#include "ContigID.h"
#include "ContigPath.h"
#include "ContigProperties.h"
#include "DataBase/DB.h"
#include "DataBase/Options.h"
#include "Functional.h"
#include "Graph/ContigGraph.h"
#include "Graph/ContigGraphAlgorithms.h"
#include "Graph/DirectedGraph.h"
#include "Graph/GraphIO.h"
#include "IOUtil.h"
#include "Uncompress.h"
#include "config.h"
#include <algorithm>
#include <cassert>
#include <cerrno>
#include <cstdlib>
#include <cstring> // for strerror
#include <fstream>
#include <functional>
#include <getopt.h>
#include <iostream>
#include <map>
#include <vector>

using namespace std;

#define PROGRAM "PathOverlap"

DB db;

static const char* VERSION_MESSAGE =
    PROGRAM " (ABySS) " VERSION "\n"
            "Written by Shaun Jackman and Tony Raymond.\n"
            "\n"
            "Copyright 2014 Canada's Michael Smith Genome Sciences Centre\n";

static const char* USAGE_MESSAGE =
    "Usage: " PROGRAM " -k<kmer> [OPTION]... ADJ PATH\n"
    "Find paths that overlap. Either output the graph of overlapping\n"
    "paths, assemble overlapping paths into larger paths, or trim the\n"
    "overlapping paths.\n"
    "\n"
    " Arguments:\n"
    "\n"
    "  ADJ   contig adjacency graph\n"
    "  PATH  sequences of contig IDs\n"
    "\n"
    " Options:\n"
    "\n"
    "  -k, --kmer=N          k-mer size\n"
    "  -g, --graph=FILE      write the contig adjacency graph to FILE\n"
    "  -r, --repeats=FILE    write repeat contigs to FILE\n"
    "      --overlap         find overlapping paths [default]\n"
    "      --assemble        assemble overlapping paths\n"
    "      --trim            trim overlapping paths\n"
    "      --adj             output the graph in ADJ format [default]\n"
    "      --asqg            output the graph in ASQG format\n"
    "      --dot             output the graph in GraphViz format\n"
    "      --gfa             output the graph in GFA1 format\n"
    "      --gfa1            output the graph in GFA1 format\n"
    "      --gfa2            output the graph in GFA2 format\n"
    "      --gv              output the graph in GraphViz format\n"
    "      --sam             output the graph in SAM format\n"
    "      --SS              expect contigs to be oriented correctly\n"
    "      --no-SS           no assumption about contig orientation [default]\n"
    "  -v, --verbose         display verbose output\n"
    "      --help            display this help and exit\n"
    "      --version         output version information and exit\n"
    "      --db=FILE         specify path of database repository in FILE\n"
    "      --library=NAME    specify library NAME for sqlite\n"
    "      --strain=NAME     specify strain NAME for sqlite\n"
    "      --species=NAME    specify species NAME for sqlite\n"
    "\n"
    "Report bugs to <" PACKAGE_BUGREPORT ">.\n";

namespace opt {
string db;
dbVars metaVars;
unsigned k;

/** Output format. */
int format; // used by ContigProperties

/** Write the contig adjacency graph to this file. */
static string graphPath;

/** Output the IDs of contigs in overlaps to this file. */
static string repeatContigs;

/** Run a strand-specific RNA-Seq assembly. */
static int ss;

/** Mode of operation. */
enum
{
	/** Find overlapping paths, do not assemble. */
	OVERLAP,
	/** Assemble overlapping paths. */
	ASSEMBLE,
	/** Trim overlapping paths. */
	TRIM,
};
static int mode;

static int verbose;
}

static const char* shortopts = "g:k:r:v";

enum
{
	OPT_HELP = 1,
	OPT_VERSION,
	OPT_DB,
	OPT_LIBRARY,
	OPT_STRAIN,
	OPT_SPECIES
};
// enum { OPT_HELP = 1, OPT_VERSION };

