void Side2Seq::convertSequence(const SGSequence* seq)
{
// we exclude the very first and last sides as they don't induce breaks
// (very first start woult have forward == true, for example..)
SGSide start = SGSide(SGPosition(seq->getID(), 0), false);
SGSide end = SGSide(SGPosition(seq->getID(), seq->getLength() - 1), true);
set<SGSide> cutSides;
if (seq->getLength() > 1)
{
getIncidentJoins(start, end, cutSides);
}
if (_chop > 0)
{
getChopSides(seq, cutSides);
}
cleanCutSides(cutSides);
SGPosition first(seq->getID(), 0);
int firstIdx = _outGraph->getNumSequences();
for (set<SGSide>::iterator i = cutSides.begin(); i != cutSides.end(); ++i)
{
SGPosition last = i->getBase();
assert(last.getSeqID() == first.getSeqID());
if (i->getForward() == true)
{
// left side of base: don't include this position
last.setPos(last.getPos() - 1);
}
// add it
addOutSequence(seq, first, last);
// add one because segments inclusive
first.setPos(last.getPos() + 1);
}
// need to do one segment at end
SGPosition last(seq->getID(), seq->getLength() - 1);
addOutSequence(seq, first, last);
// chain all the added seqeunces with new joins
for (int j = firstIdx + 1; j < _outGraph->getNumSequences(); ++j)
{
const SGSequence* fs = _outGraph->getSequence(j-1);
const SGSequence* ts = _outGraph->getSequence(j);
SGSide side1(SGPosition(fs->getID(), fs->getLength() - 1), false);
SGSide side2(SGPosition(ts->getID(), 0), true);
const SGJoin* newJoin = _outGraph->addJoin(new SGJoin(side1, side2));
verifyOutJoin(newJoin);
}
}
