X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=cea595695796d021188d7a41d6a8cad8b3768d67;hb=61f1a8b75ea5ce352d6214c34fbdcd58bafbbb73;hp=f9de1156ee4d9e6ec0aea5fb99009c7d137858c6;hpb=d6509fcf3a8cc90616e18cb22cec97f85c722bb8;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f9de115..cea5956 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,25 +1,37 @@
 /*
- * 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 2.8.2)
+ * 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.
- * 
+ * 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/>.
+ * 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.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.MessageManager;
 
-import jalview.analysis.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
 
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
@@ -44,7 +56,7 @@ public class Alignment implements AlignmentI
   public static final int PROTEIN = 0;
 
   public static final int NUCLEOTIDE = 1;
-  
+
   public boolean hasRNAStructure = false;
 
   /** DOCUMENT ME!! */
@@ -111,7 +123,7 @@ public class Alignment implements AlignmentI
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
-    throw new Error("Alignment(CigarArray) not yet implemented");
+    throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
     // this(compactAlignment.refCigars);
   }
 
@@ -125,18 +137,23 @@ public class Alignment implements AlignmentI
   {
     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;
+    }
     synchronized (sequences)
     {
       return sequences.toArray(new SequenceI[sequences.size()]);
@@ -144,6 +161,17 @@ public class Alignment implements AlignmentI
   }
 
   /**
+   * Returns a map of lists of sequences keyed by sequence name.
+   * 
+   * @return
+   */
+  @Override
+  public Map<String, List<SequenceI>> getSequencesByName()
+  {
+    return AlignmentUtils.getSequencesByName(this);
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @param i
@@ -151,6 +179,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public SequenceI getSequenceAt(int i)
   {
     synchronized (sequences)
@@ -168,6 +197,7 @@ public class Alignment implements AlignmentI
    * 
    * @param snew
    */
+  @Override
   public void addSequence(SequenceI snew)
   {
     if (dataset != null)
@@ -198,7 +228,9 @@ public class Alignment implements AlignmentI
       }
     }
     if (hiddenSequences != null)
+    {
       hiddenSequences.adjustHeightSequenceAdded();
+    }
   }
 
   /**
@@ -206,6 +238,7 @@ public class Alignment implements AlignmentI
    * 
    * @param snew
    */
+  @Override
   public void setSequenceAt(int i, SequenceI snew)
   {
     SequenceI oldseq = getSequenceAt(i);
@@ -221,15 +254,19 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getGroups()
+  @Override
+  public List<SequenceGroup> getGroups()
   {
     return groups;
   }
 
+  @Override
   public void finalize()
   {
     if (getDataset() != null)
+    {
       getDataset().removeAlignmentRef();
+    }
 
     dataset = null;
     sequences = null;
@@ -256,6 +293,7 @@ public class Alignment implements AlignmentI
    * @param s
    *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(SequenceI s)
   {
     deleteSequence(findIndex(s));
@@ -267,6 +305,7 @@ public class Alignment implements AlignmentI
    * @param i
    *          DOCUMENT ME!
    */
+  @Override
   public void deleteSequence(int i)
   {
     if (i > -1 && i < getHeight())
@@ -281,7 +320,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
    */
   @Override
@@ -302,14 +341,13 @@ public class Alignment implements AlignmentI
     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)
   {
     ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
@@ -338,6 +376,7 @@ public class Alignment implements AlignmentI
   }
 
   /**    */
+  @Override
   public void addGroup(SequenceGroup sg)
   {
     synchronized (groups)
@@ -362,7 +401,7 @@ public class Alignment implements AlignmentI
             return;
           }
         }
-
+        sg.setContext(this);
         groups.add(sg);
       }
     }
@@ -428,6 +467,7 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
   public void deleteAllGroups()
   {
     synchronized (groups)
@@ -436,11 +476,16 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(null);
       }
+      for (SequenceGroup sg : groups)
+      {
+        sg.setContext(null);
+      }
       groups.clear();
     }
   }
 
