* @param seqs SeqCigar[]
*/
public Alignment(SeqCigar[] alseqs) {
- SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter, new ColumnSelection());
+ SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter, new ColumnSelection(), null);
initAlignment(seqs);
}
/**
return null;
}
+ public SequenceI [] findSequenceMatch(String name)
+ {
+ Vector matches = new Vector();
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i).getName().equals(name))
+ {
+ matches.addElement(getSequenceAt(i));
+ }
+ i++;
+ }
+
+ SequenceI [] result = new SequenceI[matches.size()];
+ for(i=0; i<result.length; i++)
+ result[i] = (SequenceI)matches.elementAt(i);
+
+ return result;
+
+ }
+
/** */
public int findIndex(SequenceI s)
),
getSequenceAt(i).getStart(),
getSequenceAt(i).getEnd());
-
+ seqs[i].sequenceFeatures = getSequenceAt(i).getSequenceFeatures();
+ getSequenceAt(i).setSequenceFeatures(null);
getSequenceAt(i).setDatasetSequence(seqs[i]);
}
}