X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=75b18d9f0fcf0d83de9b20c3df37f0ffbcfc2e23;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=64b79b7416d1381b1cb921bcef718354f36f41c7;hpb=482e093c4670a813c9eec254990178b209e32dbc;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 64b79b7..75b18d9 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,37 +1,54 @@
 /*
- * 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 2.9)
+ * Copyright (C) 2015 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
+ * 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.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.MessageManager;
 
-import jalview.analysis.*;
+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
  */
+/**
+ * @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 +58,8 @@ public class Alignment implements AlignmentI
 
   public static final int NUCLEOTIDE = 1;
 
+  public boolean hasRNAStructure = false;
+
   /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
 
@@ -48,6 +67,8 @@ public class Alignment implements AlignmentI
 
   public Hashtable alignmentProperties;
 
+  private Set<AlignedCodonFrame> codonFrameList = new LinkedHashSet<AlignedCodonFrame>();
+
   private void initAlignment(SequenceI[] seqs)
   {
     int i = 0;
@@ -61,13 +82,35 @@ 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]);
+    }
+
+  }
+
+  /**
+   * 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);
   }
 
   /**
@@ -84,7 +127,7 @@ public class Alignment implements AlignmentI
    * Make a new alignment from an array of SeqCigars
    * 
    * @param seqs
-   *                SeqCigar[]
+   *          SeqCigar[]
    */
   public Alignment(SeqCigar[] alseqs)
   {
@@ -100,51 +143,73 @@ public class Alignment implements AlignmentI
    * appropriately.
    * 
    * @param compactAlignment
-   *                CigarArray
+   *          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)
+    {
       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!
+   *          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 +218,7 @@ public class Alignment implements AlignmentI
    * 
    * @param snew
    */
+  @Override
   public void addSequence(SequenceI snew)
   {
     if (dataset != null)
@@ -172,15 +238,19 @@ public class Alignment implements AlignmentI
     }
     if (sequences == null)
     {
-      initAlignment(new SequenceI[]
-      { snew });
+      initAlignment(new SequenceI[] { snew });
     }
     else
     {
-      sequences.addElement(snew);
+      synchronized (sequences)
+      {
+        sequences.add(snew);
+      }
     }
     if (hiddenSequences != null)
+    {
       hiddenSequences.adjustHeightSequenceAdded();
+    }
   }
 
   /**
@@ -188,12 +258,14 @@ 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);
+    synchronized (sequences)
+    {
+      deleteSequence(i);
+      sequences.set(i, snew);
+    }
   }
 
   /**
@@ -201,15 +273,19 @@ 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)
+    {
       getDataset().removeAlignmentRef();
+    }
 
     dataset = null;
     sequences = null;
@@ -234,8 +310,9 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(SequenceI s)
   {
     deleteSequence(findIndex(s));
@@ -245,118 +322,204 @@ 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);
-      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!
+  /*
+   * (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)
+        {
+          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);
@@ -367,6 +530,7 @@ 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 +540,9 @@ 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 +583,7 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  @Override
   public SequenceI[] findSequenceMatch(String name)
   {
     Vector matches = new Vector();
@@ -447,6 +613,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
    */
+  @Override
   public int findIndex(SequenceI s)
   {
     int i = 0;
@@ -467,8 +634,10 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+   * @see
+   * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
+  @Override
   public int findIndex(SearchResults results)
   {
     int i = 0;
@@ -489,6 +658,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getHeight()
   {
     return sequences.size();
@@ -499,6 +669,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getWidth()
   {
     int maxLength = -1;
@@ -518,17 +689,19 @@ 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));
+      }
     }
   }
 
@@ -537,38 +710,87 @@ 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;
+        }
       }
     }
 
     return true;
   }
 
+  /**
+   * 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)
    * 
-   * @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)
@@ -594,26 +816,66 @@ public class Alignment implements AlignmentI
         continue;
       }
       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!
+   * 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)
     {
@@ -621,22 +883,35 @@ 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)
@@ -669,16 +944,16 @@ 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)
@@ -691,6 +966,7 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
   public boolean isNucleotide()
   {
     if (type == NUCLEOTIDE)
@@ -703,6 +979,14 @@ 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)
@@ -717,7 +1001,7 @@ public class Alignment implements AlignmentI
         currentSeq = getSequenceAt(i);
         if (currentSeq.getDatasetSequence() != null)
         {
-          seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+          seqs[i] = currentSeq.getDatasetSequence();
         }
         else
         {
@@ -730,6 +1014,27 @@ public class Alignment implements AlignmentI
     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();
   }
@@ -747,11 +1052,13 @@ public class Alignment implements AlignmentI
     alignmentRefs++;
   }
 
+  @Override
   public Alignment getDataset()
   {
     return dataset;
   }
 
+  @Override
   public boolean padGaps()
   {
     boolean modified = false;
@@ -794,39 +1101,47 @@ 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
+   * 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];
+    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++)
+      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)
+            ends[i * 2] = j;
+            hitres = true;
+          }
+          else
+          {
+            ends[i * 2 + 1] = j;
+            if (j - ends[i * 2] > maxLength)
             {
-              maxLength = j-ends[i*2];
+              maxLength = j - ends[i * 2];
             }
           }
         }
@@ -835,50 +1150,56 @@ public class Alignment implements AlignmentI
 