   /**    */
+  @Override
   public void deleteGroup(SequenceGroup g)
   {
     synchronized (groups)
@@ -449,11 +494,13 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(g);
         groups.remove(g);
+        g.setContext(null);
       }
     }
   }
 
   /**    */
+  @Override
   public SequenceI findName(String name)
   {
     return findName(name, false);
@@ -464,6 +511,7 @@ 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);
@@ -475,6 +523,7 @@ 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)
   {
 
@@ -515,6 +564,7 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  @Override
   public SequenceI[] findSequenceMatch(String name)
   {
     Vector matches = new Vector();
@@ -544,6 +594,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
    */
+  @Override
   public int findIndex(SequenceI s)
   {
     int i = 0;
@@ -567,6 +618,7 @@ public class Alignment implements AlignmentI
    * @see
    * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
+  @Override
   public int findIndex(SearchResults results)
   {
     int i = 0;
@@ -587,6 +639,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getHeight()
   {
     return sequences.size();
@@ -597,6 +650,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getWidth()
   {
     int maxLength = -1;
@@ -618,6 +672,7 @@ public class Alignment implements AlignmentI
    * @param gc
    *          DOCUMENT ME!
    */
+  @Override
   public void setGapCharacter(char gc)
   {
     gapCharacter = gc;
@@ -636,6 +691,7 @@ public class Alignment implements AlignmentI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getGapCharacter()
   {
     return gapCharacter;
@@ -646,6 +702,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#isAligned()
    */
+  @Override
   public boolean isAligned()
   {
     return isAligned(false);
@@ -656,6 +713,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#isAligned(boolean)
    */
+  @Override
   public boolean isAligned(boolean includeHidden)
   {
     int width = getWidth();
@@ -683,11 +741,13 @@ 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;
@@ -715,13 +775,16 @@ public class Alignment implements AlignmentI
         continue;
       }
       if (tIndex < temp.length)
+      {
         temp[tIndex++] = annotations[i];
+      }
     }
 
     if (swap)
     {
       annotations = temp;
-      if (unhook) {
+      if (unhook)
+      {
         unhookAnnotation(aa);
       }
     }
@@ -752,6 +815,7 @@ public class Alignment implements AlignmentI
    * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
    * AlignmentAnnotation)
    */
+  @Override
   public void addAnnotation(AlignmentAnnotation aa)
   {
     addAnnotation(aa, -1);
@@ -763,12 +827,14 @@ 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)
     {
@@ -804,6 +870,7 @@ public class Alignment implements AlignmentI
     annotations = temp;
   }
 
+  @Override
   public void setAnnotationIndex(AlignmentAnnotation aa, int index)
   {
     if (aa == null || annotations == null || annotations.length - 1 < index)
@@ -845,6 +912,7 @@ public class Alignment implements AlignmentI
     return annotations;
   }
 
+  @Override
   public void setNucleotide(boolean b)
   {
     if (b)
@@ -857,6 +925,7 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
   public boolean isNucleotide()
   {
     if (type == NUCLEOTIDE)
@@ -868,12 +937,15 @@ 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)
@@ -888,7 +960,7 @@ public class Alignment implements AlignmentI
         currentSeq = getSequenceAt(i);
         if (currentSeq.getDatasetSequence() != null)
         {
-          seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+          seqs[i] = currentSeq.getDatasetSequence();
         }
         else
         {
@@ -901,6 +973,27 @@ public class Alignment implements AlignmentI
     else if (dataset == null && data != null)
     {
       dataset = data;
+      for (int i = 0; i < getHeight(); i++)
+      {
+        SequenceI currentSeq = getSequenceAt(i);
+        SequenceI dsq = currentSeq.getDatasetSequence();
+        if (dsq == null)
+        {
+          dsq = currentSeq.createDatasetSequence();
+          dataset.addSequence(dsq);
+        }
+        else
+        {
+          while (dsq.getDatasetSequence() != null)
+          {
+            dsq = dsq.getDatasetSequence();
+          }
+          if (dataset.findIndex(dsq) == -1)
+          {
+            dataset.addSequence(dsq);
+          }
+        }
+      }
     }
     dataset.addAlignmentRef();
   }
@@ -918,11 +1011,13 @@ public class Alignment implements AlignmentI
     alignmentRefs++;
   }
 
