From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 5 Dec 2006 17:55:26 +0000 (+0000)
Subject: Sequence is char []
X-Git-Tag: Release_2_3~520
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git

Sequence is char []
---

diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java
index 49faa50..00d9000 100644
--- a/src/jalview/commands/ChangeCaseCommand.java
+++ b/src/jalview/commands/ChangeCaseCommand.java
@@ -71,7 +71,7 @@ public class ChangeCaseCommand implements CommandI
       start = regions[r][0];
       for (int s = 0; s < seqs.length; s++)
       {
-        sequence = seqs[s].getSequence();
+        sequence = seqs[s].getSequenceAsString();
         StringBuffer newSeq = new StringBuffer();
 
         if (regions[r][1] > sequence.length())
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 72d82aa..be11d44 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -207,7 +207,7 @@ public class EditCommand implements CommandI
       if(command.seqs[i].getLength()>command.position)
       {
         command.string[i] = command.seqs[i].getSequence(command.position,
-            command.position + command.number).toCharArray();
+            command.position + command.number);
 
         command.seqs[i].deleteChars(command.position,
                                     command.position + command.number);
@@ -235,7 +235,8 @@ public class EditCommand implements CommandI
         else
           command.al.addSequence(command.seqs[i]);
       }
-      tmp = new StringBuffer(command.seqs[i].getSequence());
+      tmp = new StringBuffer();
+      tmp.append(command.seqs[i].getSequence());
 
       if(command.string!=null && command.string[i]!=null)
       {
diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index ddd6b76..ba39381 100644
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -60,7 +60,7 @@ public class RemoveGapsCommand  extends EditCommand
       deletedCols = 0;
       startCol = -1;
       endCol = -1;
-      sequence = seqs[s].getSequence(start, end+1).toCharArray();
+      sequence = seqs[s].getSequence(start, end+1);
 
       jSize = sequence.length;
       for (j=0; j<jSize; j++)
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 6051aa6..b5f31bc 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -137,7 +137,7 @@ public class Alignment implements AlignmentI
         {
           Sequence ds = new Sequence(snew.getName(),
                                      AlignSeq.extractGaps("-. ",
-              snew.getSequence()),
+              snew.getSequenceAsString()),
                                      snew.getStart(),
                                      snew.getEnd());
 
@@ -401,9 +401,9 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < sequences.size(); i++)
         {
             Sequence seq = (Sequence) sequences.elementAt(i);
-            seq.setSequence( seq.getSequence().replace('.', gc) );
-            seq.setSequence( seq.getSequence().replace('-', gc) );
-            seq.setSequence( seq.getSequence().replace(' ', gc) );
+            seq.setSequence( seq.getSequenceAsString().replace('.', gc) );
+            seq.setSequence( seq.getSequenceAsString().replace('-', gc) );
+            seq.setSequence( seq.getSequenceAsString().replace(' ', gc) );
         }
     }
 
@@ -589,7 +589,7 @@ public class Alignment implements AlignmentI
             seqs[i] = new Sequence(currentSeq.getName(),
                                    AlignSeq.extractGaps(
                                        jalview.util.Comparison.GapChars,
-                                       currentSeq.getSequence()
+                                       currentSeq.getSequenceAsString()
                                    ),
                                    currentSeq.getStart(),
                                    currentSeq.getEnd());
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index e668470..58b379b 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -51,7 +51,7 @@ public class AlignmentView
     width = seqcigararray.getWidth(); // visible width
   }
   /**
-   * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment 
+   * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment
    * @param sdata
    * @param firstcol
    */
@@ -244,7 +244,7 @@ public class AlignmentView
                 }
                 else
                 {
-                  alignment[s].setSequence(alignment[s].getSequence() +
+                  alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                            mseq[s].getSequence());
                   if (mseq[s].getStart() <= mseq[s].getEnd())
                   {
@@ -276,7 +276,7 @@ public class AlignmentView
                   }
                   else
                   {
-                    alignment[s].setSequence(alignment[s].getSequence() +
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                              oseq.getSequence());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
@@ -303,7 +303,7 @@ public class AlignmentView
             }
             else
             {
-              alignment[s].setSequence(alignment[s].getSequence() +
+              alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                        hseq.getSequence());
               if (hseq.getEnd() >= hseq.getStart())
               {
@@ -332,7 +332,7 @@ public class AlignmentView
               }
               else
               {
-                alignment[s].setSequence(alignment[s].getSequence() +
+                alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                          mseq[s].getSequence());
                 if (mseq[s].getEnd() >= mseq[s].getStart())
                 {
@@ -366,7 +366,7 @@ public class AlignmentView
                   }
                   else
                   {
-                    alignment[s].setSequence(alignment[s].getSequence() +
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
                                              oseq.getSequence());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
@@ -397,7 +397,7 @@ public class AlignmentView
   }
   /**
    * 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. 
+   * 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() {
@@ -429,7 +429,7 @@ public class AlignmentView
           viscontigs[nvis+1]=contigs[contig+1]-1; // end is inclusive
           nvis+=2;
         }
-        start = contigs[contig + 1] + contigs[contig + 2];              
+        start = contigs[contig + 1] + contigs[contig + 2];
       }
       if (start<fwidth) {
         viscontigs[nvis] = start;
@@ -442,8 +442,8 @@ public class AlignmentView
     }
   }
   /**
-   * 
-   * @return position of first visible column of AlignmentView within its parent's alignment reference frame 
+   *
+   * @return position of first visible column of AlignmentView within its parent's alignment reference frame
    */
   public int getAlignmentOrigin() {
     // TODO Auto-generated method stub
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index af10e1d..49e3543 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -49,7 +49,7 @@ public class BinarySequence extends Sequence
     public void encode()
     {
         // Set all matrix to 0
-        dbinary = new double[getSequence().length() * 21];
+        dbinary = new double[getSequence().length * 21];
 
         int nores = 21;
 
@@ -58,13 +58,13 @@ public class BinarySequence extends Sequence
             dbinary[i] = 0.0;
         }
 
-        for (int i = 0; i < getSequence().length(); i++)
+        for (int i = 0; i < getSequence().length; i++)
         {
             int aanum = 20;
 
             try
             {
-                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];
             }
             catch (NullPointerException e)
             {
@@ -86,20 +86,20 @@ public class BinarySequence extends Sequence
     public void blosumEncode()
     {
         // Set all matrix to 0
-        dbinary = new double[getSequence().length() * 21];
+        dbinary = new double[getSequence().length * 21];
 
         int nores = 21;
 
         //for (int i = 0; i < dbinary.length; i++) {
         //  dbinary[i] = 0.0;
         //}
-        for (int i = 0; i < getSequence().length(); i++)
+        for (int i = 0; i < getSequence().length; i++)
         {
             int aanum = 20;
 
             try
             {
-                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];
             }
             catch (NullPointerException e)
             {
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 3c1d6f1..e51afd0 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -737,7 +737,7 @@ public class ColumnSelection
     {
       for(i=0; i<iSize; i++)
       {
-        selection[i] = seqs[i].getSequence(start, end);
+        selection[i] = seqs[i].getSequenceAsString(start, end);
       }
     }
 
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 74a7812..34e8487 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -59,7 +59,7 @@ public class SeqCigar
   public String getSequenceString(char GapChar)
   {
     return (length == 0) ? "" :
-        (String) getSequenceAndDeletions(refseq.getSequence().substring(start, end), GapChar)[0];
+        (String) getSequenceAndDeletions(refseq.getSequenceAsString(start, end), GapChar)[0];
   }
 
