Method performNetworkTrim

Parallel/NetworkSequenceCollection.cpp:850–911

Distributed trimming function. */

/** Distributed trimming function. */
size_t NetworkSequenceCollection::performNetworkTrim()
{
	Timer timer("NetworkTrim");
	NetworkSequenceCollection* seqCollection = this;
	size_t numBranchesRemoved = 0;

	// The branch ids
	uint64_t branchGroupID = 0;

	for (iterator iter = seqCollection->begin();
			iter != seqCollection->end(); ++iter) {
		if (iter->second.deleted())
			continue;

		extDirection dir;
		// dir will be set to the trimming direction if the sequence
		// can be trimmed.
		SeqContiguity status = AssemblyAlgorithms::checkSeqContiguity(
				*iter, dir);
		if (status == SC_CONTIGUOUS)
			continue;
		else if(status == SC_ISLAND)
		{
			seqCollection->mark(iter->first);
			numBranchesRemoved++;
			continue;
		}

		bool inserted = m_activeBranchGroups.insert(
				BranchGroupMap::value_type(branchGroupID,
					BranchGroup(dir, 1, iter->first,
						BranchRecord(dir))))
			.second;
		assert(inserted);
		(void)inserted;

		generateExtensionRequest(branchGroupID, 0, iter->first);
		branchGroupID++;
		numBranchesRemoved += processBranchesTrim();
		seqCollection->pumpNetwork();

		// Primitive load balancing
		if(m_activeBranchGroups.size() > MAX_ACTIVE)
		{
			while(m_activeBranchGroups.size() > LOW_ACTIVE)
			{
				seqCollection->pumpNetwork();
				numBranchesRemoved += processBranchesTrim();
			}
		}
	}

	// Clear out the remaining branches
	while(!m_activeBranchGroups.empty())
	{
		numBranchesRemoved += processBranchesTrim();
		seqCollection->pumpNetwork();
	}