X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=04977e852fcd85d83afaee169af0423b76b7468f;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=3689433aefcdcba248a8c16fdb0d005f187a436f;hpb=9efc6af45120e24f7a11cc8ce6409139844e5001;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3689433..04977e8 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.datamodel;
 
@@ -22,18 +21,30 @@ import java.util.*;
 
 import jalview.analysis.*;
 
-/** Data structure to hold and manipulate a multiple sequence alignment
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
  */
-public class Alignment
-    implements AlignmentI
+/**
+ * @author JimP
+ * 
+ */
+public class Alignment implements AlignmentI
 {
   protected Alignment dataset;
+
   protected Vector sequences;
+
   protected Vector groups = new Vector();
+
   protected char gapCharacter = '-';
+
   protected int type = NUCLEOTIDE;
+
   public static final int PROTEIN = 0;
+
   public static final int NUCLEOTIDE = 1;
+  
+  public boolean hasRNAStructure = false;
 
   /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
@@ -64,8 +75,9 @@ public class Alignment
 
   }
 
-  /** Make an alignment from an array of Sequences.
-   *
+  /**
+   * Make an alignment from an array of Sequences.
+   * 
    * @param sequences
    */
   public Alignment(SequenceI[] seqs)
@@ -75,20 +87,25 @@ public class Alignment
 
   /**
    * Make a new alignment from an array of SeqCigars
-   * @param seqs SeqCigar[]
+   * 
+   * @param seqs
+   *          SeqCigar[]
    */
   public Alignment(SeqCigar[] alseqs)
   {
-    SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter,
-        new ColumnSelection(), null);
+    SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
+            gapCharacter, new ColumnSelection(), null);
     initAlignment(seqs);
   }
 
   /**
-   * Make a new alignment from an CigarArray
-   * JBPNote - can only do this when compactAlignment does not contain hidden regions.
-   * JBPNote - must also check that compactAlignment resolves to a set of SeqCigars - or construct them appropriately.
-   * @param compactAlignment CigarArray
+   * Make a new alignment from an CigarArray JBPNote - can only do this when
+   * compactAlignment does not contain hidden regions. JBPNote - must also check
+   * that compactAlignment resolves to a set of SeqCigars - or construct them
+   * appropriately.
+   * 
+   * @param compactAlignment
+   *          CigarArray
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
@@ -98,7 +115,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Vector getSequences()
@@ -108,7 +125,7 @@ public class Alignment
 
   public SequenceI[] getSequencesArray()
   {
-    if (sequences==null)
+    if (sequences == null)
       return null;
     SequenceI[] reply = new SequenceI[sequences.size()];
     for (int i = 0; i < sequences.size(); i++)
@@ -120,14 +137,15 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *          DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceI getSequenceAt(int i)
   {
-    if (i < sequences.size())
+    if (i>-1 && i < sequences.size())
     {
       return (SequenceI) sequences.elementAt(i);
     }
@@ -135,8 +153,9 @@ public class Alignment
     return null;
   }
 
-  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   *
+  /**
+   * Adds a sequence to the alignment. Recalculates maxLength and size.
+   * 
    * @param snew
    */
   public void addSequence(SequenceI snew)
@@ -156,17 +175,22 @@ public class Alignment
         snew = adding;
       }
     }
-    if (sequences==null) {
-      initAlignment(new SequenceI[] { snew });
-    } else {
+    if (sequences == null)
+    {
+      initAlignment(new SequenceI[]
+      { snew });
+    }
+    else
+    {
       sequences.addElement(snew);
     }
-    if (hiddenSequences!=null)
+    if (hiddenSequences != null)
       hiddenSequences.adjustHeightSequenceAdded();
   }
 