   /**
@@ -73,7 +73,7 @@ public class SeqCigar
     {
       return null;
     }
-    Object[] edit_result = getSequenceAndDeletions(refseq.getSequence().substring(start,end),
+    Object[] edit_result = getSequenceAndDeletions(refseq.getSequenceAsString(start,end),
         GapChar);
     if (edit_result == null)
     {
@@ -113,7 +113,7 @@ public class SeqCigar
     }
     if (_s<0)
       throw new Error("Implementation Error: _s="+_s);
-    String seq_string = seq.getSequence();
+    String seq_string = seq.getSequenceAsString();
     if (_e==0 || _e<_s || _e>seq_string.length())
       _e=seq_string.length();
     // resolve start and end positions relative to ungapped reference sequence
@@ -375,7 +375,7 @@ public class SeqCigar
     for (int i = 0; i < alseqs.length; i++)
     {
       alseqs_string[i]=alseqs[i].getRefSeq().
-          getSequence().substring(alseqs[i].start,alseqs[i].end);
+          getSequenceAsString(alseqs[i].start,alseqs[i].end);
       gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i], gapCharacter); // gapped sequence, {start, start col, end. endcol}, hidden regions {{start, end, col}})
       if (gs_regions[i] == null)
       {
@@ -561,7 +561,7 @@ public class SeqCigar
       {
         int e = st + rs;
         sub_se_gp.deleteRange(st, e);
-        String ssgapedseq = sub_se_gp.getSeq('-').getSequence();
+        String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
         System.out.println(st + "," + e + "\t:" + ssgapedseq);
         st -=3;
       }
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 7df3eaf..4687116 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -18,7 +18,6 @@
 */
 package jalview.datamodel;
 
-import java.awt.*;
 
 import java.util.*;
 
@@ -33,7 +32,7 @@ public class Sequence implements SequenceI
 {
   SequenceI datasetSequence;
   String name;
-  private String sequence;
+  private char [] sequence;
   String description;
   int start;
   int end;
@@ -64,12 +63,20 @@ public class Sequence implements SequenceI
   public Sequence(String name, String sequence, int start, int end)
   {
     this.name = name;
-    this.sequence = sequence;
+    this.sequence = sequence.toCharArray();
     this.start = start;
     this.end = end;
-
     parseId();
+    checkValidRange();
+  }
 
+  public Sequence(String name, char [] sequence, int start, int end)
+  {
+    this.name = name;
+    this.sequence = sequence;
+    this.start = start;
+    this.end = end;
+    parseId();
     checkValidRange();
   }
 
@@ -96,11 +103,9 @@ public class Sequence implements SequenceI
     if (end < 1)
     {
       int endRes = 0;
-      char ch;
-      for (int j = 0; j < sequence.length(); j++)
+      for (int j = 0; j < sequence.length; j++)
       {
-        ch = sequence.charAt(j);
-        if (!jalview.util.Comparison.isGap( (ch)))
+        if (!jalview.util.Comparison.isGap( sequence[j] ))
         {
           endRes++;
         }
@@ -328,7 +333,7 @@ public class Sequence implements SequenceI
    */
   public int getLength()
   {
-    return this.sequence.length();
+    return this.sequence.length;
   }
 
   /**
@@ -338,18 +343,25 @@ public class Sequence implements SequenceI
    */
   public void setSequence(String seq)
   {
-    this.sequence = seq;
+    this.sequence = seq.toCharArray();
     checkValidRange();
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String getSequence()
+
+  public String getSequenceAsString()
+  {
+    return new String(sequence);
+  }
+
+  public String getSequenceAsString(int start, int end)
+  {
+    return new String(getSequence(start, end));
+  }
+
+
+  public char [] getSequence()
   {
-    return this.sequence;
+    return sequence;
   }
 
   /**
@@ -360,22 +372,26 @@ public class Sequence implements SequenceI
    *
    * @return DOCUMENT ME!
    */
-  public String getSequence(int start, int end)
+  public char [] getSequence(int start, int end)
   {
     // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
-    if (start >= sequence.length())
+    if (start >= sequence.length)
     {
-      return "";
+      System.out.println("DOES THIS GET CALLED???");
     }
 
-    if (end >= sequence.length())
+    if (end >= sequence.length)
     {
-      end = sequence.length();
+      end = sequence.length;
     }
 
-    return this.sequence.substring(start, end);
+    char [] reply = new char[end-start];
+    System.arraycopy(sequence, start, reply, 0, end-start);
+
+    return reply;
   }
 
+
   /**
    * make a new Sequence object from start to end (including gaps) over this seqeunce
    * @param start int
@@ -386,8 +402,8 @@ public class Sequence implements SequenceI
   {
     if (start < 0)
       start = 0;
-    String seq = getSequence(start, end);
-    if (seq == "")
+    char [] seq = getSequence(start, end);
+    if (seq.length == 0)
       return null;
     int nstart = findPosition(start);
     int nend = findPosition(end) - 1;
@@ -407,9 +423,9 @@ public class Sequence implements SequenceI
    */
   public char getCharAt(int i)
   {
-    if (i < sequence.length())
+    if (i < sequence.length)
     {
-      return sequence.charAt(i);
+      return sequence[i];
     }
     else
     {
@@ -450,9 +466,9 @@ public class Sequence implements SequenceI
     int j = start;
     int i = 0;
 
-    while ( (i < sequence.length()) && (j <= end) && (j <= pos))
+    while ( (i < sequence.length) && (j <= end) && (j <= pos))
     {
-      if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
+      if (!jalview.util.Comparison.isGap(sequence[i]))
       {
         j++;
       }
@@ -481,10 +497,10 @@ public class Sequence implements SequenceI
   {
     int j = 0;
     int pos = start;
-    int seqlen = sequence.length();
+    int seqlen = sequence.length;
     while ( (j < i) && (j < seqlen))
     {
-      if (!jalview.util.Comparison.isGap( (sequence.charAt(j))))
+      if (!jalview.util.Comparison.isGap( sequence[j] ))
       {
         pos++;
       }
@@ -503,14 +519,14 @@ public class Sequence implements SequenceI
   public int[] gapMap()
   {
     String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
-        GapChars, sequence);
+        GapChars, new String(sequence));
     int[] map = new int[seq.length()];
     int j = 0;
     int p = 0;
 
-    while (j < sequence.length())
+    while (j < sequence.length)
     {
-      if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
+      if (!jalview.util.Comparison.isGap(sequence[j]))
       {
         map[p++] = j;
       }
@@ -525,38 +541,30 @@ public class Sequence implements SequenceI
    * 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())
+    if (i >= sequence.length)
     {
       return;
     }
 
-    if (j >= sequence.length())
+    char [] tmp;
+
+    if (j >= sequence.length)
     {
-      sequence = sequence.substring(0, i);
+      tmp = new char[i];
+      System.arraycopy(sequence,0,tmp,0,i);
     }
     else
     {
-      sequence = sequence.substring(0, i) + sequence.substring(j);
+      tmp = new char[sequence.length-j+i];
+      System.arraycopy(sequence,0,tmp,0,i);
+      System.arraycopy(sequence,j,tmp,i,sequence.length-j);
     }
+
+    sequence = tmp;
   }
 
   /**
@@ -568,27 +576,32 @@ public class Sequence implements SequenceI
    */
   public void insertCharAt(int i, int length, char c)
   {
-    StringBuffer tmp;
+    char [] tmp = new char[sequence.length+length];
 
-    if (i >= sequence.length())
+    if (i >= sequence.length)
     {
-      tmp = new StringBuffer(sequence);
+      System.arraycopy(sequence, 0, tmp, 0, sequence.length);
+      i = sequence.length;
     }
     else
-      tmp = new StringBuffer(sequence.substring(0, i));
+   {
+      System.arraycopy(sequence, 0, tmp, 0, i);
+   }
+
 
