X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=2289ac6314196fe08a62aa4797c8ef5897f0cc58;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=4057773aefccaff82cce16f2c15012d22debcce2;hpb=fd3e9637614543e5e6f039a0ad10dd5c59b6136f;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 4057773..2289ac6 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,13 +20,21 @@
  */
 package jalview.datamodel;
 
+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.Collections;
 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;
 
 /**
@@ -38,12 +46,11 @@ import java.util.Vector;
  */
 public class Alignment implements AlignmentI
 {
-  protected Alignment dataset;
+  private Alignment dataset;
 
   protected List<SequenceI> sequences;
 
-  protected List<SequenceGroup> groups = java.util.Collections
-          .synchronizedList(new ArrayList<SequenceGroup>());
+  protected List<SequenceGroup> groups;
 
   protected char gapCharacter = '-';
 
@@ -55,18 +62,21 @@ public class Alignment implements AlignmentI
 
   public boolean hasRNAStructure = false;
 
-  /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
 
-  HiddenSequences hiddenSequences = new HiddenSequences(this);
+  HiddenSequences hiddenSequences;
 
   public Hashtable alignmentProperties;
 
+  private List<AlignedCodonFrame> codonFrameList;
+
   private void initAlignment(SequenceI[] seqs)
   {
-    int i = 0;
+    groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
+    hiddenSequences = new HiddenSequences(this);
+    codonFrameList = new ArrayList<AlignedCodonFrame>();
 
-    if (jalview.util.Comparison.isNucleotide(seqs))
+    if (Comparison.isNucleotide(seqs))
     {
       type = NUCLEOTIDE;
     }
@@ -75,10 +85,9 @@ public class Alignment implements AlignmentI
       type = PROTEIN;
     }
 
-    sequences = java.util.Collections
-            .synchronizedList(new ArrayList<SequenceI>());
+    sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
 
-    for (i = 0; i < seqs.length; i++)
+    for (int i = 0; i < seqs.length; i++)
     {
       sequences.add(seqs[i]);
     }
@@ -86,6 +95,29 @@ public class Alignment implements AlignmentI
   }
 
   /**
+   * 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
@@ -119,15 +151,12 @@ public class Alignment implements AlignmentI
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
-    throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
+    throw new Error(
+            MessageManager
+                    .getString("error.alignment_cigararray_not_implemented"));
     // this(compactAlignment.refCigars);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
   @Override
   public List<SequenceI> getSequences()
   {
@@ -157,6 +186,17 @@ 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
@@ -187,23 +227,25 @@ public class Alignment implements AlignmentI
   {
     if (dataset != null)
     {
+
       // maintain dataset integrity
-      if (snew.getDatasetSequence() != null)
-      {
-        getDataset().addSequence(snew.getDatasetSequence());
-      }
-      else
+      SequenceI dsseq = snew.getDatasetSequence();
+      if (dsseq == null)
       {
         // derive new sequence
         SequenceI adding = snew.deriveSequence();
-        getDataset().addSequence(adding.getDatasetSequence());
         snew = adding;
+        dsseq = snew.getDatasetSequence();
+      }
+      if (getDataset().findIndex(dsseq) == -1)
+      {
+        getDataset().addSequence(dsseq);
       }
+
     }
     if (sequences == null)
     {
-      initAlignment(new SequenceI[]
-      { snew });
+      initAlignment(new SequenceI[] { snew });
     }
     else
     {
@@ -218,19 +260,22 @@ public class Alignment implements AlignmentI
     }
   }
 
-  /**
-   * Adds a sequence to the alignment. Recalculates maxLength and size.
-   * 
-   * @param snew
-   */
   @Override
-  public void setSequenceAt(int i, SequenceI snew)
+  public SequenceI replaceSequenceAt(int i, SequenceI snew)
   {
-    SequenceI oldseq = getSequenceAt(i);
-    deleteSequence(i);
     synchronized (sequences)
     {
-      sequences.set(i, snew);
+      if (sequences.size() > i)
+      {
+        return sequences.set(i, snew);
+
+      }
+      else
+      {
+        sequences.add(snew);
+        hiddenSequences.adjustHeightSequenceAdded();
+      }
+      return null;
     }
   }
 
@@ -246,13 +291,23 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void finalize()
+  public void finalize() throws Throwable
   {
     if (getDataset() != null)
     {
       getDataset().removeAlignmentRef();
     }
 
