X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=7f035b4b3234092abfcd507feb04a47872e7a64a;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=42559c620ad74ca9837f73da38af6dca0eb9ec91;hpb=d803f2708fc809fb8be7547727e6ab62c0451989;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 42559c6..7f035b4 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,26 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * 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
  */
@@ -32,9 +31,10 @@ 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 = '-';
 
@@ -44,6 +44,8 @@ public class Alignment implements AlignmentI
 
   public static final int NUCLEOTIDE = 1;
 
+  public boolean hasRNAStructure = false;
+
   /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
 
@@ -64,11 +66,12 @@ public class Alignment implements AlignmentI
       type = PROTEIN;
     }
 
-    sequences = new Vector();
+    sequences = java.util.Collections
+            .synchronizedList(new ArrayList<SequenceI>());
 
     for (i = 0; i < seqs.length; i++)
     {
-      sequences.addElement(seqs[i]);
+      sequences.add(seqs[i]);
     }
 
   }
@@ -116,21 +119,30 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getSequences()
+  @Override
+  public List<SequenceI> getSequences()
   {
     return sequences;
   }
 
+  @Override
+  public List<SequenceI> getSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to
+    // work on this.
+    return sequences;
+  }
+
+  @Override
   public SequenceI[] getSequencesArray()
   {
     if (sequences == null)
       return null;
-    SequenceI[] reply = new SequenceI[sequences.size()];
-    for (int i = 0; i < sequences.size(); i++)
+    synchronized (sequences)
     {
-      reply[i] = (SequenceI) sequences.elementAt(i);
+      return sequences.toArray(new SequenceI[sequences.size()]);
     }
-    return reply;
   }
 
   /**
@@ -141,13 +153,16 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public SequenceI getSequenceAt(int i)
   {
-    if (i>-1 && i < sequences.size())
+    synchronized (sequences)
     {
-      return (SequenceI) sequences.elementAt(i);
+      if (i > -1 && i < sequences.size())
+      {
+        return sequences.get(i);
+      }
     }
-
     return null;
   }
 
@@ -156,6 +171,7 @@ public class Alignment implements AlignmentI
    * 
    * @param snew
    */
+  @Override
   public void addSequence(SequenceI snew)
   {
     if (dataset != null)
@@ -180,7 +196,10 @@ public class Alignment implements AlignmentI
     }
     else
     {
-      sequences.addElement(snew);
+      synchronized (sequences)
+      {
+        sequences.add(snew);
+      }
     }
     if (hiddenSequences != null)
       hiddenSequences.adjustHeightSequenceAdded();
@@ -191,12 +210,15 @@ public class Alignment implements AlignmentI
    * 
    * @param snew
    */
+  @Override
   public void setSequenceAt(int i, SequenceI snew)
   {
     SequenceI oldseq = getSequenceAt(i);
-    deleteSequence(oldseq);
-
-    sequences.setElementAt(snew, i);
+    deleteSequence(i);
+    synchronized (sequences)
+    {
+      sequences.set(i, snew);
+    }
   }
 
   /**
@@ -204,11 +226,13 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getGroups()
+  @Override
+  public List<SequenceGroup> getGroups()
   {
     return groups;
   }
 
+  @Override
   public void finalize()
   {
     if (getDataset() != null)
@@ -239,6 +263,7 @@ public class Alignment implements AlignmentI
    * @param s
    *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(SequenceI s)
   {
     deleteSequence(findIndex(s));
@@ -250,95 +275,105 @@ public class Alignment implements AlignmentI
    * @param i
    *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(int i)
   {
     if (i > -1 && i < getHeight())
     {
-      sequences.removeElementAt(i);
+      synchronized (sequences)
+      {
+        sequences.remove(i);
+      }
       hiddenSequences.adjustHeightSequenceDeleted(i);
     }
   }
 