     maxLength++;
     // now edit the flanking gaps to justify to either left or right
-    int cLength,extent,diff;
+    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
+
+      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])
+        if (extent > ends[i * 2 + 1])
         {
-          current.deleteChars(ends[i*2+1]+1, extent);
+          current.deleteChars(ends[i * 2 + 1] + 1, extent);
           modified = true;
         }
-        if (ends[i*2]>diff)
+        if (ends[i * 2] > diff)
         {
-          current.deleteChars(0, ends[i*2]-diff);
+          current.deleteChars(0, ends[i * 2] - diff);
           modified = true;
-        } else {
-          if (ends[i*2]<diff)
+        }
+        else
+        {
+          if (ends[i * 2] < diff)
           {
-            current.insertCharAt(0, diff-ends[i*2],gapCharacter);
+            current.insertCharAt(0, diff - ends[i * 2], gapCharacter);
             modified = true;
           }
         }
-      } else {
+      }
+      else
+      {
         // left justify
-        if (ends[i*2]>0)
+        if (ends[i * 2] > 0)
         {
-          current.deleteChars(0, ends[i*2]);
+          current.deleteChars(0, ends[i * 2]);
           modified = true;
-          ends[i*2+1]-=ends[i*2];
-          extent-=ends[i*2];
+          ends[i * 2 + 1] -= ends[i * 2];
+          extent -= ends[i * 2];
         }
-        if (extent>maxLength)
+        if (extent > maxLength)
         {
-          current.deleteChars(maxLength+1, extent);
+          current.deleteChars(maxLength + 1, extent);
           modified = true;
-        } else {
-          if (extent<maxLength)
+        }
+        else
+        {
+          if (extent < maxLength)
           {
-            current.insertCharAt(extent, maxLength-extent,gapCharacter);
+            current.insertCharAt(extent, maxLength - extent, gapCharacter);
             modified = true;
           }
         }
@@ -887,105 +1208,118 @@ public class Alignment implements AlignmentI
     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)
+    {
       alignmentProperties = new Hashtable();
+    }
 
     alignmentProperties.put(key, value);
   }
 
+  @Override
   public Object getProperty(Object key)
   {
     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)
+   * @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)
+   * @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)
+  /**
+   * Sets the codon frame mappings (replacing any existing mappings).
    * 
-   * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+   * @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;
   }
@@ -993,61 +1327,54 @@ 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)
-      return false;
-    boolean removed = false;
-    int i = 0, iSize = codonFrameList.length;
-    while (i < iSize)
     {
-      if (codonFrameList[i] == codons)
-      {
-        removed = true;
-        if (i + 1 < iSize)
-        {
-          System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
-                  - i - 1);
-        }
-        iSize--;
-      }
-      else
-      {
-        i++;
-      }
+      return false;
     }
-    return removed;
+    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();
+    boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
-    boolean hashidden = toappend.getHiddenSequences()!=null && toappend.getHiddenSequences().hiddenSequences!=null;
+    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();
+    List<SequenceI> sqs = (hashidden) ? toappend.getHiddenSequences()
+            .getFullAlignment().getSequences() : toappend.getSequences();
     if (sqs != null)
     {
-      Enumeration sq = sqs.elements();
-      while (sq.hasMoreElements())
+      synchronized (sqs)
       {
-        SequenceI addedsq=(SequenceI) sq.nextElement();
-        if (!samegap)
+        for (SequenceI addedsq : sqs)
         {
-          char[] oldseq = addedsq.getSequence();
-          for (int c=0;c<oldseq.length;c++)
+          if (!samegap)
           {
-            if (oldseq[c]==oldc)
+            char[] oldseq = addedsq.getSequence();
+            for (int c = 0; c < oldseq.length; c++)
             {
-              oldseq[c] = gapCharacter;
+              if (oldseq[c] == oldc)
+              {
+                oldseq[c] = gapCharacter;
+              }
             }
           }
+          addSequence(addedsq);
         }
-        addSequence(addedsq);
       }
     }
     AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
@@ -1055,75 +1382,370 @@ public class Alignment implements AlignmentI
     {
       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();
+
+    this.codonFrameList.addAll(toappend.getCodonFrames());
+
+    List<SequenceGroup> sg = toappend.getGroups();
     if (sg != null)
     {
-      Enumeration el = sg.elements();
-      while (el.hasMoreElements())
+      for (SequenceGroup _sg : sg)
       {
-        addGroup((SequenceGroup) el.nextElement());
+        addGroup(_sg);
       }
     }
-    if (toappend.getHiddenSequences()!=null)
+    if (toappend.getHiddenSequences() != null)
     {
       HiddenSequences hs = toappend.getHiddenSequences();
-      if (hiddenSequences==null)
+      if (hiddenSequences == null)
       {
         hiddenSequences = new HiddenSequences(this);
       }
-      if (hs.hiddenSequences!=null)
+      if (hs.hiddenSequences != null)
       {
-        for (int s=0;s<hs.hiddenSequences.length; s++)
+        for (int s = 0; s < hs.hiddenSequences.length; s++)
         {
           // hide the newly appended sequence in the alignment
-          if (hs.hiddenSequences[s]!=null)
+          if (hs.hiddenSequences[s] != null)
           {
             hiddenSequences.hideSequence(hs.hiddenSequences[s]);
           }
         }
       }
     }
-    if (toappend.getProperties()!=null)
+    if (toappend.getProperties() != null)
     {
-      // we really can't do very much here - just try to concatenate strings where property collisions occur.
+      // 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 != null)
         {
-          if (ourval.getClass().equals(toapprop.getClass()) && !ourval.equals(toapprop))
+          if (ourval.getClass().equals(toapprop.getClass())
+                  && !ourval.equals(toapprop))
           {
             if (ourval instanceof String)
             {
               // append strings
-              this.setProperty(k, ((String) ourval)+"; "+((String) toapprop));
-            } else {
+              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);
+                  ((Vector) ourval).addElement(theirv);
                 }
               }
             }
           }
-        } else {
+        }
+        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 (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;
+    }
+  }
+
+  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 hasValidSeq;
+  }
 }