*/
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;
/**
}
/**
+ * 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
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)
{
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;
+ }
}