X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=ed65dd50ab4c417aac1463dbed8468b4f1026ddc;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=23fe0573aa1c86a2fcbf4d7345228b91a3002860;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 23fe057..ed65dd5 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 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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 = '-';
 
@@ -43,7 +43,7 @@ public class Alignment implements AlignmentI
   public static final int PROTEIN = 0;
 
   public static final int NUCLEOTIDE = 1;
-  
+
   public boolean hasRNAStructure = false;
 
   /** DOCUMENT ME!! */
@@ -66,11 +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]);
     }
 
   }
@@ -118,28 +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.
+    // 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;
   }
 
   /**
@@ -150,13 +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;
   }
 
@@ -165,6 +171,7 @@ public class Alignment implements AlignmentI
    * 
    * @param snew
    */
+  @Override
   public void addSequence(SequenceI snew)
   {
     if (dataset != null)
@@ -189,7 +196,10 @@ public class Alignment implements AlignmentI
     }
     else
     {
-      sequences.addElement(snew);
+      synchronized (sequences)
+      {
+        sequences.add(snew);
+      }
     }
     if (hiddenSequences != null)
       hiddenSequences.adjustHeightSequenceAdded();
@@ -200,12 +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);
+    }
   }
 
   /**
@@ -213,11 +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)
@@ -248,6 +263,7 @@ public class Alignment implements AlignmentI
    * @param s
    *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(SequenceI s)
   {
     deleteSequence(findIndex(s));
@@ -259,95 +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++)
+          {
+            if (!sequences.contains(sg.getSequenceAt(i)))
+            {
+              sg.deleteSequence(sg.getSequenceAt(i), false);
+              iSize--;
+              i--;
+            }
+          }
+
+          if (sg.getSize() < 1)
           {
-            sg.deleteSequence(sg.getSequenceAt(i), false);
-            iSize--;
-            i--;
+            return;
           }
         }
 
-        if (sg.getSize() < 1)
-        {
-          return;
-        }
+        groups.add(sg);
       }
-
-      groups.addElement(sg);
     }
   }
 
@@ -411,26 +437,35 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
   public void deleteAllGroups()
   {
-    if (annotations != null)
+    synchronized (groups)
     {
-      removeAnnotationForGroup(null);
+      if (annotations != null)
+      {
+        removeAnnotationForGroup(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);
+      }
     }
   }
 
   /**    */
+  @Override
   public SequenceI findName(String name)
   {
     return findName(name, false);
@@ -441,6 +476,7 @@ 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);
@@ -452,6 +488,7 @@ 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)
   {
 
@@ -492,6 +529,7 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  @Override
   public SequenceI[] findSequenceMatch(String name)
   {
     Vector matches = new Vector();
@@ -521,6 +559,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
    */
+  @Override
   public int findIndex(SequenceI s)
   {
     int i = 0;
@@ -544,6 +583,7 @@ public class Alignment implements AlignmentI
    * @see
    * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
+  @Override
   public int findIndex(SearchResults results)
   {
     int i = 0;
@@ -564,6 +604,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getHeight()
   {
     return sequences.size();
@@ -574,6 +615,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getWidth()
   {
     int maxLength = -1;
@@ -595,15 +637,17 @@ 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));
+      }
     }
   }
 
@@ -612,6 +656,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getGapCharacter()
   {
     return gapCharacter;
@@ -622,6 +667,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#isAligned()
    */
+  @Override
   public boolean isAligned()
   {
     return isAligned(false);
@@ -632,6 +678,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#isAligned(boolean)
    */
+  @Override
   public boolean isAligned(boolean includeHidden)
   {
     int width = getWidth();
@@ -659,11 +706,13 @@ 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;
@@ -697,7 +746,8 @@ public class Alignment implements AlignmentI
     if (swap)
     {
       annotations = temp;
-      if (unhook) {
+      if (unhook)
+      {
         unhookAnnotation(aa);
       }
     }
@@ -728,6 +778,7 @@ public class Alignment implements AlignmentI
    * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
    * AlignmentAnnotation)
    */
+  @Override
   public void addAnnotation(AlignmentAnnotation aa)
   {
     addAnnotation(aa, -1);
@@ -739,12 +790,14 @@ 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;
+    if (aa.getRNAStruc() != null)
+    {
+      hasRNAStructure = true;
     }
-    
+
     int aSize = 1;
     if (annotations != null)
     {
@@ -780,6 +833,7 @@ public class Alignment implements AlignmentI
     annotations = temp;
   }
 
