static Locus *extractConnectedComponents(IDnum locusCount)
{
Locus *loci = allocateLocusArray(locusCount);
Locus *locus;
IDnum index;
IDnum locusIndex = 0;
IDnum nodeIndex;
Node *node;
resetNodeStatus(graph);
for (index = 1; index <= nodeCount(graph); index++) {
node = getNodeInGraph(graph, index);
if (!getNodeStatus(node) && getUniqueness(node)) {
locus = getLocus(loci, locusIndex++);
clearLocus(locus);
// Long contigs
fillUpComponent(node);
setLongContigCount(locus, countMarkedNodes());
while (existsMarkedNode())
addContig(locus, popNodeRecord());
// Secondary contigs
extendComponent(locus);
setContigCount(locus, getLongContigCount(locus) + countMarkedNodes());
while (existsMarkedNode())
addContig(locus, popNodeRecord());
// Mark primary nodes so that their twins are not reused
for (nodeIndex = 0;
nodeIndex < getLongContigCount(locus);
nodeIndex++)
setNodeStatus(getContig(locus, nodeIndex), true);
// Unmark secondary nodes so that they are available to other loci
for (nodeIndex = getLongContigCount(locus);
nodeIndex < getContigCount(locus); nodeIndex++)
setNodeStatus(getContig(locus, nodeIndex), false);
}
}
return loci;
}
void getFillContig(struct cnFill *fill)
{
struct liftSpec *lift, *prevLift = NULL;
struct hashEl *el;
//uglyf("fill->qName=%s, fill->qStart=%d\n", fill->qName, fill->qStart);
if ((el = hashLookup(chromHash, fill->qName)) == NULL)
errAbort("Unknown chrom: %s\n", fill->qName);
for (lift = (struct liftSpec *)el->val; lift != NULL; prevLift = lift, lift = lift->next)
{
//uglyf("lift->oldName=%s, lift->offset=%d\n", lift->oldName, lift->offset);
if (fill->qStart < lift->offset)
{
addContig(prevLift->oldName);
break;
}
}
/* last contig */
addContig(prevLift->oldName);
}
bool MIQPSolver::addContigs(const DataStore &store)
{
ContigCount = store.ContigCount;
len.resize(ContigCount);
U.resize(ContigCount);
T.resize(ContigCount);
X.resize(ContigCount);
optimized.resize(ContigCount);
for (int i = 0; i < ContigCount; i++)
if (!addContig(store[i]))
return false;
return true;
}
