X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=a2a152ad79e7d0a2e8ce251bc0d5acc5a9671d6b;hb=0ae965fc73680bdc69b06986c060ff17342c4787;hp=8c320f75ca02c8f27a3791b5efa816952dea49c4;hpb=e33cdacd2ac2836504375c538574a0f1cafec7e3;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 8c320f7..a2a152a 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,819 +1,2035 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import jalview.analysis.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.io.FastaFile;
+import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+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, AutoCloseable
+{
+  private Alignment dataset;
 
-import jalview.util.*;
+  private List<SequenceI> sequences;
 
-import java.util.*;
+  protected List<SequenceGroup> groups;
 
-/** Data structure to hold and manipulate a multiple sequence alignment
- */
-public class Alignment implements AlignmentI
-{
-    protected Alignment dataset;
-    protected Vector sequences;
-    protected Vector groups = new Vector();
-    protected char gapCharacter = '-';
-    protected int type = NUCLEOTIDE;
-    public static final int PROTEIN = 0;
-    public static final int NUCLEOTIDE = 1;
+  protected char gapCharacter = '-';
 
-    /** DOCUMENT ME!! */
-    public AlignmentAnnotation[] annotations;
+  private boolean nucleotide = true;
 
-    HiddenSequences hiddenSequences = new HiddenSequences(this);
+  public boolean hasRNAStructure = false;
 
-    private void initAlignment(SequenceI[] seqs) {
-      int i=0;
+  public AlignmentAnnotation[] annotations;
 
-      if( jalview.util.Comparison.isNucleotide(seqs))
-        type = NUCLEOTIDE;
-      else
-        type = PROTEIN;
+  HiddenSequences hiddenSequences;
+
+  HiddenColumns hiddenCols;
+
+  public Hashtable alignmentProperties;
+
+  private List<AlignedCodonFrame> codonFrameList;
+
+  private void initAlignment(SequenceI[] seqs)
+  {
+    groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
+    hiddenSequences = new HiddenSequences(this);
+    hiddenCols = new HiddenColumns();
+    codonFrameList = new ArrayList<>();
+
+    nucleotide = Comparison.isNucleotide(seqs);
+
+    sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
+
+    for (int i = 0; i < seqs.length; 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]);
+    }
+
+    initAlignment(seqs);
+
+    /*
+     * Share the same dataset sequence mappings (if any). 
+     */
+    if (dataset == null && al.getDataset() == null)
+    {
+      this.setCodonFrames(al.getCodonFrames());
+    }
+  }
+
+  /**
+   * Make an alignment from an array of Sequences.
+   * 
+   * @param sequences
+   */
+  public Alignment(SequenceI[] seqs)
+  {
+    initAlignment(seqs);
+  }
+
+  /**
+   * Make a new alignment from an array of SeqCigars
+   * 
+   * @param seqs
+   *          SeqCigar[]
+   */
+  public Alignment(SeqCigar[] alseqs)
+  {
+    SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
+            gapCharacter, new HiddenColumns(), null);
+    initAlignment(seqs);
+  }
+
+  /**
+   * Make a new alignment from an CigarArray JBPNote - can only do this when
+   * compactAlignment does not contain hidden regions. JBPNote - must also check
+   * that compactAlignment resolves to a set of SeqCigars - or construct them
+   * appropriately.
+   * 
+   * @param compactAlignment
+   *          CigarArray
+   */
+  public static AlignmentI createAlignment(CigarArray compactAlignment)
+  {
+    throw new Error(MessageManager
+            .getString("error.alignment_cigararray_not_implemented"));
+    // this(compactAlignment.refCigars);
+  }
+
+  @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;
+    }
+    synchronized (sequences)
+    {
+      return sequences.toArray(new SequenceI[sequences.size()]);
+    }
+  }
+
+  /**
+   * Returns a map of lists of sequences keyed by sequence name.
+   * 
+   * @return
+   */
+  @Override
+  public Map<String, List<SequenceI>> getSequencesByName()
+  {
+    return AlignmentUtils.getSequencesByName(this);
+  }
+
+  @Override
+  public SequenceI getSequenceAt(int i)
+  {
+    synchronized (sequences)
+    {
+
+      if (i > -1 && i < sequences.size())
+      {
+        return sequences.get(i);
+      }
+    }
+
+    return null;
+  }
+
+  @Override
+  public SequenceI getSequenceAtAbsoluteIndex(int i)
+  {
+    SequenceI seq = null;
+    if (getHiddenSequences().getSize() > 0)
+    {
+      seq = getHiddenSequences().getHiddenSequence(i);
+      if (seq == null)
+      {
+        // didn't find the sequence in the hidden sequences, get it from the
+        // alignment
+        int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i);
+        seq = getSequenceAt(index);
+      }
+    }
+    else
+    {
+      seq = getSequenceAt(i);
+    }
+    return seq;
+  }
 
-      sequences = new Vector();
+  /**
+   * Adds a sequence to the alignment. Recalculates maxLength and size. Note
+   * this currently does not recalculate whether or not the alignment is
+   * nucleotide, so mixed alignments may have undefined behaviour.
+   * 
+   * @param snew
+   */
+  @Override
+  public void addSequence(SequenceI snew)
+  {
+    if (dataset != null)
+    {
 
-      for (i = 0; i < seqs.length; i++)
+      // maintain dataset integrity
+      SequenceI dsseq = snew.getDatasetSequence();
+      if (dsseq == null)
       {
-        sequences.addElement(seqs[i]);
+        // derive new sequence
+        SequenceI adding = snew.deriveSequence();
+        snew = adding;
+        dsseq = snew.getDatasetSequence();
+      }
+      if (getDataset().findIndex(dsseq) == -1)
+      {
+        getDataset().addSequence(dsseq);
       }
 
     }
-    /** Make an alignment from an array of Sequences.
-     *
-     * @param sequences
-     */
-    public Alignment(SequenceI[] seqs)
+    if (sequences == null)
     {
-      initAlignment(seqs);
+      initAlignment(new SequenceI[] { snew });
     }
-    /**
-     * Make a new alignment from an array of SeqCigars
-     * @param seqs SeqCigar[]
-     */
-    public Alignment(SeqCigar[] alseqs) {
+    else
+    {
+      synchronized (sequences)
+      {
+        sequences.add(snew);
+      }
+    }
+    if (hiddenSequences != null)
+    {
+      hiddenSequences.adjustHeightSequenceAdded();
+    }
+  }
+
+  @Override
+  public SequenceI replaceSequenceAt(int i, SequenceI snew)
+  {
+    synchronized (sequences)
+    {
+      if (sequences.size() > i)
+      {
+        return sequences.set(i, snew);
 
