// ==========================================================================
//                 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
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// DAMAGE.
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// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef TESTS_SEQ_IO_TEST_EASY_SEQ_IO_H_
#define TESTS_SEQ_IO_TEST_EASY_SEQ_IO_H_

#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/seq_io.h>

// ---------------------------------------------------------------------------
// Test recognition of supported file types.
// ---------------------------------------------------------------------------

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_recognize_file_type_gz_fasta)
{
#if SEQAN_HAS_ZLIB
    // Build path to file.
    seqan2::CharString filePath = getAbsolutePath("/tests/seq_io/test_dna.fa.gz");

    // Create SequenceStream object.
    SeqFileIn seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    SEQAN_ASSERT(isEqual(format(seqIO), Fasta()));
#endif  // #if SEQAN_HAS_ZLIB
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_recognize_file_type_bz2_fasta)
{
#if SEQAN_HAS_BZIP2
    // Build path to file.
    seqan2::CharString filePath = getAbsolutePath("/tests/seq_io/test_dna.fa.bz2");

    // Create SequenceStream object.
    SeqFileIn seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    SEQAN_ASSERT(isEqual(format(seqIO), Fasta()));
#endif  // #if SEQAN_HAS_BZIP2
}

// ---------------------------------------------------------------------------
// Test recognition of supported file formats.
// ---------------------------------------------------------------------------

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_recognize_file_format_text_fasta)
{
    // Build path to file.
    seqan2::CharString filePath = getAbsolutePath("/tests/seq_io/test_dna.fa");

    // Create SequenceStream object.
    SeqFileIn seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    SEQAN_ASSERT(isEqual(format(seqIO), Fasta()));
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_recognize_file_format_text_fastq)
{
    // Build path to file.
    seqan2::CharString filePath = getAbsolutePath("/tests/seq_io/test_dna.fq");

    // Create SequenceStream object.
    SeqFileIn seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    SEQAN_ASSERT(isEqual(format(seqIO), Fastq()));
}

// ---------------------------------------------------------------------------
// Test reading with different interfaces.
// ---------------------------------------------------------------------------

template <typename TId, typename TSeq>
void testSeqIOSequenceFileReadRecordTextFasta()
{
    // Build path to file.
    seqan2::CharString filePath = getAbsolutePath("/tests/seq_io/test_dna.fa");

    // Create SequenceStream object.
    SeqFileIn seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    TId id;
    TSeq seq;

    readRecord(id, seq, seqIO);
    SEQAN_ASSERT_EQ(id, "seq1");
    SEQAN_ASSERT_EQ(seq, "CGATCGATAAT");

    readRecord(id, seq, seqIO);
    SEQAN_ASSERT_EQ(id, "seq2");
    SEQAN_ASSERT_EQ(seq, "CCTCTCTCTCCCT");

    readRecord(id, seq, seqIO);
    SEQAN_ASSERT_EQ(id, "seq3");
    SEQAN_ASSERT_EQ(seq, "CCCCCCCC");

    SEQAN_ASSERT(atEnd(seqIO));
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_read_record_text_fasta)
{
    testSeqIOSequenceFileReadRecordTextFasta<seqan2::CharString, seqan2::Dna5String>();
    testSeqIOSequenceFileReadRecordTextFasta<std::string, std::string>();
    testSeqIOSequenceFileReadRecordTextFasta<std::string, seqan2::Dna5String>();
    testSeqIOSequenceFileReadRecordTextFasta<seqan2::CharString, std::string>();
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_read_all_text_fasta)
{
    // Build path to file.
    seqan2::CharString filePath = getAbsolutePath("/tests/seq_io/test_dna.fa");

    // Create SequenceStream object.
    SeqFileIn seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    seqan2::StringSet<seqan2::CharString> ids;
    seqan2::StringSet<seqan2::Dna5String> seqs;

    readRecords(ids, seqs, seqIO);
    SEQAN_ASSERT_EQ(length(seqs), 3u);
    SEQAN_ASSERT_EQ(ids[0], "seq1");
    SEQAN_ASSERT_EQ(seqs[0], "CGATCGATAAT");
    SEQAN_ASSERT_EQ(ids[1], "seq2");
    SEQAN_ASSERT_EQ(seqs[1], "CCTCTCTCTCCCT");
    SEQAN_ASSERT_EQ(ids[2], "seq3");
    SEQAN_ASSERT_EQ(seqs[2], "CCCCCCCC");

