
+    }
+    /**
+     * set the tab title for a subjob
+     * @param name String
+     * @param which int
+     */
+    public void setProgressName(String name, int which) {
+      if (subjobs!=null) {
+        subjobs.setTitleAt(which, name);
+        subjobs.revalidate();
+        subjobs.repaint();
+      }
+      JScrollPane c=(JScrollPane) jobPanes.get(which);
+      c.getViewport().getComponent(0).setName(name);
+      c.repaint();
+    }
+
+    /**
+     * Gui action for cancelling the current job, if possible.
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void cancel_actionPerformed(ActionEvent e)
+    {
+        if (!serviceIsCancellable)
+        {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "This job cannot be cancelled.\nJust close the window.", "Cancel job",
+                JOptionPane.WARNING_MESSAGE);
+        }
+        else
+        {
+            frame.setClosable(true);
+            thisService.cancelJob();
+        }
+    }
+
+    public void setResultsReady()
+    {
+      frame.setClosable(true);
+      buttonPanel.remove(cancel);
+      buttonPanel.add(showResultsNewFrame);
+      buttonPanel.add(mergeResults);
+      buttonPanel.setLayout(new GridLayout(2,1,5,5));
+      buttonPanel.validate();
+      validate();
+    }
+
+
+  class AnimatedPanel extends JPanel implements Runnable
+    {
+        long startTime = 0;
+        BufferedImage offscreen;
+
+        public void run()
+        {
+            startTime = System.currentTimeMillis();
+            Graphics2D g = null;
+
+            while (currentStatus < STATE_STOPPED_OK)
+            {
+                try
+                {
+                    Thread.sleep(50);
+
+                    int units = (int) ( (System.currentTimeMillis() - startTime) /
+                                       10f);
+                    angle += units;
+                    angle %= 360;
+                    startTime = System.currentTimeMillis();
+
+                    if (offscreen == null || offscreen.getWidth(this) != getWidth()
+                        || offscreen.getHeight(this) != getHeight())
+                    {
+                      offscreen = new BufferedImage(getWidth(), getHeight(),
+                                                    BufferedImage.TYPE_INT_ARGB);
+                      g = (Graphics2D) offscreen.getGraphics();
+                    }
+
+                    g.setColor(Color.white);
+                    g.fillRect(0, 0, getWidth(), getHeight());
+
+                    g.setFont(new Font("Arial", Font.BOLD, 12));
+                    g.setColor(Color.black);
+
+                    switch (currentStatus)
+                    {
+                      case STATE_QUEUING:
+                        g.drawString(title.concat(" - queuing"), 60, 30);
+
+                        break;
+
+                      case STATE_RUNNING:
+                        g.drawString(title.concat(" - running"), 60, 30);
+
+                        break;
+
+                      case STATE_STOPPED_OK:
+                        g.drawString(title.concat(" - complete"), 60, 30);
+
+                        break;
+
+                      case STATE_CANCELLED_OK:
+                        g.drawString(title.concat(" - job cancelled!"), 60, 30);
+
+                        break;
+
+                      case STATE_STOPPED_ERROR:
+                        g.drawString(title.concat(" - job error!"), 60, 30);
+
+                        break;
+
+                      case STATE_STOPPED_SERVERERROR:
+                        g.drawString(title.concat(" - Server Error! (try later)"),
+                                     60,
+                                     30);
+
+                        break;
+                    }
+
+
+                    if (currentStatus >= STATE_STOPPED_OK)
+                      angle = 0;
+
+                    if (image != null)
+                    {
+                      g.rotate(Math.toRadians(angle), 28, 28);
+                      g.drawImage(image, 10, 10, this);
+                      g.rotate( -Math.toRadians(angle), 28, 28);
+                    }
+
+
+                    repaint();
+                }
+                catch (Exception ex)
+                {
+                }
+            }
+
+            cancel.setEnabled(false);
+        }
+
+        public void paintComponent(Graphics g1)
+        {
+            g1.drawImage(offscreen, 0,0,this);
+        }
+    }
+}
diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index b8912e2..d51bc76 100644
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -118,9 +118,18 @@ class MsaWSThread extends Thread implements WSClientI {
         this.seqs = new vamsas.objects.simple.SequenceSet();
         this.seqs.setSeqs(seqarray);
     }
+    /**
+     * 
+     * @return true if getAlignment will return a valid alignment result.
+     */
+    public boolean hasResults() {
+      if (subjobComplete && result!=null && jobs[0].result.isFinished())
+        return true;
+      return false;
+    }
     public Object[] getAlignment() {
       
-      if (result!=null) {
+      if (result!=null && result.isFinished()) {
         SequenceI[] alseqs=null;
         char alseq_gapchar='-';
         int alseq_l=0;
@@ -640,7 +649,7 @@ class MsaWSThread extends Thread implements WSClientI {
         nwidth+=width;  
       }
     } else {
-      if (jobs[0].subjobComplete && jobs[0].result!=null) {
+      if (jobs[0].hasResults()) {
         Object[] alg = jobs[0].getAlignment();
         alignment = (SequenceI[]) alg[0];
         alorders.add(alg[1]);
@@ -667,8 +676,27 @@ class MsaWSThread extends Thread implements WSClientI {
           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;
+            int r=l;
+            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 + " Region "+i+" Ordering",
+            af.addSortByOrderMenuItem(WebServiceName + ((String) names.get(i))+" Ordering",
                 (AlignmentOrder) alorders.get(i));              
           }
         }