+    int index = i;
     while (length > 0)
     {
-      tmp.append(c);
+      tmp[ index++ ] = c;
       length--;
     }
 
-    if (i < sequence.length())
+    if (i < sequence.length)
     {
-      tmp.append(sequence.substring(i));
+      System.arraycopy(sequence, i, tmp, index, sequence.length-i );
     }
 
-    sequence = tmp.toString();
+    sequence = tmp;
   }
 
   public void insertCharAt(int i, char c)
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index a8327cf..bb5e799 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,8 +20,6 @@ package jalview.datamodel;
 
 import java.util.*;
 
-import java.awt.*;
-
 
 /**
  * DOCUMENT ME!
@@ -100,7 +98,7 @@ public interface SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getSequence();
+    public String getSequenceAsString();
 
     /**
      * DOCUMENT ME!
@@ -110,7 +108,24 @@ public interface SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getSequence(int start, int end);
+    public String getSequenceAsString(int start, int end);
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char [] getSequence();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char [] getSequence(int start, int end);
     /**
      * create a new sequence object from start to end of this sequence
      * @param start int
@@ -174,12 +189,6 @@ public interface SequenceI
      */
     public void deleteChars(int i, int j);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void deleteCharAt(int i);
 
     /**
      * DOCUMENT ME!
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fb2047e..05ba166 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -317,7 +317,7 @@ public class AlignViewport
             cons.findQuality();
           }
 
-          String sequence = cons.getConsSequence().getSequence();
+          char [] sequence = cons.getConsSequence().getSequence();
           float minR;
           float minG;
           float minB;
@@ -352,7 +352,7 @@ public class AlignViewport
           {
             float value = 0;
 
-            c = sequence.charAt(i);
+            c = sequence[i];
 
             if (Character.isDigit(c))
               value = (int) (c - '0');
@@ -1513,7 +1513,7 @@ public class AlignViewport
       } else {
         for(i=0; i<iSize; i++)
         {
-          selection[i] = seqs[i].getSequence(start, end);
+          selection[i] = seqs[i].getSequenceAsString(start, end);
         }
 
       }
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4268353..4d73aa6 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -400,7 +400,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()};
       if (dseqs[0]==null) {
         dseqs[0] = new Sequence(sq);
-        dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sq.getSequence()));
+        dseqs[0].setSequence(
+            jalview.analysis.AlignSeq.extractGaps(
+                jalview.util.Comparison.GapChars,
+                sq.getSequenceAsString()));
+
         sq.setDatasetSequence(dseqs[0]);
       }
       Alignment ds=new Alignment(dseqs);
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index beef70c..003200d 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -309,7 +309,7 @@ public class FeatureRenderer
           int pady = (y1 + av.charHeight) - av.charHeight / 5;
           for (i = fstart; i <= fend; i++)
           {
-            s = seq.getSequence().charAt(i);
+            s = seq.getCharAt(i);
 
             if (jalview.util.Comparison.isGap(s))
             {
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e1431a9..2c37b44 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -229,7 +229,7 @@ public class Finder extends GFinder
                 continue;
             }
 
-            item = seq.getSequence();
+            item = seq.getSequenceAsString();
             if(!caseSensitive.isSelected())
               item = item.toUpperCase();
 
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index b2a5ede..9fcbb6e 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -282,14 +282,12 @@ public class IdCanvas extends JPanel
                 drawIdString(gg, s, i, 0, ypos);
               }
 
-                if(labels!=null)
+                if(labels!=null && av.showAnnotation)
                 {
                   gg.translate(0, ypos+(alheight * av.charHeight));
                   labels.drawComponent(gg, getWidth());
                   gg.translate(0, -ypos-(alheight * av.charHeight));
                 }
-
-
             }
         }
         else
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 4bd951c..a9763d3 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -232,7 +232,7 @@ public class Jalview2XML
               vamsasSeq = new Sequence();
               vamsasSeq.setId(id + "");
               vamsasSeq.setName(jds.getName());
-              vamsasSeq.setSequence(jds.getSequence());
+              vamsasSeq.setSequence(jds.getSequenceAsString());
               vamsasSeq.setDescription(jds.getDescription());
 
               if (jds.getDatasetSequence().getDBRef() != null)
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index ec896d5..e7a580e 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -166,8 +166,8 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
               if(omitHidden==null)
               {
-                seqi = originalSequences[i].getSequence(start, end);
-                seqj = originalSequences[j].getSequence(start, end);
+                seqi = originalSequences[i].getSequenceAsString(start, end);
+                seqj = originalSequences[j].getSequenceAsString(start, end);
               }
               else
               {
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 3f3f9cc..0756299 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -417,7 +417,7 @@ public class SequenceFetcher
             /////////////////////////////
             Sequence ds = new Sequence(sequences[i].getName(),
                                        AlignSeq.extractGaps("-. ",
-                sequences[i].getSequence()),
+                sequences[i].getSequenceAsString()),
                                        sequences[i].getStart(),
                                        sequences[i].getEnd());
             sequences[i].setDatasetSequence(ds);
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 8d7755c..6c7fb37 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -104,7 +104,7 @@ public class SequenceRenderer
     {
         if (cs != null)
         {
-            resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+            resBoxColour = cs.findColour(seq.getCharAt(i), i);
         }
         else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
         {
@@ -236,12 +236,12 @@ public class SequenceRenderer
            && !av.getColourText()
            && av.thresholdTextColour==0)
         {
-          if(av.renderGaps)
-          graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
-         else
+          if (av.renderGaps)
+            graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
+          else
          {
            char gap = av.getGapCharacter();
-           graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1);
+           graphics.drawString( seq.getSequenceAsString(start, end+1).replace(gap, ' '), 0, y1);
          }
         }
         else
@@ -387,7 +387,7 @@ public class SequenceRenderer
           {
             if (i < seq.getLength())
             {
-              s = seq.getSequence().charAt(i);
+              s = seq.getCharAt(i);
             }
 
             charOffset = (av.charWidth - fm.charWidth(s)) / 2;
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a8afd43..a39f4ca 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -343,7 +343,7 @@ public class UserDefinedColours extends GUserDefinedColours
 
           try
           {
-            col = oldColourScheme.findColour(aa, -1);
+            col = oldColourScheme.findColour(aa.charAt(0), -1);
           }
           catch (Exception ex)
           {    }
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 0691d82..85f23a4 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -111,12 +111,12 @@ public abstract class AlignFile extends FileParse
     }
 
     // Checks whether sequence is valid aa characters
-    protected boolean isValidProteinSequence(String sequence)
+    protected boolean isValidProteinSequence(char [] sequence)
     {
-        for (int i = 0; i < sequence.length(); i++)
-            if (jalview.schemes.ResidueProperties.aaIndex[sequence.charAt(i)]==-1)
+        for (int i = 0; i < sequence.length; i++)
+            if (jalview.schemes.ResidueProperties.aaIndex[sequence[i]]==-1)
             {
-                invalidCharacter = sequence.charAt(i);
+                invalidCharacter = sequence[i];
                 return false;
             }
 
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 08b5862..04861a2 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -356,7 +356,7 @@ public class AnnotationFile
         for(int j=0; j<annotations.length; j++)
         {
           if(annotations[j]!=null)
-            annotations[j].colour = ucs.findColour("A");
+            annotations[j].colour = ucs.findColour('A');
         }
       }
     }
@@ -414,7 +414,7 @@ public class AnnotationFile
     if(st.hasMoreTokens())
     {
       UserColourScheme ucs = new UserColourScheme(st.nextToken());
-      colour = ucs.findColour("A");
+      colour = ucs.findColour('A');
     }
 
     annotation.setThreshold(new GraphLine(value, label, colour));
diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index ceeac64..4a9e777 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -188,9 +188,9 @@ public class BLCFile extends AlignFile
         {
             out.append(">" + printId(s[i]) +"\n");
 
