{
int fpos=seq.getStart(),lpos= seq.getEnd();
int start = 0;
- int end = seq.getLength();
if (hiddenColumns == null || hiddenColumns.size() == 0)
{
- return new int[] { seq.findIndex(fpos), seq.findIndex(lpos), fpos,
+ return new int[] { seq.findIndex(fpos) - 1, seq.findIndex(lpos) - 1,
+ fpos,
lpos };
}
List<int[]> regions = getHiddenColumns();
int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq
.getLength(), hideEnd = -1;
- int visPrev = 0, visNext = 0, base = 0;
+ int visPrev = 0, visNext = 0;
boolean foundStart = false;
for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
&& p < pLen; p++)
while (hideEnd < p && rcount < regions.size())
{
int[] region = regions.get(rcount++);
- visNext += region[1] + 1 - region[0];
- visPrev = visNext-1;
+ visPrev = visNext;
+ visNext += region[0] - visPrev;
hideStart = region[0];
hideEnd = region[1];
}