X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=ef961d09c419da80074f27865f49b066212d6459;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=a88fa9e88c21755ff7b02d0de5b4e0d9c0903f0e;hpb=ed52d72ae281a74a5496a605e51159931caa925c;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index a88fa9e..ef961d0 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,40 +1,65 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * 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.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT 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 distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+/**
+ * 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 List<SequenceI> sequences;
+
+  protected List<SequenceGroup> groups = java.util.Collections
+          .synchronizedList(new ArrayList<SequenceGroup>());
+
   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;
 
@@ -42,6 +67,8 @@ public class Alignment
 
   public Hashtable alignmentProperties;
 
+  private Set<AlignedCodonFrame> codonFrameList = new LinkedHashSet<AlignedCodonFrame>();
+
   private void initAlignment(SequenceI[] seqs)
   {
     int i = 0;
@@ -55,17 +82,40 @@ public class Alignment
       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]);
+    }
+
+  }
+
+  /**
+   * Make a 'copy' alignment - sequences have new copies of features and
+   * annotations, but share the original dataset sequences.
+   */
+  public Alignment(AlignmentI al)
+  {
+    SequenceI[] seqs = al.getSequencesArray();
+    for (int i = 0; i < seqs.length; i++)
+    {
+      seqs[i] = new Sequence(seqs[i]);
     }
 
+    /*
+     * Share the same dataset sequence mappings (if any). TODO: find a better
+     * place for these to live (alignment dataset?).
+     */
+    this.codonFrameList = ((Alignment) al).codonFrameList;
+
+    initAlignment(seqs);
   }
 
-  /** Make an alignment from an array of Sequences.
-   *
+  /**
+   * Make an alignment from an array of Sequences.
+   * 
    * @param sequences
    */
   public Alignment(SequenceI[] seqs)
@@ -75,70 +125,100 @@ 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)
   {
-    throw new Error("Alignment(CigarArray) not yet implemented");
+    throw new Error(
+            MessageManager
+                    .getString("error.alignment_cigararray_not_implemented"));
     // this(compactAlignment.refCigars);
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @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)
+    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;
+  }
+
+  /**
+   * Returns a map of lists of sequences keyed by sequence name.
+   * 
+   * @return
+   */
+  @Override
+  public Map<String, List<SequenceI>> getSequencesByName()
+  {
+    return AlignmentUtils.getSequencesByName(this);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *          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;
   }
 
-  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   *
+  /**
+   * Adds a sequence to the alignment. Recalculates maxLength and size.
+   * 
    * @param snew
    */
+  @Override
   public void addSequence(SequenceI snew)
   {
     if (dataset != null)
@@ -156,41 +236,56 @@ public class Alignment
         snew = adding;
       }
     }
-    if (sequences==null) {
+    if (sequences == null)
+    {
       initAlignment(new SequenceI[] { snew });
-    } else {
-      sequences.addElement(snew);
     }
-    if (hiddenSequences!=null)
+    else
+    {
+      synchronized (sequences)
+      {
+        sequences.add(snew);
+      }
+    }
+    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
    */
+  @Override
   public void setSequenceAt(int i, SequenceI snew)
   {
-    SequenceI oldseq = getSequenceAt(i);
-    deleteSequence(oldseq);
-
-    sequences.setElementAt(snew, i);
+    synchronized (sequences)
+    {
+      deleteSequence(i);
+      sequences.set(i, snew);
+    }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
-  public Vector getGroups()
+  @Override
+  public List<SequenceGroup> getGroups()
   {
     return groups;
   }
 
+  @Override
   public void finalize()
   {
-    if(getDataset()!=null)
+    if (getDataset() != null)
+    {
       getDataset().removeAlignmentRef();
+    }
 
     dataset = null;
     sequences = null;
@@ -200,11 +295,12 @@ 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();
     }
@@ -212,9 +308,11 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
+   * 
+   * @param s
+   *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(SequenceI s)
   {
     deleteSequence(findIndex(s));
@@ -222,147 +320,242 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+   * 
+   * @param i
+   *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(int i)
   {
     if (i > -1 && i < getHeight())
     {
-      sequences.removeElementAt(i);
-      hiddenSequences.adjustHeightSequenceDeleted(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!
-   *
-   * @return DOCUMENT ME!
+  /*
+   * (non-Javadoc)
+   * 
+   * @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)
+        {
+          this.deleteGroup(sg);
+          gSize--;
+          continue;
+        }
 