-            if (s[i].getSequence().length() > max)
+            if (s[i].getSequence().length > max)
             {
-                max = s[i].getSequence().length();
+                max = s[i].getSequence().length;
             }
 
             i++;
@@ -204,9 +204,9 @@ public class BLCFile extends AlignFile
 
             while ((i < s.length) && (s[i] != null))
             {
-                if (s[i].getSequence().length() > j)
+                if (s[i].getSequence().length > j)
                 {
-                    out.append(s[i].getSequence().substring(j, j + 1));
+                    out.append(s[i].getSequenceAsString(j, j + 1));
                 }
                 else
                 {
diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index e3f83ee..b43e3ea 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -164,9 +164,9 @@ public class ClustalFile
     {
       String tmp = printId(s[i]);
 
-      if (s[i].getSequence().length() > max)
+      if (s[i].getSequence().length > max)
       {
-        max = s[i].getSequence().length();
+        max = s[i].getSequence().length;
       }
 
       if (tmp.length() > maxid)
@@ -198,16 +198,16 @@ public class ClustalFile
         int start = i * len;
         int end = start + len;
 
-        if ( (end < s[j].getSequence().length()) &&
-            (start < s[j].getSequence().length()))
+        if ( (end < s[j].getSequence().length) &&
+            (start < s[j].getSequence().length))
         {
-          out.append(s[j].getSequence().substring(start, end));
+          out.append(s[j].getSequenceAsString(start, end));
         }
         else
         {
-          if (start < s[j].getSequence().length())
+          if (start < s[j].getSequence().length)
           {
-            out.append(s[j].getSequence().substring(start));
+            out.append(s[j].getSequenceAsString().substring(start));
           }
         }
 
diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index 4a6044f..bd3c733 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -305,7 +305,8 @@ public class DBRefFetcher implements Runnable
         System.out.println("Adding dbref to " + sequence.getName() + " : " +
                            entry.getAccession().elementAt(0).toString());
 
-        String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence()).
+        String nonGapped = AlignSeq.extractGaps("-. ",
+                                                sequence.getSequenceAsString()).
             toUpperCase();
 
         int absStart = entry.getUniprotSequence().getContent().indexOf(
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 6e3ced8..f257c6c 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -73,7 +73,7 @@ public class FastaFile extends AlignFile
                 {
                     if (count != 0)
                     {
-                      if (!isValidProteinSequence(sb.toString()))
+                      if (!isValidProteinSequence(sb.toString().toCharArray()))
                       {
                         throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
                                               +" : "+seq.getName()
@@ -98,7 +98,7 @@ public class FastaFile extends AlignFile
 
         if (count > 0)
         {
-            if (!isValidProteinSequence(sb.toString()))
+            if (!isValidProteinSequence(sb.toString().toCharArray()))
             {
                 throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
                                       +" : "+seq.getName()
@@ -144,11 +144,11 @@ public class FastaFile extends AlignFile
 
                 if (end < s[i].getLength())
                 {
-                    out.append(s[i].getSequence(start, end) + "\n");
+                    out.append(s[i].getSequenceAsString(start, end) + "\n");
                 }
                 else if (start < s[i].getLength())
                 {
-                    out.append(s[i].getSequence(start, s[i].getLength()) + "\n");
+                    out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
                 }
             }
 
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 42b032d..e4fd38e 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -125,7 +125,7 @@ public class FeaturesFile extends AlignFile
             else
             {
               UserColourScheme ucs = new UserColourScheme(st.nextToken());
-              colours.put(type, ucs.findColour("A"));
+              colours.put(type, ucs.findColour('A'));
               if (st.hasMoreElements())
               {
                 String link = st.nextToken();
@@ -230,7 +230,7 @@ public class FeaturesFile extends AlignFile
             {
               // Probably the old style groups file
               UserColourScheme ucs = new UserColourScheme(type);
-              colours.put(type, ucs.findColour("A"));
+              colours.put(type, ucs.findColour('A'));
             }
 
             sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 577e874..07a0068 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -42,9 +42,9 @@ public class JnetAnnotationMaker
     // in the future we could search for the query
     // sequence in the alignment before calling this function.
     SequenceI seqRef = al.getSequenceAt(firstSeq);
-    int width = preds[0].getSequence().length();
+    int width = preds[0].getSequence().length;
     int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
-    if ((delMap!=null && delMap.length > width) || (delMap==null && gapmap.length!=width)) 
+    if ((delMap!=null && delMap.length > width) || (delMap==null && gapmap.length!=width))
     {
       throw (new Exception(
           "Number of residues in "+(delMap==null ? "" : " mapped ")+"supposed query sequence ('" +
@@ -127,7 +127,7 @@ public class JnetAnnotationMaker
             for (int j = 0; j < width; j++)
             {
             annotations[gapmap[delMap[j]]] = new Annotation(preds[i].getCharAt(
-                j) + "", "", ' ', 0);            
+                j) + "", "", ' ', 0);
             }
           }
         }
@@ -178,4 +178,4 @@ public class JnetAnnotationMaker
      */
 
   }
-}
\ No newline at end of file
+}
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index c06757b..61b3528 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -145,7 +145,7 @@ public class MSFfile extends AlignFile
 
                 // Replace ~ with a sensible gap character
                 seq = seq.replace('~', '-');
-                if (!isValidProteinSequence(seq))
+                if (!isValidProteinSequence(seq.toCharArray()))
                 {
                     throw new IOException(AppletFormatAdapter.
                                           INVALID_CHARACTERS
@@ -227,9 +227,11 @@ public class MSFfile extends AlignFile
         while ((i < seqs.length) && (seqs[i] != null))
         {
           // Replace all internal gaps with . and external spaces with ~
-          s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequence().replace('-', '.'));
+          s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequenceAsString().replace('-', '.'));
+
+          StringBuffer sb = new StringBuffer();
+          sb.append(s[i].getSequence());
 
-          StringBuffer sb = new StringBuffer(s[i].getSequence());
           for (int ii = 0; ii < sb.length(); ii++)
           {
             if (sb.charAt(ii) == '.')
@@ -252,9 +254,9 @@ public class MSFfile extends AlignFile
 
             s[i].setSequence(sb.toString());
 
-            if (s[i].getSequence().length() > max)
+            if (s[i].getSequence().length > max)
             {
-                max = s[i].getSequence().length();
+                max = s[i].getSequence().length;
             }
 
             i++;
@@ -270,13 +272,13 @@ public class MSFfile extends AlignFile
         int [] checksums = new int[s.length];
         while ( i < s.length )
         {
-          checksums[i] = checkSum(s[i].getSequence());
+          checksums[i] = checkSum(s[i].getSequenceAsString());
           bigChecksum += checksums[i];
           i++;
         }
 
         long maxNB = 0;
-        out.append("   MSF: " + s[0].getSequence().length() + "   Type: " +
+        out.append("   MSF: " + s[0].getSequence().length + "   Type: " +
             (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum%10000) + "   ..\n\n\n");
 
         String[] nameBlock = new String[s.length];
@@ -289,7 +291,7 @@ public class MSFfile extends AlignFile
             nameBlock[i] = new String("  Name: " + printId(s[i])+" ");
 
             idBlock[i] = new String("Len: " +
-                    maxLenpad.form(s[i].getSequence().length()) + "  Check: " +
+                    maxLenpad.form(s[i].getSequence().length) + "  Check: " +
                     maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
 
             if (s[i].getName().length() > maxid)
@@ -350,10 +352,10 @@ public class MSFfile extends AlignFile
                     int start = (i * 50) + (k * 10);
                     int end = start + 10;
 
