// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2010, 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
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef TESTS_FILE_TEST_FILE_H_
#define TESTS_FILE_TEST_FILE_H_

#include <seqan/align.h>
#include <seqan/find.h>

using namespace std;
using namespace seqan;

SEQAN_DEFINE_TEST(test_file_stream)
{
	//string => stream
	String<char> str_1("The first test file string.");
 
    char buffer[1023];
    strcpy(buffer, SEQAN_TEMP_FILENAME());
    
	fstream strm_1;
	strm_1.open(buffer, ios_base::out | ios_base::trunc | ios_base::binary);
    
	strm_1 << str_1;
	strm_1.close();
    
	//assign stream => string
	String<char> str_3 = "";
	fstream strm_3;
	strm_3.open(buffer, ios_base::in | ios_base::binary);
	strm_3 >> str_3;
	strm_3.close();
	SEQAN_ASSERT_EQ(length(str_3), length(str_1));
	SEQAN_ASSERT_EQ(str_3, str_1);
    
    strcpy(buffer, SEQAN_TEMP_FILENAME());

	//const string => stream
	fstream strm_4;
	strm_4.open(buffer, ios_base::out | ios_base::trunc | ios_base::binary);
	strm_4 << "Testfile";
	strm_4.close();
    
	String<char> str_5 = "";
	fstream strm_5;
	strm_5.open(buffer, ios_base::in | ios_base::binary);
	strm_5 >> str_5;
	strm_5.close();
	SEQAN_ASSERT_EQ(str_5, "Testfile");
    
    
    //	String<char> str_4("This test file was made by " __FILE__ " too.\n");
    
    /*
     str_2 = "";
     fstream strm_3;
     strm_3.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     assign(str_2, strm_3, Insist());
     strm_3.close();
     SEQAN_ASSERT_EQ(str_2, str_1);
     
     str_2 = "";
     fstream strm_4;
     strm_4.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     assign(str_2, strm_4, 9, Insist());
     strm_4.close();
     SEQAN_ASSERT_EQ(str_2, "This test");
     
     String<char> str_3;
     fstream strm_5;
     strm_5.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     assign(str_3, strm_5, 9, Generous());
     strm_5.close();
     SEQAN_ASSERT_EQ(str_3, "This test");
     
     str_2 = "";
     fstream strm_6;
     strm_6.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     assign(str_2, strm_6, Limit());
     strm_6.close();
     SEQAN_ASSERT_EQ(str_2, str_1);
     
     str_2 = "";
     fstream strm_7;
     strm_7.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     assign(str_2, strm_7, 9, Limit());
     strm_7.close();
     SEQAN_ASSERT_EQ(str_2, "This test");
     
     char str_4[200];
     fstream strm_8;
     strm_8.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     assign(str_4, strm_8);
     strm_8.close();
     SEQAN_ASSERT_EQ(str_4, str_1);
     
     fstream strm_9;
     strm_9.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     assign(str_4, strm_9, 9);
     strm_9.close();
     SEQAN_ASSERT(isEqual(str_4, "This test"));
     
     //____________________________________________________________________________
     //append stream => string
     String<char> str_5("Start");
     append(str_5, str_1);
     
     String<char> str_6("Start");
     fstream strm_10;
     strm_10.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(str_6, strm_10);
     strm_10.close();
     SEQAN_ASSERT_EQ(str_6, str_5);
     
     String<char> str_7("Start");
     fstream strm_11;
     strm_11.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(str_7, strm_11, 14, Generous());
     strm_11.close();
     SEQAN_ASSERT_EQ(str_7, "StartThis test");
     
     String<char> str_8("Start");
     fstream strm_11a;
     strm_11a.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(str_8, strm_11a, 200, Generous());
     strm_11a.close();
     SEQAN_ASSERT_EQ(str_8, str_5);
     
     str_2 = "Start";
     fstream strm_12;
     strm_12.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(str_2, strm_12, Insist());
     strm_12.close();
     SEQAN_ASSERT_EQ(str_2, str_5);
     
     str_2 = "Start";
     fstream strm_13;
     strm_13.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(str_2, strm_13, 14, Insist());
     strm_13.close();
     SEQAN_ASSERT_EQ(str_2, "StartThis test");
     
     str_2 = "Start";
     fstream strm_14;
     strm_14.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(str_2, strm_14, Limit());
     strm_14.close();
     SEQAN_ASSERT_EQ(str_2, str_5);
     
     str_2 = "Start";
     fstream strm_15;
     strm_15.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(str_2, strm_15, 14, Limit());
     strm_15.close();
     SEQAN_ASSERT_EQ(str_2, "StartThis test");
     
     assign(str_4, "Start");
     fstream strm_16;
     strm_16.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(str_4, strm_16);
     strm_16.close();
     SEQAN_ASSERT_EQ(str_4, str_5);
     
     assign(str_4, "Start");
     fstream strm_17;
     strm_17.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(str_4, strm_17, 14);
     strm_17.close();
     SEQAN_ASSERT_EQ(isEqual(str_4, "StartThis test"));
     
