// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2024, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// 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
//       documentation and/or other materials provided with the distribution.
//     * 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
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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// DAMAGE.
//
// ==========================================================================
// Author: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
// ==========================================================================
// Tests for seqan/stream/write_fasta_fastq.h
// ==========================================================================


#ifndef TEST_STREAM_TEST_STREAM_WRITE_FASTA_H_
#define TEST_STREAM_TEST_STREAM_WRITE_FASTA_H_

using namespace seqan2;

SEQAN_DEFINE_TEST(test_stream_write_record_fasta_default)
{
    CharString outStream;
    CharString meta1 = "meta1";
    CharString meta2 = "  meta2 ";
    Dna5String seq1 = "CGATN";
    Dna5String seq2 = "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN";

    writeRecord(outStream, meta1, seq1, Fasta());
    writeRecord(outStream, meta2, seq2, Fasta());

    char const * EXPECTED =
            ">meta1\n"
            "CGATN\n"
            ">  meta2 \n"
            "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN\n"
            "CCCAAATTTNCCCAAATTTNCCCAAATTTN\n";
    SEQAN_ASSERT_EQ(outStream, EXPECTED);
}

// Test that no empty lines are written if (seq_len % line_len) == 0.
SEQAN_DEFINE_TEST(test_stream_write_record_fasta_no_empty_lines)
{
    using namespace seqan2;

    String<char> outStream;

    CharString meta1 = "meta1";
    CharString meta2 = "meta2";
    Dna5String seq1 = "CCCAAATTTN""CCCAAATTTN";
    Dna5String seq2 = "CGATN";
    SEQAN_ASSERT_EQ(length(seq1), 20u);

    SequenceOutputOptions options;
    options.lineLength = 10;

    writeRecord(outStream, meta1, seq1, Fasta(), options);
    writeRecord(outStream, meta2, seq2, Fasta(), options);

    char const * EXPECTED =
            ">meta1\n"
            "CCCAAATTTN\n"
            "CCCAAATTTN\n"
            ">meta2\n"
            "CGATN\n";
    SEQAN_ASSERT_EQ(outStream, CharString(EXPECTED));
}

SEQAN_DEFINE_TEST(test_stream_write_record_fasta_nolinebreaks)
{
    CharString outStream;
    CharString meta1 = "meta1";
    CharString meta2 = "  meta2 ";
    Dna5String seq1 = "CGATN";
    Dna5String seq2 = "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN";

    writeRecord(outStream, meta1, seq1, Fasta(), SequenceOutputOptions(0));
    writeRecord(outStream, meta2, seq2, Fasta(), SequenceOutputOptions(0));

    char const * EXPECTED =
            ">meta1\n"
            "CGATN\n"
            ">  meta2 \n"
            "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN"
            "CCCAAATTTNCCCAAATTTNCCCAAATTTN\n";
    SEQAN_ASSERT_EQ(outStream, EXPECTED);
}

SEQAN_DEFINE_TEST(test_stream_write_record_fastq_default_separate_qual)
{
    CharString outStream;
    CharString meta1 = "meta1";
    CharString meta2 = "  meta2 ";
    Dna5String seq1 = "CGATN";
    Dna5String seq2 = "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN";
    CharString qual1 = "!!!!!";
    CharString qual2 = "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";

    writeRecord(outStream, meta1, seq1, qual1, Fastq());
    writeRecord(outStream, meta2, seq2, qual2, Fastq());

    char const * EXPECTED =
            "@meta1\n"
            "CGATN\n"
            "+\n"
            "!!!!!\n"
            "@  meta2 \n"
            "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN\n"
            "+\n"
            "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
    SEQAN_ASSERT_EQ(outStream, EXPECTED);
}