-                    if ((end < s[j].getSequence().length()) &&
-                            (start < s[j].getSequence().length()))
+                    if ((end < s[j].getSequence().length) &&
+                            (start < s[j].getSequence().length))
                     {
-                        out.append(s[j].getSequence().substring(start, end));
+                        out.append(s[j].getSequence(start, end));
 
                         if (k < 4)
                         {
@@ -366,9 +368,9 @@ public class MSFfile extends AlignFile
                     }
                     else
                     {
-                        if (start < s[j].getSequence().length())
+                        if (start < s[j].getSequence().length)
                         {
-                            out.append(s[j].getSequence().substring(start));
+                            out.append(s[j].getSequenceAsString().substring(start));
                             out.append("\n");
                         }
                         else
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index fa9a28b..8b05171 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -114,7 +114,7 @@ public class PIRFile
 
     while ( (i < s.length) && (s[i] != null))
     {
-      String seq = s[i].getSequence();
+      String seq = s[i].getSequenceAsString();
       seq = seq + "*";
 
 
diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index bbd441c..7cb381d 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -138,9 +138,9 @@ public class PfamFile
     {
       String tmp = printId(s[i]);
 
-      if (s[i].getSequence().length() > max)
+      if (s[i].getSequence().length > max)
       {
-        max = s[i].getSequence().length();
+        max = s[i].getSequence().length;
       }
 
       if (tmp.length() > maxid)
@@ -162,7 +162,7 @@ public class PfamFile
     {
       out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));
 
-      out.append(s[j].getSequence() + "\n");
+      out.append(s[j].getSequenceAsString() + "\n");
       j++;
     }
 
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index fa77802..be16169 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -80,21 +80,21 @@ public class PileUpfile  extends MSFfile
     int[] checksums = new int[s.length];
     while (i < s.length)
     {
-      checksums[i] = checkSum(s[i].getSequence());
+      checksums[i] = checkSum(s[i].getSequenceAsString());
       bigChecksum += checksums[i];
       i++;
     }
 
-    out.append("   MSF: " + s[0].getSequence().length() +
+    out.append("   MSF: " + s[0].getSequence().length +
                "   Type: P    Check:  " + bigChecksum%10000 + "   ..\n\n\n");
 
     i=0;
     while ( (i < s.length) && (s[i] != null))
     {
-      String seq = s[i].getSequence();
+      String seq = s[i].getSequenceAsString();
       out.append(" Name: " + printId(s[i]) +
                  " oo  Len:  " +
-                 s[i].getSequence().length() + "  Check:  " + checksums[i] +
+                 seq.length() + "  Check:  " + checksums[i] +
                  "  Weight:  1.00\n");
 
       if (seq.length() > max)
@@ -142,10 +142,10 @@ public class PileUpfile  extends MSFfile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ( (end < s[j].getSequence().length()) &&
-              (start < s[j].getSequence().length()))
+          if ( (end < s[j].getSequence().length) &&
+              (start < s[j].getSequence().length))
           {
-            out.append(s[j].getSequence().substring(start, end));
+            out.append(s[j].getSequence(start, end));
 
             if (k < 4)
             {
@@ -158,9 +158,9 @@ public class PileUpfile  extends MSFfile
           }
           else
           {
-            if (start < s[j].getSequence().length())
+            if (start < s[j].getSequence().length)
             {
-              out.append(s[j].getSequence().substring(start));
+              out.append(s[j].getSequenceAsString().substring(start));
               out.append("\n");
             }
             else
diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index 395a251..2f43f03 100755
--- a/src/jalview/io/VamsasDatastore.java
+++ b/src/jalview/io/VamsasDatastore.java
@@ -45,11 +45,11 @@ import org.exolab.castor.xml.*;
 import org.exolab.castor.mapping.Mapping;
 
 /*
- * 
+ *
  * static {
  * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
  * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
- * 
+ *
  */
 
 public class VamsasDatastore {
@@ -84,11 +84,11 @@ public class VamsasDatastore {
    * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data
    * with the total price back and print the XML in the console Marshaller
    * marshaller = new Marshaller( new FileWriter(file) );
-   * 
+   *
    * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) {
    * e.printStackTrace(); } }
-   * 
-   * 
+   *
+   *
    */
   /**
    * @return the Vobject bound to Jalview datamodel object
@@ -100,7 +100,7 @@ public class VamsasDatastore {
   }
 
   /**
-   * 
+   *
    * @param vobj
    * @return Jalview datamodel object bound to the vamsas document object
    */
@@ -126,11 +126,11 @@ public class VamsasDatastore {
       if (id==null || vobj.getVorbaId()==null)
         Cache.log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);
     }
-    
+
     if (vobj2jv.containsKey(vobj.getVorbaId()) && !((VorbaId)vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) {
       Cache.log.debug("Warning? Overwriting existing vamsas id binding for "+vobj.getVorbaId(), new Exception("Overwriting vamsas id binding."));
     }
-    else if (jv2vobj.containsKey(jvobj) && !((VorbaId)jv2vobj.get(jvobj)).equals(vobj.getVorbaId())) 
+    else if (jv2vobj.containsKey(jvobj) && !((VorbaId)jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
     {
       Cache.log.debug("Warning? Overwriting existing jalview object binding for "+jvobj, new Exception("Overwriting jalview object binding."));
     }
@@ -139,12 +139,12 @@ public class VamsasDatastore {
     // we just update the hash's regardless!
     vobj2jv.put(vobj.getVorbaId(), jvobj);
     // JBPNote - better implementing a hybrid invertible hash.
-    jv2vobj.put(jvobj, vobj.getVorbaId());   
+    jv2vobj.put(jvobj, vobj.getVorbaId());
   }
 
   /**
    * put the alignment viewed by AlignViewport into cdoc.
-   * 
+   *
    * @param av alignViewport to be stored
    * @param aFtitle title for alignment
    */
@@ -197,7 +197,7 @@ public class VamsasDatastore {
           sequence = new Sequence();
           bindjvvobj(sq, sequence);
           sq.setVamsasId(sequence.getVorbaId().getId());
-          sequence.setSequence(sq.getSequence());
+          sequence.setSequence(sq.getSequenceAsString());
           sequence.setDictionary(dict);
           sequence.setName(jal.getDataset().getSequenceAt(i).getName());
           sequence.setStart(jal.getDataset().getSequenceAt(i).getStart());
@@ -282,7 +282,7 @@ public class VamsasDatastore {
       // ////////////////////////////////////////////
       // Save the Alignments
 
-      Alignment alignment = (Alignment) getjv2vObj(av); // this is so we can get the alignviewport back 
+      Alignment alignment = (Alignment) getjv2vObj(av); // this is so we can get the alignviewport back
       if (alignment == null)
       {
         alignment = new Alignment();
@@ -306,7 +306,7 @@ public class VamsasDatastore {
         {
           alseq = new AlignmentSequence();
           // TODO: VAMSAS: translate lowercase symbols to annotation ?
-          alseq.setSequence(jal.getSequenceAt(i).getSequence());
+          alseq.setSequence(jal.getSequenceAt(i).getSequenceAsString());
           alseq.setName(jal.getSequenceAt(i).getName());
           alseq.setStart(jal.getSequenceAt(i).getStart());
           alseq.setEnd(jal.getSequenceAt(i).getEnd());
@@ -555,7 +555,7 @@ public class VamsasDatastore {
                 an.addProperty(newProperty("jalview:graphType",null,
                     ((aa[i].graph==jalview.datamodel.AlignmentAnnotation.BAR_GRAPH) ? "BAR_GRAPH" : "LINE_GRAPH")));
 