-      SequenceI[] seqs = new SequenceI[alseqs.length];
-      for (int i=0; i<alseqs.length; i++) {
-        seqs[i] = alseqs[i].getSeq(this.gapCharacter);
       }
-      initAlignment(seqs);
+      else
+      {
+        sequences.add(snew);
+        hiddenSequences.adjustHeightSequenceAdded();
+      }
+      return null;
     }
-    /**
-     * Make a new alignment from an CigarArray
-     * JBPNote - can only do this when compactAlignment does not contain hidden regions.
-     * JBPNote - must also check that compactAlignment resolves to a set of SeqCigars - or construct them appropriately.
-     * @param compactAlignment CigarArray
-     */
-    public Alignment(CigarArray compactAlignment) {
-      throw new Error("Alignment(CigarArray) not yet implemented");
-      // this(compactAlignment.refCigars);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  @Override
+  public List<SequenceGroup> getGroups()
+  {
+    return groups;
+  }
+
+  @Override
+  public void close()
+  {
+    if (getDataset() != null)
+    {
+      try
+      {
+        getDataset().removeAlignmentRef();
+      } catch (Throwable e)
+      {
+        e.printStackTrace();
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getSequences()
+    nullReferences();
+  }
+
+  /**
+   * Defensively nulls out references in case this object is not garbage
+   * collected
+   */
+  void nullReferences()
+  {
+    dataset = null;
+    sequences = null;
+    groups = null;
+    annotations = null;
+    hiddenSequences = null;
+  }
+
+  /**
+   * decrement the alignmentRefs counter by one and null references if it goes
+   * to zero.
+   * 
+   * @throws Throwable
+   */
+  private void removeAlignmentRef() throws Throwable
+  {
+    if (--alignmentRefs == 0)
     {
-        return sequences;
+      nullReferences();
     }
+  }
 
-    public SequenceI [] getSequencesArray()
+  @Override
+  public void deleteSequence(SequenceI s)
+  {
+    synchronized (sequences)
     {
-      SequenceI [] reply = new SequenceI[sequences.size()];
-      for(int i=0; i<sequences.size(); i++)
+      deleteSequence(findIndex(s));
+    }
+  }
+
+  @Override
+  public void deleteSequence(int i)
+  {
+    synchronized (sequences)
+    {
+      if (i > -1 && i < getHeight())
       {
-        reply[i] = (SequenceI)sequences.elementAt(i);
+        sequences.remove(i);
+        hiddenSequences.adjustHeightSequenceDeleted(i);
       }
-      return reply;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI getSequenceAt(int i)
+  @Override
+  public void deleteHiddenSequence(int i)
+  {
+    synchronized (sequences)
     {
-        if (i < sequences.size())
+      if (i > -1 && i < getHeight())
+      {
+        sequences.remove(i);
+      }
+    }
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+   */
+  @Override
+  public SequenceGroup findGroup(SequenceI seq, int position)
+  {
+    synchronized (groups)
+    {
+      for (SequenceGroup sg : groups)
+      {
+        if (sg.getSequences(null).contains(seq))
         {
-            return (SequenceI) sequences.elementAt(i);
+          if (position >= sg.getStartRes() && position <= sg.getEndRes())
+          {
+            return sg;
+          }
         }
+      }
+    }
+    return null;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
+   */
+  @Override
+  public SequenceGroup[] findAllGroups(SequenceI s)
+  {
+    ArrayList<SequenceGroup> temp = new ArrayList<>();
 
-        return null;
+    synchronized (groups)
+    {
+      int gSize = groups.size();
+      for (int i = 0; i < gSize; i++)
+      {
+        SequenceGroup sg = groups.get(i);
+        if (sg == null || sg.getSequences() == null)
+        {
+          this.deleteGroup(sg);
+          gSize--;
+          continue;
+        }
+
+        if (sg.getSequences().contains(s))
+        {
+          temp.add(sg);
+        }
+      }
     }
+    SequenceGroup[] ret = new SequenceGroup[temp.size()];
+    return temp.toArray(ret);
+  }
 
-    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-     *
-     * @param snew
-     */
-    public void addSequence(SequenceI snew)
+  /**    */
+  @Override
+  public void addGroup(SequenceGroup sg)
+  {
+    synchronized (groups)
     {
-      if(dataset!=null)
+      if (!groups.contains(sg))
       {
-        if(snew.getDatasetSequence()!=null)
+        if (hiddenSequences.getSize() > 0)
         {
-          System.out.println(snew.getName());
-          getDataset().addSequence(snew.getDatasetSequence());
+          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)
+          {
+            return;
+          }
+        }
+        sg.setContext(this, true);
+        groups.add(sg);
+      }
+    }
+  }
+
+  /**
+   * 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
         {
-          Sequence ds = new Sequence(snew.getName(),
-                                     AlignSeq.extractGaps("-. ",
-              snew.getSequence()),
-                                     snew.getStart(),
-                                     snew.getEnd());
+          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;
+    }
+  }
 
-          snew.setDatasetSequence(ds);
-          getDataset().addSequence(ds);
+  @Override
+  public void deleteAllGroups()
+  {
+    synchronized (groups)
+    {
+      if (annotations != null)
+      {
+        removeAnnotationForGroup(null);
+      }
+      for (SequenceGroup sg : groups)
+      {
+        sg.setContext(null, false);
+      }
+      groups.clear();
+    }
+  }
+
+  /**    */
+  @Override
+  public void deleteGroup(SequenceGroup g)
+  {
+    synchronized (groups)
+    {
+      if (groups.contains(g))
+      {
+        removeAnnotationForGroup(g);
+        groups.remove(g);
+        g.setContext(null, false);
+      }
+    }
+  }
+
+  /**    */
+  @Override
+  public SequenceI findName(String name)
+  {
+    return findName(name, false);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+   */
+  @Override
+  public SequenceI findName(String token, boolean b)
+  {
+    return findName(null, token, b);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+   * boolean)
+   */
+  @Override
+  public SequenceI findName(SequenceI startAfter, String token, boolean b)
+  {
+
+    int i = 0;
+    SequenceI sq = null;
+    String sqname = null;
+    int nseq = sequences.size();
+    if (startAfter != null)
+    {
+      // try to find the sequence in the alignment
+      boolean matched = false;
+      while (i < nseq)
+      {
+        if (getSequenceAt(i++) == startAfter)
+        {
+          matched = true;
+          break;
         }
       }
+      if (!matched)
+      {
+        i = 0;
+      }
+    }
+    while (i < nseq)
+    {
+      sq = getSequenceAt(i);
+      sqname = sq.getName();
+      if (sqname.equals(token) // exact match
+              || (b && // allow imperfect matches - case varies
+                      (sqname.equalsIgnoreCase(token))))
+      {
+        return getSequenceAt(i);
+      }
 
-      sequences.addElement(snew);
+      i++;
     }
 
+    return null;
+  }
+
+  @Override
+  public SequenceI[] findSequenceMatch(String name)
+  {
+    Vector matches = new Vector();
+    int i = 0;
 