-  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   *
+  /**
+   * Adds a sequence to the alignment. Recalculates maxLength and size.
+   * 
    * @param snew
    */
   public void setSequenceAt(int i, SequenceI snew)
@@ -179,7 +203,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Vector getGroups()
@@ -189,7 +213,7 @@ public class Alignment
 
   public void finalize()
   {
-    if(getDataset()!=null)
+    if (getDataset() != null)
       getDataset().removeAlignmentRef();
 
     dataset = null;
@@ -200,11 +224,12 @@ public class Alignment
   }
 
   /**
-   * decrement the alignmentRefs counter by one and call finalize if it goes to zero.
+   * decrement the alignmentRefs counter by one and call finalize if it goes to
+   * zero.
    */
   private void removeAlignmentRef()
   {
-    if (--alignmentRefs==0)
+    if (--alignmentRefs == 0)
     {
       finalize();
     }
@@ -212,8 +237,9 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
+   * 
+   * @param s
+   *          DOCUMENT ME!
    */
   public void deleteSequence(SequenceI s)
   {
@@ -222,8 +248,9 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+   * 
+   * @param i
+   *          DOCUMENT ME!
    */
   public void deleteSequence(int i)
   {
@@ -252,9 +279,10 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   *
+   * 
+   * @param s
+   *          DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceGroup[] findAllGroups(SequenceI s)
@@ -317,10 +345,71 @@ public class Alignment
   }
 
   /**
-   * DOCUMENT ME!
+   * remove any annotation that references gp
+   * 
+   * @param gp
+   *          (if null, removes all group associated annotation)
    */
+  private void removeAnnotationForGroup(SequenceGroup gp)
+  {
+    if (annotations == null || annotations.length == 0)
+    {
+      return;
+    }
+    // remove annotation very quickly
+    AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+    int i, p, k;
+    if (gp == null)
+    {
+      for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+      {
+        if (annotations[i].groupRef != null)
+        {
+          todelete[p++] = annotations[i];
+        }
+        else
+        {
+          tokeep[k++] = annotations[i];
+        }
+      }
+    }
+    else
+    {
+      for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+      {
+        if (annotations[i].groupRef == gp)
+        {
+          todelete[p++] = annotations[i];
+        }
+        else
+        {
+          tokeep[k++] = annotations[i];
+        }
+      }
+    }
+    if (p > 0)
+    {
+      // clear out the group associated annotation.
+      for (i = 0; i < p; i++)
+      {
+        unhookAnnotation(todelete[i]);
+        todelete[i] = null;
+      }
+      t = new AlignmentAnnotation[k];
+      for (i = 0; i < k; i++)
+      {
+        t[i] = tokeep[i];
+      }
+      annotations = t;
+    }
+  }
+
   public void deleteAllGroups()
   {
+    if (annotations != null)
+    {
+      removeAnnotationForGroup(null);
+    }
     groups.removeAllElements();
   }
 
@@ -329,6 +418,7 @@ public class Alignment
   {
     if (groups.contains(g))
     {
+      removeAnnotationForGroup(g);
       groups.removeElement(g);
     }
   }
@@ -336,24 +426,54 @@ public class Alignment
   /**    */
   public SequenceI findName(String name)
   {
-    return findName(name,false);
+    return findName(name, false);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
    */
   public SequenceI findName(String token, boolean b)
   {
+    return findName(null, token, b);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+   * boolean)
+   */
+  public SequenceI findName(SequenceI startAfter, String token, boolean b)
+  {
 
     int i = 0;
-    SequenceI sq=null;
-    String sqname=null;
+    SequenceI sq = null;
+    String sqname = null;
+    if (startAfter != null)
+    {
+      // try to find the sequence in the alignment
+      boolean matched = false;
+      while (i < sequences.size())
+      {
+        if (getSequenceAt(i++) == startAfter)
+        {
+          matched = true;
+          break;
+        }
+      }
+      if (!matched)
+      {
+        i = 0;
+      }
+    }
     while (i < sequences.size())
     {
       sq = getSequenceAt(i);
       sqname = sq.getName();
       if (sqname.equals(token) // exact match
-          || (b && // allow imperfect matches - case varies 
+              || (b && // allow imperfect matches - case varies
               (sqname.equalsIgnoreCase(token))))
       {
         return getSequenceAt(i);
@@ -364,6 +484,7 @@ public class Alignment
 
     return null;
   }
+
   public SequenceI[] findSequenceMatch(String name)
   {
     Vector matches = new Vector();
@@ -388,7 +509,11 @@ public class Alignment
 