static const struct option longopts[] = { { "graph", required_argument, NULL, 'g' },
	                                      { "kmer", required_argument, NULL, 'k' },
	                                      { "assemble", no_argument, &opt::mode, opt::ASSEMBLE },
	                                      { "overlap", no_argument, &opt::mode, opt::OVERLAP },
	                                      { "trim", no_argument, &opt::mode, opt::TRIM },
	                                      { "adj", no_argument, &opt::format, ADJ },
	                                      { "asqg", no_argument, &opt::format, ASQG },
	                                      { "dot", no_argument, &opt::format, DOT },
	                                      { "gfa", no_argument, &opt::format, GFA1 },
	                                      { "gfa1", no_argument, &opt::format, GFA1 },
	                                      { "gfa2", no_argument, &opt::format, GFA2 },
	                                      { "gv", no_argument, &opt::format, DOT },
	                                      { "sam", no_argument, &opt::format, SAM },
	                                      { "SS", no_argument, &opt::ss, 1 },
	                                      { "no-SS", no_argument, &opt::ss, 0 },
	                                      { "repeats", required_argument, NULL, 'r' },
	                                      { "verbose", no_argument, NULL, 'v' },
	                                      { "help", no_argument, NULL, OPT_HELP },
	                                      { "version", no_argument, NULL, OPT_VERSION },
	                                      { "db", required_argument, NULL, OPT_DB },
	                                      { "library", required_argument, NULL, OPT_LIBRARY },
	                                      { "strain", required_argument, NULL, OPT_STRAIN },
	                                      { "species", required_argument, NULL, OPT_SPECIES },
	                                      { NULL, 0, NULL, 0 } };

/** A vertex of the overlap graph. */
struct Vertex
{
	unsigned id;
	bool sense;

	/** The number of single-end contigs. */
	static unsigned s_offset;

	Vertex(unsigned id, bool sense)
	  : id(id)
	  , sense(sense)
	{}

	bool operator==(const Vertex& v) const { return id == v.id && sense == v.sense; }

	ContigNode descriptor() const { return ContigNode(s_offset + id, sense); }
};

unsigned Vertex::s_offset;

/** An alignment of two overlapping contigs. */
struct Overlap
{
	Vertex source;
	Vertex target;

	/** Overlap measured in number of contigs. */
	unsigned overlap;

	/** Overlap measured in bp. */
	int distance;

	Overlap(const Vertex& source, const Vertex& target, unsigned overlap, int distance)
	  : source(source)
	  , target(target)
	  , overlap(overlap)
	  , distance(distance)
	{}
};

/** The contig IDs that have been removed from paths. */
static vector<ContigID> s_trimmedContigs;

/** The contig graph. */
typedef DirectedGraph<ContigProperties, Distance> DG;
typedef ContigGraph<DG> Graph;

typedef vector<ContigPath> Paths;

/** Return whether this vertex is a path or a contig. */
static bool
isPath(const ContigNode& u)
{
	return u.id() >= Vertex::s_offset;
}

/** Return a path, complemented if necessary. */
static ContigPath
getPath(const Paths& paths, const ContigNode& u)
{
	if (isPath(u)) {
		unsigned i = u.id() - Vertex::s_offset;
		return u.sense() ? reverseComplement(paths[i]) : paths[i];
	} else
		return ContigPath(1, u);
}

/** Read contig paths from the specified file.
 * @param g the contig adjacency graph
 * @param inPath the file of contig paths
 * @param[out] pathIDs the path IDs
 * @return the paths
 */
static Paths
readPaths(Graph& g, const string& inPath, vector<string>& pathIDs)
{
	typedef graph_traits<Graph>::vertex_descriptor V;

	assert(pathIDs.empty());
	ifstream fin(inPath.c_str());
	if (opt::verbose > 0)
		cerr << "Reading `" << inPath << "'..." << endl;
	if (inPath != "-")
		assert_good(fin, inPath);
	istream& in = inPath == "-" ? cin : fin;

	assert_good(in, inPath);
	Paths paths;
	string id;
	ContigPath path;
	while (in >> id >> path) {
		if (path.empty()) {
			// Remove this contig from the graph.
			V u = find_vertex(id, false, g);
			clear_vertex(u, g);
			remove_vertex(u, g);
		} else {
			pathIDs.push_back(id);
			paths.push_back(path);
		}
	}
	assert(in.eof());
	return paths;
}

typedef multimap<ContigNode, Vertex> SeedMap;

