*/
public String getSequenceString(char GapChar)
{
- return (length == 0) ? "" : (String) getSequenceAndDeletions(refseq
- .getSequenceAsString(start, end), GapChar)[0];
+ return (length == 0) ? "" : (String) getSequenceAndDeletions(
+ refseq.getSequenceAsString(start, end), GapChar)[0];
}
/**
{
return null;
}
- Object[] edit_result = getSequenceAndDeletions(refseq
- .getSequenceAsString(start, end), GapChar);
+ Object[] edit_result = getSequenceAndDeletions(
+ refseq.getSequenceAsString(start, end), GapChar);
if (edit_result == null)
{
throw new Error(
"Implementation Error - unexpected null from getSequenceAndDeletions");
}
int bounds[] = (int[]) edit_result[1];
- seq = new Sequence(refseq.getName(), (String) edit_result[0], refseq
- .getStart()
- + start + bounds[0], refseq.getStart() + start
- + ((bounds[2] == 0) ? -1 : bounds[2]));
+ seq = new Sequence(refseq.getName(), (String) edit_result[0],
+ refseq.getStart() + start + bounds[0], refseq.getStart()
+ + start + ((bounds[2] == 0) ? -1 : bounds[2]));
seq.setDescription(refseq.getDescription());
int sstart = seq.getStart(), send = seq.getEnd();
// seq.checkValidRange(); probably not needed
}
else
{
- ds = new Sequence(seq.getName(), ungapped, seq.getStart(), seq
- .getStart()
- + ungapped.length() - 1);
+ ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
+ seq.getStart() + ungapped.length() - 1);
// JBPNote: this would be consistent but may not be useful
// seq.setDatasetSequence(ds);
}
}
else
{
- g_seqs[s].insert(inspos, alseqs_string[i].substring(
- region[0], region[1] + 1));
+ g_seqs[s].insert(inspos,
+ alseqs_string[i].substring(region[0], region[1] + 1));
}
}
shifts.addShift(region[2], insert.length); // update shift in
{
int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
SequenceI ref = alseqs[i].getRefSeq();
- seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(), ref
- .getStart()
- + alseqs[i].start + bounds[0], ref.getStart()
- + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
+ seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
+ ref.getStart() + alseqs[i].start + bounds[0], ref.getStart()
+ + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
seqs[i].setDatasetSequence(ref);
seqs[i].setDescription(ref.getDescription());
}