-    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-     *
-     * @param snew
-     */
-    public void setSequenceAt(int i, SequenceI snew)
+    while (i < sequences.size())
     {
-        SequenceI oldseq = getSequenceAt(i);
-        deleteSequence(oldseq);
+      if (getSequenceAt(i).getName().equals(name))
+      {
+        matches.addElement(getSequenceAt(i));
+      }
+      i++;
+    }
 
-        sequences.setElementAt(snew, i);
+    SequenceI[] result = new SequenceI[matches.size()];
+    for (i = 0; i < result.length; i++)
+    {
+      result[i] = (SequenceI) matches.elementAt(i);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getGroups()
+    return result;
+
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+   */
+  @Override
+  public int findIndex(SequenceI s)
+  {
+    int i = 0;
+
+    while (i < sequences.size())
     {
-        return groups;
+      if (s == getSequenceAt(i))
+      {
+        return i;
+      }
+
+      i++;
     }
 
-    /** Takes out columns consisting entirely of gaps (-,.," ")
-     */
-    public void removeGaps()
+    return -1;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+   */
+  @Override
+  public int findIndex(SearchResultsI results)
+  {
+    int i = 0;
+
+    while (i < sequences.size())
     {
-        SequenceI[] seqs = getVisibleAndRepresentedSeqs();
-        int j, jSize = seqs.length;
+      if (results.involvesSequence(getSequenceAt(i)))
+      {
+        return i;
+      }
+      i++;
+    }
+    return -1;
+  }
 
-        int width = 0;
-        for (int i = 0; i < jSize; i++)
+  @Override
+  public int getHeight()
+  {
+    return sequences.size();
+  }
+
+  @Override
+  public int getAbsoluteHeight()
+  {
+    return sequences.size() + getHiddenSequences().getSize();
+  }
+
+  @Override
+  public int getWidth()
+  {
+    int maxLength = -1;
+
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
+    }
+    return maxLength;
+  }
+
+  @Override
+  public int getVisibleWidth()
+  {
+    int w = getWidth();
+    if (hiddenCols != null)
+    {
+      w -= hiddenCols.getSize();
+    }
+    return w;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param gc
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void setGapCharacter(char gc)
+  {
+    gapCharacter = gc;
+    synchronized (sequences)
+    {
+      for (SequenceI seq : sequences)
+      {
+        seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+                .replace('-', gc).replace(' ', gc));
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  @Override
+  public char getGapCharacter()
+  {
+    return gapCharacter;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#isAligned()
+   */
+  @Override
+  public boolean isAligned()
+  {
+    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 (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
+      {
+        if (getSequenceAt(i).getLength() != width)
         {
-          if (seqs[i].getLength() > width)
-          {
-            width = seqs[i].getLength();
-          }
+          return false;
         }
+      }
+    }
 
-        int startCol = -1, endCol = -1;
-        boolean delete = true;
-        for (int i = 0; i < width; i++)
-        {
-            delete = true;
+    return true;
+  }
 
-            for (j = 0; j < jSize; j++)
-            {
-                if (seqs[j].getLength() > i)
-                {
-                    if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
-                    {
-                        if(delete)
-                          endCol = i;
-
-                        delete = false;
-                        break;
-                    }
-                }
-            }
+  @Override
+  public boolean isHidden(int alignmentIndex)
+  {
+    return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null);
+  }
 
-            if(delete && startCol==-1)
-            {
-              startCol = i;
-            }
+  /**
+   * Delete all annotations, including auto-calculated if the flag is set true.
+   * Returns true if at least one annotation was deleted, else false.
+   * 
+   * @param includingAutoCalculated
+   * @return
+   */
+  @Override
+  public boolean deleteAllAnnotations(boolean includingAutoCalculated)
+  {
+    boolean result = false;
+    for (AlignmentAnnotation alan : getAlignmentAnnotation())
+    {
+      if (!alan.autoCalculated || includingAutoCalculated)
+      {
+        deleteAnnotation(alan);
+        result = true;
+      }
+    }
+    return result;
+  }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+   * AlignmentAnnotation)
+   */
+  @Override
+  public boolean deleteAnnotation(AlignmentAnnotation aa)
+  {
+    return deleteAnnotation(aa, true);
+  }
 
-            if (!delete && startCol > -1)
-            {
-              deleteColumns(seqs, startCol, endCol);
-              width -= (endCol - startCol);
-              i -= (endCol - startCol);
-              startCol = -1;
-              endCol = -1;
-            }
-        }
+  @Override
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+  {
+    int aSize = 1;
 
-        if (delete && startCol > -1)
+    if (annotations != null)
+    {
+      aSize = annotations.length;
+    }
+
+    if (aSize < 1)
+    {
+      return false;
+    }
+
+    AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+
+    boolean swap = false;
+    int tIndex = 0;
+
+    for (int i = 0; i < aSize; i++)
+    {
+      if (annotations[i] == aa)
+      {
+        swap = true;
+        continue;
+      }
+      if (tIndex < temp.length)
+      {
+        temp[tIndex++] = annotations[i];
+      }
+    }
+
+    if (swap)
+    {
+      annotations = temp;
+      if (unhook)
+      {
+        unhookAnnotation(aa);
+      }
+    }
+    return swap;
+  }
+
+  /**
+   * remove any object references associated with this annotation
+   * 
+   * @param aa
+   */
+  private void unhookAnnotation(AlignmentAnnotation aa)
+  {
+    if (aa.sequenceRef != null)
+    {
+      aa.sequenceRef.removeAlignmentAnnotation(aa);
+    }
+    if (aa.groupRef != null)
+    {
+      // probably need to do more here in the future (post 2.5.0)
+      aa.groupRef = null;
+    }
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * AlignmentAnnotation)
+   */
+  @Override
+  public void addAnnotation(AlignmentAnnotation aa)
+  {
+    addAnnotation(aa, -1);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * AlignmentAnnotation, int)
+   */
+  @Override
+  public void addAnnotation(AlignmentAnnotation aa, int pos)
+  {
+    if (aa.getRNAStruc() != null)
+    {
+      hasRNAStructure = true;
+    }
+
+    int aSize = 1;
+    if (annotations != null)
+    {
+      aSize = annotations.length + 1;
+    }
+
+    AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+    int i = 0;
+    if (pos == -1 || pos >= aSize)
+    {
+      temp[aSize - 1] = aa;
+    }
+    else
+    {
+      temp[pos] = aa;
+    }
+    if (aSize > 1)
+    {
+      int p = 0;
+      for (i = 0; i < (aSize - 1); i++, p++)
+      {
+        if (p == pos)
+        {
+          p++;
+        }
+        if (p < temp.length)
         {
-          deleteColumns(seqs, startCol, endCol);
+          temp[p] = annotations[i];
         }
+      }
     }
 