/** Index the first and last contig of each path to facilitate finding
 * overlaps between paths. */
static SeedMap
makeSeedMap(const Paths& paths)
{
	SeedMap seedMap;
	for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) {
		if (it->empty())
			continue;
		assert(!it->front().ambiguous());
		seedMap.insert(make_pair(it->front(), Vertex(it - paths.begin(), false)));
		assert(!it->back().ambiguous());
		seedMap.insert(make_pair(it->back() ^ 1, Vertex(it - paths.begin(), true)));
	}
	return seedMap;
}

/** Check whether path starts with the sequence [first, last). */
static bool
startsWith(
    ContigPath path,
    bool rc,
    ContigPath::const_iterator first,
    ContigPath::const_iterator last)
{
	if (rc)
		reverseComplement(path.begin(), path.end());
	assert(*first == path.front());
	assert(first < last);
	return unsigned(last - first) > path.size() ? false : equal(first, last, path.begin());
}

/** Check whether path starts with the sequence [first, last). */
static unsigned
findOverlap(
    const Graph& g,
    const Paths& paths,
    ContigPath::const_iterator first,
    ContigPath::const_iterator last,
    const Vertex& v,
    int& distance)
{
	if (!startsWith(paths[v.id], v.sense, first, last))
		return 0;
	distance = -addProp(g, first, last).length;
	return last - first;
}

typedef vector<Overlap> Overlaps;

/** Find every path that overlaps with the specified path. */
static void
findOverlaps(
    const Graph& g,
    const Paths& paths,
    const SeedMap& seedMap,
    const Vertex& v,
    Overlaps& overlaps)
{
	ContigPath rc;
	if (v.sense) {
		rc = paths[v.id];
		reverseComplement(rc.begin(), rc.end());
	}
	const ContigPath& path = v.sense ? rc : paths[v.id];

	for (ContigPath::const_iterator it = path.begin(); it != path.end(); ++it) {
		if (it->ambiguous())
			continue;

		pair<SeedMap::const_iterator, SeedMap::const_iterator> range = seedMap.equal_range(*it);
		for (SeedMap::const_iterator seed = range.first; seed != range.second; ++seed) {
			if (v == seed->second)
				continue;
			int distance = 0;
			unsigned overlap = findOverlap(g, paths, it, path.end(), seed->second, distance);
			if (overlap > 0)
				overlaps.push_back(Overlap(v, seed->second, overlap, distance));
		}
	}
}

/** Find every pair of overlapping paths. */
static Overlaps
findOverlaps(const Graph& g, const Paths& paths)
{
	SeedMap seedMap = makeSeedMap(paths);

	Overlaps overlaps;
	for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) {
		unsigned i = it - paths.begin();
		findOverlaps(g, paths, seedMap, Vertex(i, false), overlaps);
		findOverlaps(g, paths, seedMap, Vertex(i, true), overlaps);
	}
	return overlaps;
}

/** Record the trimmed contigs. */
static void
recordTrimmedContigs(ContigPath::const_iterator first, ContigPath::const_iterator last)
{
	for (ContigPath::const_iterator it = first; it != last; ++it)
		if (!it->ambiguous())
			s_trimmedContigs.push_back(it->contigIndex());
}

/** Remove ambiguous contigs from the ends of the path. */
static void
removeAmbiguousContigs(ContigPath& path)
{
	if (!path.empty() && path.back().ambiguous())
		path.erase(path.end() - 1);
	if (!path.empty() && path.front().ambiguous())
		path.erase(path.begin());
}