-  /**    */
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+   */
+  @Override
   public SequenceGroup findGroup(SequenceI s)
   {
-    for (int i = 0; i < this.groups.size(); i++)
+    synchronized (groups)
     {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
-      if (sg.getSequences(null).contains(s))
+      for (int i = 0; i < this.groups.size(); i++)
       {
-        return sg;
+        SequenceGroup sg = groups.get(i);
+
+        if (sg.getSequences(null).contains(s))
+        {
+          return sg;
+        }
       }
     }
-
     return null;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
+  /*
+   * (non-Javadoc)
    * 
-   * @return DOCUMENT ME!
+   * @see
+   * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
    */
+  @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-    Vector temp = new Vector();
+    ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
 
-    int gSize = groups.size();
-    for (int i = 0; i < gSize; i++)
+    synchronized (groups)
     {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-      if (sg == null || sg.getSequences(null) == null)
+      int gSize = groups.size();
+      for (int i = 0; i < gSize; i++)
       {
-        this.deleteGroup(sg);
-        gSize--;
-        continue;
-      }
+        SequenceGroup sg = groups.get(i);
+        if (sg == null || sg.getSequences(null) == null)
+        {
+          this.deleteGroup(sg);
+          gSize--;
+          continue;
+        }
 
-      if (sg.getSequences(null).contains(s))
-      {
-        temp.addElement(sg);
+        if (sg.getSequences(null).contains(s))
+        {
+          temp.add(sg);
+        }
       }
     }
-
     SequenceGroup[] ret = new SequenceGroup[temp.size()];
-
-    for (int i = 0; i < temp.size(); i++)
-    {
-      ret[i] = (SequenceGroup) temp.elementAt(i);
-    }
-
-    return ret;
+    return temp.toArray(ret);
   }
 
   /**    */
+  @Override
   public void addGroup(SequenceGroup sg)
   {
-    if (!groups.contains(sg))
+    synchronized (groups)
     {
-      if (hiddenSequences.getSize() > 0)
+      if (!groups.contains(sg))
       {
-        int i, iSize = sg.getSize();
-        for (i = 0; i < iSize; i++)
+        if (hiddenSequences.getSize() > 0)
         {
-          if (!sequences.contains(sg.getSequenceAt(i)))
+          int i, iSize = sg.getSize();
+          for (i = 0; i < iSize; i++)
           {
-            sg.deleteSequence(sg.getSequenceAt(i), false);
-            iSize--;
-            i--;
+            if (!sequences.contains(sg.getSequenceAt(i)))
+            {
+              sg.deleteSequence(sg.getSequenceAt(i), false);
+              iSize--;
+              i--;
+            }
           }
-        }
 
-        if (sg.getSize() < 1)
-        {
-          return;
+          if (sg.getSize() < 1)
+          {
+            return;
+          }
         }
+        sg.setContext(this);
+        groups.add(sg);
       }
-
-      groups.addElement(sg);
     }
   }
 
@@ -402,26 +437,39 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
   public void deleteAllGroups()
   {
-    if (annotations != null)
+    synchronized (groups)
     {
-      removeAnnotationForGroup(null);
+      if (annotations != null)
+      {
+        removeAnnotationForGroup(null);
+      }
+      for (SequenceGroup sg:groups) {
+        sg.setContext(null);
+      }
+      groups.clear();
     }
-    groups.removeAllElements();
   }
 
   /**    */
+  @Override
   public void deleteGroup(SequenceGroup g)
   {
-    if (groups.contains(g))
+    synchronized (groups)
     {
-      removeAnnotationForGroup(g);
-      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);
@@ -432,6 +480,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
    */
+  @Override
   public SequenceI findName(String token, boolean b)
   {
     return findName(null, token, b);
@@ -443,6 +492,7 @@ public class Alignment implements AlignmentI
    * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
    * boolean)
    */
+  @Override
   public SequenceI findName(SequenceI startAfter, String token, boolean b)
   {
 
@@ -483,6 +533,7 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  @Override
   public SequenceI[] findSequenceMatch(String name)
   {
     Vector matches = new Vector();
@@ -512,6 +563,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
    */
+  @Override
   public int findIndex(SequenceI s)
   {
     int i = 0;
@@ -535,6 +587,7 @@ public class Alignment implements AlignmentI
    * @see
    * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
+  @Override
   public int findIndex(SearchResults results)
   {
     int i = 0;
@@ -555,6 +608,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getHeight()
   {
     return sequences.size();
@@ -565,6 +619,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getWidth()
   {
     int maxLength = -1;
@@ -586,15 +641,17 @@ public class Alignment implements AlignmentI
    * @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));
+      }
     }
   }
 