     //____________________________________________________________________________
     //replace stream => string
     String<char> str_9("start ");
     append(str_9, str_1);
     append(str_9, " end");
     
     String<char> str_10("start middle end");
     fstream strm_18;
     strm_18.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     replace(str_10, 6, 12, strm_18);
     strm_18.close();
     SEQAN_ASSERT(str_10 == str_9);
     
     str_10 = "start middle end";
     fstream strm_19;
     strm_19.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     replace(str_10, 6, 12, strm_19, 15);
     strm_19.close();
     SEQAN_ASSERT(str_10 == "start This test");
     
     str_10 = "start middle end";
     fstream strm_20;
     strm_20.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     replace(str_10, 6, 12, strm_20, Limit());
     strm_20.close();
     SEQAN_ASSERT(str_10 == str_9);
     
     str_10 = "start middle end";
     fstream strm_21;
     strm_21.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     replace(str_10, 6, 12, strm_21, 15, Limit());
     strm_21.close();
     SEQAN_ASSERT(str_10 == "start This test");
     
     assign(str_4, "start middle end");
     fstream strm_22;
     strm_22.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     replace(str_4, 6, 12, strm_22);
     strm_22.close();
     SEQAN_ASSERT(str_4 == str_9);
     
     assign(str_4, "start middle end");
     fstream strm_23;
     strm_23.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     replace(str_4, 6, 12, strm_23, 15);
     strm_23.close();
     SEQAN_ASSERT(isEqual(str_4, "start This test"));
     
     //____________________________________________________________________________
     //Test limited string => stream
     
     fstream strm_24;
     strm_24.open(TEST_PATH "testfile.txt", ios_base::out | ios_base::trunc | ios_base::binary);
     write(strm_24, str_1, 9);
     strm_24.close();
     
     fstream strm_25;
     strm_25.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     strm_25 >> str_2;
     strm_25.close();
     SEQAN_ASSERT(isEqual(str_2, "This test"));
     
     //____________________________________________________________________________
     //Test stream => segment
     
     str_2 = "begin middle end";
     Segment<String<char> > seg_1(str_2, 6, 12);
     fstream strm_26;
     strm_26.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     strm_26 >> seg_1;
     strm_26.close();
     SEQAN_ASSERT(isEqual(str_2, "begin This test end"));
     
     str_2 = "begin middle end";
     Segment<String<char> > seg_2(str_2, 6, 12);
     fstream strm_27;
     strm_27.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     append(seg_2, strm_27);
     strm_27.close();
     SEQAN_ASSERT(isEqual(str_2, "begin middleThis test end"));
     
     str_2 = "begin one two three end";
     Segment<String<char> > seg_3(str_2, 6, 19);
     fstream strm_28;
     strm_28.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     replace(seg_3, 4, 7, strm_28);
     strm_28.close();
     SEQAN_ASSERT(isEqual(str_2, "begin one This test three end"));
     
     //____________________________________________________________________________
     */
}

//////////////////////////////////////////////////////////////////////////////

SEQAN_DEFINE_TEST(test_file_cstream)
{
    //____________________________________________________________________________
    //string => stream: create testfile
    
	String<char> str_1("This test file was made by " __FILE__ ".\n");

    char buffer[1024];
    strcpy(buffer, SEQAN_TEMP_FILENAME());

	FILE * file_1 = fopen(buffer, "w");
	file_1 << str_1;
	fclose(file_1);
    
    /*
     //assign FILE => string
     //____________________________________________________________________________
     
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     String<char> str_2;
     assign(str_2, file_1);
     fclose(file_1);
     SEQAN_ASSERT(str_2 == str_1);
     
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     assign(str_2, file_1, 9);
     fclose(file_1);
     SEQAN_ASSERT(str_2 == "This test");
     
     char str_3[200]="";
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     assign(str_3, file_1);
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_3, str_1));
     
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     assign(str_3, file_1, 9);
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_3, "This test"));
     
     //____________________________________________________________________________
     //append FILE => string
     
     String<char> str_5("Start");
     append(str_5, str_1);
     
     assign(str_2, "Start");
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     append(str_2, file_1);
     fclose(file_1);
     SEQAN_ASSERT(str_2 == str_5);
     
     assign(str_2, "Start");
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     append(str_2, file_1, 14);
     fclose(file_1);
     SEQAN_ASSERT(str_2 == "StartThis test");
     
     assign(str_3, "Start");
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     append(str_3, file_1);
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_3, str_5));
     
     assign(str_3, "Start");
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     append(str_3, file_1, 14);
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_3, "StartThis test"));
     
     //____________________________________________________________________________
     //replace FILE => string
     