-    /** Removes a range of columns (start to end inclusive).
-     *
-     * @param seqs Sequences to remove columns from
-     * @param start Start column in the alignment
-     * @param end End column in the alignment
-     */
-    public void deleteColumns(SequenceI [] seqs, int start, int end)
+    annotations = temp;
+  }
+
+  @Override
+  public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+  {
+    if (aa == null || annotations == null || annotations.length - 1 < index)
     {
-      for(int i=0; i<seqs.length; i++)
-        seqs[i].deleteChars(start, end);
+      return;
     }
 
+    int aSize = annotations.length;
+    AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void trimLeft(int i)
+    temp[index] = aa;
+
+    for (int i = 0; i < aSize; i++)
+    {
+      if (i == index)
+      {
+        continue;
+      }
+
+      if (i < index)
+      {
+        temp[i] = annotations[i];
+      }
+      else
+      {
+        temp[i] = annotations[i - 1];
+      }
+    }
+
+    annotations = temp;
+  }
+
+  @Override
+  /**
+   * returns all annotation on the alignment
+   */
+  public AlignmentAnnotation[] getAlignmentAnnotation()
+  {
+    return annotations;
+  }
+
+  @Override
+  public boolean isNucleotide()
+  {
+    return nucleotide;
+  }
+
+  @Override
+  public boolean hasRNAStructure()
+  {
+    // TODO can it happen that structure is removed from alignment?
+    return hasRNAStructure;
+  }
+
+  @Override
+  public void setDataset(AlignmentI data)
+  {
+    if (dataset == null && data == null)
     {
-        SequenceI[] seqs = getVisibleAndRepresentedSeqs();
-        int j, jSize = seqs.length;
-        for (j = 0; j < jSize; j++)
+      createDatasetAlignment();
+    }
+    else if (dataset == null && data != null)
+    {
+      if (data == this)
+      {
+        throw new IllegalArgumentException("Circular dataset reference");
+      }
+      if (!(data instanceof Alignment))
+      {
+        throw new Error(
+                "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference");
+      }
+      dataset = (Alignment) data;
+      for (int i = 0; i < getHeight(); i++)
+      {
+        SequenceI currentSeq = getSequenceAt(i);
+        SequenceI dsq = currentSeq.getDatasetSequence();
+        if (dsq == null)
         {
-            int newstart = seqs[j].findPosition(i);
+          dsq = currentSeq.createDatasetSequence();
+          dataset.addSequence(dsq);
+        }
+        else
+        {
+          while (dsq.getDatasetSequence() != null)
+          {
+            dsq = dsq.getDatasetSequence();
+          }
+          if (dataset.findIndex(dsq) == -1)
+          {
+            dataset.addSequence(dsq);
+          }
+        }
+      }
+    }
+    dataset.addAlignmentRef();
+  }
 
-            if(i>seqs[j].getLength())
+  /**
+   * add dataset sequences to seq for currentSeq and any sequences it references
+   */
+  private void resolveAndAddDatasetSeq(SequenceI currentSeq,
+          Set<SequenceI> seqs, boolean createDatasetSequence)
+  {
+    SequenceI alignedSeq = currentSeq;
+    if (currentSeq.getDatasetSequence() != null)
+    {
+      currentSeq = currentSeq.getDatasetSequence();
+    }
+    else
+    {
+      if (createDatasetSequence)
+      {
+        currentSeq = currentSeq.createDatasetSequence();
+      }
+    }
+
+    List<SequenceI> toProcess = new ArrayList<>();
+    toProcess.add(currentSeq);
+    while (toProcess.size() > 0)
+    {
+      // use a queue ?
+      SequenceI curDs = toProcess.remove(0);
+
+      if (!seqs.add(curDs))
+      {
+        continue;
+      }
+      // iterate over database references, making sure we add forward referenced
+      // sequences
+      if (curDs.getDBRefs() != null)
+      {
+        for (DBRefEntry dbr : curDs.getDBRefs())
+        {
+          if (dbr.getMap() != null && dbr.getMap().getTo() != null)
+          {
+            if (dbr.getMap().getTo() == alignedSeq)
             {
-              sequences.removeElement(seqs[j]);
-              j--;
-              jSize--;
+              /*
+               * update mapping to be to the newly created dataset sequence
+               */
+              dbr.getMap().setTo(currentSeq);
             }
-            else
+            if (dbr.getMap().getTo().getDatasetSequence() != null)
             {
-              seqs[j].setStart(newstart);
-              seqs[j].setSequence(seqs[j].getSequence().substring(i));
+              throw new Error("Implementation error: Map.getTo() for dbref "
+                      + dbr + " from " + curDs.getName()
+                      + " is not a dataset sequence.");
             }
+            // we recurse to add all forward references to dataset sequences via
+            // DBRefs/etc
+            toProcess.add(dbr.getMap().getTo());
+          }
         }
+      }
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void trimRight(int i)
+  /**
+   * Creates a new dataset for this alignment. Can only be done once - if
+   * dataset is not null this will not be performed.
+   */
+  public void createDatasetAlignment()
+  {
+    if (dataset != null)
     {
-        SequenceI[] seqs = getVisibleAndRepresentedSeqs();
-        int j, jSize = seqs.length;
-        for (j = 0; j < jSize; j++)
-        {
-            int newend = seqs[j].findPosition(i);
+      return;
+    }
+    // try to avoid using SequenceI.equals at this stage, it will be expensive
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<>();
 
-            seqs[j].setEnd(newend);
-            if(seqs[j].getLength()>i)
-              seqs[j].setSequence(seqs[j].getSequence().substring(0, i + 1));
+    for (int i = 0; i < getHeight(); i++)
+    {
+      SequenceI currentSeq = getSequenceAt(i);
+      resolveAndAddDatasetSeq(currentSeq, seqs, true);
+    }
+
+    // verify all mappings are in dataset
+    for (AlignedCodonFrame cf : codonFrameList)
+    {
+      for (SequenceToSequenceMapping ssm : cf.getMappings())
+      {
+        if (!seqs.contains(ssm.getFromSeq()))
+        {
+          resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false);
+        }
+        if (!seqs.contains(ssm.getMapping().getTo()))
+        {
+          resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false);
         }
+      }
     }
+    // finally construct dataset
+    dataset = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+    // move mappings to the dataset alignment
+    dataset.codonFrameList = this.codonFrameList;
+    this.codonFrameList = null;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     */
-    public void deleteSequence(SequenceI s)
+  /**
+   * reference count for number of alignments referencing this one.
+   */
+  int alignmentRefs = 0;
+
+  /**
+   * increase reference count to this alignment.
+   */
+  private void addAlignmentRef()
+  {
+    alignmentRefs++;
+  }
+
+  @Override
+  public Alignment getDataset()
+  {
+    return dataset;
+  }
+
+  @Override
+  public boolean padGaps()
+  {
+    boolean modified = false;
+
+    // Remove excess gaps from the end of alignment
+    int maxLength = -1;
+
+    SequenceI current;
+    int nseq = sequences.size();
+    for (int i = 0; i < nseq; i++)
     {
-        for (int i = 0; i < getHeight(); i++)
+      current = getSequenceAt(i);
+      for (int j = current.getLength(); j > maxLength; j--)
+      {
+        if (j > maxLength
+                && !jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
-            if (getSequenceAt(i) == s)
-            {
-                deleteSequence(i);
-            }
+          maxLength = j;
+          break;
         }
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void deleteSequence(int i)
+    maxLength++;
+
+    int cLength;
+    for (int i = 0; i < nseq; i++)
     {
-        sequences.removeElementAt(i);
+      current = getSequenceAt(i);
+      cLength = current.getLength();
+
+      if (cLength < maxLength)
+      {
+        current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
+        modified = true;
+      }
+      else if (current.getLength() > maxLength)
+      {
+        current.deleteChars(maxLength, current.getLength());
+      }
     }
+    return modified;
+  }
 
