X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=5d97fe3bd3759235e7ad84571297bc079157e568;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=08c04f5b779f3b73c27cdba8baf081912a48d199;hpb=961b10e4c895aadb7fc9df82a641c6c53c0d5c70;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 08c04f5..5d97fe3 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,37 +1,40 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
 import java.util.*;
 
-import jalview.analysis.*;
-
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
+/**
+ * @author JimP
+ * 
+ */
 public class Alignment implements AlignmentI
 {
   protected Alignment dataset;
 
-  protected Vector sequences;
+  protected List<SequenceI> sequences;
 
-  protected Vector groups = new Vector();
+  protected List<SequenceGroup> groups = java.util.Collections
+          .synchronizedList(new ArrayList<SequenceGroup>());
 
   protected char gapCharacter = '-';
 
@@ -41,6 +44,8 @@ public class Alignment implements AlignmentI
 
   public static final int NUCLEOTIDE = 1;
 
+  public boolean hasRNAStructure = false;
+
   /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
 
@@ -61,11 +66,12 @@ public class Alignment implements AlignmentI
       type = PROTEIN;
     }
 
-    sequences = new Vector();
+    sequences = java.util.Collections
+            .synchronizedList(new ArrayList<SequenceI>());
 
     for (i = 0; i < seqs.length; i++)
     {
-      sequences.addElement(seqs[i]);
+      sequences.add(seqs[i]);
     }
 
   }
@@ -84,7 +90,7 @@ public class Alignment implements AlignmentI
    * Make a new alignment from an array of SeqCigars
    * 
    * @param seqs
-   *                SeqCigar[]
+   *          SeqCigar[]
    */
   public Alignment(SeqCigar[] alseqs)
   {
@@ -100,7 +106,7 @@ public class Alignment implements AlignmentI
    * appropriately.
    * 
    * @param compactAlignment
-   *                CigarArray
+   *          CigarArray
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
@@ -113,38 +119,50 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getSequences()
+  @Override
+  public List<SequenceI> getSequences()
   {
     return sequences;
   }
 
+  @Override
+  public List<SequenceI> getSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to
+    // work on this.
+    return sequences;
+  }
+
+  @Override
   public SequenceI[] getSequencesArray()
   {
     if (sequences == null)
       return null;
-    SequenceI[] reply = new SequenceI[sequences.size()];
-    for (int i = 0; i < sequences.size(); i++)
+    synchronized (sequences)
     {
-      reply[i] = (SequenceI) sequences.elementAt(i);
+      return sequences.toArray(new SequenceI[sequences.size()]);
     }
-    return reply;
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public SequenceI getSequenceAt(int i)
   {
-    if (i < sequences.size())
+    synchronized (sequences)
     {
-      return (SequenceI) sequences.elementAt(i);
+      if (i > -1 && i < sequences.size())
+      {
+        return sequences.get(i);
+      }
     }
-
     return null;
   }
 
@@ -153,6 +171,7 @@ public class Alignment implements AlignmentI
    * 
    * @param snew
    */
+  @Override
   public void addSequence(SequenceI snew)
   {
     if (dataset != null)
@@ -177,7 +196,10 @@ public class Alignment implements AlignmentI
     }
     else
     {
-      sequences.addElement(snew);
+      synchronized (sequences)
+      {
+        sequences.add(snew);
+      }
     }
     if (hiddenSequences != null)
       hiddenSequences.adjustHeightSequenceAdded();
@@ -188,12 +210,15 @@ public class Alignment implements AlignmentI
    * 
    * @param snew
    */
+  @Override
   public void setSequenceAt(int i, SequenceI snew)
   {
     SequenceI oldseq = getSequenceAt(i);
-    deleteSequence(oldseq);
-
-    sequences.setElementAt(snew, i);
+    deleteSequence(i);
+    synchronized (sequences)
+    {
+      sequences.set(i, snew);
+    }
   }
 
   /**
@@ -201,11 +226,13 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getGroups()
+  @Override
+  public List<SequenceGroup> getGroups()
   {
     return groups;
   }
 
+  @Override
   public void finalize()
   {
     if (getDataset() != null)
@@ -234,8 +261,9 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(SequenceI s)
   {
     deleteSequence(findIndex(s));
@@ -245,118 +273,203 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(int i)
   {
     if (i > -1 && i < getHeight())
     {
-      sequences.removeElementAt(i);
+      synchronized (sequences)
+      {
+        sequences.remove(i);
+      }
       hiddenSequences.adjustHeightSequenceDeleted(i);
     }
   }
 