   }
 
-  /**    */
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+   */
   public int findIndex(SequenceI s)
   {
     int i = 0;
@@ -406,9 +531,30 @@ public class Alignment
     return -1;
   }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+   */
+  public int findIndex(SearchResults results)
+  {
+    int i = 0;
+
+    while (i < sequences.size())
+    {
+      if (results.involvesSequence(getSequenceAt(i)))
+      {
+        return i;
+      }
+      i++;
+    }
+    return -1;
+  }
+
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getHeight()
@@ -418,7 +564,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getWidth()
@@ -438,8 +584,9 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param gc DOCUMENT ME!
+   * 
+   * @param gc
+   *          DOCUMENT ME!
    */
   public void setGapCharacter(char gc)
   {
@@ -448,17 +595,14 @@ public class Alignment
     for (int i = 0; i < sequences.size(); i++)
     {
       Sequence seq = (Sequence) sequences.elementAt(i);
-      seq.setSequence(seq.getSequenceAsString()
-                      .replace('.', gc)
-                      .replace('-', gc)
-                      .replace(' ', gc)
-          );
+      seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+              .replace('-', gc).replace(' ', gc));
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public char getGapCharacter()
@@ -466,30 +610,55 @@ public class Alignment
     return gapCharacter;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#isAligned()
    */
   public boolean isAligned()
   {
-    int width = getWidth();
+    return isAligned(false);
+  }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+   */
+  public boolean isAligned(boolean includeHidden)
+  {
+    int width = getWidth();
+    if (hiddenSequences == null || hiddenSequences.getSize() == 0)
+    {
+      includeHidden = true; // no hidden sequences to check against.
+    }
     for (int i = 0; i < sequences.size(); i++)
     {
-      if (getSequenceAt(i).getLength() != width)
+      if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
       {
-        return false;
+        if (getSequenceAt(i).getLength() != width)
+        {
+          return false;
+        }
       }
     }
 
     return true;
   }
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+   * AlignmentAnnotation)
    */
   public boolean deleteAnnotation(AlignmentAnnotation aa)
   {
+    return deleteAnnotation(aa, true);
+  }
+  
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+  {
     int aSize = 1;
 
     if (annotations != null)
@@ -504,36 +673,71 @@ public class Alignment
 
     AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
 
-    boolean swap=false;
+    boolean swap = false;
     int tIndex = 0;
 
     for (int i = 0; i < aSize; i++)
     {
       if (annotations[i] == aa)
       {
-        swap=true;
+        swap = true;
         continue;
       }
-      if (tIndex<temp.length)
+      if (tIndex < temp.length)
         temp[tIndex++] = annotations[i];
     }
 
     if (swap)
     {
       annotations = temp;
-      if(aa.sequenceRef!=null)
-        aa.sequenceRef.removeAlignmentAnnotation(aa);
+      if (unhook) {
+        unhookAnnotation(aa);
+      }
     }
     return swap;
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param aa DOCUMENT ME!
+   * remove any object references associated with this annotation
+   * 
+   * @param aa
+   */
+  private void unhookAnnotation(AlignmentAnnotation aa)
+  {
+    if (aa.sequenceRef != null)
+    {
+      aa.sequenceRef.removeAlignmentAnnotation(aa);
+    }
+    if (aa.groupRef != null)
+    {
+      // probably need to do more here in the future (post 2.5.0)
+      aa.groupRef = null;
+    }
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * AlignmentAnnotation)
    */
   public void addAnnotation(AlignmentAnnotation aa)
   {
+    addAnnotation(aa, -1);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * AlignmentAnnotation, int)
+   */
+  public void addAnnotation(AlignmentAnnotation aa, int pos)
+  {
+    if(aa.getRNAStruc()!= null){
+      hasRNAStructure=true;
+    }
+    
     int aSize = 1;
     if (annotations != null)
     {
@@ -541,16 +745,28 @@ public class Alignment
     }
 
     AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
-    temp[aSize - 1] = aa;
-
     int i = 0;
-
+    if (pos == -1 || pos >= aSize)
+    {
+      temp[aSize - 1] = aa;
+    }
+    else
+    {
+      temp[pos] = aa;
+    }
     if (aSize > 1)
     {
-      for (i = 0; i < (aSize - 1); i++)
+      int p = 0;
+      for (i = 0; i < (aSize - 1); i++, p++)
       {
-        temp[i] = annotations[i];
+        if (p == pos)
+        {
+          p++;
+        }
+        if (p < temp.length)
+        {
+          temp[p] = annotations[i];
+        }
       }
     }
 
@@ -591,7 +807,7 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public AlignmentAnnotation[] getAlignmentAnnotation()
@@ -622,6 +838,11 @@ public class Alignment
       return false;
     }
   }
+  
+  public boolean hasRNAStructure(){
+    //TODO can it happen that structure is removed from alignment?
+    return hasRNAStructure;
+  }
 
   public void setDataset(Alignment data)
   {
@@ -653,10 +874,12 @@ public class Alignment
     }
     dataset.addAlignmentRef();
   }
+
   /**
    * reference count for number of alignments referencing this one.
    */
-  int alignmentRefs=0;
+  int alignmentRefs = 0;
+
   /**
    * increase reference count to this alignment.
    */
@@ -674,7 +897,7 @@ public class Alignment
   {
     boolean modified = false;
 
-    //Remove excess gaps from the end of alignment
+    // Remove excess gaps from the end of alignment
     int maxLength = -1;
 
     SequenceI current;
@@ -683,8 +906,8 @@ public class Alignment
       current = getSequenceAt(i);
       for (int j = current.getLength(); j > maxLength; j--)
       {
-        if (j > maxLength && !jalview.util.Comparison.isGap(
-            current.getCharAt(j)))
+        if (j > maxLength
+                && !jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
           maxLength = j;
           break;
@@ -695,16 +918,14 @@ public class Alignment
     maxLength++;
 
     int cLength;
-    for (int i = 0; i < sequences.size();
-         i++)
+    for (int i = 0; i < sequences.size(); i++)
     {
       current = getSequenceAt(i);
       cLength = current.getLength();
 
       if (cLength < maxLength)
       {
-        current.insertCharAt(cLength,
-                             maxLength - cLength, gapCharacter);
+        current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
         modified = true;
       }
       else if (current.getLength() > maxLength)
@@ -715,6 +936,111 @@ public class Alignment
     return modified;
   }
 