-                /** and on and on.. 
+                /** and on and on..
                  vProperty=new Property();
                   vProperty.setName("jalview:graphThreshhold");
                   vProperty.setContent(aa[i].threshold);
@@ -653,7 +653,7 @@ public class VamsasDatastore {
 
   /**
    * correctly create a RangeAnnotation from a jalview sequence feature
-   * 
+   *
    * @param dsa
    *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
    * @param feature
@@ -695,7 +695,7 @@ public class VamsasDatastore {
   /**
    * correctly creates provenance for trees calculated on an alignment by
    * jalview.
-   * 
+   *
    * @param jal
    * @param tp
    * @return
@@ -722,7 +722,7 @@ public class VamsasDatastore {
       prov.getEntry(0).getParam(0).setName("treeType");
       prov.getEntry(0).getParam(0).setType("utf8");
       prov.getEntry(0).getParam(0).setContent("NJ");
-      
+
       int ranges[] = tp.getTree().seqData.getVisibleContigs();
       // VisibleContigs are with respect to alignment coordinates. Still need offsets
       int start= tp.getTree().seqData.getAlignmentOrigin();
@@ -739,7 +739,7 @@ public class VamsasDatastore {
   }
 
   /**
-   * 
+   *
    * @param tp
    * @return Object[] { AlignmentView, AlignmentI - reference alignment for
    *         input }
@@ -795,7 +795,7 @@ public class VamsasDatastore {
   /**
    * get start<end range of segment, adjusting for inclusivity flag and
    * polarity.
-   *  
+   *
    * @param visSeg
    * @param ensureDirection when true - always ensure start is less than end.
    * @return int[] { start, end, direction} where direction==1 for range running from end to start.
@@ -818,7 +818,7 @@ public class VamsasDatastore {
   }
 
   /**
-   * 
+   *
    * @param annotation
    * @return true if annotation is not to be stored in document
    */
@@ -950,14 +950,14 @@ public class VamsasDatastore {
         }
 
         if (dataset.getAlignmentCount()>0) {
-          // LOAD ALIGNMENTS from DATASET 
+          // LOAD ALIGNMENTS from DATASET
 
           for (int al=0,nal=dataset.getAlignmentCount(); al<nal; al++) {
             org.vamsas.objects.core.Alignment alignment = dataset.getAlignment(al);
             AlignViewport av = (AlignViewport) getvObj2jv(alignment);
             jalview.datamodel.AlignmentI jal=null;
             if (av!=null)
-              jal = av.getAlignment(); 
+              jal = av.getAlignment();
             iSize = alignment.getAlignmentSequenceCount();
             boolean newal=(jal==null) ? true : false;
             Vector newasAnnots=new Vector();
@@ -988,7 +988,7 @@ public class VamsasDatastore {
                     valseq.getSequence().replace(valGapchar, gapChar),
                     valseq.getStart(),
                     valseq.getEnd()  );
-                
+
                 Vobject datsetseq = (Vobject)valseq.getRefid();
                 if (datsetseq!=null) {
                   alseq.setDatasetSequence((SequenceI)getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
@@ -1018,7 +1018,7 @@ public class VamsasDatastore {
                       // basically do this:
                       // int se[] = getBounds(vasannot[a]);
                       // asa.update(getjAlignmentAnnotation(jal, vasannot[a])); //  update from another annotation object in place.
-                      // asa.createSequenceMapping(alseq, se[0], false); 
+                      // asa.createSequenceMapping(alseq, se[0], false);
 
                     }
                   }
@@ -1155,18 +1155,18 @@ public class VamsasDatastore {
     // summary flags saying what we found over the set of annotation rows.
     boolean[] AeContent = new boolean[] { false, false, false, false, false};
     int[] rangeMap = getMapping(annotation);
-    jalview.datamodel.Annotation[][] anot=new jalview.datamodel.Annotation[][] { 
+    jalview.datamodel.Annotation[][] anot=new jalview.datamodel.Annotation[][] {
         new jalview.datamodel.Annotation[rangeMap.length],
         new jalview.datamodel.Annotation[rangeMap.length]
     };
-    boolean mergeable=true; //false  if 'after positions cant be placed on same annotation row as positions. 
-    
+    boolean mergeable=true; //false  if 'after positions cant be placed on same annotation row as positions.
+
     if (annotation.getAnnotationElementCount()>0) {
       AnnotationElement ae[] = annotation.getAnnotationElement();
       for (int aa = 0; aa < ae.length; aa++)
       {
         int pos = ae[aa].getPosition()-1;// pos counts from 1 to (|seg.start-seg.end|+1)
-        if (pos>=0 && pos<rangeMap.length) { 
+        if (pos>=0 && pos<rangeMap.length) {
           int row=ae[aa].getAfter()?1:0;
           if (anot[row][pos]!=null) {
             // only time this should happen is if the After flag is set.
@@ -1275,8 +1275,8 @@ public class VamsasDatastore {
     }
     if (parsedRangeAnnotation==null) {
       Cache.log.debug("Inserting empty annotation row elements for a whole-alignment annotation.");
-      
-      
+
+
     } else {
       if (parsedRangeAnnotation[3]!=null) {
         Cache.log.warn("Ignoring 'After' annotation row in "+annotation.getVorbaId());
@@ -1315,7 +1315,7 @@ public class VamsasDatastore {
             // make tooltip and display char value
             if (!has[HASDESCSTR]) arow[i].description = arow[i].value + "";
             if (!has[HASDC]) arow[i].displayCharacter=arow[i].value+"";
-          } 
+          }
         }
         int type=jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
         if (has[HASHPHOB]) {
@@ -1338,7 +1338,7 @@ public class VamsasDatastore {
         org.vamsas.objects.core.Property[] props=annotation.getProperty();
         for (int p=0;p<props.length; p++) {
           if (props[p].getName().equalsIgnoreCase("jalview:graphType")) {
-            try { 
+            try {
               // probably a jalview annotation graph so recover the visualization hints.
               jan.graph = jalview.datamodel.AlignmentAnnotation.getGraphValueFromString(props[p].getContent());
             } catch (Exception e) {
@@ -1356,7 +1356,7 @@ public class VamsasDatastore {
 
       return jan;
 
-    } 
+    }
 
     return null;
   }
@@ -1442,7 +1442,7 @@ public class VamsasDatastore {
             posList.add(new Integer(p));
           }
         }
-      } 
+      }
       else if (dseta.getPosCount() > 0)
       {
         int pos = dseta.getPos(0).getI();
@@ -1463,7 +1463,7 @@ public class VamsasDatastore {
     }
     return null;
   }
-  /* not needed now. 
+  /* not needed now.
    * Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov) {
     jalview.datamodel.ProvenanceEntry[] entries = null;
     // TODO: fix App and Action here.
@@ -1519,7 +1519,7 @@ public class VamsasDatastore {
   }
 
   /**
-   * 
+   *
    * @return default initial provenance list for a Jalview created vamsas
    *         object.
    */
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 6a06f90..e2910ee 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -286,7 +286,7 @@ public class WSWUBlastClient
               Data inputs[] = new Data[1];
               Data input= new Data();
               input.setType("sequence");
-              input.setContent(AlignSeq.extractGaps("-. ",sequence.getSequence()));
+              input.setContent(AlignSeq.extractGaps("-. ",sequence.getSequenceAsString()));
               inputs[0]=input;
 
               WSWUBlastService service = new WSWUBlastServiceLocator();
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 1a44c7f..b9bccc0 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -172,7 +172,8 @@ public class GFinder
           if(sequences!=null && sequences.length>0)
           {
             str = jalview.analysis.AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars, sequences[0].getSequence());
+                jalview.util.Comparison.GapChars,
+                sequences[0].getSequenceAsString());
 
             textfield.setText(str);
           }
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 4a78aa1..20b0885 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -126,7 +126,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n)
+    public Color findColour(char c)
     {
         return Color.red;
     }
@@ -139,15 +139,15 @@ public class AnnotationColourGradient extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n, int j)
+    public Color findColour(char c, int j)
     {
         Color currentColour = Color.white;
 