-      if (sg.getSequences(null).contains(s))
-      {
-        temp.addElement(sg);
+        if (sg.getSequences().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);
+    return findName(name, false);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
    */
+  @Override
   public SequenceI findName(String token, boolean b)
   {
     return findName(null, token, b);
   }
-  
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String, boolean)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+   * boolean)
    */
+  @Override
   public SequenceI findName(SequenceI startAfter, String token, boolean b)
   {
-  
+
     int i = 0;
-    SequenceI sq=null;
-    String sqname=null;
-    if (startAfter!=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())
+      boolean matched = false;
+      while (i < sequences.size())
       {
-        if (getSequenceAt(i++)==startAfter)
+        if (getSequenceAt(i++) == startAfter)
         {
           matched = true;
           break;
@@ -370,7 +563,7 @@ public class Alignment
       }
       if (!matched)
       {
-        i=0;
+        i = 0;
       }
     }
     while (i < sequences.size())
@@ -378,7 +571,7 @@ public class Alignment
       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);
@@ -389,6 +582,8 @@ public class Alignment
 
     return null;
   }
+
+  @Override
   public SequenceI[] findSequenceMatch(String name)
   {
     Vector matches = new Vector();
@@ -413,7 +608,12 @@ public class Alignment
 
   }
 
-  /**    */
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+   */
+  @Override
   public int findIndex(SequenceI s)
   {
     int i = 0;
@@ -431,11 +631,34 @@ public class Alignment
     return -1;
   }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+   */
+  @Override
+  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!
    */
+  @Override
   public int getHeight()
   {
     return sequences.size();
@@ -443,9 +666,10 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getWidth()
   {
     int maxLength = -1;
@@ -463,58 +687,110 @@ public class Alignment
 
   /**
    * DOCUMENT ME!
-   *
-   * @param gc DOCUMENT ME!
+   * 
+   * @param gc
+   *          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));
+      }
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getGapCharacter()
   {
     return gapCharacter;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+  /*
+   * (non-Javadoc)
+   * 
+   * @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;
+        }
       }
     }
 
     return true;
   }
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
+
+  /**
+   * Delete all annotations, including auto-calculated if the flag is set true.
+   * Returns true if at least one annotation was deleted, else false.
+   * 
+   * @param includingAutoCalculated
+   * @return
+   */
+  @Override
+  public boolean deleteAllAnnotations(boolean includingAutoCalculated)
+  {
+    boolean result = false;
+    for (AlignmentAnnotation alan : getAlignmentAnnotation())
+    {
+      if (!alan.autoCalculated || includingAutoCalculated)
+      {
+        deleteAnnotation(alan);
+        result = true;
+      }
+    }
+    return result;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @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)
@@ -529,36 +805,77 @@ 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)
+   */
+  @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)
     {
@@ -566,22 +883,35 @@ 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];
+        }
       }
     }
 
     annotations = temp;
   }
 
+  @Override
   public void setAnnotationIndex(AlignmentAnnotation aa, int index)
   {
     if (aa == null || annotations == null || annotations.length - 1 < index)
@@ -614,16 +944,16 @@ public class Alignment
     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)
@@ -636,6 +966,7 @@ public class Alignment
     }
   }
 
+  @Override
   public boolean isNucleotide()
   {
     if (type == NUCLEOTIDE)
@@ -648,6 +979,14 @@ public class Alignment
     }
   }
 
+  @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)
@@ -662,7 +1001,7 @@ public class Alignment
         currentSeq = getSequenceAt(i);
         if (currentSeq.getDatasetSequence() != null)
         {
-          seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+          seqs[i] = currentSeq.getDatasetSequence();
         }
         else
         {
@@ -675,13 +1014,36 @@ public class Alignment
     else if (dataset == null && data != null)
     {
       dataset = data;
+      for (int i = 0; i < getHeight(); i++)
+      {
+        SequenceI currentSeq = getSequenceAt(i);
+        SequenceI dsq = currentSeq.getDatasetSequence();
+        if (dsq == null)
+        {
+          dsq = currentSeq.createDatasetSequence();
+          dataset.addSequence(dsq);
+        }
+        else
+        {
+          while (dsq.getDatasetSequence() != null)
+          {
+            dsq = dsq.getDatasetSequence();
+          }
+          if (dataset.findIndex(dsq) == -1)
+          {
+            dataset.addSequence(dsq);
+          }
+        }
+      }
     }
     dataset.addAlignmentRef();
   }
+
   /**
    * reference count for number of alignments referencing this one.
    */
-  int alignmentRefs=0;
+  int alignmentRefs = 0;
+
   /**
    * increase reference count to this alignment.
    */
@@ -690,16 +1052,18 @@ public class Alignment
     alignmentRefs++;
   }
 
