// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2024, Knut Reinert, FU Berlin
// All rights reserved.
//
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// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
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//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
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//
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// ==========================================================================
// Writing of alignment data structures to streams.
// ==========================================================================

#ifndef SEQAN_TESTS_ALIGN_TEST_ALIGN_STREAM_H_
#define SEQAN_TESTS_ALIGN_TEST_ALIGN_STREAM_H_

#include <sstream>

#include <seqan/align.h>

// Test function write() on Array Gaps.

SEQAN_DEFINE_TEST(test_align_stream_gaps_write)
{
    seqan2::Gaps<seqan2::Dna5String> gaps;
    assignSource(gaps, "CGATTTAT");
    insertGaps(gaps, 8, 2);
    insertGaps(gaps, 5, 1);
    insertGaps(gaps, 0, 2);

    std::stringstream ss;
    ss << gaps;

    std::stringstream expected;
    expected << "--CGATT-TAT--";
    SEQAN_ASSERT_EQ(expected.str(), ss.str());
}

// Test operator<<() on Array Gaps.

SEQAN_DEFINE_TEST(test_align_stream_gaps_stream)
{
    seqan2::Gaps<seqan2::Dna5String> gaps;
    assignSource(gaps, "CGATTTAT");
    insertGaps(gaps, 8, 2);
    insertGaps(gaps, 5, 1);
    insertGaps(gaps, 0, 2);

    std::stringstream ss;
    ss << gaps;

    std::stringstream expected;
    expected << "--CGATT-TAT--";
    SEQAN_ASSERT_EQ(expected.str(), ss.str());
}

// Test write() on Align.

SEQAN_DEFINE_TEST(test_align_stream_align_write)
{
    seqan2::Align<seqan2::Dna5String> align;
    resize(rows(align), 2);
    assignSource(row(align, 0), "CGATTAGTG");
    assignSource(row(align, 1), "ATTAGTA");
    globalAlignment(align, seqan2::EditDistanceScore());

    std::stringstream ss;
    ss << align;

    std::stringstream expected;
    expected << "      0     .     \n"
             << "        CGATTAGTG\n"
             << "          |||||| \n"
             << "        --ATTAGTA\n\n\n";
    SEQAN_ASSERT_EQ(expected.str(), ss.str());
}

// Test operator<<() on Align.

SEQAN_DEFINE_TEST(test_align_stream_align_stream)
{
    seqan2::Align<seqan2::Dna5String> align;
    resize(rows(align), 2);
    assignSource(row(align, 0), "CGATTAGTG");
    assignSource(row(align, 1), "ATTAGTA");
    globalAlignment(align, seqan2::EditDistanceScore());

    std::stringstream ss;
    ss << align;

    std::stringstream expected;
    expected << "      0     .     \n"
             << "        CGATTAGTG\n"
             << "          |||||| \n"
             << "        --ATTAGTA\n\n\n";
    SEQAN_ASSERT_EQ(expected.str(), ss.str());
}

#endif  // SEQAN_TESTS_ALIGN_TEST_ALIGN_STREAM_H_