+    nullReferences();
+    super.finalize();
+  }
+
+  /**
+   * Defensively nulls out references in case this object is not garbage
+   * collected
+   */
+  void nullReferences()
+  {
     dataset = null;
     sequences = null;
     groups = null;
@@ -261,14 +316,16 @@ public class Alignment implements AlignmentI
   }
 
   /**
-   * decrement the alignmentRefs counter by one and call finalize if it goes to
-   * zero.
+   * decrement the alignmentRefs counter by one and null references if it goes
+   * to zero.
+   * 
+   * @throws Throwable
    */
-  private void removeAlignmentRef()
+  private void removeAlignmentRef() throws Throwable
   {
     if (--alignmentRefs == 0)
     {
-      finalize();
+      nullReferences();
     }
   }
 
@@ -298,8 +355,8 @@ public class Alignment implements AlignmentI
       synchronized (sequences)
       {
         sequences.remove(i);
+        hiddenSequences.adjustHeightSequenceDeleted(i);
       }
-      hiddenSequences.adjustHeightSequenceDeleted(i);
     }
   }
 
@@ -343,14 +400,14 @@ public class Alignment implements AlignmentI
       for (int i = 0; i < gSize; i++)
       {
         SequenceGroup sg = groups.get(i);
-        if (sg == null || sg.getSequences(null) == null)
+        if (sg == null || sg.getSequences() == null)
         {
           this.deleteGroup(sg);
           gSize--;
           continue;
         }
 
-        if (sg.getSequences(null).contains(s))
+        if (sg.getSequences().contains(s))
         {
           temp.add(sg);
         }
@@ -720,6 +777,28 @@ public class Alignment implements AlignmentI
     return true;
   }
 
+  /**
+   * Delete all annotations, including auto-calculated if the flag is set true.
+   * Returns true if at least one annotation was deleted, else false.
+   * 
+   * @param includingAutoCalculated
+   * @return
+   */
+  @Override
+  public boolean deleteAllAnnotations(boolean includingAutoCalculated)
+  {
+    boolean result = false;
+    for (AlignmentAnnotation alan : getAlignmentAnnotation())
+    {
+      if (!alan.autoCalculated || includingAutoCalculated)
+      {
+        deleteAnnotation(alan);
+        result = true;
+      }
+    }
+    return result;
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -931,33 +1010,20 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setDataset(Alignment data)
+  public void setDataset(AlignmentI data)
   {
     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
-      SequenceI[] seqs = new SequenceI[getHeight()];
-      SequenceI currentSeq;
-      for (int i = 0; i < getHeight(); i++)
-      {
-        currentSeq = getSequenceAt(i);
-        if (currentSeq.getDatasetSequence() != null)
-        {
-          seqs[i] = currentSeq.getDatasetSequence();
-        }
-        else
-        {
-          seqs[i] = currentSeq.createDatasetSequence();
-        }
-      }
-
-      dataset = new Alignment(seqs);
+      createDatasetAlignment();
     }
     else if (dataset == null && data != null)
     {
-      dataset = data;
+      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);
@@ -984,6 +1050,111 @@ public class Alignment implements AlignmentI
   }
 
   /**
+   * 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();
+      }
+    }
+    if (seqs.contains(currentSeq))
+    {
+      return;
+    }
+    List<SequenceI> toProcess = new ArrayList<SequenceI>();
+    toProcess.add(currentSeq);
+    while (toProcess.size() > 0)
+    {
+      // use a queue ?
+      SequenceI curDs = toProcess.remove(0);
+      if (seqs.contains(curDs))
+      {
+        continue;
+      }
+      seqs.add(curDs);
+      // 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)
+            {
+              /*
+               * update mapping to be to the newly created dataset sequence
+               */
+              dbr.getMap().setTo(currentSeq);
+            }
+            if (dbr.getMap().getTo().getDatasetSequence() != null)
+            {
+              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());
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * 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)
+    {
+      return;
+    }
+    // try to avoid using SequenceI.equals at this stage, it will be expensive
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
+
+    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;
+  }
+
+  /**
    * reference count for number of alignments referencing this one.
    */
   int alignmentRefs = 0;
@@ -1205,43 +1376,18 @@ public class Alignment implements AlignmentI
     return alignmentProperties;
   }
 