SEQAN_DEFINE_TEST(test_stream_write_record_fastq_default_qual_in_seq)
{
    CharString outStream;
    CharString meta1 = "meta1";
    CharString meta2 = "  meta2 ";
    String<Dna5Q> seq1 = "CGATN";
    assignQualities(seq1, CharString("!!!!!"));
    String<Dna5Q> seq2 = "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN";
    assignQualities(seq2, CharString("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"));

    writeRecord(outStream, meta1, seq1, Fastq());
    writeRecord(outStream, meta2, seq2, Fastq());

    char const * EXPECTED =
            "@meta1\n"
            "CGATN\n"
            "+\n"
            "!!!!!\n"
            "@  meta2 \n"
            "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN\n"
            "+\n"
            "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
    SEQAN_ASSERT_EQ(outStream, EXPECTED);
}

SEQAN_DEFINE_TEST(test_stream_write_record_fastq_linebreaks_qualmeta)
{
    CharString outStream;
    CharString meta1 = "meta1";
    CharString meta2 = "  meta2 ";
    Dna5String seq1 = "CGATN";
    Dna5String seq2 = "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN";
    CharString qual1 = "!!!!!";
    CharString qual2 = "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!";

    writeRecord(outStream, meta1, seq1, qual1, Fastq(), SequenceOutputOptions(70, true));
    writeRecord(outStream, meta2, seq2, qual2, Fastq(), SequenceOutputOptions(70, true));

    char const * EXPECTED =
            "@meta1\n"
            "CGATN\n"
            "+meta1\n"
            "!!!!!\n"
            "@  meta2 \n"
            "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN\n"
            "CCCAAATTTNCCCAAATTTNCCCAAATTTN\n"
            "+  meta2 \n"
            "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n"
            "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
    SEQAN_ASSERT_EQ(outStream, EXPECTED);
}

//SEQAN_DEFINE_TEST(test_stream_write2_fasta_default)
//{
//    CharString outStream;
//    StringSet<CharString> metas;
//    appendValue(metas, "meta1");
//    appendValue(metas, "  meta2 ");
//    StringSet<Dna5String> seqs;
//    appendValue(seqs, "CGATN");
//    appendValue(seqs, "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN");
//
//    write2(outStream, metas, seqs, Fasta());
//
//    char const * EXPECTED =
//            ">meta1\n"
//            "CGATN\n"
//            ">  meta2 \n"
//            "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN\n"
//            "CCCAAATTTNCCCAAATTTNCCCAAATTTN\n";
//    SEQAN_ASSERT_EQ(outStream, EXPECTED);
//}
//
//SEQAN_DEFINE_TEST(test_stream_write2_fastq_default_qual_in_seq)
//{
//    CharString outStream;
//    StringSet<CharString> metas;
//    appendValue(metas, "meta1");
//    appendValue(metas, "  meta2 ");
//    StringSet<String<Dna5Q> > seqs;
//    appendValue(seqs, "CGATN");
//    assignQualities(seqs[0], CharString("!!!!!"));
//    appendValue(seqs, "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN");
//    assignQualities(seqs[1], CharString("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"));
//
//    write2(outStream, metas, seqs, Fastq());
//
//    char const * EXPECTED =
//            "@meta1\n"
//            "CGATN\n"
//            "+\n"
//            "!!!!!\n"
//            "@  meta2 \n"
//            "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN\n"
//            "+\n"
//            "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
//    SEQAN_ASSERT_EQ(outStream, EXPECTED);
//}
//
//SEQAN_DEFINE_TEST(test_stream_write2_fastq_default_separate_qual)
//{
//    CharString outStream;
//    StringSet<CharString> metas;
//    appendValue(metas, "meta1");
//    appendValue(metas, "  meta2 ");
//    StringSet<Dna5String> seqs;
//    appendValue(seqs, "CGATN");
//    appendValue(seqs, "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN");
//    StringSet<CharString> quals;
//    appendValue(quals, "!!!!!");
//    appendValue(quals, "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!");
//
//    write2(outStream, metas, seqs, quals, Fastq());
//
//    char const * EXPECTED =
//            "@meta1\n"
//            "CGATN\n"
//            "+\n"
//            "!!!!!\n"
//            "@  meta2 \n"
//            "CCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTNCCCAAATTTN\n"
//            "+\n"
//            "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
//    SEQAN_ASSERT_EQ(outStream, EXPECTED);
//}

#endif // def TEST_STREAM_TEST_STREAM_WRITE_FASTA_H_