+  /**
+   * Justify the sequences to the left or right by deleting and inserting gaps
+   * before the initial residue or after the terminal residue
+   * 
+   * @param right
+   *          true if alignment padded to right, false to justify to left
+   * @return true if alignment was changed
+   */
+  @Override
+  public boolean justify(boolean right)
+  {
+    boolean modified = false;
 
-    /**    */
-    public SequenceGroup findGroup(SequenceI s)
+    // Remove excess gaps from the end of alignment
+    int maxLength = -1;
+    int ends[] = new int[sequences.size() * 2];
+    SequenceI current;
+    for (int i = 0; i < sequences.size(); i++)
     {
-        for (int i = 0; i < this.groups.size(); i++)
+      current = getSequenceAt(i);
+      // This should really be a sequence method
+      ends[i * 2] = current.findIndex(current.getStart());
+      ends[i * 2 + 1] = current
+              .findIndex(current.getStart() + current.getLength());
+      boolean hitres = false;
+      for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
+      {
+        if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
-            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
-            if (sg.getSequences(false).contains(s))
+          if (!hitres)
+          {
+            ends[i * 2] = j;
+            hitres = true;
+          }
+          else
+          {
+            ends[i * 2 + 1] = j;
+            if (j - ends[i * 2] > maxLength)
             {
-                return sg;
+              maxLength = j - ends[i * 2];
             }
+          }
         }
-
-        return null;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceGroup[] findAllGroups(SequenceI s)
+    maxLength++;
+    // now edit the flanking gaps to justify to either left or right
+    int cLength, extent, diff;
+    for (int i = 0; i < sequences.size(); i++)
     {
-        Vector temp = new Vector();
+      current = getSequenceAt(i);
 
-        int gSize = groups.size();
-        for (int i = 0; i < gSize; i++)
+      cLength = 1 + ends[i * 2 + 1] - ends[i * 2];
+      diff = maxLength - cLength; // number of gaps to indent
+      extent = current.getLength();
+      if (right)
+      {
+        // right justify
+        if (extent > ends[i * 2 + 1])
         {
-            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            if(sg==null || sg.getSequences(false)==null)
-            {
-              this.deleteGroup(sg);
-              gSize--;
-              continue;
-            }
-
-            if (sg.getSequences(false).contains(s))
-            {
-                temp.addElement(sg);
-            }
+          current.deleteChars(ends[i * 2 + 1] + 1, extent);
+          modified = true;
         }
-
-        SequenceGroup[] ret = new SequenceGroup[temp.size()];
-
-        for (int i = 0; i < temp.size(); i++)
+        if (ends[i * 2] > diff)
+        {
+          current.deleteChars(0, ends[i * 2] - diff);
+          modified = true;
+        }
+        else
+        {
+          if (ends[i * 2] < diff)
+          {
+            current.insertCharAt(0, diff - ends[i * 2], gapCharacter);
+            modified = true;
+          }
+        }
+      }
+      else
+      {
+        // left justify
+        if (ends[i * 2] > 0)
+        {
+          current.deleteChars(0, ends[i * 2]);
+          modified = true;
+          ends[i * 2 + 1] -= ends[i * 2];
+          extent -= ends[i * 2];
+        }
+        if (extent > maxLength)
+        {
+          current.deleteChars(maxLength + 1, extent);
+          modified = true;
+        }
+        else
         {
-            ret[i] = (SequenceGroup) temp.elementAt(i);
+          if (extent < maxLength)
+          {
+            current.insertCharAt(extent, maxLength - extent, gapCharacter);
+            modified = true;
+          }
         }
-
-        return ret;
+      }
     }
+    return modified;
+  }
 
+  @Override
+  public HiddenSequences getHiddenSequences()
+  {
+    return hiddenSequences;
+  }
 
+  @Override
+  public HiddenColumns getHiddenColumns()
+  {
+    return hiddenCols;
+  }
 
-    /**    */
-    public void addGroup(SequenceGroup sg)
+  @Override
+  public CigarArray getCompactAlignment()
+  {
+    synchronized (sequences)
     {
-        if (!groups.contains(sg))
-        {
-            groups.addElement(sg);
-        }
+      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;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void deleteAllGroups()
+  @Override
+  public void setProperty(Object key, Object value)
+  {
+    if (alignmentProperties == null)
     {
-        groups.removeAllElements();
-
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            SequenceI s = getSequenceAt(i);
-            s.setColor(java.awt.Color.white);
-            i++;
-        }
+      alignmentProperties = new Hashtable();
     }
 
-    /**    */
-    public void deleteGroup(SequenceGroup g)
+    alignmentProperties.put(key, value);
+  }
+
+  @Override
+  public Object getProperty(Object key)
+  {
+    if (alignmentProperties != null)
     {
-        if (groups.contains(g))
-        {
-            groups.removeElement(g);
-        }
+      return alignmentProperties.get(key);
     }
-
-    /**    */
-    public SequenceI findName(String name)
+    else
     {
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            if (getSequenceAt(i).getName().equals(name))
-            {
-                return getSequenceAt(i);
-            }
-
-            i++;
-        }
-
-        return null;
+      return null;
     }
+  }
 
+  @Override
+  public Hashtable getProperties()
+  {
+    return alignmentProperties;
+  }
 