-  /**    */
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+   */
+  @Override
   public SequenceGroup findGroup(SequenceI s)
   {
-    for (int i = 0; i < this.groups.size(); i++)
+    synchronized (groups)
     {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
-      if (sg.getSequences(null).contains(s))
+      for (int i = 0; i < this.groups.size(); i++)
       {
-        return sg;
+        SequenceGroup sg = groups.get(i);
+
+        if (sg.getSequences(null).contains(s))
+        {
+          return sg;
+        }
       }
     }
-
     return null;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *                DOCUMENT ME!
+  /*
+   * (non-Javadoc)
    * 
-   * @return DOCUMENT ME!
+   * @see
+   * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
    */
+  @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-    Vector temp = new Vector();
+    ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
 
-    int gSize = groups.size();
-    for (int i = 0; i < gSize; i++)
+    synchronized (groups)
     {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-      if (sg == null || sg.getSequences(null) == null)
+      int gSize = groups.size();
+      for (int i = 0; i < gSize; i++)
       {
-        this.deleteGroup(sg);
-        gSize--;
-        continue;
-      }
+        SequenceGroup sg = groups.get(i);
+        if (sg == null || sg.getSequences(null) == null)
+        {
+          this.deleteGroup(sg);
+          gSize--;
+          continue;
+        }
 
-      if (sg.getSequences(null).contains(s))
-      {
-        temp.addElement(sg);
+        if (sg.getSequences(null).contains(s))
+        {
+          temp.add(sg);
+        }
       }
     }
-
     SequenceGroup[] ret = new SequenceGroup[temp.size()];
-
-    for (int i = 0; i < temp.size(); i++)
-    {
-      ret[i] = (SequenceGroup) temp.elementAt(i);
-    }
-
-    return ret;
+    return temp.toArray(ret);
   }
 
   /**    */
+  @Override
   public void addGroup(SequenceGroup sg)
   {
-    if (!groups.contains(sg))
+    synchronized (groups)
     {
-      if (hiddenSequences.getSize() > 0)
+      if (!groups.contains(sg))
       {
-        int i, iSize = sg.getSize();
-        for (i = 0; i < iSize; i++)
+        if (hiddenSequences.getSize() > 0)
         {
-          if (!sequences.contains(sg.getSequenceAt(i)))
+          int i, iSize = sg.getSize();
+          for (i = 0; i < iSize; i++)
           {
-            sg.deleteSequence(sg.getSequenceAt(i), false);
-            iSize--;
-            i--;
+            if (!sequences.contains(sg.getSequenceAt(i)))
+            {
+              sg.deleteSequence(sg.getSequenceAt(i), false);
+              iSize--;
+              i--;
+            }
           }
-        }
 
-        if (sg.getSize() < 1)
-        {
-          return;
+          if (sg.getSize() < 1)
+          {
+            return;
+          }
         }
+        sg.setContext(this);
+        groups.add(sg);
       }
-
-      groups.addElement(sg);
     }
   }
 
   /**
-   * 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;
+    }
+  }
+
+  @Override
   public void deleteAllGroups()
   {
-    groups.removeAllElements();
+    synchronized (groups)
+    {
+      if (annotations != null)
+      {
+        removeAnnotationForGroup(null);
+      }
+      for (SequenceGroup sg:groups) {
+        sg.setContext(null);
+      }
+      groups.clear();
+    }
   }
 
   /**    */
+  @Override
   public void deleteGroup(SequenceGroup g)
   {
-    if (groups.contains(g))
+    synchronized (groups)
     {
-      groups.removeElement(g);
+      if (groups.contains(g))
+      {
+        removeAnnotationForGroup(g);
+        groups.remove(g);
+        g.setContext(null);
+      }
     }
   }
 
   /**    */
+  @Override
   public SequenceI findName(String name)
   {
     return findName(name, false);
@@ -367,6 +480,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
    */
+  @Override
   public SequenceI findName(String token, boolean b)
   {
     return findName(null, token, b);
@@ -376,8 +490,9 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
-   *      boolean)
+   * boolean)
    */
+  @Override
   public SequenceI findName(SequenceI startAfter, String token, boolean b)
   {
 
@@ -418,6 +533,7 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  @Override
   public SequenceI[] findSequenceMatch(String name)
   {
     Vector matches = new Vector();
@@ -441,9 +557,13 @@ public class Alignment implements AlignmentI
     return result;
 
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
    */
+  @Override
   public int findIndex(SequenceI s)
   {
     int i = 0;
@@ -460,14 +580,19 @@ public class Alignment implements AlignmentI
 
     return -1;
   }
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
+  @Override
   public int findIndex(SearchResults results)
   {
-    int i=0;
-    
-    while (i<sequences.size())
+    int i = 0;
+
+    while (i < sequences.size())
     {
       if (results.involvesSequence(getSequenceAt(i)))
       {
@@ -483,6 +608,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getHeight()
   {
     return sequences.size();
@@ -493,6 +619,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getWidth()
   {
     int maxLength = -1;
@@ -512,17 +639,19 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param gc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void setGapCharacter(char gc)
   {
     gapCharacter = gc;
-
-    for (int i = 0; i < sequences.size(); i++)
+    synchronized (sequences)
     {
-      Sequence seq = (Sequence) sequences.elementAt(i);
-      seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
-              '-', gc).replace(' ', gc));
+      for (SequenceI seq : sequences)
+      {
+        seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+                .replace('-', gc).replace(' ', gc));
+      }
     }
   }
 