-        if ((threshold == 0) || aboveThreshold(n, j))
+        if ((threshold == 0) || aboveThreshold(c, j))
         {
           if( j<annotation.annotations.length
               && annotation.annotations[j]!=null
-              && !jalview.util.Comparison.isGap(n.charAt(0)))
+              && !jalview.util.Comparison.isGap(c))
           {
             if(  aboveAnnotationThreshold==NO_THRESHOLD
                || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
@@ -155,7 +155,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
             {
               if(colourScheme!=null)
               {
-                currentColour = colourScheme.findColour(n, j);
+                currentColour = colourScheme.findColour(c, j);
               }
               else if(range!=0)
               {
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index f2d2c98..02545a3 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -30,20 +30,18 @@ public class Blosum62ColourScheme
     super();
   }
 
-  public Color findColour(String s, int j)
+  public Color findColour(char res, int j)
   {
-
-    char res = s.charAt(0);
     if ('a' <= res && res <= 'z' )
     {
        // TO UPPERCASE !!!
-       s = String.valueOf( res -= ('a' - 'A') );
+       res -= ('a' - 'A');
     }
 
     if (consensus == null ||
         j >= consensus.length ||
         consensus[j] == null ||
-        (threshold != 0 && !aboveThreshold(s, j)))
+        (threshold != 0 && !aboveThreshold(res, j)))
     {
       return Color.white;
     }
@@ -54,7 +52,7 @@ public class Blosum62ColourScheme
     {
       String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
 
-      if (max.indexOf(s) > -1)
+      if (max.indexOf(res) > -1)
       {
         currentColour = new Color(154, 154, 255);
       }
@@ -66,8 +64,8 @@ public class Blosum62ColourScheme
 
         do
         {
-          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
-              max_aa + 1), s);
+          c += ResidueProperties.getBLOSUM62(
+              max.charAt(max_aa), res);
         }
         while (++max_aa < n);
 
diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 4c20873..eaf2a5f 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -70,23 +70,23 @@ public class ClustalxColourScheme
     int res;
     int i;
     int j = 0;
-    String seq;
+    char [] seq;
 
     while (j < seqs.size())
     {
       seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
 
-      int end_j = seq.length() - 1;
+      int end_j = seq.length - 1;
 
       for (i = start; i <= end_j; i++)
       {
-        if ( (seq.length() - 1) < i)
+        if ( (seq.length - 1) < i)
         {
           res = 23;
         }
         else
         {
-          res =  ResidueProperties.aaIndex[seq.charAt(i)];
+          res =  ResidueProperties.aaIndex[seq[i]];
         }
 
         cons2[i][res]++;
@@ -240,22 +240,22 @@ public class ClustalxColourScheme
     ResidueColour[19] = colours[0]; // V
   }
 
-  public Color findColour(String s)
+  public Color findColour(char c)
   {
     return Color.pink;
   }
 
-  public Color findColour(String s, int j)
+  public Color findColour(char c, int j)
   {
     Color currentColour;
 
 
-    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(s, j)))
+    if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(c, j)))
     {
       return Color.white;
     }
 
-    int i = ResidueProperties.aaIndex[s.charAt(0)];
+    int i = ResidueProperties.aaIndex[c];
 
     currentColour = Color.white;
 
diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index da3093e..6afa3ef 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -22,9 +22,9 @@ import java.awt.*;
 
 public interface ColourSchemeI
 {
-  public Color findColour(String aa);
+  public Color findColour(char c);
 
-  public Color findColour(String s, int j);
+  public Color findColour(char c, int j);
 
   public void setConsensus(java.util.Hashtable [] h);
 
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 4afb321..899fc60 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -44,10 +44,10 @@ public class NucleotideColourScheme extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n)
+    public Color findColour(char c)
     {
         // System.out.println("called"); log.debug
-        return colors[ResidueProperties.nucleotideIndex[n.charAt(0)]];
+        return colors[ResidueProperties.nucleotideIndex[c]];
     }
 
     /**
@@ -58,14 +58,14 @@ public class NucleotideColourScheme extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n, int j)
+    public Color findColour(char c, int j)
     {
         Color currentColour;
-        if ((threshold == 0) || aboveThreshold(n, j))
+        if ((threshold == 0) || aboveThreshold(c, j))
         {
             try
             {
-                currentColour = colors[ ResidueProperties.nucleotideIndex[n.charAt(0)]];
+                currentColour = colors[ ResidueProperties.nucleotideIndex[c]];
             }
             catch (Exception ex)
             {
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 9bd092e..8686894 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -36,12 +36,11 @@ public class PIDColourScheme
     this.thresholds = ResidueProperties.pidThresholds;
   }
 
-  public Color findColour(String s, int j)
+  public Color findColour(char c, int j)
   {
-    char res = s.charAt(0);
-    if ('a' <= res && res <= 'z')
+    if ('a' <= c && c <= 'z')
     {
-      s = String.valueOf(res -= ('a' - 'A'));
+      c -= ('a' - 'A');
     }
 
     if (consensus == null
@@ -51,7 +50,7 @@ public class PIDColourScheme
       return Color.white;
     }
 
-    if ( (threshold != 0) && !aboveThreshold(s, j))
+    if ( (threshold != 0) && !aboveThreshold(c, j))
     {
       return Color.white;
     }
@@ -64,11 +63,11 @@ public class PIDColourScheme
       return Color.white;
 
       if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&
-          consensus[j].contains(s))
+          consensus[j].contains(String.valueOf(c)))
       {
         sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
 
-        if (!jalview.util.Comparison.isGap(res))
+        if (!jalview.util.Comparison.isGap(c))
         {
           for (int i = 0; i < thresholds.length; i++)
           {
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index b905c45..df90500 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -75,21 +75,20 @@ public class ResidueColourScheme implements ColourSchemeI
     /**
     * Find a colour without an index in a sequence
     */
-   public Color findColour(String aa)
+   public Color findColour(char c)
    {
-       return colors[ResidueProperties.aaIndex[aa.charAt(0)]];
+       return colors[ResidueProperties.aaIndex[c]];
    }
 
 
 
-   public Color findColour(String s, int j)
+   public Color findColour(char c, int j)
    {
        Color currentColour;
-       int index = ResidueProperties.aaIndex[s.charAt(0)];
 
-       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+       if ((threshold == 0) || aboveThreshold(c, j))
        {
-           currentColour = colors[index];
+           currentColour = colors[ResidueProperties.aaIndex[c]];
        }
        else
        {
@@ -136,22 +135,20 @@ public class ResidueColourScheme implements ColourSchemeI
      *
      * @return DOCUMENT ME!
      */
-    public boolean aboveThreshold(String s, int j)
+    public boolean aboveThreshold(char c, int j)
     {
-      char c = s.charAt(0);
       if ('a' <= c && c <= 'z')
         {
           // TO UPPERCASE !!!
           //Faster than toUpperCase
           c -= ('a' - 'A');
-          s = String.valueOf(c);
         }
 
         if (consensus == null || consensus[j] == null)
           return false;
 
         if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&
-            consensus[j].contains(s))
+            consensus[j].contains(String.valueOf(c)))
         {
           if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
           {
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 4699dc6..1015073 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1168,14 +1168,14 @@ public class ResidueProperties
     return pog;
   }
 