/** Remove the overlapping portion of the specified contig. */
static void
removeContigs(ContigPath& path, unsigned first, unsigned last)
{
	assert(first <= path.size());
	assert(last <= path.size());
	if (first < last) {
		recordTrimmedContigs(path.begin(), path.begin() + first);
		recordTrimmedContigs(path.begin() + last, path.end());
		path.erase(path.begin() + last, path.end());
		path.erase(path.begin(), path.begin() + first);
	} else {
		recordTrimmedContigs(path.begin(), path.end());
		path.clear();
	}
	removeAmbiguousContigs(path);
}

/** Find the largest overlap for each contig and remove it. */
static void
trimOverlaps(Paths& paths, const Overlaps& overlaps)
{
	vector<unsigned> removed[2];
	removed[0].resize(paths.size());
	removed[1].resize(paths.size());

	for (Overlaps::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it) {
		unsigned& a = removed[!it->source.sense][it->source.id];
		unsigned& b = removed[it->target.sense][it->target.id];
		a = max(a, it->overlap);
		b = max(b, it->overlap);
	}

	for (Paths::iterator it = paths.begin(); it != paths.end(); ++it)
		removeContigs(
		    *it, removed[0][it - paths.begin()], it->size() - removed[1][it - paths.begin()]);
}

/** Trim the ends of paths that overlap another path. */
static void
trimOverlaps(const Graph& g, Paths& paths)
{
	for (Overlaps overlaps = findOverlaps(g, paths); !overlaps.empty();
	     overlaps = findOverlaps(g, paths)) {
		cerr << "Found " << overlaps.size() / 2 << " overlaps.\n";
		trimOverlaps(paths, overlaps);
	}
}

static inline ContigProperties
get(vertex_bundle_t, const Graph& g, ContigNode u)
{
	return u.ambiguous() ? ContigProperties(u.length() + opt::k - 1, 0) : g[u];
}

/** Add the path overlap edges to the specified graph. */
static void
addPathOverlapEdges(
    Graph& g,
    const Paths& paths,
    const vector<string>& pathIDs,
    const Overlaps& overlaps)
{
	typedef graph_traits<Graph>::vertex_descriptor V;
	const bool allowParallelEdge = opt::mode == opt::ASSEMBLE;

	// Add the path vertices.
	g_contigNames.unlock();
	for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) {
		const ContigPath& path = *it;
		const string& id = pathIDs[it - paths.begin()];
		if (!path.empty()) {
			V u = merge(g, path.begin(), path.end());
			put(vertex_name, g, u, id);
		}
	}
	g_contigNames.lock();

	// Remove the single-end contigs that are in paths.
	for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it)
		remove_vertex_if(
		    g, it->begin(), it->end(), [](const ContigNode& c) { return !c.ambiguous(); });

	// Add the path edges.
	for (Overlaps::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it) {
		V u = it->source.descriptor();
		V v = it->target.descriptor();
		if (allowParallelEdge || !edge(u, v, g).second)
			add_edge(u, v, it->distance, static_cast<DG&>(g));
		else if (opt::verbose > 0)
			cerr << "ambiguous overlap: " << get(vertex_name, g, u) << " -> "
			     << get(vertex_name, g, v) << '\n';
	}
}

typedef graph_traits<Graph>::edge_descriptor edge_descriptor;

/** A property map giving the number of contigs by which two paths
 * overlap. */
typedef map<edge_descriptor, unsigned> OverlapMap;

/** Return the number of contigs by which the two paths overlap. */
static unsigned
getOverlap(
    const OverlapMap& pmap,
    graph_traits<Graph>::vertex_descriptor u,
    graph_traits<Graph>::vertex_descriptor v)
{
	if (isPath(u) && isPath(v)) {
		// Both vertices are paths.
		OverlapMap::const_iterator it = pmap.find(edge_descriptor(u, v));
		return it == pmap.end() ? 0 : it->second;
	} else {
		// One of the two vertices is a contig.
		return 0;
	}
}