+  @Override
   public Alignment getDataset()
   {
     return dataset;
   }
 
+  @Override
   public boolean padGaps()
   {
     boolean modified = false;
@@ -974,6 +1069,7 @@ 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;
@@ -1071,11 +1167,13 @@ public class Alignment implements AlignmentI
     return modified;
   }
 
+  @Override
   public HiddenSequences getHiddenSequences()
   {
     return hiddenSequences;
   }
 
+  @Override
   public CigarArray getCompactAlignment()
   {
     synchronized (sequences)
@@ -1096,19 +1194,27 @@ public class Alignment implements AlignmentI
   public void setProperty(Object key, Object value)
   {
     if (alignmentProperties == null)
+    {
       alignmentProperties = new Hashtable();
+    }
 
     alignmentProperties.put(key, value);
   }
 
+  @Override
   public Object getProperty(Object key)
   {
     if (alignmentProperties != null)
+    {
       return alignmentProperties.get(key);
+    }
     else
+    {
       return null;
+    }
   }
 
+  @Override
   public Hashtable getProperties()
   {
     return alignmentProperties;
@@ -1123,10 +1229,13 @@ public class Alignment implements AlignmentI
    * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
    * )
    */
+  @Override
   public void addCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null)
+    {
       return;
+    }
     if (codonFrameList == null)
     {
       codonFrameList = new AlignedCodonFrame[]
@@ -1144,6 +1253,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
    */
+  @Override
   public AlignedCodonFrame getCodonFrame(int index)
   {
     return codonFrameList[index];
@@ -1155,18 +1265,25 @@ public class Alignment implements AlignmentI
    * @see
    * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
+  @Override
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
     if (seq == null || codonFrameList == null)
+    {
       return null;
+    }
     Vector cframes = new Vector();
     for (int f = 0; f < codonFrameList.length; f++)
     {
       if (codonFrameList[f].involvesSequence(seq))
+      {
         cframes.addElement(codonFrameList[f]);
+      }
     }
     if (cframes.size() == 0)
+    {
       return null;
+    }
     AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
     cframes.copyInto(cfr);
     return cfr;
@@ -1177,6 +1294,7 @@ public class Alignment implements AlignmentI
    * 
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
+  @Override
   public AlignedCodonFrame[] getCodonFrames()
   {
     return codonFrameList;
@@ -1188,10 +1306,13 @@ public class Alignment implements AlignmentI
    * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
    * AlignedCodonFrame)
    */
+  @Override
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null || codonFrameList == null)
+    {
       return false;
+    }
     boolean removed = false;
     int i = 0, iSize = codonFrameList.length;
     while (i < iSize)
@@ -1214,6 +1335,7 @@ public class Alignment implements AlignmentI
     return removed;
   }
 
+  @Override
   public void append(AlignmentI toappend)
   {
     if (toappend == this)
@@ -1263,7 +1385,7 @@ public class Alignment implements AlignmentI
     List<SequenceGroup> sg = toappend.getGroups();
     if (sg != null)
     {
-      for (SequenceGroup _sg:sg)
+      for (SequenceGroup _sg : sg)
       {
         addGroup(_sg);
       }
@@ -1333,23 +1455,28 @@ 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)
     {
@@ -1364,10 +1491,12 @@ 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);
       }
@@ -1375,4 +1504,183 @@ public class Alignment implements AlignmentI
     return aa;
   }
 