     String<char> str_9("start ");
     append(str_9, str_1);
     append(str_9, " end");
     
     assign(str_2, "start middle end");
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     replace(str_2, 6, 12, file_1);
     fclose(file_1);
     SEQAN_ASSERT(str_2 == str_9);
     
     assign(str_2, "start middle end");
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     replace(str_2, 6, 12, file_1, 15);
     fclose(file_1);
     SEQAN_ASSERT(str_2 == "start This test");
     
     assign(str_3, "start middle end");
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     replace(str_3, 6, 12, file_1);
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_3, str_9));
     
     assign(str_3, "start middle end");
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     replace(str_3, 6, 12, file_1, 15);
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_3, "start This test"));
     
     //____________________________________________________________________________
     // assign string => FILE
     
     str_1 = "first seqan string test";
     FILE * file_2 = fopen(TEST_PATH "testfile.txt", "w");
     write(file_2, str_1, 18);
     fclose(file_2);
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     file_1 >> str_2;
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_2, infix(str_1, 0, 18)));
     
     assign(str_3, "first char array test");
     FILE * file_2 = fopen("testfile2.txt", "w");
     write(file_2, str_3);
     fclose(file_2);
     file_1 = fopen("testfile2.txt", "r");
     file_1 >> str_2;
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_2, str_3));
     
     assign(str_3, "second char array test");
     file_2 = fopen(TEST_PATH "testfile.txt", "w");
     write(file_2, str_3, 17);
     fclose(file_2);
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     file_1 >> str_2;
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_2, infix(str_3, 0, 17)));
     
     char const * str_20 = "first const char array test";
     file_2 = fopen(TEST_PATH "testfile.txt", "w");
     write(file_2, str_20);
     fclose(file_2);
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     file_1 >> str_2;
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_2, str_20));
     
     char const * str_21 = "second const char array test";
     file_2 = fopen(TEST_PATH "testfile.txt", "w");
     write(file_2, str_21, 23);
     fclose(file_2);
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     file_1 >> str_2;
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_2, infix(str_21, 0, 23)));
     
     String<char> str_22("begin middle end");
     Segment<String<char> > infix_1(str_22, 6, 12);
     file_2 = fopen(TEST_PATH "testfile.txt", "w");
     write(file_2, infix_1);
     fclose(file_2);
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     file_1 >> str_2;
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_2, infix_1));
     
     assign(infix_1, "prefix suffix");
     file_2 = fopen(TEST_PATH "testfile.txt", "w");
     write(file_2, infix_1, 6);
     fclose(file_2);
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     file_1 >> str_2;
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_2, infix(infix_1, 0, 6)));
     
     file_2 = fopen(TEST_PATH "testfile.txt", "w");
     write(file_2, 'a');
     fclose(file_2);
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     file_1 >> str_2;
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_2, 'a'));
     
     file_2 = fopen(TEST_PATH "testfile.txt", "w");
     write(file_2, 'a', 6);
     fclose(file_2);
     file_1 = fopen(TEST_PATH "testfile.txt", "r");
     file_1 >> str_2;
     fclose(file_1);
     SEQAN_ASSERT(isEqual(str_2, 'a'));
     */
    
    //____________________________________________________________________________
    
}
//////////////////////////////////////////////////////////////////////////////

SEQAN_DEFINE_TEST(test_file_raw)
{
    //____________________________________________________________________________

    char buffer[1024];
    strcpy(buffer, SEQAN_TEMP_FILENAME());

	//write
	FILE * file_3 = fopen(buffer, "w");
	String<char> str_3("this is a test string"); 
	write(file_3, str_3);
	fclose(file_3);
    
	FILE * file_4 = fopen(buffer, "r");
	SEQAN_ASSERT(file_4);
    
	//readID
	String<char> str_4("init");
	readID(file_4, str_4, Raw());
	SEQAN_ASSERT_EQ(str_4, "");
    
	//read
	read(file_4, str_4);
	SEQAN_ASSERT_EQ(str_4, str_3);
	fclose(file_4);
    
	//read limit
	FILE * file_4b = fopen(buffer, "r");
	SEQAN_ASSERT(file_4b);
    
	read(file_4b, str_4, 4);
	SEQAN_ASSERT_EQ(str_4, "this");
	fclose(file_4b);
    
    //____________________________________________________________________________
    // raw and stingstream
    
	str_3 = "hello you fellow";
	stringstream ss_1;
	write(ss_1, str_3);
    
	read(ss_1, str_4, Raw());
	SEQAN_ASSERT_EQ(str_4, str_3);
    
    
	str_3 = "gogogo dududu";
	stringstream ss_2;
	write(ss_2, str_3);
	read(ss_2, str_4, 5);
	SEQAN_ASSERT_EQ(str_4, "gogog");
    
    
    //	::std::cout << sstream_1;
    
    /*
     //string => stream
     String<char> str_1("The first test file string.");
     
     fstream strm_1;
     strm_1.open(TEST_PATH "testfile.txt", ios_base::out | ios_base::trunc | ios_base::binary);
     strm_1 << str_1;
     strm_1.close();
     
     //assign stream => string
     String<char> str_3 = "";
     fstream strm_3;
     strm_3.open(TEST_PATH "testfile.txt", ios_base::in | ios_base::binary);
     strm_3 >> str_3;
     strm_3.close();
     SEQAN_ASSERT(str_3 == str_1);
     */
    