/** Merge a sequence of overlapping paths. */
static ContigPath
mergePaths(const Paths& paths, const OverlapMap& overlaps, const ContigPath& merge)
{
	assert(!merge.empty());
	ContigNode u = merge.front();
	ContigPath path(getPath(paths, u));
	for (ContigPath::const_iterator it = merge.begin() + 1; it != merge.end(); ++it) {
		ContigNode v = *it;
		ContigPath vpath(getPath(paths, v));
		unsigned overlap = getOverlap(overlaps, u, v);
		assert(path.size() > overlap);
		assert(vpath.size() > overlap);
		assert(equal(path.end() - overlap, path.end(), vpath.begin()));
		path.insert(path.end(), vpath.begin() + overlap, vpath.end());
		u = v;
	}
	return path;
}

/** Return true if the edge e is a path overlap. */
struct IsPathOverlap : unary_function<edge_descriptor, bool>
{
	IsPathOverlap(const Graph& g, const OverlapMap& pmap, const IsPositive<Graph>& pred)
	  : m_g(g)
	  , m_pmap(pmap)
	  , m_isPositive(pred)
	{}
	bool operator()(edge_descriptor e) const
	{
		bool stranded = true;
		if (opt::ss)
			stranded = m_isPositive(e);
		return stranded && getOverlap(m_pmap, source(e, m_g), target(e, m_g));
	}

  private:
	const Graph& m_g;
	const OverlapMap& m_pmap;
	const IsPositive<Graph>& m_isPositive;
};

/** Assemble overlapping paths. */
static void
assembleOverlappingPaths(Graph& g, Paths& paths, vector<string>& pathIDs)
{
	if (paths.empty())
		return;

	// Find overlapping paths.
	Overlaps overlaps = findOverlaps(g, paths);
	addPathOverlapEdges(g, paths, pathIDs, overlaps);

	// Create a property map of path overlaps.
	OverlapMap overlapMap;
	for (Overlaps::const_iterator it = overlaps.begin(); it != overlaps.end(); ++it)
		overlapMap.insert(OverlapMap::value_type(
		    OverlapMap::key_type(it->source.descriptor(), it->target.descriptor()), it->overlap));

	// Assemble unambiguously overlapping paths.
	Paths merges;
	assemble_if(g, back_inserter(merges), IsPathOverlap(g, overlapMap, IsPositive<Graph>(g)));

	// Merge overlapping paths.
	g_contigNames.unlock();
	assert(!pathIDs.empty());
	setNextContigName(pathIDs.back());
	for (Paths::const_iterator it = merges.begin(); it != merges.end(); ++it) {
		string name = createContigName();
		if (opt::verbose > 0)
			cerr << name << '\t' << *it << '\n';
		Vertex u(paths.size(), false);
		put(vertex_name, g, u.descriptor(), name);
		pathIDs.push_back(name);
		paths.push_back(mergePaths(paths, overlapMap, *it));

		// Remove the merged paths.
		for (ContigPath::const_iterator it2 = it->begin(); it2 != it->end(); ++it2) {
			if (isPath(*it2))
				paths[it2->id() - Vertex::s_offset].clear();
		}
	}
	g_contigNames.lock();
}

int
main(int argc, char** argv)
{
	string commandLine;
	{
		ostringstream ss;
		char** last = argv + argc - 1;
		copy(argv, last, ostream_iterator<const char*>(ss, " "));
		ss << *last;
		commandLine = ss.str();
	}

	if (!opt::db.empty())
		opt::metaVars.resize(3);

