X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=cea595695796d021188d7a41d6a8cad8b3768d67;hb=61f1a8b75ea5ce352d6214c34fbdcd58bafbbb73;hp=4057773aefccaff82cce16f2c15012d22debcce2;hpb=fd3e9637614543e5e6f039a0ad10dd5c59b6136f;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 4057773..cea5956 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,13 +20,17 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
 import jalview.util.MessageManager;
 
 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;
 
 /**
@@ -157,6 +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
@@ -1489,6 +1504,27 @@ 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)
@@ -1573,4 +1609,78 @@ public class Alignment implements AlignmentI
   {
     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;
+  }
 }