+  @Override
   public void setAnnotationIndex(AlignmentAnnotation aa, int index)
   {
     if (aa == null || annotations == null || annotations.length - 1 < index)
@@ -821,6 +875,7 @@ public class Alignment implements AlignmentI
     return annotations;
   }
 
+  @Override
   public void setNucleotide(boolean b)
   {
     if (b)
@@ -833,6 +888,7 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
   public boolean isNucleotide()
   {
     if (type == NUCLEOTIDE)
@@ -844,12 +900,15 @@ public class Alignment implements AlignmentI
       return false;
     }
   }
-  
-  public boolean hasRNAStructure(){
-    //TODO can it happen that structure is removed from 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)
@@ -864,7 +923,7 @@ public class Alignment implements AlignmentI
         currentSeq = getSequenceAt(i);
         if (currentSeq.getDatasetSequence() != null)
         {
-          seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+          seqs[i] = currentSeq.getDatasetSequence();
         }
         else
         {
@@ -894,11 +953,13 @@ public class Alignment implements AlignmentI
     alignmentRefs++;
   }
 
+  @Override
   public Alignment getDataset()
   {
     return dataset;
   }
 
+  @Override
   public boolean padGaps()
   {
     boolean modified = false;
@@ -950,6 +1011,7 @@ 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;
@@ -1047,23 +1109,30 @@ 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)
@@ -1072,6 +1141,7 @@ public class Alignment implements AlignmentI
     alignmentProperties.put(key, value);
   }
 
+  @Override
   public Object getProperty(Object key)
   {
     if (alignmentProperties != null)
@@ -1080,6 +1150,7 @@ public class Alignment implements AlignmentI
       return null;
   }
 
+  @Override
   public Hashtable getProperties()
   {
     return alignmentProperties;
@@ -1094,6 +1165,7 @@ public class Alignment implements AlignmentI
    * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
    * )
    */
+  @Override
   public void addCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null)
@@ -1115,6 +1187,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
    */
+  @Override
   public AlignedCodonFrame getCodonFrame(int index)
   {
     return codonFrameList[index];
@@ -1126,6 +1199,7 @@ public class Alignment implements AlignmentI
    * @see
    * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
+  @Override
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
     if (seq == null || codonFrameList == null)
@@ -1148,6 +1222,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
+  @Override
   public AlignedCodonFrame[] getCodonFrames()
   {
     return codonFrameList;
@@ -1159,6 +1234,7 @@ public class Alignment implements AlignmentI
    * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
    * AlignedCodonFrame)
    */
+  @Override
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null || codonFrameList == null)
@@ -1185,8 +1261,13 @@ 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();
@@ -1194,26 +1275,27 @@ 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();
@@ -1229,7 +1311,7 @@ public class Alignment implements AlignmentI
     List<SequenceGroup> sg = toappend.getGroups();
     if (sg != null)
     {
-      for (SequenceGroup _sg:sg)
+      for (SequenceGroup _sg : sg)
       {
         addGroup(_sg);
       }
@@ -1299,23 +1381,28 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
-          SequenceI seqRef, SequenceGroup groupRef)
+  public AlignmentAnnotation findOrCreateAnnotation(String name,
+          String calcId, boolean autoCalc, SequenceI seqRef,
+          SequenceGroup groupRef)
   {
-    for (AlignmentAnnotation annot : 
-            getAlignmentAnnotation())
+    assert (name != null);
+    if (annotations != null)
     {
-      if (annot.autoCalculated == autoCalc
-              && annot.getCalcId().equals(name)
-              && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+      for (AlignmentAnnotation annot : getAlignmentAnnotation())
       {
-        return annot;
+        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(name));
+    annot.setCalcId(new String(calcId));
     annot.autoCalculated = autoCalc;
     if (seqRef != null)
     {
@@ -1330,10 +1417,12 @@ public class Alignment implements AlignmentI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa=new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation a:getAlignmentAnnotation())
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation a : getAlignmentAnnotation())
     {
-      if (a.getCalcId()==calcId || (a.getCalcId()!=null && calcId!=null && a.getCalcId().equals(calcId)))
+      if (a.getCalcId() == calcId
+              || (a.getCalcId() != null && calcId != null && a.getCalcId()
+                      .equals(calcId)))
       {
         aa.add(a);
       }
@@ -1341,4 +1430,72 @@ public class Alignment implements AlignmentI
     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;
+}
 }