/**
 ** Copyright (c) 2010 Illumina, Inc.
 **
 ** 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).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 **/

#include <iostream>
#include <sstream>
#include <string>
#include <boost/filesystem.hpp>

using namespace std;

#include "RegistryName.hh"
#include "testPairStats.hh"

#include "common/RelOrient.hh"
#include "common/PairStats.hh"
#include "common/Exceptions.hh"

CPPUNIT_TEST_SUITE_NAMED_REGISTRATION(TestPairStats, registryName("PairStats"));

const boost::filesystem::path projDirPath = ".";

using casava::common::RelOrient;
//using casava::common::LanePairStats;
using casava::common::PairStats;

/*****************************************************************************/

void TestPairStats::setUp()
{
}

/*****************************************************************************/

void TestPairStats::tearDown()
{
}

/*****************************************************************************/

void TestPairStats::testConstructor()
{
    try
    {
        PairStats pairStats(projDirPath);
    }
    catch(const casava::common::CasavaException &e)
    {
        std::cerr << e.getContext() << ": " << e.getMessage() << std::endl;
        CPPUNIT_ASSERT(false);
    }
}

/*****************************************************************************/

void TestPairStats::testLoad()
{
    PairStats pairStats(projDirPath);

    const float numLowSds(5);
    const float numHighSds(3);
    pairStats.setNumSds(numLowSds, numHighSds);

    //const std::string laneKey("EAS51_210:1");
    const std::string instrument = "EAS51";
    const int run = 210;
    const int lane = 1;
    const std::string barcode = "ACGTTA";
    //const unsigned int read1Len(pairStats.getReadLen(instrument, run, lane, barcode, 1));
    //const unsigned int read2Len(pairStats.getReadLen(instrument, run, lane, barcode, 2));

    //const unsigned int expectedRead1Len(100);
    //const unsigned int expectedRead2Len(100);
    // disabling un-maintained tests
    //CPPUNIT_ASSERT_EQUAL(expectedRead1Len, read1Len);
    //CPPUNIT_ASSERT_EQUAL(expectedRead2Len, read2Len);

    RelOrient relOrient;
    double minSize(0.0);
    double maxSize(0.0);
    pairStats.getBounds(instrument, run, lane, barcode, relOrient, minSize, maxSize);

    RelOrient expectedRelOrient("Rp");
    //CPPUNIT_ASSERT(expectedRelOrient == relOrient);
    //CPPUNIT_ASSERT_EQUAL(double(236.0), minSize);
    //CPPUNIT_ASSERT_EQUAL(double(362.0), maxSize);
}

/*****************************************************************************/