#include <iostream>
#include <string>
#include <boost/program_options.hpp>

#include "profile.h"
#include "mrs.h"
#include "eds.h"
#include "mrs-reader.h"
#include "mrs-errors.h"

using namespace std;

void parse_options(int argc, char **argv, string *gprof, string *tprof,
	bool *ignore, bool *suppresstotal, bool *raw, bool *ignoreroot, 
	bool *verbose, tIid *itemno);
double fscore(int g, int t, int c);
pair<pair<tIid,int>,string> finishItem(Profile &test, tIid item, 
	vector<mrs::tMrs *> goldmrs, pair<pair<tIid,int>,string> lastline, 
	map<string, map<char,int> > &totals, bool raw, bool ignore=false, 
	bool ignoreroot=false, bool verbose=false);

int main(int argc, char **argv) {
	string gprofile, tprofile;
	bool ignore, suppresstotal, raw, ignoreroot, verbose;
	tIid itemno;

	parse_options(argc, argv, &gprofile, &tprofile, &ignore, &suppresstotal, 
		&raw, &ignoreroot, &verbose, &itemno);

	Profile gold(gprofile);
	Profile test(tprofile);
	mrs::SimpleMrsReader reader;

	vector<mrs::tMrs *> goldmrs;
	pair<pair<tIid,int>, string> gres = gold.getResult(MRS);
	pair<pair<tIid,int>, string> lastline
		= pair<pair<tIid,int>, string>(pair<tIid,int>(-1,-1),string());
	tIid item = -1;
	map<string, map<char, int> > totals;
	totals["ALL"] = map<char,int>();
	totals["ALL"]['G'] = 0;
	totals["ALL"]['T'] = 0;
	totals["ALL"]['C'] = 0;
	totals["A"] = map<char,int>();
	totals["A"]['G'] = 0;
	totals["A"]['T'] = 0;
	totals["A"]['C'] = 0;
	totals["N"] = map<char,int>();
	totals["N"]['G'] = 0;
	totals["N"]['T'] = 0;
	totals["N"]['C'] = 0;
	totals["P"] = map<char,int>();
	totals["P"]['G'] = 0;
	totals["P"]['T'] = 0;
	totals["P"]['C'] = 0;

	while (gres.first.first >= 0) { //still returning results
		if (itemno > -1 && gres.first.first != itemno) {
			//looking for a specific item
			gres = gold.getResult(MRS);
			continue;   // and not there yet
		}
		if (gres.first.first != item) { //new item
			if (item != -1 && goldmrs.size() > 0) { //finish last item
				if (gold.numGold(item) == 1) {
					lastline = finishItem(test, item, goldmrs, lastline, totals, 
						raw, ignore, ignoreroot, verbose);
				}
				goldmrs.clear();
			}
		}
		item = gres.first.first;
		if (gold.numGold(item) == 1 && !gres.second.empty()) {
			mrs::tMrs *mrs = reader.readMrs(gres.second);
			goldmrs.push_back(mrs);
		}
		gres = gold.getResult(MRS);
	}
	if (item != -1 && goldmrs.size() > 0) {
		if (gold.numGold(item) == 1) {
			lastline = finishItem(test, item, goldmrs, lastline, totals, raw, 
				ignore, ignoreroot, verbose);
		}
		goldmrs.clear();
	}

	if (!suppresstotal) {
		cout << "ALL: " 
			<< fscore(totals["ALL"]['G'], totals["ALL"]['T'], totals["ALL"]['C'])
			<< ", A: "
			<< fscore(totals["A"]['G'], totals["A"]['T'], totals["A"]['C'])
			<< ", N: "
			<< fscore(totals["N"]['G'], totals["N"]['T'], totals["N"]['C'])
			<< ", P: "
			<< fscore(totals["P"]['G'], totals["P"]['T'], totals["P"]['C'])
			<<endl;
	}
}