-    /**    */
-    public int findIndex(SequenceI s)
+  /**
+   * Adds the given mapping to the stored set. Note this may be held on the
+   * dataset alignment.
+   */
+  @Override
+  public void addCodonFrame(AlignedCodonFrame codons)
+  {
+    List<AlignedCodonFrame> acfs = getCodonFrames();
+    if (codons != null && acfs != null && !acfs.contains(codons))
     {
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            if (s == getSequenceAt(i))
-            {
-                return i;
-            }
-
-            i++;
-        }
-
-        return -1;
+      acfs.add(codons);
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getHeight()
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+   */
+  @Override
+  public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
+  {
+    if (seq == null)
     {
-        return sequences.size();
+      return null;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWidth()
+    List<AlignedCodonFrame> cframes = new ArrayList<>();
+    for (AlignedCodonFrame acf : getCodonFrames())
     {
-        int maxLength = -1;
-
-        for (int i = 0; i < sequences.size(); i++)
-        {
-            if (getSequenceAt(i).getLength() > maxLength)
-            {
-                maxLength = getSequenceAt(i).getLength();
-            }
-        }
-
-        return maxLength;
+      if (acf.involvesSequence(seq))
+      {
+        cframes.add(acf);
+      }
     }
+    return cframes;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMaxIdLength()
+  /**
+   * Sets the codon frame mappings (replacing any existing mappings). Note the
+   * mappings are set on the dataset alignment instead if there is one.
+   * 
+   * @see jalview.datamodel.AlignmentI#setCodonFrames()
+   */
+  @Override
+  public void setCodonFrames(List<AlignedCodonFrame> acfs)
+  {
+    if (dataset != null)
     {
-        int max = 0;
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            SequenceI seq = getSequenceAt(i);
-            String tmp = seq.getName() + "/" + seq.getStart() + "-" +
-                seq.getEnd();
-
-            if (tmp.length() > max)
-            {
-                max = tmp.length();
-            }
+      dataset.setCodonFrames(acfs);
+    }
+    else
+    {
+      this.codonFrameList = acfs;
+    }
+  }
 
-            i++;
-        }
+  /**
+   * Returns the set of codon frame mappings. Any changes to the returned set
+   * will affect the alignment. The mappings are held on (and read from) the
+   * dataset alignment if there is one.
+   * 
+   * @see jalview.datamodel.AlignmentI#getCodonFrames()
+   */
+  @Override
+  public List<AlignedCodonFrame> getCodonFrames()
+  {
+    // TODO: Fix this method to fix failing AlignedCodonFrame tests
+    // this behaviour is currently incorrect. method should return codon frames
+    // for just the alignment,
+    // selected from dataset
+    return dataset != null ? dataset.getCodonFrames() : codonFrameList;
+  }
 
-        return max;
+  /**
+   * Removes the given mapping from the stored set. Note that the mappings are
+   * held on the dataset alignment if there is one.
+   */
+  @Override
+  public boolean removeCodonFrame(AlignedCodonFrame codons)
+  {
+    List<AlignedCodonFrame> acfs = getCodonFrames();
+    if (codons == null || acfs == null)
+    {
+      return false;
     }
+    return acfs.remove(codons);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gc DOCUMENT ME!
-     */
-    public void setGapCharacter(char gc)
+  @Override
+  public void append(AlignmentI toappend)
+  {
+    // TODO JAL-1270 needs test coverage
+    // currently tested for use in jalview.gui.SequenceFetcher
+    char oldc = toappend.getGapCharacter();
+    boolean samegap = oldc == getGapCharacter();
+    boolean hashidden = toappend.getHiddenSequences() != null
+            && toappend.getHiddenSequences().hiddenSequences != null;
+    // get all sequences including any hidden ones
+    List<SequenceI> sqs = (hashidden)
+            ? toappend.getHiddenSequences().getFullAlignment()
+                    .getSequences()
+            : toappend.getSequences();
+    if (sqs != null)
     {
-        gapCharacter = gc;
-
-        for (int i = 0; i < sequences.size(); i++)
+      // avoid self append deadlock by
+      List<SequenceI> toappendsq = new ArrayList<>();
+      synchronized (sqs)
+      {
+        for (SequenceI addedsq : sqs)
         {
-            Sequence seq = (Sequence) sequences.elementAt(i);
-            seq.setSequence( seq.getSequence().replace('.', gc) );
-            seq.setSequence( seq.getSequence().replace('-', gc) );
-            seq.setSequence( seq.getSequence().replace(' ', gc) );
+          if (!samegap)
+          {
+            addedsq.replace(oldc, gapCharacter);
+          }
+          toappendsq.add(addedsq);
         }
+      }
+      for (SequenceI addedsq : toappendsq)
+      {
+        addSequence(addedsq);
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter()
+    AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+    for (int a = 0; alan != null && a < alan.length; a++)
     {
-        return gapCharacter;
+      addAnnotation(alan[a]);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getAAFrequency()
+    // use add method
+    getCodonFrames().addAll(toappend.getCodonFrames());
+
+    List<SequenceGroup> sg = toappend.getGroups();
+    if (sg != null)
     {
-        return AAFrequency.calculate(sequences, 0, getWidth());
+      for (SequenceGroup _sg : sg)
+      {
+        addGroup(_sg);
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean isAligned()
+    if (toappend.getHiddenSequences() != null)
     {
-        int width = getWidth();
-
-        for (int i = 0; i < sequences.size(); i++)
+      HiddenSequences hs = toappend.getHiddenSequences();
+      if (hiddenSequences == null)
+      {
+        hiddenSequences = new HiddenSequences(this);
+      }
+      if (hs.hiddenSequences != null)
+      {
+        for (int s = 0; s < hs.hiddenSequences.length; s++)
+        {
+          // hide the newly appended sequence in the alignment
+          if (hs.hiddenSequences[s] != null)
+          {
+            hiddenSequences.hideSequence(hs.hiddenSequences[s]);
+          }
+        }
+      }
+    }
+    if (toappend.getProperties() != null)
+    {
+      // we really can't do very much here - just try to concatenate strings
+      // where property collisions occur.
+      Enumeration key = toappend.getProperties().keys();
+      while (key.hasMoreElements())
+      {
+        Object k = key.nextElement();
+        Object ourval = this.getProperty(k);
+        Object toapprop = toappend.getProperty(k);
+        if (ourval != null)
         {
-            if (getSequenceAt(i).getLength() != width)
+          if (ourval.getClass().equals(toapprop.getClass())
+                  && !ourval.equals(toapprop))
+          {
+            if (ourval instanceof String)
+            {
+              // append strings
+              this.setProperty(k,
+                      ((String) ourval) + "; " + ((String) toapprop));
+            }
+            else
             {
-                return false;
+              if (ourval instanceof Vector)
+              {
+                // append vectors
+                Enumeration theirv = ((Vector) toapprop).elements();
+                while (theirv.hasMoreElements())
+                {
+                  ((Vector) ourval).addElement(theirv);
+                }
+              }
             }
+          }
+        }
+        else
+        {
+          // just add new property directly
+          setProperty(k, toapprop);
         }
 
-        return true;
+      }
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param aa DOCUMENT ME!
-     */
-    public void deleteAnnotation(AlignmentAnnotation aa)
+  @Override
+  public AlignmentAnnotation findOrCreateAnnotation(String name,
+          String calcId, boolean autoCalc, SequenceI seqRef,
+          SequenceGroup groupRef)
+  {
+    if (annotations != null)
     {
-        int aSize = 1;
-
-        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)
         {
-            aSize = annotations.length;
+          return annot;
         }
+      }
+    }
+    AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
+            new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
+    annot.hasText = false;
+    if (calcId != null)
+    {
+      annot.setCalcId(new String(calcId));
+    }
+    annot.autoCalculated = autoCalc;
+    if (seqRef != null)
+    {
+      annot.setSequenceRef(seqRef);
+    }
+    annot.groupRef = groupRef;
+    addAnnotation(annot);
 