-  public static int getBLOSUM62(String A1, String A2)
+  public static int getBLOSUM62(char c1, char c2)
   {
     int pog = 0;
 
     try
     {
-      int a = aaIndex[A1.charAt(0)];
-      int b = aaIndex[A2.charAt(0)];
+      int a = aaIndex[c1];
+      int b = aaIndex[c2];
 
       pog = ResidueProperties.BLOSUM62[a][b];
     }
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 4cd9fd3..1c9525c 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -82,18 +82,16 @@ public class ScoreColourScheme extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String s, int j)
+    public Color findColour(char c, int j)
     {
         if (threshold > 0)
         {
-            if (!aboveThreshold(s, j))
+            if (!aboveThreshold(c, j))
             {
                 return Color.white;
             }
         }
 
-        char c = s.charAt(0);
-
         if (jalview.util.Comparison.isGap(c))
         {
             return Color.white;
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index c029b31..00f8f6f 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -186,14 +186,14 @@ public class UserColourScheme
 
 
 
-  public Color findColour(String s, int j)
+  public Color findColour(char c, int j)
   {
       Color currentColour;
-      int index = ResidueProperties.aaIndex[s.charAt(0)];
+      int index = ResidueProperties.aaIndex[c];
 
-      if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+      if ((threshold == 0) || aboveThreshold(c, j))
       {
-        if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
+        if(lowerCaseColours!=null && 'a' <= c && c <= 'z')
           currentColour = lowerCaseColours[index];
         else
           currentColour = colors[index];
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index a4d8b1f..863e80e 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -60,7 +60,7 @@ public class JPredClient
    * @param title String
    * @param msa boolean
    * @param alview AlignmentView
-   * @param viewonly if true then the prediction will be made just on the concatenated visible regions 
+   * @param viewonly if true then the prediction will be made just on the concatenated visible regions
    */
   private void startJPredClient(String title, boolean msa,
                                 jalview.datamodel.AlignmentView alview, AlignFrame parentFrame, boolean viewonly)
@@ -89,13 +89,13 @@ public class JPredClient
       int spos=0;
       int i=0;
       if (viscontigs!=null) {
-        // Construct the delMap - mapping from the positions within the input to Jnet to the contigs in the original sequence  
-        
+        // Construct the delMap - mapping from the positions within the input to Jnet to the contigs in the original sequence
+
         delMap = new int[seq.getEnd()-seq.getStart()+1];
         int gapMap[] = seq.gapMap();
         for (int contig = 0; contig<viscontigs.length; contig += 2)
         {
-           
+
           while (spos<gapMap.length && gapMap[spos]<viscontigs[contig]) {
             spos++;
           }
@@ -106,11 +106,11 @@ public class JPredClient
         int tmap[] = new int[i];
         System.arraycopy(delMap, 0, tmap, 0, i);
         delMap=tmap;
-      } 
+      }
     }
     if (msa && msf.length > 1)
     {
-      
+
       String altitle = "JNet prediction on "+(viewonly?"visible ":"") + seq.getName() +
           " using alignment from " + title;
 
@@ -119,22 +119,22 @@ public class JPredClient
       {
         aln[i] = msf[i].getSeq('-');
       }
-      
-      
+
+
       Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
       if (viewonly) {
         // Remove hidden regions from sequence objects.
         String seqs[] = alview.getSequenceStrings('-');
         for (int i = 0, j = msf.length; i < j; i++)
-        { 
+        {
           aln[i].setSequence(seqs[i]);
-        } 
+        }
         seq.setSequence(seqs[0]);
-      }  
+      }
       wsInfo.setProgressText("Job details for "+(viewonly?"visible ":"")+"MSA based prediction (" +
           title + ") on sequence :\n>" + seq.getName() +
           "\n" +
-          AlignSeq.extractGaps("-. ", seq.getSequence()) +
+          AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
           "\n");
       JPredThread jthread = new JPredThread(wsInfo, altitle, server,
                                             SequenceInfo, aln, delMap, alview, parentFrame, WsURL);
@@ -155,10 +155,10 @@ public class JPredClient
         // Remove hidden regions from input sequence
         String seqs[] = alview.getSequenceStrings('-');
         seq.setSequence(seqs[0]);
-      } 
+      }
       wsInfo.setProgressText("Job details for prediction on "+(viewonly?"visible ":"")+"sequence :\n>" +
           seqname + "\n" +
-          AlignSeq.extractGaps("-. ", seq.getSequence()) +
+          AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
           "\n");
       JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
                                             SequenceInfo, seq, delMap, alview, parentFrame);
@@ -203,7 +203,7 @@ public class JPredClient
 
     wsInfo.setProgressText("Job details for MSA based prediction (" +
                            title + ") on sequence :\n>" + seq.getName() + "\n" +
-                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
                            "\n");
     SequenceI aln[] = new SequenceI[msf.length];
     for (int i = 0, j = msf.length; i < j; i++)
@@ -232,7 +232,7 @@ public class JPredClient
     }
     wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
                            seq.getName() + "\n" +
-                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
                            "\n");
     String altitle = "JNet prediction for sequence " + seq.getName() + " from " +
         title;
diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 15b8bd8..f2592ff 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -142,7 +142,7 @@ implements WSClientI
                                                  gc);
 
           SequenceI profileseq=al.getSequenceAt(FirstSeq);
-          profileseq.setSequence(sqs[msaIndex].getSequence());
+          profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
         }
 
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
@@ -181,7 +181,7 @@ implements WSClientI
             sb.append(gc);
           }
           for (int s=1,ns=al.getHeight(); s<ns; s++) {
-            String sq = al.getSequenceAt(s).getSequence();
+            String sq = al.getSequenceAt(s).getSequenceAsString();
             int diff=gapMap[r]-sq.length();
             if (diff>0) {
               // pad gaps
@@ -225,7 +225,7 @@ implements WSClientI
           for (int s=0,ns=al.getHeight(); s<ns; s++) {
             SequenceI sqobj = al.getSequenceAt(s);
             if (sqobj!=profileseq) {
-              String sq = al.getSequenceAt(s).getSequence();
+              String sq = al.getSequenceAt(s).getSequenceAsString();
               if (sq.length()<=spos+offset) {
                 // pad sequence
                 int diff=spos+offset-sq.length()-1;
@@ -252,7 +252,7 @@ implements WSClientI
           sb.append(gc);
         }
         for (int s=1,ns=al.getHeight(); s<ns; s++) {
-          String sq = al.getSequenceAt(s).getSequence();
+          String sq = al.getSequenceAt(s).getSequenceAsString();
           // pad sequence
           int diff=origseq.getLength()-sq.length();
           while (diff>0) {
@@ -268,7 +268,8 @@ implements WSClientI
     {
       super();
       this.predMap = delMap;
-      String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());
+      String sq = AlignSeq.extractGaps(Comparison.GapChars,
+                                       seq.getSequenceAsString());
       if (sq.length() >= 20)
       {
         this.SequenceInfo = SequenceInfo;
diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 3fd5fbc..cd14a24 100644
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -127,20 +127,20 @@ class MsaWSThread
         {
           seqarray[n] = new vamsas.objects.simple.Sequence();
           seqarray[n].setId(newname);
-          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequence()
+          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
                                : AlignSeq.extractGaps(
                                    jalview.util.Comparison.GapChars, seqs[i]
-                                   .getSequence()));
+                                   .getSequenceAsString()));
         }
         else
         {
           String empty = null;
           if (seqs[i].getEnd() >= seqs[i].getStart())
           {
-            empty = (submitGaps) ? seqs[i].getSequence()
+            empty = (submitGaps) ? seqs[i].getSequenceAsString()
                 : AlignSeq.extractGaps(
                     jalview.util.Comparison.GapChars, seqs[i]
-                    .getSequence());
+                    .getSequenceAsString());
           }
           emptySeqs.add(new String[]
                         {newname, empty});