/*
 * =====================================================================================
 *
 *       Filename:  FASTAReader_gtest.cpp
 *
 *    Description:  Test common/FASTAReader.h
 *
 *        Version:  1.0
 *        Created:  10/29/2012 05:18:52 PM
 *       Revision:  none
 *       Compiler:  gcc
 *
 *         Author:  Yuan Li (yli), yli@pacificbiosciences.com
 *        Company:  Pacific Biosciences
 *
 * =====================================================================================
 */

#include <gtest/gtest.h>

#include <pbdata/testdata.h>
#include <pbdata/FASTAReader.hpp>

class FASTAReaderTest : public ::testing::Test
{
public:
    void SetUp()
    {
        std::string filename(fastaFile1);
        reader.Initialize(filename);
    }

    void TearDown()
    {
        reader.Close();
        seq.Free();
    }

    FASTAReader reader;
    FASTASequence seq;
};

TEST_F(FASTAReaderTest, GetNext)
{
    reader.GetNext(seq);
    EXPECT_EQ(strcmp(seq.title, "read1"), 0);
    EXPECT_EQ(seq.length, 100u);
    std::string expected_seq(
        "AAAAAGGGGGCCCCCACGGCAGCCAGATTTAAATTGAGGGCCCCCCCTTT"
        "GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
    EXPECT_EQ(strcmp((char*)seq.seq, expected_seq.c_str()), 0);

    reader.GetNext(seq);
    EXPECT_EQ(std::strcmp(seq.title, "read2"), 0);
    EXPECT_EQ(seq.length, 99u);
}

TEST_F(FASTAReaderTest, ReadAllSequences)
{
    std::vector<FASTASequence> seqs;
    reader.ReadAllSequences(seqs);

    EXPECT_EQ(seqs.size(), 12u);
    EXPECT_EQ(std::strcmp(seqs[11].title, "read2x"), 0);

    std::string expected_seq(
        "AAAAAGGGGGCCCACGGCAGCCAGATTTAAATTGAGGGCAACCCCCCTTT"
        "GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
    EXPECT_EQ(strcmp((char*)seqs[11].seq, expected_seq.c_str()), 0);
}