#include "applications/ExportExample.hh"

/**
 * Project     : CASAVA
 * Module      : $RCSfile: ExportExample.cpp,v $
 * @author     : Lukasz Szajkowski
 * Copyright   : Copyright (c) Illumina 2008, 2009. All rights reserved.
 *
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 *
 */
#include <iostream>

#include <stdlib.h>
#include <stdio.h>

#include "common/Alignment.hh"


namespace ca {
namespace applications {

using namespace std;
using namespace casava::common;


int ExportExample::run() {
	std::ostringstream os;
	cout << "[" << "Start" << "]\n";


	const casava::common::Compression &noCompression =
			casava::common::CompressionFactory::none();
	//casava::common::SequenceWriter sequenceWriter(qseqFilePath.string() + saveSuffix_, noCompression);
	const casava::common::Alignment defaultAlignment;
	const casava::common::Tile customTile("a name", 11, 12, 13);
	const casava::common::Spot customSpot(customTile, 24, 25);
	const casava::common::Sequence customSequence(customSpot, "ACG", 37, "asdf",
			"qwerty", true);
	const casava::common::Match match1("chr.X", "contig1", 10,
			casava::common::Match::Forward);
	const casava::common::Match match2("chr.Y", "contig2", 20,
			casava::common::Match::Reverse);
	const casava::common::Alignment customAlignment(customSequence, match1,
			"descr.1", 1, match2, 2);

	std::string exportFilePath1 = "./s_1_1_export.txt";
	std::string exportFilePath2 = "./s_1_2_export.txt";

	std::string exportFilePath3 = "./s_1_2_export_final.txt";

	casava::common::Ofstream stream(exportFilePath1, noCompression);
	//stream.open(exportFilePath);
	if (stream.is_open() && stream.good()) {
		cout << "Writing " << exportFilePath1 << "\n";
	} else {
		cout << "Error: failed to open. Qval files will not be produced."
				<< exportFilePath1 << "\n";
		exit(1);
	}
	stream << customAlignment;
	casava::common::AlignmentWriter alignmentWriter(exportFilePath2, noCompression);
	//alignmentWriter.open(exportFilePath2);

	if (alignmentWriter.is_open() && alignmentWriter.good()) {
		cout << "Writing " << exportFilePath2 << "\n";
	} else {
		cout << "Error: failed to open. Qval files will not be produced."
				<< exportFilePath2 << "\n";
		exit(1);
	}
	alignmentWriter << customAlignment;
	alignmentWriter.put(customAlignment);
	alignmentWriter.close();
	casava::common::AlignmentReader alignmentReader(exportFilePath2,
			noCompression);

	if (alignmentReader && alignmentReader.good()) {
		cout << "Reading from " << exportFilePath2 << "\n";
	} else {
		cout << "Error: failed to open. Qval files will not be produced."
				<< exportFilePath2 << "\n";
		exit(1);
	}
	casava::common::AlignmentWriter alignmentWriterFinal(exportFilePath3,
			noCompression);
	casava::common::Alignment newAlignment;
	while (alignmentReader.get(newAlignment) && alignmentReader.good()) {
		cout << "Line\n";
		alignmentWriterFinal << newAlignment;
	}
	//alignmentWriterFinal.put(newAlignment);
	//count << newAlignment;
	cout << "[" << "End" << "]\n";
	return 0;
}
}
} // end namespace casava{ namespace { applications