    SEQAN_ASSERT(atEnd(seqIO));
}

// ---------------------------------------------------------------------------
// Test writing with different interfaces.
// ---------------------------------------------------------------------------

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_write_record_text_fasta)
{
    // Build path to file.
    seqan2::CharString filePath = SEQAN_TEMP_FILENAME();
    append(filePath, ".fa");

    // Create SequenceStream object.
    SeqFileOut seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    seqan2::StringSet<seqan2::CharString> ids;
    appendValue(ids, "seq1");
    appendValue(ids, "seq2");
    appendValue(ids, "seq3");
    seqan2::StringSet<seqan2::Dna5String> seqs;
    appendValue(seqs, "CGATCGATAAT");
    appendValue(seqs, "CCTCTCTCTCCCT");
    appendValue(seqs, "CCCCCCCC");

    writeRecords(seqIO, ids, seqs);

    close(seqIO);  // Make sure we can read this later.

    seqan2::CharString pathToExpected = getAbsolutePath("/tests/seq_io/test_dna.fa");
    SEQAN_ASSERT_MSG(seqan2::_compareTextFilesAlt(toCString(pathToExpected), toCString(filePath)), "Output should match example.");
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_write_all_text_fasta)
{
    // Build path to file.
    seqan2::CharString filePath = SEQAN_TEMP_FILENAME();
    append(filePath, ".fa");

    // Create SequenceStream object.
    SeqFileOut seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    seqan2::StringSet<seqan2::CharString> ids;
    appendValue(ids, "seq1");
    appendValue(ids, "seq2");
    appendValue(ids, "seq3");
    seqan2::StringSet<seqan2::Dna5String> seqs;
    appendValue(seqs, "CGATCGATAAT");
    appendValue(seqs, "CCTCTCTCTCCCT");
    appendValue(seqs, "CCCCCCCC");

    writeRecords(seqIO, ids, seqs);

    close(seqIO);  // Make sure we can read this later.

    seqan2::CharString pathToExpected = getAbsolutePath("/tests/seq_io/test_dna.fa");
    SEQAN_ASSERT_MSG(seqan2::_compareTextFilesAlt(toCString(pathToExpected), toCString(filePath)), "Output should match example.");
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_write_record_text_fastq_no_qual)
{
    // Build path to file.
    seqan2::CharString filePath = SEQAN_TEMP_FILENAME();
    append(filePath, ".fq");
    seqan2::CharString pathToExpected = getAbsolutePath("/tests/seq_io/test_dna.fq");

    // Create SequenceStream object.
    SeqFileIn seqIn(toCString(pathToExpected));
    SeqFileOut seqOut(toCString(filePath));

    // Check that the file type and format are set correctly.
    seqan2::StringSet<seqan2::CharString> ids;
    seqan2::StringSet<seqan2::Dna5QString> seqs;

    readRecords(ids, seqs, seqIn);
    writeRecords(seqOut, ids, seqs);

    close(seqIn);
    close(seqOut);  // Make sure we can read this later.

    SEQAN_ASSERT_MSG(seqan2::_compareTextFilesAlt(toCString(pathToExpected), toCString(filePath)), "Output should match example.");
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_write_record_text_fastq_with_qual)
{
    // Build path to file.
    seqan2::CharString filePath = SEQAN_TEMP_FILENAME();
    append(filePath, ".fq");

    // Create SequenceStream object.
    SeqFileOut seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    seqan2::StringSet<seqan2::CharString> ids;
    appendValue(ids, "seq1");
    appendValue(ids, "seq2");
    appendValue(ids, "seq3");
    seqan2::StringSet<seqan2::Dna5String> seqs;
    appendValue(seqs, "CGATCGATAAT");
    appendValue(seqs, "CCTCTCTCTCCCT");
    appendValue(seqs, "CCCCCCCC");
    seqan2::StringSet<seqan2::CharString> quals;
    appendValue(quals, "IIIIIIIIIII");
    appendValue(quals, "IIIIIIIIIIIII");
    appendValue(quals, "IIIIIIII");

    writeRecords(seqIO, ids, seqs, quals);

    close(seqIO);  // Make sure we can read this later.

