rstart = Long.parseLong(stindx);
} catch (Exception e)
{
- System.err.println("Couldn't parse '" + stindx
- + "' as start of row");
+ System.err.println(
+ "Couldn't parse '" + stindx + "' as start of row");
// inAlignments = false;
// warn for this line
}
rend = Long.parseLong(endindx);
} catch (Exception e)
{
- System.err.println("Couldn't parse '" + endindx
- + "' as end of row");
+ System.err.println(
+ "Couldn't parse '" + endindx + "' as end of row");
// inAlignments = false;
// warn for this line
{
padseq = true; // prepend gaps to new sequences in this block
seqentry = new Object[] { new StringBuffer(),
- new long[] { rstart, rend } };
+ new long[]
+ { rstart, rend } };
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);
{
Sequence newseq = new Sequence(idstring,
- ((StringBuffer) seqentry[0]).toString(),
+ ((StringBuffer) seqentry[0]).toString(),
(int) ((long[]) seqentry[1])[0],
(int) ((long[]) seqentry[1])[1]);
if (newseq.getEnd() == 0)