+  @Override
   public Alignment getDataset()
   {
     return dataset;
   }
 
+  @Override
   public boolean padGaps()
   {
     boolean modified = false;
 
-    //Remove excess gaps from the end of alignment
+    // Remove excess gaps from the end of alignment
     int maxLength = -1;
 
     SequenceI current;
@@ -708,8 +1072,8 @@ 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;
@@ -720,16 +1084,14 @@ 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)
@@ -740,123 +1102,650 @@ 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
+   */
+  @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)
+    if (alignmentProperties == null)
+    {
       alignmentProperties = new Hashtable();
+    }
 
-    alignmentProperties.put(key,value);
+    alignmentProperties.put(key, value);
   }
 
+  @Override
   public Object getProperty(Object key)
   {
-    if(alignmentProperties!=null)
+    if (alignmentProperties != null)
+    {
       return alignmentProperties.get(key);
+    }
     else
+    {
       return null;
+    }
   }
 
+  @Override
   public Hashtable getProperties()
   {
     return alignmentProperties;
   }
-  AlignedCodonFrame[] codonFrameList=null;
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+   * )
    */
+  @Override
   public void addCodonFrame(AlignedCodonFrame codons)
   {
-    if (codons==null)
-      return;
-    if (codonFrameList==null)
+    if (codons != null)
     {
-      codonFrameList = new AlignedCodonFrame[] { codons };
-      return;
+      codonFrameList.add(codons);
     }
-    AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
-    System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
-    t[codonFrameList.length] = codons;
-    codonFrameList = t;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
-  public AlignedCodonFrame getCodonFrame(int index)
+  @Override
+  public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
   {
-    return codonFrameList[index];
+    if (seq == null)
+    {
+      return null;
+    }
+    List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+    for (AlignedCodonFrame acf : codonFrameList)
+    {
+      if (acf.involvesSequence(seq))
+      {
+        cframes.add(acf);
+      }
+    }
+    return cframes;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+  /**
+   * Sets the codon frame mappings (replacing any existing mappings).
+   * 
+   * @see jalview.datamodel.AlignmentI#setCodonFrames()
    */
-  public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+  @Override
+  public void setCodonFrames(Set<AlignedCodonFrame> acfs)
   {
-    if (seq==null || codonFrameList==null)
-      return null;
-    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)
-      return null;
-    AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
-    cframes.copyInto(cfr);
-    return cfr;
+    this.codonFrameList = acfs;
   }
 