-  AlignedCodonFrame[] codonFrameList = null;
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see
-   * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
-   * )
+  /**
+   * Adds the given mapping to the stored set. Note this may be held on the
+   * dataset alignment.
    */
   @Override
   public void addCodonFrame(AlignedCodonFrame codons)
   {
-    if (codons == null)
+    List<AlignedCodonFrame> acfs = getCodonFrames();
+    if (codons != null && acfs != null && !acfs.contains(codons))
     {
-      return;
+      acfs.add(codons);
     }
-    if (codonFrameList == null)
-    {
-      codonFrameList = new AlignedCodonFrame[]
-      { codons };
-      return;
-    }
-    AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
-    System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
-    t[codonFrameList.length] = codons;
-    codonFrameList = t;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
-   */
-  @Override
-  public AlignedCodonFrame getCodonFrame(int index)
-  {
-    return codonFrameList[index];
   }
 
   /*
@@ -1251,83 +1397,78 @@ public class Alignment implements AlignmentI
    * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
   @Override
-  public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+  public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
   {
-    if (seq == null || codonFrameList == null)
+    if (seq == null)
     {
       return null;
     }
-    Vector cframes = new Vector();
-    for (int f = 0; f < codonFrameList.length; f++)
+    List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+    for (AlignedCodonFrame acf : getCodonFrames())
     {
-      if (codonFrameList[f].involvesSequence(seq))
+      if (acf.involvesSequence(seq))
       {
-        cframes.addElement(codonFrameList[f]);
+        cframes.add(acf);
       }
     }
-    if (cframes.size() == 0)
+    return cframes;
+  }
+
+  /**
+   * 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)
+    {
+      dataset.setCodonFrames(acfs);
+    }
+    else
     {
-      return null;
+      this.codonFrameList = acfs;
     }
-    AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
-    cframes.copyInto(cfr);
-    return cfr;
   }
 
-  /*
-   * (non-Javadoc)
+  /**
+   * 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 AlignedCodonFrame[] getCodonFrames()
+  public List<AlignedCodonFrame> getCodonFrames()
   {
-    return codonFrameList;
+    // 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;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
-   * AlignedCodonFrame)
+  /**
+   * 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)
   {
-    if (codons == null || codonFrameList == null)
+    List<AlignedCodonFrame> acfs = getCodonFrames();
+    if (codons == null || acfs == null)
     {
       return false;
     }
-    boolean removed = false;
-    int i = 0, iSize = codonFrameList.length;
-    while (i < iSize)
-    {
-      if (codonFrameList[i] == codons)
-      {
-        removed = true;
-        if (i + 1 < iSize)
-        {
-          System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
-                  - i - 1);
-        }
-        iSize--;
-      }
-      else
-      {
-        i++;
-      }
-    }
-    return removed;
+    return acfs.remove(codons);
   }
 
   @Override
   public void append(AlignmentI toappend)
   {
-    if (toappend == this)
-    {
-      System.err.println("Self append may cause a deadlock.");
-    }
-    // TODO test this method for a future 2.5 release
+    // TODO JAL-1270 needs test coverage
     // currently tested for use in jalview.gui.SequenceFetcher
     boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
@@ -1338,6 +1479,8 @@ public class Alignment implements AlignmentI
             .getFullAlignment().getSequences() : toappend.getSequences();
     if (sqs != null)
     {
+      // avoid self append deadlock by
+      List<SequenceI> toappendsq = new ArrayList<SequenceI>();
       synchronized (sqs)
       {
         for (SequenceI addedsq : sqs)
@@ -1353,20 +1496,23 @@ public class Alignment implements AlignmentI
               }
             }
           }
-          addSequence(addedsq);
+          toappendsq.add(addedsq);
         }
       }
+      for (SequenceI addedsq : toappendsq)
+      {
+        addSequence(addedsq);
+      }
     }
     AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
     for (int a = 0; alan != null && a < alan.length; a++)
     {
       addAnnotation(alan[a]);
     }
-    AlignedCodonFrame[] acod = toappend.getCodonFrames();
-    for (int a = 0; acod != null && a < acod.length; a++)
-    {
-      this.addCodonFrame(acod[a]);
-    }
+
+    // use add method
+    getCodonFrames().addAll(toappend.getCodonFrames());
+
     List<SequenceGroup> sg = toappend.getGroups();
     if (sg != null)
     {
@@ -1489,6 +1635,27 @@ 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)
@@ -1550,6 +1717,41 @@ public class Alignment implements AlignmentI
     }
   }
 
