}
return seq;
}
- public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, int start, int end) {
+ public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, long start, long end) {
if (refseq!=null) {
AlignmentSequence asq = new AlignmentSequence();
asq.setName(name);
asq.setSequence(alSequence);
asq.setRefid(refseq);
+ if (end>refseq.getEnd() || end<start || end==-1)
+ end = refseq.getEnd();
+ asq.setEnd(end);
if (start<refseq.getStart())
start = refseq.getStart();
asq.setStart(start);
- if (end>refseq.getEnd())
- end = refseq.getEnd();
- asq.setEnd(end);
return asq;
}
return null;