@@ -531,25 +660,44 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getGapCharacter()
   {
     return gapCharacter;
   }
 
-  /**
-   * DOCUMENT ME!
+  /*
+   * (non-Javadoc)
    * 
-   * @return DOCUMENT ME!
+   * @see jalview.datamodel.AlignmentI#isAligned()
    */
+  @Override
   public boolean isAligned()
   {
-    int width = getWidth();
+    return isAligned(false);
+  }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+   */
+  @Override
+  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;
+        }
       }
     }
 
@@ -559,10 +707,18 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
+   * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+   * AlignmentAnnotation)
    */
+  @Override
   public boolean deleteAnnotation(AlignmentAnnotation aa)
   {
+    return deleteAnnotation(aa, true);
+  }
+
+  @Override
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+  {
     int aSize = 1;
 
     if (annotations != null)
@@ -594,20 +750,58 @@ public class Alignment implements AlignmentI
     if (swap)
     {
       annotations = temp;
-      if (aa.sequenceRef != null)
-        aa.sequenceRef.removeAlignmentAnnotation(aa);
+      if (unhook)
+      {
+        unhookAnnotation(aa);
+      }
     }
     return swap;
   }
 
   /**
-   * DOCUMENT ME!
+   * remove any object references associated with this annotation
    * 
    * @param aa
-   *                DOCUMENT ME!
    */
+  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)
+   */
+  @Override
   public void addAnnotation(AlignmentAnnotation aa)
   {
+    addAnnotation(aa, -1);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * AlignmentAnnotation, int)
+   */
+  @Override
+  public void addAnnotation(AlignmentAnnotation aa, int pos)
+  {
+    if (aa.getRNAStruc() != null)
+    {
+      hasRNAStructure = true;
+    }
+
     int aSize = 1;
     if (annotations != null)
     {
@@ -615,22 +809,35 @@ public class Alignment implements AlignmentI
     }
 
     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];
+        }
       }
     }
 
     annotations = temp;
   }
 
+  @Override
   public void setAnnotationIndex(AlignmentAnnotation aa, int index)
   {
     if (aa == null || annotations == null || annotations.length - 1 < index)
@@ -663,16 +870,16 @@ public class Alignment implements AlignmentI
     annotations = temp;
   }
 
+  @Override
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * returns all annotation on the alignment
    */
   public AlignmentAnnotation[] getAlignmentAnnotation()
   {
     return annotations;
   }
 
+  @Override
   public void setNucleotide(boolean b)
   {
     if (b)
@@ -685,6 +892,7 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
   public boolean isNucleotide()
   {
     if (type == NUCLEOTIDE)
@@ -697,6 +905,14 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public boolean hasRNAStructure()
+  {
+    // TODO can it happen that structure is removed from alignment?
+    return hasRNAStructure;
+  }
+
+  @Override
   public void setDataset(Alignment data)
   {
     if (dataset == null && data == null)
@@ -711,7 +927,7 @@ public class Alignment implements AlignmentI
         currentSeq = getSequenceAt(i);
         if (currentSeq.getDatasetSequence() != null)
         {
-          seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+          seqs[i] = currentSeq.getDatasetSequence();
         }
         else
         {
@@ -741,11 +957,13 @@ public class Alignment implements AlignmentI
     alignmentRefs++;
   }
 
+  @Override
   public Alignment getDataset()
   {
     return dataset;
   }
 
+  @Override
   public boolean padGaps()
   {
     boolean modified = false;
@@ -789,23 +1007,136 @@ public class Alignment implements AlignmentI
     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
+   */
+  @Override
+  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;
+  }
+
+  @Override
   public HiddenSequences getHiddenSequences()
   {
     return hiddenSequences;
   }
 
+  @Override
   public CigarArray getCompactAlignment()
   {
-    SeqCigar alseqs[] = new SeqCigar[sequences.size()];
-    for (int i = 0; i < sequences.size(); i++)
+    synchronized (sequences)
     {
-      alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+      SeqCigar alseqs[] = new SeqCigar[sequences.size()];
+      int i = 0;
+      for (SequenceI seq : sequences)
+      {
+        alseqs[i++] = new SeqCigar(seq);
+      }
+      CigarArray cal = new CigarArray(alseqs);
+      cal.addOperation(CigarArray.M, getWidth());
+      return cal;
     }
-    CigarArray cal = new CigarArray(alseqs);
-    cal.addOperation(CigarArray.M, getWidth());
-    return cal;
   }
 