    //____________________________________________________________________________
}


void Test_Fasta_Read(const char * path)
{
    //____________________________________________________________________________
    // FASTA from C stream
    
	FILE * file_1 = fopen(path, "rb");
	SEQAN_ASSERT(file_1);
    
	String<Dna> str_1;
	read(file_1, str_1, Fasta());
	SEQAN_ASSERT_EQ(str_1, "ACGT");
    
	String<char> str_2;
    
	read(file_1, str_2, Fasta());
	SEQAN_ASSERT(empty(str_2));
    
	read(file_1, str_2, Fasta());
	SEQAN_ASSERT_EQ(length(str_2), 1065u);
    
	read(file_1, str_2, Fasta());
	SEQAN_ASSERT_EQ(length(str_2), 200u);
    
	fclose(file_1);
    
    //____________________________________________________________________________
    // FASTA from iostream
    
	fstream strm_1;
	strm_1.open(path, ios_base::in | ios_base::binary);
	read(strm_1, str_2, Fasta());
	strm_1.close();
	SEQAN_ASSERT_EQ(str_2, "ACGT");
}

SEQAN_DEFINE_TEST(test_file_fasta_crlf)
{
    char buffer[1023];
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_crlf.txt");
    Test_Fasta_Read(buffer);
}

SEQAN_DEFINE_TEST(test_file_fasta_cr)
{
    char buffer[1023];
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_cr.txt");
    Test_Fasta_Read(buffer);
}

SEQAN_DEFINE_TEST(test_file_fasta_lf)
{
    char buffer[1023];
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_lf.txt");
    Test_Fasta_Read(buffer);
}

SEQAN_DEFINE_TEST(test_file_fasta_write)
{
    //____________________________________________________________________________
    // FASTA to C stream
    
    char tmpFilename[1024];
    strcpy(tmpFilename, SEQAN_TEMP_FILENAME());
    
	FILE * file_3 = fopen(tmpFilename, "wb");
	String<Dna> str_3("acgtufacgtufacgtufacgtufacgtufacgtufacgtufacgtufaaaaaaaaaauuuuuuuuucccccccccccggggg"); 
	write(file_3, str_3, "Identifier1", Fasta());
	write(file_3, "", "Empty Entry", Fasta());
	write(file_3, str_3, "Identifier2", Fasta());
	fclose(file_3);
    
	//test it
	FILE * file_4 = fopen(tmpFilename, "rb");
	SEQAN_ASSERT(file_4);
    
	String<char> str_4;
	readID(file_4, str_4, Fasta());
	SEQAN_ASSERT_EQ(str_4, "Identifier1");
    
	String<Dna> str_4a;
	read(file_4, str_4a, Fasta());
	SEQAN_ASSERT_EQ(str_4a, str_3);
    
	String<Dna> str_empty;
	read(file_4, str_empty, Fasta());
	SEQAN_ASSERT(empty(str_empty));
    
	read(file_4, str_4a, Fasta());
	SEQAN_ASSERT_EQ(str_4a, str_3);
	fclose(file_4);
    
    //____________________________________________________________________________
    // Test virtual file format object //outdated!!
    /*
     FileFormat<FILE *, String<Dna>, Fasta> fasta_format;
     FileFormat<FILE *, String<Dna> > & ff = fasta_format;
     
     //write
     FILE * file_5 = fopen(TEST_PATH "my_fasta.txt", "w");
     String<Dna> str_5("acgt"); 
     write(file_5, str_5, "Identifier3", ff);
     write(file_5, str_5, "Identifier4", ff);
     write(file_5, str_5, "Identifier5", ff);
     write(file_5, str_5, "Identifier6", ff);
     fclose(file_5);
     
     //readID
     FILE * file_6 = fopen(TEST_PATH "my_fasta.txt", "r");
     SEQAN_ASSERT(file_6);
     
     String<char> str_6;
     readID(file_6, str_6, ff);
     SEQAN_ASSERT(str_6 == "Identifier3");
     
     char str_6b[100];
     readID(file_6, str_6b, ff);
     SEQAN_ASSERT(isEqual(str_6b, "Identifier3"));
     
     //read
     String<Dna> str_7;
     read(file_6, str_7, ff);
     SEQAN_ASSERT(str_7 == str_5);
     
     read(file_6, str_7, 2, ff);
     SEQAN_ASSERT(str_7 == "ac");
     
     readID(file_6, str_6, ff);
     SEQAN_ASSERT(str_6 == "Identifier5");
     
     //goNext
     goNext(file_6, ff);
     
     readID(file_6, str_6, ff);
     SEQAN_ASSERT(str_6 == "Identifier6");
     fclose(file_6)
     
     //comparison
     SEQAN_ASSERT(ff == fasta_format);
     SEQAN_ASSERT(ff == Fasta());
     SEQAN_ASSERT(Fasta() == ff);
     