-  /* (non-Javadoc)
+  /**
+   * Returns the set of codon frame mappings. Any changes to the returned set
+   * will affect the alignment.
+   * 
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
-  public AlignedCodonFrame[] getCodonFrames()
+  @Override
+  public Set<AlignedCodonFrame> getCodonFrames()
   {
     return codonFrameList;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+   * AlignedCodonFrame)
    */
+  @Override
   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)
+    }
+    return codonFrameList.remove(codons);
+  }
+
+  @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]);
+    }
+
+    this.codonFrameList.addAll(toappend.getCodonFrames());
+
+    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;
+  }
+
+  /**
+   * Returns an iterable collection of any annotations that match on given
+   * sequence ref, calcId and label (ignoring null values).
+   */
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+          String calcId, String label)
+  {
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation ann : getAlignmentAnnotation())
+    {
+      if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+              && ann.sequenceRef != null && ann.sequenceRef == seq
+              && ann.label != null && ann.label.equals(label))
+      {
+        aa.add(ann);
+      }
+    }
+    return aa;
+  }
+
+  @Override
+  public void moveSelectedSequencesByOne(SequenceGroup sg,
+          Map<SequenceI, SequenceCollectionI> map, boolean up)
+  {
+    synchronized (sequences)
     {
-      if (codonFrameList[i]==codons)
+      if (up)
       {
-        removed=true;
-        if (i+1<iSize)
+
+        for (int i = 1, iSize = sequences.size(); i < iSize; i++)
         {
-          System.arraycopy(codonFrameList,i+1,codonFrameList, i, iSize-i-1);
+          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);
         }
-        iSize--;
       }
       else
       {
-        i++;
+        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;
+    }
+  }
+
+  private SequenceI seqrep = null;
+
+  /**
+   * 
+   * @return the representative sequence for this group
+   */
+  public SequenceI getSeqrep()
+  {
+    return seqrep;
+  }
+
+  /**
+   * set the representative sequence for this group. Note - this affects the
+   * interpretation of the Hidereps attribute.
+   * 
+   * @param seqrep
+   *          the seqrep to set (null means no sequence representative)
+   */
+  public void setSeqrep(SequenceI seqrep)
+  {
+    this.seqrep = seqrep;
+  }
+
+  /**
+   * 
+   * @return true if group has a sequence representative
+   */
+  public boolean hasSeqrep()
+  {
+    return seqrep != null;
+  }
+
+  @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;
+  }
+
+  /**
+   * Align this alignment like the given (mapped) one.
+   */
+  @Override
+  public int alignAs(AlignmentI al)
+  {
+    /*
+     * Currently retains unmapped gaps (in introns), regaps mapped regions
+     * (exons)
+     */
+    return alignAs(al, false, true);
+  }
+
+  /**
+   * Align this alignment 'the same as' the given one. Mapped sequences only are
+   * realigned. If both of the same type (nucleotide/protein) then align both
+   * identically. If this is nucleotide and the other is protein, make 3 gaps
+   * for each gap in the protein sequences. If this is protein and the other is
+   * nucleotide, insert a gap for each 3 gaps (or part thereof) between
+   * nucleotide bases. If this is protein and the other is nucleotide, gaps
+   * protein to match the relative ordering of codons in the nucleotide.
+   * 
+   * Parameters control whether gaps in exon (mapped) and intron (unmapped)
+   * regions are preserved. Gaps that connect introns to exons are treated
+   * conservatively, i.e. only preserved if both intron and exon gaps are
+   * preserved.
+   * 
+   * @param al
+   * @param preserveMappedGaps
+   *          if true, gaps within and between mapped codons are preserved
+   * @param preserveUnmappedGaps
+   *          if true, gaps within and between unmapped codons are preserved
+   */
+  // @Override
+  public int alignAs(AlignmentI al, boolean preserveMappedGaps,
+          boolean preserveUnmappedGaps)
+  {
+    // TODO should this method signature be the one in the interface?
+    int count = 0;
+    boolean thisIsNucleotide = this.isNucleotide();
+    boolean thatIsProtein = !al.isNucleotide();
+    if (!thatIsProtein && !thisIsNucleotide)
+    {
+      return AlignmentUtils.alignProteinAsDna(this, al);
+    }
+
+    char thisGapChar = this.getGapCharacter();
+    String gap = thisIsNucleotide && thatIsProtein ? String
+            .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
+            : String.valueOf(thisGapChar);
+
+    // TODO handle intron regions? Needs a 'holistic' alignment of dna,
+    // not just sequence by sequence. But how to 'gap' intron regions?
+
+    /*
+     * Get mappings from 'that' alignment's sequences to this.
+     */
+    for (SequenceI alignTo : getSequences())
+    {
+      count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
+              preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
+    }
+    return count;
+  }
+
+  /**
+   * Returns the alignment in Fasta format. Behaviour of this method is not
+   * guaranteed between versions.
+   */
+  @Override
+  public String toString()
+  {
+    return new FastaFile().print(getSequencesArray());
+  }
+
+  /**
+   * Returns the set of distinct sequence names. No ordering is guaranteed.
+   */
+  @Override
+  public Set<String> getSequenceNames()
+  {
+    Set<String> names = new HashSet<String>();
+    for (SequenceI seq : getSequences())
+    {
+      names.add(seq.getName());
+    }
+    return names;
+  }
+
+  @Override
+  public boolean hasValidSequence()
+  {
+    boolean hasValidSeq = false;
+    for (SequenceI seq : getSequences())
+    {
+      if ((seq.getEnd() - seq.getStart()) > 0)
+      {
+        hasValidSeq = true;
+        break;
       }
     }
-    return removed;
+    return hasValidSeq;
   }
 }