	bool die = false;
	for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) {
		istringstream arg(optarg != NULL ? optarg : "");
		switch (c) {
		case '?':
			die = true;
			break;
		case 'g':
			arg >> opt::graphPath;
			break;
		case 'k':
			arg >> opt::k;
			break;
		case 'r':
			arg >> opt::repeatContigs;
			break;
		case 'v':
			opt::verbose++;
			break;
		case OPT_HELP:
			cout << USAGE_MESSAGE;
			exit(EXIT_SUCCESS);
		case OPT_VERSION:
			cout << VERSION_MESSAGE;
			exit(EXIT_SUCCESS);
		case OPT_DB:
			arg >> opt::db;
			break;
		case OPT_LIBRARY:
			arg >> opt::metaVars[0];
			break;
		case OPT_STRAIN:
			arg >> opt::metaVars[1];
			break;
		case OPT_SPECIES:
			arg >> opt::metaVars[2];
			break;
		}
		if (optarg != NULL && !arg.eof()) {
			cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n";
			exit(EXIT_FAILURE);
		}
	}

	if (opt::k <= 0) {
		cerr << PROGRAM ": missing -k,--kmer option\n";
		die = true;
	}

	if (argc - optind < 2) {
		cerr << PROGRAM ": missing arguments\n";
		die = true;
	} else if (argc - optind > 2) {
		cerr << PROGRAM ": too many arguments\n";
		die = true;
	}

	if (die) {
		cerr << "Try `" << PROGRAM << " --help' for more information.\n";
		exit(EXIT_FAILURE);
	}

	const char* adjPath = argv[optind++];
	if (opt::verbose > 0)
		cerr << "Reading `" << adjPath << "'..." << endl;
	ifstream fin(adjPath);
	assert_good(fin, adjPath);
	Graph g;
	fin >> g;
	Vertex::s_offset = g.num_vertices() / 2;

	string pathsFile(argv[optind++]);
	vector<string> pathIDs;
	Paths paths = readPaths(g, pathsFile, pathIDs);

	switch (opt::mode) {
	case opt::OVERLAP:
		// Find overlapping paths, do not assemble.
		addPathOverlapEdges(g, paths, pathIDs, findOverlaps(g, paths));
		paths.clear();
		if (opt::graphPath.empty())
			opt::graphPath = "-";
		break;

	case opt::ASSEMBLE:
		// Assemble overlapping paths.
		assembleOverlappingPaths(g, paths, pathIDs);
		break;

	case opt::TRIM:
		// Trim overlapping paths.
		trimOverlaps(g, paths);
		// Remove paths consisting of a single contig.
		for_each_if(
		    paths.begin(),
		    paths.end(),
		    [](ContigPath& c) { return c.clear(); },
		    [](const ContigPath& c) { return c.size() == 1; });
		// Add the paths to the graph.
		addPathOverlapEdges(g, paths, pathIDs, Overlaps());
		break;
	}

	// Output the paths.
	for (Paths::const_iterator it = paths.begin(); it != paths.end(); ++it) {
		if (it->empty())
			continue;
		assert(it->size() != 1);
		cout << pathIDs[it - paths.begin()] << '\t' << *it << '\n';
	}
	assert(cout.good());

	// Output the graph.
	if (!opt::graphPath.empty()) {
		ofstream fout;
		ostream& out = opt::graphPath == "-" ? cout : (fout.open(opt::graphPath.c_str()), fout);
		assert_good(out, opt::graphPath);
		write_graph(out, g, PROGRAM, commandLine);
		assert_good(out, opt::graphPath);
	}

	// Output the repeat contigs.
	if (!opt::repeatContigs.empty()) {
		sort(s_trimmedContigs.begin(), s_trimmedContigs.end());
		s_trimmedContigs.erase(
		    unique(s_trimmedContigs.begin(), s_trimmedContigs.end()), s_trimmedContigs.end());
		ofstream out(opt::repeatContigs.c_str());
		assert_good(out, opt::repeatContigs);
		for (vector<ContigID>::const_iterator it = s_trimmedContigs.begin();
		     it != s_trimmedContigs.end();
		     ++it)
			out << get(g_contigNames, *it) << '\n';
		assert_good(out, opt::repeatContigs);
	}

	if (!opt::db.empty()) {
		init(db, opt::db, opt::verbose, PROGRAM, opt::getCommand(argc, argv), opt::metaVars);
		addToDb(db, "SS", opt::ss);
		addToDb(db, "K", opt::k);
	}

	return 0;
}