+  /**
+   * Justify the sequences to the left or right by deleting and inserting gaps
+   * before the initial residue or after the terminal residue
+   * 
+   * @param right
+   *          true if alignment padded to right, false to justify to left
+   * @return true if alignment was changed
+   */
+  public boolean justify(boolean right)
+  {
+    boolean modified = false;
+
+    // Remove excess gaps from the end of alignment
+    int maxLength = -1;
+    int ends[] = new int[sequences.size() * 2];
+    SequenceI current;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      current = getSequenceAt(i);
+      // This should really be a sequence method
+      ends[i * 2] = current.findIndex(current.getStart());
+      ends[i * 2 + 1] = current.findIndex(current.getStart()
+              + current.getLength());
+      boolean hitres = false;
+      for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
+      {
+        if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+        {
+          if (!hitres)
+          {
+            ends[i * 2] = j;
+            hitres = true;
+          }
+          else
+          {
+            ends[i * 2 + 1] = j;
+            if (j - ends[i * 2] > maxLength)
+            {
+              maxLength = j - ends[i * 2];
+            }
+          }
+        }
+      }
+    }
+
+    maxLength++;
+    // now edit the flanking gaps to justify to either left or right
+    int cLength, extent, diff;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      current = getSequenceAt(i);
+
+      cLength = 1 + ends[i * 2 + 1] - ends[i * 2];
+      diff = maxLength - cLength; // number of gaps to indent
+      extent = current.getLength();
+      if (right)
+      {
+        // right justify
+        if (extent > ends[i * 2 + 1])
+        {
+          current.deleteChars(ends[i * 2 + 1] + 1, extent);
+          modified = true;
+        }
+        if (ends[i * 2] > diff)
+        {
+          current.deleteChars(0, ends[i * 2] - diff);
+          modified = true;
+        }
+        else
+        {
+          if (ends[i * 2] < diff)
+          {
+            current.insertCharAt(0, diff - ends[i * 2], gapCharacter);
+            modified = true;
+          }
+        }
+      }
+      else
+      {
+        // left justify
+        if (ends[i * 2] > 0)
+        {
+          current.deleteChars(0, ends[i * 2]);
+          modified = true;
+          ends[i * 2 + 1] -= ends[i * 2];
+          extent -= ends[i * 2];
+        }
+        if (extent > maxLength)
+        {
+          current.deleteChars(maxLength + 1, extent);
+          modified = true;
+        }
+        else
+        {
+          if (extent < maxLength)
+          {
+            current.insertCharAt(extent, maxLength - extent, gapCharacter);
+            modified = true;
+          }
+        }
+      }
+    }
+    return modified;
+  }
+
   public HiddenSequences getHiddenSequences()
   {
     return hiddenSequences;
@@ -725,7 +1051,7 @@ public class Alignment
     SeqCigar alseqs[] = new SeqCigar[sequences.size()];
     for (int i = 0; i < sequences.size(); i++)
     {
-      alseqs[i] = new SeqCigar( (SequenceI) sequences.elementAt(i));
+      alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
     }
     CigarArray cal = new CigarArray(alseqs);
     cal.addOperation(CigarArray.M, getWidth());
@@ -734,15 +1060,15 @@ public class Alignment
 
   public void setProperty(Object key, Object value)
   {
-    if(alignmentProperties==null)
+    if (alignmentProperties == null)
       alignmentProperties = new Hashtable();
 
-    alignmentProperties.put(key,value);
+    alignmentProperties.put(key, value);
   }
 
