/*
* The characters of the aligned sequence e.g. "-cGT-ACgTG-"
*/
- private final char[] alignedSeq;
+ private final SequenceI alignedSeq;
/*
* the sequence start residue
*/
public AlignedCodonIterator(SequenceI seq, char gapChar)
{
- this.alignedSeq = seq.getSequence();
+ this.alignedSeq = seq;
this.start = seq.getStart();
this.gap = gapChar;
fromRanges = map.getFromRanges().iterator();
if (toPosition <= currentToRange[1])
{
SequenceI seq = Mapping.this.to;
- char pep = seq.getSequence()[toPosition - seq.getStart()];
+ char pep = seq.getCharAt(toPosition - seq.getStart());
toPosition++;
return String.valueOf(pep);
}
* allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
*/
int truePos = sequencePos - (start - 1);
- while (alignedBases < truePos && alignedColumn < alignedSeq.length)
+ int length = alignedSeq.getLength();
+ while (alignedBases < truePos && alignedColumn < length)
{
- char c = alignedSeq[alignedColumn++];
+ char c = alignedSeq.getCharAt(alignedColumn++);
if (c != gap && !Comparison.isGap(c))
{
alignedBases++;
SequenceFeature[] vf = new SequenceFeature[frange.length / 2];
for (int i = 0, v = 0; i < frange.length; i += 2, v++)
{
- vf[v] = new SequenceFeature(f);
- vf[v].setBegin(frange[i]);
- vf[v].setEnd(frange[i + 1]);
+ vf[v] = new SequenceFeature(f, frange[i], frange[i + 1],
+ f.getFeatureGroup(), f.getScore());
if (frange.length > 2)
{
vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
return vf;
}
}
- if (false) // else
- {
- int[] word = getWord(f.getBegin());
- if (word[0] < word[1])
- {
- f.setBegin(word[0]);
- }
- else
- {
- f.setBegin(word[1]);
- }
- word = getWord(f.getEnd());
- if (word[0] > word[1])
- {
- f.setEnd(word[0]);
- }
- else
- {
- f.setEnd(word[1]);
- }
- }
+
// give up and just return the feature.
return new SequenceFeature[] { f };
}
to = tto;
}
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#finalize()
- */
- @Override
- protected void finalize() throws Throwable
- {
- map = null;
- to = null;
- super.finalize();
- }
-
/**
* Returns an iterator which can serve up the aligned codon column positions
* and their corresponding peptide products