+  private SequenceI seqrep = null;
+
+  /**
+   * 
+   * @return the representative sequence for this group
+   */
+  @Override
+  public SequenceI getSeqrep()
+  {
+    return seqrep;
+  }
+
+  /**
+   * set the representative sequence for this group. Note - this affects the
+   * interpretation of the Hidereps attribute.
+   * 
+   * @param seqrep
+   *          the seqrep to set (null means no sequence representative)
+   */
+  @Override
+  public void setSeqrep(SequenceI seqrep)
+  {
+    this.seqrep = seqrep;
+  }
+
+  /**
+   * 
+   * @return true if group has a sequence representative
+   */
+  @Override
+  public boolean hasSeqrep()
+  {
+    return seqrep != null;
+  }
+
   @Override
   public int getEndRes()
   {
@@ -1573,4 +1775,175 @@ public class Alignment implements AlignmentI
   {
     return dataset;
   }
+
+  /**
+   * Align this alignment like the given (mapped) one.
+   */
+  @Override
+  public int alignAs(AlignmentI al)
+  {
+    /*
+     * Currently retains unmapped gaps (in introns), regaps mapped regions
+     * (exons)
+     */
+    return alignAs(al, false, true);
+  }
+
+  /**
+   * Align this alignment 'the same as' the given one. Mapped sequences only are
+   * realigned. If both of the same type (nucleotide/protein) then align both
+   * identically. If this is nucleotide and the other is protein, make 3 gaps
+   * for each gap in the protein sequences. If this is protein and the other is
+   * nucleotide, insert a gap for each 3 gaps (or part thereof) between
+   * nucleotide bases. If this is protein and the other is nucleotide, gaps
+   * protein to match the relative ordering of codons in the nucleotide.
+   * 
+   * Parameters control whether gaps in exon (mapped) and intron (unmapped)
+   * regions are preserved. Gaps that connect introns to exons are treated
+   * conservatively, i.e. only preserved if both intron and exon gaps are
+   * preserved. 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 AlignmentUtils.alignProteinAsDna(this, al);
+    }
+    else if (thatIsProtein && thisIsNucleotide)
+    {
+      return AlignmentUtils.alignCdsAsProtein(this, al);
+    }
+    return AlignmentUtils.alignAs(this, al);
+  }
+
+  /**
+   * Returns the alignment in Fasta format. Behaviour of this method is not
+   * guaranteed between versions.
+   */
+  @Override
+  public String toString()
+  {
+    return new FastaFile().print(getSequencesArray());
+  }
+
+  /**
+   * Returns the set of distinct sequence names. No ordering is guaranteed.
+   */
+  @Override
+  public Set<String> getSequenceNames()
+  {
+    Set<String> names = new HashSet<String>();
+    for (SequenceI seq : getSequences())
+    {
+      names.add(seq.getName());
+    }
+    return names;
+  }
+
+  @Override
+  public boolean hasValidSequence()
+  {
+    boolean hasValidSeq = false;
+    for (SequenceI seq : getSequences())
+    {
+      if ((seq.getEnd() - seq.getStart()) > 0)
+      {
+        hasValidSeq = true;
+        break;
+      }
+    }
+    return hasValidSeq;
+  }
+
+  /**
+   * 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)
+    {
+      for (AlignedCodonFrame mapping : getCodonFrames())
+      {
+        count += mapping.realiseWith(seq);
+      }
+    }
+    return count;
+  }
+
+  /**
+   * 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)
+      {
+        return acf;
+      }
+    }
+    return null;
+  }
+
+  @Override
+  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+  {
+    int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
+    int startPos = alignmentStartEnd[0];
+    int endPos = alignmentStartEnd[1];
+
+    int[] lowestRange = new int[] { -1, -1 };
+    int[] higestRange = new int[] { -1, -1 };
+
+    for (int[] hiddenCol : hiddenCols)
+    {
+      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+    }
+
+    if (lowestRange[0] == -1 && lowestRange[1] == -1)
+    {
+      startPos = alignmentStartEnd[0];
+    }
+    else
+    {
+      startPos = lowestRange[1] + 1;
+    }
+
+    if (higestRange[0] == -1 && higestRange[1] == -1)
+    {
+      endPos = alignmentStartEnd[1];
+    }
+    else
+    {
+      endPos = higestRange[0] - 1;
+    }
+    return new int[] { startPos, endPos };
+  }
 }