@@ -603,6 +660,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getGapCharacter()
   {
     return gapCharacter;
@@ -613,6 +671,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#isAligned()
    */
+  @Override
   public boolean isAligned()
   {
     return isAligned(false);
@@ -623,6 +682,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#isAligned(boolean)
    */
+  @Override
   public boolean isAligned(boolean includeHidden)
   {
     int width = getWidth();
@@ -650,8 +710,15 @@ public class Alignment implements AlignmentI
    * @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)
@@ -683,7 +750,10 @@ public class Alignment implements AlignmentI
     if (swap)
     {
       annotations = temp;
-      unhookAnnotation(aa);
+      if (unhook)
+      {
+        unhookAnnotation(aa);
+      }
     }
     return swap;
   }
@@ -712,6 +782,7 @@ public class Alignment implements AlignmentI
    * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
    * AlignmentAnnotation)
    */
+  @Override
   public void addAnnotation(AlignmentAnnotation aa)
   {
     addAnnotation(aa, -1);
@@ -723,8 +794,14 @@ public class Alignment implements AlignmentI
    * @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)
     {
@@ -760,6 +837,7 @@ public class Alignment implements AlignmentI
     annotations = temp;
   }
 
+  @Override
   public void setAnnotationIndex(AlignmentAnnotation aa, int index)
   {
     if (aa == null || annotations == null || annotations.length - 1 < index)
@@ -792,16 +870,16 @@ public class Alignment implements AlignmentI
     annotations = temp;
   }
 
+  @Override
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * returns all annotation on the alignment
    */
   public AlignmentAnnotation[] getAlignmentAnnotation()
   {
     return annotations;
   }
 
+  @Override
   public void setNucleotide(boolean b)
   {
     if (b)
@@ -814,6 +892,7 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
   public boolean isNucleotide()
   {
     if (type == NUCLEOTIDE)
@@ -826,6 +905,14 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public boolean hasRNAStructure()
+  {
+    // TODO can it happen that structure is removed from alignment?
+    return hasRNAStructure;
+  }
+
+  @Override
   public void setDataset(Alignment data)
   {
     if (dataset == null && data == null)
@@ -840,7 +927,7 @@ public class Alignment implements AlignmentI
         currentSeq = getSequenceAt(i);
         if (currentSeq.getDatasetSequence() != null)
         {
-          seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+          seqs[i] = currentSeq.getDatasetSequence();
         }
         else
         {
@@ -870,11 +957,13 @@ public class Alignment implements AlignmentI
     alignmentRefs++;
   }
 
+  @Override
   public Alignment getDataset()
   {
     return dataset;
   }
 
+  @Override
   public boolean padGaps()
   {
     boolean modified = false;
@@ -926,6 +1015,7 @@ public class Alignment implements AlignmentI
    *          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;
@@ -1023,23 +1113,30 @@ 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)
@@ -1048,6 +1145,7 @@ public class Alignment implements AlignmentI
     alignmentProperties.put(key, value);
   }
 
+  @Override
   public Object getProperty(Object key)
   {
     if (alignmentProperties != null)
@@ -1056,6 +1154,7 @@ public class Alignment implements AlignmentI
       return null;
   }
 
+  @Override
   public Hashtable getProperties()
   {
     return alignmentProperties;
@@ -1070,6 +1169,7 @@ public class Alignment implements AlignmentI
    * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
    * )
    */
+  @Override
   public void addCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null)
@@ -1091,6 +1191,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
    */
+  @Override
   public AlignedCodonFrame getCodonFrame(int index)
   {
     return codonFrameList[index];
@@ -1102,6 +1203,7 @@ public class Alignment implements AlignmentI
    * @see
    * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
+  @Override
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
     if (seq == null || codonFrameList == null)
@@ -1124,6 +1226,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
+  @Override
   public AlignedCodonFrame[] getCodonFrames()
   {
     return codonFrameList;
@@ -1135,6 +1238,7 @@ public class Alignment implements AlignmentI
    * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
    * AlignedCodonFrame)
    */
+  @Override
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null || codonFrameList == null)
@@ -1161,8 +1265,13 @@ public class Alignment implements AlignmentI
     return removed;
   }
 