     SEQAN_ASSERT(!(ff != fasta_format));
     SEQAN_ASSERT(ff != Raw());
     SEQAN_ASSERT(Raw() != ff);
     */
}

//////////////////////////////////////////////////////////////////////////////

SEQAN_DEFINE_TEST(test_file_fasta_align)
{
    //____________________________________________________________________________
    // FASTA Align from C stream
    
    char buffer[1023];
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_align.txt");
    
	FILE * file_1 = fopen(buffer, "r");
	SEQAN_ASSERT(file_1);
	
	Align<String<char>, ArrayGaps> align;
	read(file_1, align, FastaAlign());
	SEQAN_ASSERT_EQ(source(row(align,0)), "MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII");
	SEQAN_ASSERT_EQ(length(source(row(align,1))), 362u);
	SEQAN_ASSERT_EQ(length(source(row(align,2))), 335u);
	String<String<char> > str_ids1;
	readIDs(file_1, str_ids1, FastaAlign());
	SEQAN_ASSERT_EQ(value(str_ids1,0), "CYS1_DICDI");
	SEQAN_ASSERT_EQ(value(str_ids1,1), "ALEU_HORVU");
	SEQAN_ASSERT_EQ(value(str_ids1,2), "CATH_HUMAN");
    
	fclose(file_1);
    
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_align_dna.txt");
    
	FILE * file_11 = fopen(buffer, "r");
	SEQAN_ASSERT(file_11);
	
	Align<String<Dna>, ArrayGaps> align11;
	read(file_11, align11, FastaAlign());
	SEQAN_ASSERT_EQ(source(row(align11,0)), "CTACGAAAGGTCGTGTCACGATGTCCGCAAGGGATGGCATTGCATAGAGGAATTGATTGCAACCTACGAAA");
	SEQAN_ASSERT_EQ(source(row(align11,1)), "CTTAATGTCCCGCGTACAAGGGATAGCATGTGGCATAGAGGAATAGAATAGCAGCCTACGAAA");
	String<String<char> > str_ids11;
	readIDs(file_11, str_ids11, FastaAlign());
	SEQAN_ASSERT_EQ(value(str_ids11,0), "SEQ1");
	SEQAN_ASSERT_EQ(value(str_ids11,1), "SEQ2");
	fclose(file_11);
    
    strcpy(buffer, SEQAN_TEMP_FILENAME());

	FILE * file_44 = fopen(buffer, "w");
	write(file_44, align11, str_ids11, FastaAlign());
	fclose(file_44);
    
    //____________________________________________________________________________
    // FASTA  Align from iostream
    
	Align<String<char>, ArrayGaps> align2;
	fstream strm_1;
    
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_align.txt");
	strm_1.open(buffer, ios_base::in | ios_base::binary);
	read(strm_1, align2, FastaAlign());
	strm_1.close();
	SEQAN_ASSERT_EQ(source(row(align2,0)), "MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII");
	SEQAN_ASSERT_EQ(length(source(row(align2,1))), 362u);
	SEQAN_ASSERT_EQ(length(source(row(align2,2))), 335u);
    
	Align<String<Dna>, ArrayGaps> align22;
	fstream strm_12;

    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_align_dna.txt");
	strm_12.open(buffer, ios_base::in | ios_base::binary);
	read(strm_12, align22, FastaAlign());
	strm_12.close();
	SEQAN_ASSERT_EQ(source(row(align22,0)), "CTACGAAAGGTCGTGTCACGATGTCCGCAAGGGATGGCATTGCATAGAGGAATTGATTGCAACCTACGAAA");
	SEQAN_ASSERT_EQ(source(row(align22,1)), "CTTAATGTCCCGCGTACAAGGGATAGCATGTGGCATAGAGGAATAGAATAGCAGCCTACGAAA");
    
    //____________________________________________________________________________
    // FASTA Align to C stream
    
	Align<String<char>, ArrayGaps> align3;
	resize(rows(align3), 2);
	assignSource(row(align3, 0), "abcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyz");
	insertGaps(row(align3, 0), 2, 3);
	assignSource(row(align3, 1), "xyz");
    
	String<char> id1("Seq1"); 
	String<char> id2("Seq2"); 
	String<String<char> > str_ids;
	appendValue(str_ids, id1);
	appendValue(str_ids, id2);
    
    strcpy(buffer, SEQAN_TEMP_FILENAME());
    
	FILE * file_2 = fopen(buffer, "w");
	write(file_2, align3, str_ids, FastaAlign());
	fclose(file_2);
    
	//test it
	FILE * file_3 = fopen(buffer, "r");
	SEQAN_ASSERT(file_3);
    
	String<String<char> > str_ids2;
	readIDs(file_3, str_ids2, FastaAlign());
	SEQAN_ASSERT_EQ(value(str_ids2,0), "Seq1");
	SEQAN_ASSERT_EQ(value(str_ids2,1), "Seq2");
	Align<String<char>, ArrayGaps> align4;
	read(file_3, align4, FastaAlign());
	SEQAN_ASSERT_EQ(source(row(align4,1)), "xyz");
    
	fclose(file_3);
    