+  @Override
   public void setProperty(Object key, Object value)
   {
     if (alignmentProperties == null)
@@ -814,6 +1145,7 @@ public class Alignment implements AlignmentI
     alignmentProperties.put(key, value);
   }
 
+  @Override
   public Object getProperty(Object key)
   {
     if (alignmentProperties != null)
@@ -822,6 +1154,7 @@ public class Alignment implements AlignmentI
       return null;
   }
 
+  @Override
   public Hashtable getProperties()
   {
     return alignmentProperties;
@@ -832,8 +1165,11 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   * @see
+   * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+   * )
    */
+  @Override
   public void addCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null)
@@ -855,6 +1191,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
    */
+  @Override
   public AlignedCodonFrame getCodonFrame(int index)
   {
     return codonFrameList[index];
@@ -863,8 +1200,10 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+   * @see
+   * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
+  @Override
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
     if (seq == null || codonFrameList == null)
@@ -887,6 +1226,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
+  @Override
   public AlignedCodonFrame[] getCodonFrames()
   {
     return codonFrameList;
@@ -895,8 +1235,10 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+   * AlignedCodonFrame)
    */
+  @Override
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null || codonFrameList == null)
@@ -923,4 +1265,251 @@ public class Alignment implements AlignmentI
     return removed;
   }
 
+  @Override
+  public void append(AlignmentI toappend)
+  {
+    if (toappend == this)
+    {
+      System.err.println("Self append may cause a deadlock.");
+    }
+    // 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
+    List<SequenceI> sqs = (hashidden) ? toappend.getHiddenSequences()
+            .getFullAlignment().getSequences() : toappend.getSequences();
+    if (sqs != null)
+    {
+      synchronized (sqs)
+      {
+        for (SequenceI addedsq : sqs)
+        {
+          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]);
+    }
+    List<SequenceGroup> sg = toappend.getGroups();
+    if (sg != null)
+    {
+      for (SequenceGroup _sg : sg)
+      {
+        addGroup(_sg);
+      }
+    }
+    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);
+        }
+
+      }
+    }
+  }
+
+  @Override
+  public AlignmentAnnotation findOrCreateAnnotation(String name,
+          String calcId, boolean autoCalc, SequenceI seqRef,
+          SequenceGroup groupRef)
+  {
+    assert (name != null);
+    if (annotations != null)
+    {
+      for (AlignmentAnnotation annot : getAlignmentAnnotation())
+      {
+        if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+                && (calcId == null || annot.getCalcId().equals(calcId))
+                && annot.sequenceRef == seqRef
+                && annot.groupRef == groupRef)
+        {
+          return annot;
+        }
+      }
+    }
+    AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
+            new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
+    annot.hasText = false;
+    annot.setCalcId(new String(calcId));
+    annot.autoCalculated = autoCalc;
+    if (seqRef != null)
+    {
+      annot.setSequenceRef(seqRef);
+    }
+    annot.groupRef = groupRef;
+    addAnnotation(annot);
+
+    return annot;
+  }
+
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+  {
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation a : getAlignmentAnnotation())
+    {
+      if (a.getCalcId() == calcId
+              || (a.getCalcId() != null && calcId != null && a.getCalcId()
+                      .equals(calcId)))
+      {
+        aa.add(a);
+      }
+    }
+    return aa;
+  }
+
+  @Override
+  public void moveSelectedSequencesByOne(SequenceGroup sg,
+          Map<SequenceI, SequenceCollectionI> map, boolean up)
+  {
+    synchronized (sequences)
+    {
+      if (up)
+      {
+
+        for (int i = 1, iSize = sequences.size(); i < iSize; i++)
+        {
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
+
+          SequenceI temp = sequences.get(i - 1);
+          if (sg.getSequences(null).contains(temp))
+          {
+            continue;
+          }
+
+          sequences.set(i, temp);
+          sequences.set(i - 1, seq);
+        }
+      }
+      else
+      {
+        for (int i = sequences.size() - 2; i > -1; i--)
+        {
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
+
+          SequenceI temp = sequences.get(i + 1);
+          if (sg.getSequences(map).contains(temp))
+          {
+            continue;
+          }
+
+          sequences.set(i, temp);
+          sequences.set(i + 1, seq);
+        }
+      }
+
+    }
+  }
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+   alignmentAnnotation.validateRangeAndDisplay();
+   if (isNucleotide() && alignmentAnnotation.isValidStruc())
+   {
+     hasRNAStructure = true;
+   }
+ }
+ @Override
+public int getEndRes()
+{
+  return getWidth()-1;
+}@Override
+public int getStartRes()
+{
+  return 0;
+}
+
+/* In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+@Override
+public AnnotatedCollectionI getContext()
+{
+  return dataset;
+}
 }