C++ ContigPaths::front方法代码示例

/** Return the consensus sequence of the specified gap. */
static ContigPath fillGap(const Graph& g,
		const AmbPathConstraint& apConstraint,
		vector<bool>& seen,
		ofstream& outFasta)
{
	if (opt::verbose > 1)
		cerr << "\n* "
			<< get(vertex_name, g, apConstraint.source) << ' '
			<< apConstraint.dist << "N "
			<< get(vertex_name, g, apConstraint.dest) << '\n';

	Constraints constraints;
	constraints.push_back(Constraint(apConstraint.dest,
				apConstraint.dist + opt::distanceError));

	ContigPaths solutions;
	unsigned numVisited = 0;
	constrainedSearch(g, apConstraint.source,
			constraints, solutions, numVisited);
	bool tooComplex = numVisited >= opt::maxCost;

	for (ContigPaths::iterator solIt = solutions.begin();
			solIt != solutions.end(); solIt++)
		solIt->insert(solIt->begin(), apConstraint.source);

	ContigPath consensus;
	bool tooManySolutions = solutions.size() > opt::numBranches;
	if (tooComplex) {
		stats.tooComplex++;
		if (opt::verbose > 1)
			cerr << solutions.size() << " paths (too complex)\n";
	} else if (tooManySolutions) {
		stats.numTooManySolutions++;
		if (opt::verbose > 1)
			cerr << solutions.size() << " paths (too many)\n";
	} else if (solutions.empty()) {
		stats.numNoSolutions++;
		if (opt::verbose > 1)
			cerr << "no paths\n";
	} else if (solutions.size() == 1) {
		if (opt::verbose > 1)
			cerr << "1 path\n" << solutions.front() << '\n';
		stats.numMerged++;
	} else {
		assert(solutions.size() > 1);
		if (opt::verbose > 2)
			copy(solutions.begin(), solutions.end(),
					ostream_iterator<ContigPath>(cerr, "\n"));
		else if (opt::verbose > 1)
			cerr << solutions.size() << " paths\n";
		consensus = align(g, solutions, outFasta);
		if (!consensus.empty()) {
			stats.numMerged++;
			// Mark contigs that are used in a consensus.
			markSeen(seen, solutions, true);
			if (opt::verbose > 1)
				cerr << consensus << '\n';
		} else
			stats.notMerged++;
	}
	return consensus;
}

/** Return an ambiguous path that agrees with all the given paths. */
static ContigPath constructAmbiguousPath(const Graph &g,
		const ContigNode& origin, const ContigPaths& paths)
{
	assert(!paths.empty());

	// Find the size of the smallest path.
	const ContigPath& firstSol = paths.front();
	size_t min_len = firstSol.size();
	for (ContigPaths::const_iterator it = paths.begin() + 1;
			it != paths.end(); ++it)
		min_len = min(min_len, it->size());

	// Find the longest prefix.
	ContigPath vppath;
	size_t longestPrefix;
	bool commonPrefix = true;
	for (longestPrefix = 0;
			longestPrefix < min_len; longestPrefix++) {
		const ContigNode& common_path_node = firstSol[longestPrefix];
		for (ContigPaths::const_iterator solIter = paths.begin();
				solIter != paths.end(); ++solIter) {
			const ContigNode& pathnode = (*solIter)[longestPrefix];
			if (pathnode != common_path_node) {
				// Found the longest prefix.
				commonPrefix = false;
				break;
			}
		}
		if (!commonPrefix)
			break;
		vppath.push_back(common_path_node);
	}

	// Find the longest suffix.
	ContigPath vspath;
	size_t longestSuffix;
	bool commonSuffix = true;
	for (longestSuffix = 0;
			longestSuffix < min_len-longestPrefix; longestSuffix++) {
		const ContigNode& common_path_node
			= firstSol[firstSol.size()-longestSuffix-1];
		for (ContigPaths::const_iterator solIter = paths.begin();
				solIter != paths.end(); ++solIter) {
			const ContigNode& pathnode
				= (*solIter)[solIter->size()-longestSuffix-1];
			if (pathnode != common_path_node) {
				// Found the longest suffix.
				commonSuffix = false;
				break;
			}
		}
		if (!commonSuffix)
			break;
		vspath.push_back(common_path_node);
	}

	ContigPath out;
	out.reserve(vppath.size() + 1 + vspath.size());
	out.insert(out.end(), vppath.begin(), vppath.end());
	if (longestSuffix > 0) {
		const ContigPath& longestPath(
				*max_element(paths.begin(), paths.end(),
					ComparePathLength(g, origin)));
		unsigned length = calculatePathLength(g, origin, longestPath,
				longestPrefix, longestSuffix);