    //____________________________________________________________________________
    // Dna5 File format output
    
	Align<String<Dna>, ArrayGaps> align5;
	resize(rows(align5), 2);
	assignSource(row(align5, 0), "aaccggtt");
	assignSource(row(align5, 1), "accgtttt");
	globalAlignment(align5, SimpleScore(), NeedlemanWunsch());
    
    
    //____________________________________________________________________________
    // Test virtual file format object //outdated!!
	/*
     FileFormat<FILE *, String<char>, FastaAlign> fasta_format;
     FileFormat<FILE *, String<char> > & ff = fasta_format;
     
     //write
     FILE * file_4 = fopen(TEST_PATH "my_fasta_align.txt", "w");
     
     Align<String<char>, ArrayGaps> align5;
     resize(rows(align5), 2);
     assignSource(row(align5, 0), "abc");
     insertGaps(row(align5, 0), 2, 3);
     assignSource(row(align5, 1), "xyz");
     
     String<char> id4_1("Seq1"); 
     String<char> id4_2("Seq2"); 
     String<String<char> > str_ids4;
     appendValue(str_ids4, id4_1);
     appendValue(str_ids4, id4_2);
     
     write(file_4, align5, str_ids4, ff);
     fclose(file_4);
     */
	// ??? ToDo ???
}


//////////////////////////////////////////////////////////////////////////////

SEQAN_DEFINE_TEST(test_file_cgviz)
{
    //____________________________________________________________________________
    // Read FASTA Align from C stream
    
    char buffer[1023];
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_align.txt");
    
	FILE * file_1 = fopen(buffer, "r");
	SEQAN_ASSERT(file_1);
	
	Align<String<char>, ArrayGaps> align;
	read(file_1, align, FastaAlign());
	SEQAN_ASSERT_EQ(source(row(align,0)), "MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII");
	SEQAN_ASSERT_EQ(length(source(row(align,1))), 362u);
	SEQAN_ASSERT_EQ(length(source(row(align,2))), 335u);
	String<String<char> > str_ids1;
	readIDs(file_1, str_ids1, FastaAlign());
	SEQAN_ASSERT_EQ(value(str_ids1,0), "CYS1_DICDI");
	SEQAN_ASSERT_EQ(value(str_ids1,1), "ALEU_HORVU");
	SEQAN_ASSERT_EQ(value(str_ids1,2), "CATH_HUMAN");
	fclose(file_1);
    
    
    //____________________________________________________________________________
    // Output in CGViz format
    
    strcpy(buffer, SEQAN_TEMP_FILENAME());
    
	FILE * file_2 = fopen(buffer, "w");
	write(file_2, align, str_ids1, CGViz());
	fclose(file_2);
    
    // To read this file in CGViz:
    // java -jar CGViz-1.0beta1.jar -i <data_file>
    //
    // Reference:
    // CGViz - a highly configurable viewer for biomolecular data
    // www-ab.informatik.uni-tuebingen.de/software/cgviz/welcome.html
}

//////////////////////////////////////////////////////////////////////////////

SEQAN_DEFINE_TEST(test_file_embl)
{
    char fl_path[1024];
    strcpy(fl_path, SEQAN_PATH_TO_ROOT());
    strcat(fl_path, "/core/tests/file/embl_crlf.txt");
    
    char fl_out_path[1024];
    strcpy(fl_out_path, SEQAN_TEMP_FILENAME());
    
	FILE * fl = fopen(fl_path, "rb");
	SEQAN_ASSERT(fl);
    
	FILE *fl_out = fopen(fl_out_path, "wb");
	SEQAN_ASSERT(fl_out);
    
	String<char> data;
	String<char> meta;
    
	readMeta(fl, meta, Embl());
	read(fl, data, Embl());
    
	SEQAN_ASSERT_EQ(length(meta), 1652u);
	SEQAN_ASSERT_EQ(length(data), 281u);
    
	write(fl_out, data, meta, Embl());
    
	readMeta(fl, meta, Embl());
	read(fl, data, Embl());
    
	SEQAN_ASSERT_EQ(data, "ACGT");
    
	write(fl_out, data, meta, Embl());
    
	fclose(fl_out);
	fclose(fl);
    
	SEQAN_ASSERT(_compareTextFiles(fl_path, fl_out_path));
    
    //____________________________________________________________________________
    // test reading data without reading meta before
    
	fl = fopen(fl_path, "rb");
	SEQAN_ASSERT(fl);
    
	read(fl, data, Embl());
    
	SEQAN_ASSERT_EQ(length(data), 281u);
	fclose(fl);
    
}

//////////////////////////////////////////////////////////////////////////////

SEQAN_DEFINE_TEST(test_file_genbank)
{
    char fl_path[1024];
    strcpy(fl_path, SEQAN_PATH_TO_ROOT());
    strcat(fl_path, "/core/tests/file/genbank_crlf.txt");
    
    char fl_out_path[1024];
    strcpy(fl_out_path, SEQAN_TEMP_FILENAME());