-        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
-
-        int tIndex = 0;
-
-        for (int i = 0; i < aSize; i++)
-        {
-            if (annotations[i] == aa)
-            {
-                continue;
-            }
-
-            temp[tIndex] = annotations[i];
-            tIndex++;
-        }
+    return annot;
+  }
 
-        annotations = temp;
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+  {
+    AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+    if (alignmentAnnotation != null)
+    {
+      return AlignmentAnnotation.findAnnotation(
+              Arrays.asList(getAlignmentAnnotation()), calcId);
     }
+    return Arrays.asList(new AlignmentAnnotation[] {});
+  }
 
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+          String calcId, String label)
+  {
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
+  }
 
-    public void adjustSequenceAnnotations()
+  @Override
+  public void moveSelectedSequencesByOne(SequenceGroup sg,
+          Map<SequenceI, SequenceCollectionI> map, boolean up)
+  {
+    synchronized (sequences)
     {
-      if(annotations!=null)
+      if (up)
       {
-        for (int a = 0; a < annotations.length; a++)
+
+        for (int i = 1, iSize = sequences.size(); i < iSize; i++)
         {
-          if (annotations[a].sequenceRef != null)
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
+
+          SequenceI temp = sequences.get(i - 1);
+          if (sg.getSequences(null).contains(temp))
           {
-            annotations[a].adjustForAlignment();
+            continue;
           }
+
+          sequences.set(i, temp);
+          sequences.set(i - 1, seq);
         }
       }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param aa DOCUMENT ME!
-     */
-    public void addAnnotation(AlignmentAnnotation aa)
-    {
-        int aSize = 1;
-        if (annotations != null)
+      else
+      {
+        for (int i = sequences.size() - 2; i > -1; i--)
         {
-            aSize = annotations.length + 1;
-        }
-
-        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
-        temp[aSize-1] = aa;
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
 
-        int i = 0;
+          SequenceI temp = sequences.get(i + 1);
+          if (sg.getSequences(map).contains(temp))
+          {
+            continue;
+          }
 
-        if (aSize > 1)
-        {
-            for (i = 0; i < (aSize-1); i++)
-            {
-                temp[i] = annotations[i];
-            }
+          sequences.set(i, temp);
+          sequences.set(i + 1, seq);
         }
+      }
 
-        annotations = temp;
     }
+  }
 
-    public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+  @Override
+  public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+  {
+    alignmentAnnotation.validateRangeAndDisplay();
+    if (isNucleotide() && alignmentAnnotation.isValidStruc())
     {
-      if(aa==null || annotations==null || annotations.length-1<index)
-        return;
+      hasRNAStructure = true;
+    }
+  }
 
-      int aSize = annotations.length;
-      AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+  private SequenceI seqrep = null;
 
-      temp[index] = aa;
+  /**
+   * 
+   * @return the representative sequence for this group
+   */
+  @Override
+  public SequenceI getSeqrep()
+  {
+    return seqrep;
+  }
 
-      for (int i = 0; i < aSize; i++)
-      {
-        if(i==index)
-          continue;
+  /**
+   * 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)
+   */
+  @Override
+  public void setSeqrep(SequenceI seqrep)
+  {
+    this.seqrep = seqrep;
+  }
 
-        if(i<index)
-          temp[i] = annotations[i];
-        else
-          temp[i] = annotations[i-1];
-      }
+  /**
+   * 
+   * @return true if group has a sequence representative
+   */
+  @Override
+  public boolean hasSeqrep()
+  {
+    return seqrep != null;
+  }
 
-        annotations = temp;
-    }
+  @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;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+  /**
+   * Align this alignment like the given (mapped) one.
+   */
+  @Override
+  public int alignAs(AlignmentI al)
+  {
+    /*
+     * Currently retains unmapped gaps (in introns), regaps mapped regions
+     * (exons)
      */
-    public AlignmentAnnotation[] getAlignmentAnnotation()
+    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. TODO: check caveats below where the implementation fails
+   * 
+   * @param al
+   *          - must have same dataset, and sequences in al must have equivalent
+   *          dataset sequence and start/end bounds under given mapping
+   * @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?
+    // JBPComment - yes - neither flag is used, so should be deleted.
+    boolean thisIsNucleotide = this.isNucleotide();
+    boolean thatIsProtein = !al.isNucleotide();
+    if (!thatIsProtein && !thisIsNucleotide)
     {
-        return annotations;
+      return AlignmentUtils.alignProteinAsDna(this, al);
     }
-
-    public void setNucleotide(boolean b)
+    else if (thatIsProtein && thisIsNucleotide)
     {
-      if(b)
-        type = NUCLEOTIDE;
-      else
-        type = PROTEIN;
+      return AlignmentUtils.alignCdsAsProtein(this, al);
     }
+    return AlignmentUtils.alignAs(this, al);
+  }
 
-    public boolean isNucleotide()
+  /**
+   * Returns the alignment in Fasta format. Behaviour of this method is not
+   * guaranteed between versions.
+   */
+  @Override
+  public String toString()
+  {
+    return new FastaFile().print(getSequencesArray(), true);
+  }
+
+  /**
+   * Returns the set of distinct sequence names. No ordering is guaranteed.
+   */
+  @Override
+  public Set<String> getSequenceNames()
+  {
+    Set<String> names = new HashSet<>();
+    for (SequenceI seq : getSequences())
     {
-      if(type==NUCLEOTIDE)
-        return true;
-      else
-        return false;
+      names.add(seq.getName());
     }
+    return names;
+  }
 
-    public void setDataset(Alignment data)
+  @Override
+  public boolean hasValidSequence()
+  {
+    boolean hasValidSeq = false;
+    for (SequenceI seq : getSequences())
     {
-      if(dataset==null && data==null)
-      {
-        // Create a new dataset for this alignment.
-        // Can only be done once, if dataset is not null
-        // This will not be performed
-        Sequence[] seqs = new Sequence[getHeight()];
-        for (int i = 0; i < getHeight(); i++)
-        {
-          if(getSequenceAt(i).getDatasetSequence()!=null)
-          {
-            seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();
-          }
-          else
-          {
-            seqs[i] = new Sequence(getSequenceAt(i).getName(),
-                                   AlignSeq.extractGaps(
-                                       jalview.util.Comparison.GapChars,
-                                       getSequenceAt(i).getSequence()
-                                   ),
-                                   getSequenceAt(i).getStart(),
-                                   getSequenceAt(i).getEnd());
-
-            getSequenceAt(i).setDatasetSequence(seqs[i]);
-          }
-        }
-
-        dataset = new Alignment(seqs);
-      }
-      else if(dataset==null && data!=null)
+      if ((seq.getEnd() - seq.getStart()) > 0)
       {
-        dataset = data;
+        hasValidSeq = true;
+        break;
       }
     }
+    return hasValidSeq;
+  }
 