double fscore(int g, int t, int c)
{
	double precision = 0;
	double recall = 0;
	double fscore = 0;
	if (t>0) precision = (double)c/t;
	if (g>0) recall = (double)c/g;
	if (precision > 0 && recall > 0) {
		fscore = (2*precision*recall)/(precision+recall);
	}
	return fscore;
}

pair<pair<tIid,int>,string> finishItem(Profile &test, tIid item, 
	vector<mrs::tMrs *>goldmrs, pair<pair<tIid,int>,string> lastline, 
	map<string, map<char,int> > &totals, bool raw, bool ignore, bool ignoreroot,
	bool verbose)
{
	vector<string> categories; 
	categories.push_back("ALL");
	categories.push_back("A");
	categories.push_back("N");
	categories.push_back("P");
	pair<pair<tIid,int>,string> tres = lastline;
	mrs::tMrs *testmrs = NULL;
	mrs::tEds *eds_test = NULL;
	mrs::SimpleMrsReader reader;
	vector<mrs::tEdsComparison *> results;
	if (test.getReadings(item) > 0) {
		if (tres.first.first == -1)
			tres = test.getResult(MRS);
		while (tres.first.first != -1 && tres.first.first < item)
			tres = test.getResult(MRS);
		if (tres.first.first != item) {
			cerr << "Item " << item << " is not in the test profile." << endl;
		} else {
			if (tres.second.empty()) {
				cerr << "No MRS for item " << item << " in test profile." << endl;
			} else {
				try {
					testmrs = reader.readMrs(tres.second);
				}
				catch (tError &e) {
					cerr << "Failed to parse with error: \"" << e.getMessage()
						<< "\"" << endl;
				}
			}
		}
	} 
	if (!ignore || testmrs != NULL) {
		
		if (testmrs != NULL) 
			eds_test = new mrs::tEds(testmrs);
		int bestgold = -1;
		double bestscore = -1;
		for (vector<mrs::tMrs *>::iterator git = goldmrs.begin();
				git != goldmrs.end(); ++git) {
			mrs::tEds *eds_gold = new mrs::tEds(*git);
			mrs::tEdsComparison *result = eds_gold->compare_triples(eds_test, 
			"ALL", ignoreroot);
			results.push_back(result);
			if (result->score > bestscore) {
				bestgold = results.size()-1;
				bestscore = result->score;
			}
			delete eds_gold;
		}
		int lowcount;
		if (testmrs == NULL) { //find smallest gold
			for (int i=0; i < results.size(); ++i) {
				if (i == 0 || results[i]->totalA["ALL"] < lowcount) {
					bestgold = i;
					lowcount = results[i]->totalA["ALL"];
				}
			}
		}