	FILE * fl = fopen(fl_path, "rb");
	SEQAN_ASSERT(fl);
    
	FILE *fl_out = fopen(fl_out_path, "wb");
	SEQAN_ASSERT(fl_out);
    
	String<char> data;
	String<char> meta;
    
	readMeta(fl, meta, Genbank());
	read(fl, data, Genbank());
    
	write(fl_out, data, meta, Genbank());
    
	SEQAN_ASSERT_EQ(length(meta), 4167u);
	SEQAN_ASSERT_EQ(length(data), 5028u);
    
	readMeta(fl, meta, Embl());
	read(fl, data, Genbank());
	write(fl_out, data, meta, Genbank());
    
	SEQAN_ASSERT_EQ(data, "ACGT");
    
	readMeta(fl, meta, Embl());
	read(fl, data, Genbank());
	write(fl_out, data, meta, Genbank());
    
	SEQAN_ASSERT_EQ(data, "CATAGAT");
    
	fclose(fl_out);
	fclose(fl);
    
	SEQAN_ASSERT(_compareTextFiles(fl_path, fl_out_path));
}

//////////////////////////////////////////////////////////////////////////////

//____________________________________________________________________________
//test FileReader iterator
/*
SEQAN_DEFINE_TEST(test_file_reader_iterator)
{
    char buffer[1023];
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_crlf.txt");

	FILE * file_fasta = fopen(buffer, "rb");
	SEQAN_ASSERT(file_fasta);
    
	Iter<FILE *, FileReader<Fasta> > it_fasta(file_fasta);
    
	//read the first record "ACGT" from file
	SEQAN_ASSERT(!atEnd(it_fasta));
	SEQAN_ASSERT(value(it_fasta) == 'A');
	goNext(it_fasta);
	SEQAN_ASSERT(!atEnd(it_fasta));
	SEQAN_ASSERT(value(it_fasta) == 'C');
	goNext(it_fasta);
	SEQAN_ASSERT(!atEnd(it_fasta));
	SEQAN_ASSERT(value(it_fasta) == 'G');
	goNext(it_fasta);
	SEQAN_ASSERT(!atEnd(it_fasta));
	SEQAN_ASSERT(value(it_fasta) == 'T');
	goNext(it_fasta);
	SEQAN_ASSERT(atEnd(it_fasta));
    
	//scan second record = 1065 characters
	goBegin(it_fasta);
	SEQAN_ASSERT(!atEnd(it_fasta));
    
	unsigned int i = 0;
	while (!atEnd(it_fasta))
	{
		++i;
		goNext(it_fasta);
	}
	SEQAN_ASSERT(i == 1065);
    
    
	fclose(file_fasta);
}
 */

//____________________________________________________________________________
//test FileReader string

SEQAN_DEFINE_TEST(test_file_reader_string)
{
    char buffer[1023];
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_crlf.txt");
    
	FILE * file_fasta = fopen(buffer, "rb");
	SEQAN_ASSERT(file_fasta);
	goNext(file_fasta, Fasta());
	goNext(file_fasta, Fasta());
    
	String<AminoAcid, FileReader<Fasta> > str(file_fasta);
	SEQAN_ASSERT_EQ(length(str), 1065u);
	SEQAN_ASSERT_EQ(value(str, 1064), 'G');
    
	Iterator<String<AminoAcid, FileReader<Fasta> > >::Type it = begin(str);
	SEQAN_ASSERT_EQ(*it, value(str, 0));
    
	goEnd(it);
	SEQAN_ASSERT(atEnd(it));
    
	unsigned int pos = length(str);
	do
	{
		--it;
		--pos;
		SEQAN_ASSERT_EQ(position(it), pos);
		SEQAN_ASSERT_EQ(*it, value(str, pos));
	} while (!atBegin(it));
    
	SEQAN_ASSERT(pos == 0);
    
	while (it < end(str))
	{
		SEQAN_ASSERT_EQ(position(it), pos);
		SEQAN_ASSERT_EQ(*it, value(str, pos));
		++pos;
		++it;
	}
	SEQAN_ASSERT_EQ(pos, length(str));
	SEQAN_ASSERT(atEnd(it));
    
	fclose(file_fasta);
}

//____________________________________________________________________________

void Create_Long_Testfile(char * filename, Fasta const &)
{
//IOREV uses custom io, switch to File() for tests in future
    strcpy(filename, SEQAN_TEMP_FILENAME());
    
	FILE * fl = fopen(filename, "wb");
	fprintf(fl, ">testfile\n"); 
	for (unsigned int i = 0; i < 20; ++i)
	{
		::std::cout << ".";
		for (unsigned int j = 0; j < 500; ++j)
		{
			fprintf(fl, "A.........B.........C.........D.........E.........F.........G.........H.........I.........J.........\n");
		}
		fprintf(fl, "A.........B.........CHERE_IS_THE_PATTERNE.........F.........G.........H.........I.........J.........\n");
		for (unsigned int j = 501; j < 1000; ++j)
		{
			fprintf(fl, "A.........B.........C.........D.........E.........F.........G.........H.........I.........J.........\n");
		}
	}
	fclose(fl);
}

void Create_Long_Testfile(char * filename, Embl const &)
{
//IOREV uses custom io, switch to File() for tests in future
    strcpy(filename, SEQAN_TEMP_FILENAME());
    