		// Account for the overlap on the right.
		int dist = length + getDistance(g,
				longestSuffix == longestPath.size() ? origin
				: *(longestPath.rbegin() + longestSuffix),
				*(longestPath.rbegin() + longestSuffix - 1));

		// Add k-1 because it is the convention.
		int numN = dist + opt::k - 1;
		assert(numN > 0);

		out.push_back(ContigNode(numN, 'N'));
		out.insert(out.end(), vspath.rbegin(), vspath.rend());
	}
	return out;
}

/* Resolve ambiguous region using pairwise alignment
 * (Needleman-Wunsch) ('solutions' contain exactly two paths, from a
 * source contig to a dest contig)
 */
static ContigPath alignPair(const Graph& g,
		const ContigPaths& solutions, ofstream& out)
{
	assert(solutions.size() == 2);
	assert(solutions[0].size() > 1);
	assert(solutions[1].size() > 1);
	assert(solutions[0].front() == solutions[1].front());
	assert(solutions[0].back() == solutions[1].back());
	ContigPath fstSol(solutions[0].begin()+1, solutions[0].end()-1);
	ContigPath sndSol(solutions[1].begin()+1, solutions[1].end()-1);

	if (fstSol.empty() || sndSol.empty()) {
		// This entire sequence may be deleted.
		const ContigPath& sol(fstSol.empty() ? sndSol : fstSol);
		assert(!sol.empty());
		Sequence consensus(mergePath(g, sol));
		assert(consensus.size() > opt::k - 1);
		string::iterator first = consensus.begin() + opt::k - 1;
		transform(first, consensus.end(), first, ::tolower);

		unsigned match = opt::k - 1;
		float identity = (float)match / consensus.size();
		if (opt::verbose > 2)
			cerr << consensus << '\n';
		if (opt::verbose > 1)
			cerr << identity
				<< (identity < opt::identity ? " (too low)\n" : "\n");
		if (identity < opt::identity)
			return ContigPath();

		unsigned coverage = calculatePathProperties(g, sol).coverage;
		ContigNode u = outputNewContig(g,
				solutions, 1, 1, consensus, coverage, out);
		ContigPath path;
		path.push_back(solutions.front().front());
		path.push_back(u);
		path.push_back(solutions.front().back());
		return path;
	}

	Sequence fstPathContig(mergePath(g, fstSol));
	Sequence sndPathContig(mergePath(g, sndSol));
	if (fstPathContig == sndPathContig) {
		// These two paths have identical sequence.
		if (fstSol.size() == sndSol.size()) {
			// A perfect match must be caused by palindrome.
			typedef ContigPath::const_iterator It;
			pair<It, It> it = mismatch(
					fstSol.begin(), fstSol.end(), sndSol.begin());
			assert(it.first != fstSol.end());
			assert(it.second != sndSol.end());
			assert(*it.first
					== get(vertex_complement, g, *it.second));
			assert(equal(it.first+1, It(fstSol.end()), it.second+1));
			if (opt::verbose > 1)
				cerr << "Palindrome: "
					<< get(vertex_contig_name, g, *it.first) << '\n';
			return solutions[0];
		} else {
			// The paths are different lengths.
			cerr << PROGRAM ": warning: "
				"Two paths have identical sequence, which may be "
				"caused by a transitive edge in the overlap graph.\n"
				<< '\t' << fstSol << '\n'
				<< '\t' << sndSol << '\n';
			return solutions[fstSol.size() > sndSol.size() ? 0 : 1];
		}
	}

	unsigned minLength = min(
			fstPathContig.length(), sndPathContig.length());
	unsigned maxLength = max(
			fstPathContig.length(), sndPathContig.length());
	float lengthRatio = (float)minLength / maxLength;
	if (lengthRatio < opt::identity) {
		if (opt::verbose > 1)
			cerr << minLength << '\t' << maxLength
				<< '\t' << lengthRatio << "\t(different length)\n";
		return ContigPath();
	}

	NWAlignment align;
	unsigned match = alignGlobal(fstPathContig, sndPathContig,
		   	align);
	float identity = (float)match / align.size();
	if (opt::verbose > 2)
		cerr << align;
	if (opt::verbose > 1)
		cerr << identity
			<< (identity < opt::identity ? " (too low)\n" : "\n");
	if (identity < opt::identity)
		return ContigPath();

	unsigned coverage = calculatePathProperties(g, fstSol).coverage
		+ calculatePathProperties(g, sndSol).coverage;
	ContigNode u = outputNewContig(g, solutions, 1, 1,
//.........这里部分代码省略.........