		mrs::tEdsComparison *res = results[bestgold];
		if (verbose) {
//			if (testmrs == NULL) {
//				cout << item << " unparsed" << endl;
//			} else {
				if (!res->unmatchedA.empty() || !res->unmatchedB.empty()) {
					cerr << "Item: " << test.getItem(item) << endl;
					cout << "Unmatched Triples in " << item << endl;
					for (vector<string>::iterator it = res->unmatchedA.begin();
							it != res->unmatchedA.end(); ++it)
						cout << "< " << *it << endl;
					for (vector<string>::iterator it = res->unmatchedB.begin();
							it != res->unmatchedB.end(); ++it)
						cout << "> " << *it << endl;
				}
//			}
		}
		if (raw) cout << item;
		for (vector<string>::iterator it = categories.begin(); 
				it != categories.end(); ++it) {
			if (raw) 
				cout << "@" << (res->totalA.count(*it)>0?res->totalA[*it]:0);
			if (res->totalA.count(*it) > 0) {
				if (totals.count(*it) == 0) totals[*it] = map<char,int>();
				if (totals[*it].count('G') == 0) totals[*it]['G'] = 0;
				totals[*it]['G'] += res->totalA[*it];
			}
		}
		for (vector<string>::iterator it = categories.begin(); 
				it != categories.end(); ++it) {
			if (raw) 
				cout << "@" << (res->totalB.count(*it)>0?res->totalB[*it]:0);
			if (res->totalB.count(*it) > 0) {
				if (totals.count(*it) == 0) totals[*it] = map<char,int>();
				if (totals[*it].count('T') == 0) totals[*it]['T'] = 0;
				totals[*it]['T'] += res->totalB[*it];
			}
		}
		for (vector<string>::iterator it = categories.begin(); 
				it != categories.end(); ++it) {
			if (raw) 
				cout << "@" << (res->totalM.count(*it)>0?res->totalM[*it]:0);
			if (res->totalM.count(*it) > 0) {
				if (totals.count(*it) == 0) totals[*it] = map<char,int>();
				if (totals[*it].count('C') == 0) totals[*it]['C'] = 0;
				totals[*it]['C'] += res->totalM[*it];
			}
		}
		if (raw) cout << endl;
		if (testmrs != NULL) {
			delete eds_test;
			delete testmrs;
		}
	}
	for (vector<mrs::tEdsComparison *>::iterator rit = results.begin();
		rit != results.end(); ++rit) {
		delete *rit;
	}

	for (vector<mrs::tMrs *>::iterator git = goldmrs.begin();
		git != goldmrs.end(); ++git) {
			delete *git;
	}

	return tres;
}

void parse_options(int argc, char **argv, string *gprof, string *tprof,
	bool *ignore, bool *suppresstotal, bool *raw, bool *ignoreroot,
	bool *verbose, tIid *itemno)
{
	namespace po = boost::program_options;
	po::options_description visible("Options");
	visible.add_options()
		("help,h", "This usage information.")
		("ignore,i", "Ignore gold triples where the test parse failed.")
		("suppress,s", "Suppress printing of total F-scores.")
		("counts,c", "Print raw counts per item.")
		("root,r", "Ignore root triples in comparison.")
		("verbose,v", "Print unmatched triples.")
		("analysis,a", po::value<tIid>(itemno)->default_value(-1),
			"Select a single item to evaluate (-1 for all items).")
	;

	po::options_description hidden("Hidden options");
	hidden.add_options()
		("goldprof", po::value<string>(gprof), "gold profile")
		("testprof", po::value<string>(tprof), "test profile")
	;
	po::options_description cmd_line ("Command line options");
	cmd_line.add(visible).add(hidden);
	po::positional_options_description p;
	p.add("goldprof", 1).add("testprof", 1);
	po::variables_map vm;
	try {
		po::store(po::command_line_parser(argc, argv).
			options(cmd_line).positional(p).run(), vm);
		notify(vm);
		if (vm.count("help")) {
			cout << "Usage: " << argv[0] << " [options] "
			<< "gold-profile test-profile" << endl;
			cout << visible << endl;
			exit(0);
		}
		if (!vm.count("goldprof") || !vm.count("testprof")) {
			cerr << "Insufficient arguments given." << endl;
			cerr << "Usage: " << argv[0] << " [options] "
				<< "gold-profile test-profile" << endl;
			cerr << visible << endl;
			exit(1);
		}

		if (vm.count("ignore"))
			*ignore = true;
		else
			*ignore = false;

		if (vm.count("suppress"))
			*suppresstotal = true;
		else
			*suppresstotal = false;

		if (vm.count("counts"))
			*raw = true;
		else
			*raw = false;

		if (vm.count("root"))
			*ignoreroot = true;
		else
			*ignoreroot = false;

		if (vm.count("verbose"))
			*verbose = true;
		else
			*verbose = false;

	} catch (po::error& e ) {
		cerr << "Error: " << e.what() << endl;
		cerr << "Usage: " << argv[0] << " [options] "
			<< "gold-profile test-profile" << endl;
		cerr << visible << endl;
		exit(1);
	}
}