	FILE * fl = fopen(filename, "wb");
	fprintf(fl, "ID\nSQ\n"); 
	for (unsigned int i = 0; i < 20; ++i)
	{
		::std::cout << ".";
		for (unsigned int j = 0; j < 500; ++j)
		{
			fprintf(fl, "  A.........B.........C.........D.........E.........F.........G.........H.........I.........J.........\n");
		}
		fprintf(fl, "  A.........B.........CHERE_IS_THE_PATTERNE.........F.........G.........H.........I.........J.........\n");
		for (unsigned int j = 501; j < 1000; ++j)
		{
			fprintf(fl, "  A.........B.........C.........D.........E.........F.........G.........H.........I.........J.........\n");
		}
	}
	fclose(fl);
}

void Create_Long_Testfile(char * filename, Genbank const &)
{
//IOREV uses custom io, switch to File() for tests in future
    strcpy(filename, SEQAN_TEMP_FILENAME());
    
	FILE * fl = fopen(filename, "wb");
	fprintf(fl, "LOCUS\nORIGIN\n"); 
	for (unsigned int i = 0; i < 20; ++i)
	{
		::std::cout << ".";
		for (unsigned int j = 0; j < 500; ++j)
		{
			fprintf(fl, "  A.........B.........C.........D.........E.........F.........G.........H.........I.........J.........\n");
		}
		fprintf(fl, "  A.........B.........CHERE_IS_THE_PATTERNE.........F.........G.........H.........I.........J.........\n");
		for (unsigned int j = 501; j < 1000; ++j)
		{
			fprintf(fl, "  A.........B.........C.........D.........E.........F.........G.........H.........I.........J.........\n");
		}
	}
	fclose(fl);
}
//____________________________________________________________________________

//test filereader string on long files
template <typename TFormat>
void Test_FileReader_String2(TFormat const &)
{
//IOREV uses custom io, switch to File() for tests in future
    char buffer[1024];
	Create_Long_Testfile(buffer, TFormat());
    
    //____________________________________________________________________________
    // scan the file using file reader string
    
	String<char, FileReader<TFormat> > fr(buffer);
	Finder<String<char, FileReader<TFormat> > > fnd(fr);
	String<char> ndl = "HERE_IS_THE_PATTERN";
	Pattern<String<char>, Horspool> pat(ndl);
    
	::std::cout << "find patterns";
    
	for (unsigned int i = 0; i < 20; ++i)
	{
		bool found = find(fnd, pat);
        
        ::std::cout << ".";
		SEQAN_ASSERT(found);
		SEQAN_ASSERT(!fr.data_scanned);
		SEQAN_ASSERT_EQ(position(fnd), (50021 + i * 100000));
	}
    
	SEQAN_ASSERT(find(fnd, pat));
	SEQAN_ASSERT(fr.data_scanned);
    
	::std::cout << "\n";
    
    //____________________________________________________________________________
    // scan the file the old way: read the complete file into memory
    
	String<char> hay;
	FILE * fl = fopen(buffer, "rb");
	read(fl, hay, TFormat());
	fclose(fl);
    
	Finder<String<char> > fnd2(hay);
	for (unsigned int i = 0; i < 20; ++i)
	{
		bool found = find(fnd2, pat);
        
        ::std::cout << ".";
		SEQAN_ASSERT(found);
		SEQAN_ASSERT_EQ(position(fnd2), (50021 + i * 100000));
	}
    
}

/*
SEQAN_DEFINE_TEST(test_file_reader_string2_fasta)
{
	Test_FileReader_String2(Fasta());
}

SEQAN_DEFINE_TEST(test_file_reader_string2_embl)
{
	Test_FileReader_String2(Embl());
}

SEQAN_DEFINE_TEST(test_file_reader_string2_genbank)
{
	Test_FileReader_String2(Genbank());
}
*/

//____________________________________________________________________________

SEQAN_DEFINE_TEST(test_file_reader_string3)
{
    char buffer[1023];
    strcpy(buffer, SEQAN_PATH_TO_ROOT());
    strcat(buffer, "/core/tests/file/fasta_crlf.txt");
    
	FILE * file_fasta = fopen(buffer, "rb");
	SEQAN_ASSERT(file_fasta);
    
	String<AminoAcid, FileReader<Fasta> > str(file_fasta);
	String<AminoAcid> str2(str);
    
	SEQAN_ASSERT_EQ(str, str2);
    
	append(str2, str);
	SEQAN_ASSERT_EQ(str2, "ACGTACGT");
    
	fclose(file_fasta);
}

#endif  // TESTS_FILE_TEST_FILE_H_