+  /**
+   * Returns an iterable collection of any annotations that match on given
+   * sequence ref, calcId and label (ignoring null values).
+   */
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+          String calcId, String label)
+  {
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation ann : getAlignmentAnnotation())
+    {
+      if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+              && ann.sequenceRef != null && ann.sequenceRef == seq
+              && ann.label != null && ann.label.equals(label))
+      {
+        aa.add(ann);
+      }
+    }
+    return aa;
+  }
+
+  @Override
+  public void moveSelectedSequencesByOne(SequenceGroup sg,
+          Map<SequenceI, SequenceCollectionI> map, boolean up)
+  {
+    synchronized (sequences)
+    {
+      if (up)
+      {
+
+        for (int i = 1, iSize = sequences.size(); i < iSize; i++)
+        {
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
+
+          SequenceI temp = sequences.get(i - 1);
+          if (sg.getSequences(null).contains(temp))
+          {
+            continue;
+          }
+
+          sequences.set(i, temp);
+          sequences.set(i - 1, seq);
+        }
+      }
+      else
+      {
+        for (int i = sequences.size() - 2; i > -1; i--)
+        {
+          SequenceI seq = sequences.get(i);
+          if (!sg.getSequences(map).contains(seq))
+          {
+            continue;
+          }
+
+          SequenceI temp = sequences.get(i + 1);
+          if (sg.getSequences(map).contains(temp))
+          {
+            continue;
+          }
+
+          sequences.set(i, temp);
+          sequences.set(i + 1, seq);
+        }
+      }
+
+    }
+  }
+
+  @Override
+  public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+  {
+    alignmentAnnotation.validateRangeAndDisplay();
+    if (isNucleotide() && alignmentAnnotation.isValidStruc())
+    {
+      hasRNAStructure = true;
+    }
+  }
+
+  @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;
+  }
+
+  @Override
+  public int alignAs(AlignmentI al)
+  {
+    return alignAs(al, true, 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. Does nothing if alignment of protein from cDNA is
+   * requested (not yet implemented).
+   * 
+   * @param al
+   */
+//  @Override
+  public int alignAs(AlignmentI al, boolean preserveMappedGaps,
+          boolean preserveUnmappedGaps)
+  {
+    // TODO should this method signature be the one in the interface?
+    int count = 0;
+    boolean thisIsNucleotide = this.isNucleotide();
+    boolean thatIsProtein = !al.isNucleotide();
+    if (!thatIsProtein && !thisIsNucleotide)
+    {
+      System.err
+              .println("Alignment of protein from cDNA not yet implemented");
+      return 0;
+      // todo: build it - a variant of Dna.CdnaTranslate()
+    }
+
+    char thisGapChar = this.getGapCharacter();
+    String gap = thisIsNucleotide && thatIsProtein ? String
+            .valueOf(new char[]
+            { thisGapChar, thisGapChar, thisGapChar }) : String
+            .valueOf(thisGapChar);
+
+    /*
+     * Get mappings from 'that' alignment's sequences to this.
+     */
+    for (SequenceI alignTo : getSequences())
+    {
+      count += AlignmentUtils.alignSequenceAs(alignTo, al, gap, preserveMappedGaps,
+              preserveUnmappedGaps) ? 1 : 0;
+    }
+    return count;
+  }
+
+  /**
+   * Returns the alignment in Fasta format. Behaviour of this method is not
+   * guaranteed between versions.
+   */
+  @Override
+  public String toString()
+  {
+    return new FastaFile().print(getSequencesArray());
+  }
+
+  /**
+   * Returns the set of distinct sequence names. No ordering is guaranteed.
+   */
+  @Override
+  public Set<String> getSequenceNames()
+  {
+    Set<String> names = new HashSet<String>();
+    for (SequenceI seq : getSequences())
+    {
+      names.add(seq.getName());
+    }
+    return names;
+  }
 }