   public Object getProperty(Object key)
   {
-    if(alignmentProperties!=null)
+    if (alignmentProperties != null)
       return alignmentProperties.get(key);
     else
       return null;
@@ -752,26 +1078,35 @@ public class Alignment
   {
     return alignmentProperties;
   }
-  AlignedCodonFrame[] codonFrameList=null;
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+
+  AlignedCodonFrame[] codonFrameList = null;
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+   * )
    */
   public void addCodonFrame(AlignedCodonFrame codons)
   {
-    if (codons==null)
+    if (codons == null)
       return;
-    if (codonFrameList==null)
+    if (codonFrameList == null)
     {
-      codonFrameList = new AlignedCodonFrame[] { codons };
+      codonFrameList = new AlignedCodonFrame[]
+      { codons };
       return;
     }
-    AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
+    AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
     System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
     t[codonFrameList.length] = codons;
     codonFrameList = t;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
    */
   public AlignedCodonFrame getCodonFrame(int index)
@@ -779,27 +1114,32 @@ public class Alignment
     return codonFrameList[index];
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
-    if (seq==null || codonFrameList==null)
+    if (seq == null || codonFrameList == null)
       return null;
-    Vector cframes=new Vector();
-    for (int f=0;f<codonFrameList.length; f++)
+    Vector cframes = new Vector();
+    for (int f = 0; f < codonFrameList.length; f++)
     {
       if (codonFrameList[f].involvesSequence(seq))
         cframes.addElement(codonFrameList[f]);
     }
-    if (cframes.size()==0)
+    if (cframes.size() == 0)
       return null;
     AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
     cframes.copyInto(cfr);
     return cfr;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
   public AlignedCodonFrame[] getCodonFrames()
@@ -807,23 +1147,27 @@ public class Alignment
     return codonFrameList;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+   * AlignedCodonFrame)
    */
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
-    if (codons==null || codonFrameList==null)
+    if (codons == null || codonFrameList == null)
       return false;
-    boolean removed=false;
-    int i=0,iSize=codonFrameList.length;
-    while (i<iSize)
+    boolean removed = false;
+    int i = 0, iSize = codonFrameList.length;
+    while (i < iSize)
     {
-      if (codonFrameList[i]==codons)
+      if (codonFrameList[i] == codons)
       {
-        removed=true;
-        if (i+1<iSize)
+        removed = true;
+        if (i + 1 < iSize)
         {
-          System.arraycopy(codonFrameList,i+1,codonFrameList, i, iSize-i-1);
+          System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
+                  - i - 1);
         }
         iSize--;
       }
@@ -834,4 +1178,119 @@ public class Alignment
     }
     return removed;
   }
+
+  public void append(AlignmentI toappend)
+  {
+    // TODO test this method for a future 2.5 release
+    // currently tested for use in jalview.gui.SequenceFetcher
+    boolean samegap = toappend.getGapCharacter() == getGapCharacter();
+    char oldc = toappend.getGapCharacter();
+    boolean hashidden = toappend.getHiddenSequences() != null
+            && toappend.getHiddenSequences().hiddenSequences != null;
+    // get all sequences including any hidden ones
+    Vector sqs = (hashidden) ? toappend.getHiddenSequences()
+            .getFullAlignment().getSequences() : toappend.getSequences();
+    if (sqs != null)
+    {
+      Enumeration sq = sqs.elements();
+      while (sq.hasMoreElements())
+      {
+        SequenceI addedsq = (SequenceI) sq.nextElement();
+        if (!samegap)
+        {
+          char[] oldseq = addedsq.getSequence();
+          for (int c = 0; c < oldseq.length; c++)
+          {
+            if (oldseq[c] == oldc)
+            {
+              oldseq[c] = gapCharacter;
+            }
+          }
+        }
+        addSequence(addedsq);
+      }
+    }
+    AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+    for (int a = 0; alan != null && a < alan.length; a++)
+    {
+      addAnnotation(alan[a]);
+    }
+    AlignedCodonFrame[] acod = toappend.getCodonFrames();
+    for (int a = 0; acod != null && a < acod.length; a++)
+    {
+      this.addCodonFrame(acod[a]);
+    }
+    Vector sg = toappend.getGroups();
+    if (sg != null)
+    {
+      Enumeration el = sg.elements();
+      while (el.hasMoreElements())
+      {
+        addGroup((SequenceGroup) el.nextElement());
+      }
+    }
+    if (toappend.getHiddenSequences() != null)
+    {
+      HiddenSequences hs = toappend.getHiddenSequences();
+      if (hiddenSequences == null)
+      {
+        hiddenSequences = new HiddenSequences(this);
+      }
+      if (hs.hiddenSequences != null)
+      {
+        for (int s = 0; s < hs.hiddenSequences.length; s++)
+        {
+          // hide the newly appended sequence in the alignment
+          if (hs.hiddenSequences[s] != null)
+          {
+            hiddenSequences.hideSequence(hs.hiddenSequences[s]);
+          }
+        }
+      }
+    }
+    if (toappend.getProperties() != null)
+    {
+      // we really can't do very much here - just try to concatenate strings
+      // where property collisions occur.
+      Enumeration key = toappend.getProperties().keys();
+      while (key.hasMoreElements())
+      {
+        Object k = key.nextElement();
+        Object ourval = this.getProperty(k);
+        Object toapprop = toappend.getProperty(k);
+        if (ourval != null)
+        {
+          if (ourval.getClass().equals(toapprop.getClass())
+                  && !ourval.equals(toapprop))
+          {
+            if (ourval instanceof String)
+            {
+              // append strings
+              this.setProperty(k, ((String) ourval) + "; "
+                      + ((String) toapprop));
+            }
+            else
+            {
+              if (ourval instanceof Vector)
+              {
+                // append vectors
+                Enumeration theirv = ((Vector) toapprop).elements();
+                while (theirv.hasMoreElements())
+                {
+                  ((Vector) ourval).addElement(theirv);
+                }
+              }
+            }
+          }
+        }
+        else
+        {
+          // just add new property directly
+          setProperty(k, toapprop);
+        }
+
+      }
+    }
+  }
+
 }