+  @Override
   public void append(AlignmentI toappend)
   {
+    if (toappend == this)
+    {
+      System.err.println("Self append may cause a deadlock.");
+    }
     // TODO test this method for a future 2.5 release
     // currently tested for use in jalview.gui.SequenceFetcher
     boolean samegap = toappend.getGapCharacter() == getGapCharacter();
@@ -1170,26 +1279,27 @@ public class Alignment implements AlignmentI
     boolean hashidden = toappend.getHiddenSequences() != null
             && toappend.getHiddenSequences().hiddenSequences != null;
     // get all sequences including any hidden ones
-    Vector sqs = (hashidden) ? toappend.getHiddenSequences()
+    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();
@@ -1202,13 +1312,12 @@ public class Alignment implements AlignmentI
     {
       this.addCodonFrame(acod[a]);
     }
-    Vector sg = toappend.getGroups();
+    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)
@@ -1275,4 +1384,132 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public AlignmentAnnotation findOrCreateAnnotation(String name,
+          String calcId, boolean autoCalc, SequenceI seqRef,
+          SequenceGroup groupRef)
+  {
+    assert (name != null);
+    if (annotations != null)
+    {
+      for (AlignmentAnnotation annot : getAlignmentAnnotation())
+      {
+        if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+                && (calcId == null || annot.getCalcId().equals(calcId))
+                && annot.sequenceRef == seqRef
+                && annot.groupRef == groupRef)
+        {
+          return annot;
+        }
+      }
+    }
+    AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
+            new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
+    annot.hasText = false;
+    annot.setCalcId(new String(calcId));
+    annot.autoCalculated = autoCalc;
+    if (seqRef != null)
+    {
+      annot.setSequenceRef(seqRef);
+    }
+    annot.groupRef = groupRef;
+    addAnnotation(annot);
+
+    return annot;
+  }
+
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+  {
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation a : getAlignmentAnnotation())
+    {
+      if (a.getCalcId() == calcId
+              || (a.getCalcId() != null && calcId != null && a.getCalcId()
+                      .equals(calcId)))
+      {
+        aa.add(a);
+      }
+    }
+    return aa;
+  }
+
+  @Override
+  public void moveSelectedSequencesByOne(SequenceGroup sg,
+          Map<SequenceI, SequenceCollectionI> map, boolean up)
+  {
+    synchronized (sequences)
+    {
+      if (up)
+      {
+
+        for (int i = 1, iSize = sequences.size(); i < iSize; i++)
+        {
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
+
+          SequenceI temp = sequences.get(i - 1);
+          if (sg.getSequences(null).contains(temp))
+          {
+            continue;
+          }
+
+          sequences.set(i, temp);
+          sequences.set(i - 1, seq);
+        }
+      }
+      else
+      {
+        for (int i = sequences.size() - 2; i > -1; i--)
+        {
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
+
+          SequenceI temp = sequences.get(i + 1);
+          if (sg.getSequences(map).contains(temp))
+          {
+            continue;
+          }
+
+          sequences.set(i, temp);
+          sequences.set(i + 1, seq);
+        }
+      }
+
+    }
+  }
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+   alignmentAnnotation.validateRangeAndDisplay();
+   if (isNucleotide() && alignmentAnnotation.isValidStruc())
+   {
+     hasRNAStructure = true;
+   }
+ }
+ @Override
+public int getEndRes()
+{
+  return getWidth()-1;
+}@Override
+public int getStartRes()
+{
+  return 0;
+}
+
+/* In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+@Override
+public AnnotatedCollectionI getContext()
+{
+  return dataset;
+}
 }