-    public Alignment getDataset()
+  /**
+   * Update any mappings to 'virtual' sequences to compatible real ones, if
+   * present in the added sequences. Returns a count of mappings updated.
+   * 
+   * @param seqs
+   * @return
+   */
+  @Override
+  public int realiseMappings(List<SequenceI> seqs)
+  {
+    int count = 0;
+    for (SequenceI seq : seqs)
     {
-      return dataset;
+      for (AlignedCodonFrame mapping : getCodonFrames())
+      {
+        count += mapping.realiseWith(seq);
+      }
     }
+    return count;
+  }
 
-    public boolean padGaps() {
-      boolean modified=false;
-
-      //Remove excess gaps from the end of alignment
-      int maxLength = -1;
-
-      SequenceI current;
-      for (int i = 0; i < sequences.size(); i++)
+  /**
+   * Returns the first AlignedCodonFrame that has a mapping between the given
+   * dataset sequences
+   * 
+   * @param mapFrom
+   * @param mapTo
+   * @return
+   */
+  @Override
+  public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo)
+  {
+    for (AlignedCodonFrame acf : getCodonFrames())
+    {
+      if (acf.getAaForDnaSeq(mapFrom) == mapTo)
       {
-        current = getSequenceAt(i);
-        for (int j = current.getLength(); j > maxLength; j--)
-        {
-          if (j > maxLength && !jalview.util.Comparison.isGap(
-              current.getCharAt(j)))
-          {
-            maxLength = j;
-            break;
-          }
-        }
+        return acf;
       }
+    }
+    return null;
+  }
 
-      maxLength++;
+  @Override
+  public boolean setHiddenColumns(HiddenColumns cols)
+  {
+    boolean changed = cols == null ? hiddenCols != null
+            : !cols.equals(hiddenCols);
+    hiddenCols = cols;
+    return changed;
+  }
 
-      for (int i = 0; i < sequences.size();
-           i++)
-      {
-        current = getSequenceAt(i);
+  @Override
+  public void setupJPredAlignment()
+  {
+    SequenceI repseq = getSequenceAt(0);
+    setSeqrep(repseq);
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideList(repseq.getInsertions());
+    setHiddenColumns(cs);
+  }
 
-        if (current.getLength() < maxLength)
-        {
-          current.insertCharAt(maxLength - 1, gapCharacter);
-          modified=true;
-        }
-        else if(current.getLength() > maxLength)
-        {
-          current.deleteChars(maxLength, current.getLength());
-        }
-      }
-      return modified;
-    }
+  @Override
+  public HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentView input)
+  {
+    int profsqpos = 0;
 
-    public HiddenSequences getHiddenSequences()
-    {
-      return hiddenSequences;
-    }
-    SequenceI [] getVisibleAndRepresentedSeqs()
+    char gc = getGapCharacter();
+    Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+    HiddenColumns nview = (HiddenColumns) alandhidden[1];
+    SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+    return propagateInsertions(profileseq, origseq, nview);
+  }
+
+  /**
+   * 
+   * @param profileseq
+   *          sequence in al which corresponds to origseq
+   * @param al
+   *          alignment which is to have gaps inserted into it
+   * @param origseq
+   *          sequence corresponding to profileseq which defines gap map for
+   *          modifying al
+   */
+  private HiddenColumns propagateInsertions(SequenceI profileseq,
+          SequenceI origseq, HiddenColumns hc)
+  {
+    // take the set of hidden columns, and the set of gaps in origseq,
+    // and remove all the hidden gaps from hiddenColumns
+
+    // first get the gaps as a Bitset
+    // then calculate hidden ^ not(gap)
+    BitSet gaps = origseq.gapBitset();
+    hc.andNot(gaps);
+
+    // for each sequence in the alignment, except the profile sequence,
+    // insert gaps corresponding to each hidden region but where each hidden
+    // column region is shifted backwards by the number of preceding visible
+    // gaps update hidden columns at the same time
+    HiddenColumns newhidden = new HiddenColumns();
+
+    int numGapsBefore = 0;
+    int gapPosition = 0;
+    Iterator<int[]> it = hc.iterator();
+    while (it.hasNext())
     {
-      if(hiddenSequences==null || hiddenSequences.getSize()<1)
-        return getSequencesArray();
+      int[] region = it.next();
 
-      Vector seqs = new Vector();
-      SequenceI seq;
-      SequenceGroup hidden;
-      for (int i = 0; i < sequences.size(); i++)
+      // get region coordinates accounting for gaps
+      // we can rely on gaps not being *in* hidden regions because we already
+      // removed those
+      while (gapPosition < region[0])
       {
-        seq = (SequenceI) sequences.elementAt(i);
-        seqs.addElement(seq);
-        hidden = seq.getHiddenSequences();
-        if(hidden!=null)
+        gapPosition++;
+        if (gaps.get(gapPosition))
         {
-          for(int j=0; j<hidden.getSize(false); j++)
-          {
-            seqs.addElement(hidden.getSequenceAt(j));
-          }
+          numGapsBefore++;
         }
       }
-      SequenceI [] result = new SequenceI[seqs.size()];
-      for(int i=0; i<seqs.size(); i++)
-        result[i] = (SequenceI)seqs.elementAt(i);
 
-      return result;
+      int left = region[0] - numGapsBefore;
+      int right = region[1] - numGapsBefore;
 
+      newhidden.hideColumns(left, right);
+      padGaps(left, right, profileseq);
     }
+    return newhidden;
+  }
 
-  public CigarArray getCompactAlignment()
+  /**
+   * Pad gaps in all sequences in alignment except profileseq
+   * 
+   * @param left
+   *          position of first gap to insert
+   * @param right
+   *          position of last gap to insert
+   * @param profileseq
+   *          sequence not to pad
+   */
+  private void padGaps(int left, int right, SequenceI profileseq)
   {
-    SeqCigar alseqs[] = new SeqCigar[sequences.size()];
-    for (int i=0; i<sequences.size(); i++) {
-      alseqs[i] = new SeqCigar((SequenceI) sequences.get(i));
+    char gc = getGapCharacter();
+
+    // make a string with number of gaps = length of hidden region
+    StringBuilder sb = new StringBuilder();
+    for (int g = 0; g < right - left + 1; g++)
+    {
+      sb.append(gc);
+    }
+
+    // loop over the sequences and pad with gaps where required
+    for (int s = 0, ns = getHeight(); s < ns; s++)
+    {
+      SequenceI sqobj = getSequenceAt(s);
+      if ((sqobj != profileseq) && (sqobj.getLength() >= left))
+      {
+        String sq = sqobj.getSequenceAsString();
+        sqobj.setSequence(
+                sq.substring(0, left) + sb.toString() + sq.substring(left));
+      }
     }
-    return new CigarArray(alseqs);
   }
 
 }