    seqan2::CharString pathToExpected = getAbsolutePath("/tests/seq_io/test_dna.fq");
    SEQAN_ASSERT_MSG(seqan2::_compareTextFilesAlt(toCString(pathToExpected), toCString(filePath)), "Output should match example.");
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_write_all_text_fastq_no_qual)
{
    // Build path to file.
    seqan2::CharString filePath = SEQAN_TEMP_FILENAME();
    append(filePath, ".fq");

    // Create SequenceStream object.
    SeqFileOut seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    seqan2::StringSet<seqan2::CharString> ids;
    appendValue(ids, "seq1");
    appendValue(ids, "seq2");
    appendValue(ids, "seq3");
    seqan2::StringSet<seqan2::Dna5QString> seqs;
    appendValue(seqs, "CGATCGATAAT");
    appendValue(seqs, "CCTCTCTCTCCCT");
    appendValue(seqs, "CCCCCCCC");

    writeRecords(seqIO, ids, seqs);

    close(seqIO);  // Make sure we can read this later.

    seqan2::CharString pathToExpected = getAbsolutePath("/tests/seq_io/test_dna.fq");
    SEQAN_ASSERT_MSG(seqan2::_compareTextFilesAlt(toCString(pathToExpected), toCString(filePath)), "Output should match example.");
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_write_all_text_fastq_with_qual)
{
    // Build path to file.
    seqan2::CharString filePath = SEQAN_TEMP_FILENAME();
    append(filePath, ".fq");

    // Create SequenceStream object.
    SeqFileOut seqIO(toCString(filePath));

    // Check that the file type and format are set correctly.
    seqan2::StringSet<seqan2::CharString> ids;
    appendValue(ids, "seq1");
    appendValue(ids, "seq2");
    appendValue(ids, "seq3");
    seqan2::StringSet<seqan2::Dna5String> seqs;
    appendValue(seqs, "CGATCGATAAT");
    appendValue(seqs, "CCTCTCTCTCCCT");
    appendValue(seqs, "CCCCCCCC");
    seqan2::StringSet<seqan2::CharString> quals;
    appendValue(quals, "IIIIIIIIIII");
    appendValue(quals, "IIIIIIIIIIIII");
    appendValue(quals, "IIIIIIII");

    writeRecords(seqIO, ids, seqs, quals);

    close(seqIO);  // Make sure we can read this later.

    seqan2::CharString pathToExpected = getAbsolutePath("/tests/seq_io/test_dna.fq");
    SEQAN_ASSERT_MSG(seqan2::_compareTextFilesAlt(toCString(pathToExpected), toCString(filePath)), "Output should match example.");
}

// ---------------------------------------------------------------------------
// Test isOpen() functionality.
// ---------------------------------------------------------------------------

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_isOpen_fileIn)
{
    // Build path to file.
    seqan2::CharString filePath = SEQAN_PATH_TO_ROOT();
    append(filePath, "/tests/seq_io/test_dna.fa");

    // Create SequenceStream object.
    SeqFileIn seqI;
    SEQAN_ASSERT(!isOpen(seqI));

    // open file
    open(seqI, toCString(filePath));
    SEQAN_ASSERT(isOpen(seqI));

    // close file
    close(seqI);
    SEQAN_ASSERT(!isOpen(seqI));
}

SEQAN_DEFINE_TEST(test_seq_io_sequence_file_isOpen_fileOut)
{
    // Build path to file.
    seqan2::CharString filePath = SEQAN_TEMP_FILENAME();
    append(filePath, ".fa");

    // Create SequenceStream object.
    SeqFileOut  seqO;
    SEQAN_ASSERT(!isOpen(seqO));

    // open files
    open(seqO, toCString(filePath));
    SEQAN_ASSERT(isOpen(seqO));

    // close files
    close(seqO);
    SEQAN_ASSERT(!isOpen(seqO));
}

#endif  // TESTS_SEQ_IO_TEST_EASY_SEQ_IO_H_
