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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, 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: Jochen Singer <jochen.singer@fu-berlin.de>
// ==========================================================================
// This file contains functions to test the functionality of the sequence
// module.
// ==========================================================================
#ifndef TESTS_SEQUENCE_TEST_SEQUENCE_H_
#define TESTS_SEQUENCE_TEST_SEQUENCE_H_
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/stream.h>
#include <string>
using namespace seqan2;
// --------------------------------------------------------------------------
// CountingChar is used to test sequences of non simple data types.
// --------------------------------------------------------------------------
struct CountingChar
{
char value{}; // value of the object
static unsigned numConstruct; // number of constructor calls
static unsigned numDeconstruct; // number of destructor calls
CountingChar() : value()
{
numConstruct += 1;
}
CountingChar(char const & value) : value(value)
{
numConstruct += 1;
}
#if defined(__GNUC__) && !defined(__llvm__) && !defined(__INTEL_COMPILER) && (__GNUC__ >= 12)
# pragma GCC diagnostic push
# pragma GCC diagnostic ignored "-Wstringop-overflow="
#endif
CountingChar(CountingChar const & other): value(other.value)
{
numConstruct += 1;
}
#if defined(__GNUC__) && !defined(__llvm__) && !defined(__INTEL_COMPILER) && (__GNUC__ >= 12)
# pragma GCC diagnostic pop
#endif
CountingChar & operator=(CountingChar const &) = default;
~CountingChar()
{
numDeconstruct += 1;
}
static void clear()
{
numConstruct = 0;
numDeconstruct = 0;
}
operator char & ()
{
return value;
}
bool operator==(CountingChar const & other) const
{
return value == other.value;
}
bool operator!=(CountingChar const & other) const
{
return value != other.value;
}
bool operator>(CountingChar const & other) const
{
return value > other.value;
}
bool operator<(CountingChar const & other) const
{
return value < other.value;
}
};
template <typename TStream>
inline TStream & operator<<(TStream & stream, CountingChar const & countingChar)
{
stream << countingChar.value;
return stream;
}
template <typename TStream, typename TSpec>
inline TStream & operator<<(TStream & stream, seqan2::String<CountingChar, TSpec> const & string)
{
for (unsigned i = 0; i < length(string); ++i)
stream << string[i];
return stream;
}
unsigned CountingChar::numConstruct = 0;
unsigned CountingChar::numDeconstruct = 0;
template <typename TString>
void testConstructDeconstruct(TString const &, unsigned)
{}
template <typename TSpec>
void testConstructDeconstruct(String<CountingChar, TSpec> const &, unsigned minConstructions)
{
SEQAN_ASSERT_EQ(CountingChar::numConstruct, CountingChar::numDeconstruct);
SEQAN_ASSERT_GEQ(CountingChar::numConstruct, minConstructions);
}
void testConstructDeconstruct(String<CountingChar, External<> > const &, unsigned)
{}
void testConstructDeconstruct(String<CountingChar, MMap<> > const &, unsigned)
{}
template <size_t COUNT>
void testConstructDeconstruct(String<CountingChar, Array<COUNT> > const &, unsigned)
{}
template <size_t COUNT>
void testConstructDeconstruct(String<CountingChar, Block<COUNT> > const &, unsigned)
{}
template <typename TString>
void testConstructDeconstruct(TString const &str)
{
testConstructDeconstruct(str, 1u);
}
template <typename TAlphabetSpecPair_>
class StringTest : public seqan2::Test
{
public:
typedef TAlphabetSpecPair_ TString;
};
// --------------------------------------------------------------------------
// Types which are tested for very common functionality
// --------------------------------------------------------------------------
template <typename T>
class StringTestCommon : public StringTest<T>
{};
typedef
seqan2::TagList<String<Dna5, External<> >,
seqan2::TagList<String<char, External<> >,
seqan2::TagList<String< int, External<> >,
seqan2::TagList<String<CountingChar, External<> >,
seqan2::TagList<String<Dna5, MMap<> >,
seqan2::TagList<String<char, MMap<> >,
seqan2::TagList<String<int, MMap<> >,
seqan2::TagList<String<CountingChar, MMap<> >,
seqan2::TagList<String<Dna, Packed<> >,
seqan2::TagList<String<Dna5, Packed<> >,
seqan2::TagList<String<char, Packed<> >,
seqan2::TagList<String<char, Packed<> >,
seqan2::TagList<String<int, Packed<> >,
seqan2::TagList<String<Dna5, Array<100> >,
seqan2::TagList<String<char, Array<100> >,
seqan2::TagList<String<int, Array<100> >,
seqan2::TagList<String<CountingChar,Array<100> >,
seqan2::TagList<String<seqan2::Dna5, Block<> >,
seqan2::TagList<String<char, Block<> >,
seqan2::TagList<String<int, Block<> >,
seqan2::TagList<String<CountingChar,Block<> >,
seqan2::TagList<String<seqan2::Dna5, Alloc<> >,
seqan2::TagList<String<char, Alloc<> >,
seqan2::TagList<String<int, Alloc<> >,
seqan2::TagList<String<CountingChar, Alloc<> >,
seqan2::TagList<std::basic_string<char>,
seqan2::TagList<std::vector<seqan2::Dna5>,
seqan2::TagList<std::vector<char>,
seqan2::TagList<std::vector<int>,
seqan2::TagList<std::vector<CountingChar>,
seqan2::TagList<std::deque<seqan2::Dna5>,
seqan2::TagList<std::deque<char>,
seqan2::TagList<std::deque<int>,
seqan2::TagList<std::deque<CountingChar>,
seqan2::TagList<std::forward_list<seqan2::Dna5>,
seqan2::TagList<std::forward_list<char>,
seqan2::TagList<std::forward_list<int>,
seqan2::TagList<std::forward_list<CountingChar>,
seqan2::TagList<std::list<seqan2::Dna5>,
seqan2::TagList<std::list<char>,
seqan2::TagList<std::list<int>,
seqan2::TagList<std::list<CountingChar>
> > > > > > > > > > > > > > > > > > > > > > > > >
> > > > > > > > > > > > > >
> > >
StringTestCommonTypes;
SEQAN_TYPED_TEST_CASE(StringTestCommon, StringTestCommonTypes);
// ==========================================================================
// The tests start here
// ==========================================================================
// --------------------------------------------------------------------------
// default constructible
// --------------------------------------------------------------------------
// Test whether sequences are default constructible.
template <typename TString>
void testSequenceDefaultConstructible(TString & /*Tag*/)
{
CountingChar::clear();
TString string;
SEQAN_ASSERT(seqan2::begin(string) == seqan2::end(string));
}
SEQAN_TYPED_TEST(StringTestCommon, DefaultConstructible)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceDefaultConstructible(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceDefaultConstructible(constStr);
testConstructDeconstruct(str, 0);
}
// --------------------------------------------------------------------------
// copy constructible
// --------------------------------------------------------------------------
// Test whether sequences are copy constructible.
template <typename TString>
void testSequenceCopyConstructible(TString & /*Tag*/)
{
TString string1;
assign(string1, "ACGCTAGCAT");
TString string2(string1);
SEQAN_ASSERT(string1 == string2);
}
template <typename TValue>
void testSequenceCopyConstructible(String<TValue, Block<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceCopyConstructible(String<TValue, External<> > & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, CopyConstructible)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceCopyConstructible(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceCopyConstructible(constStr);
testConstructDeconstruct(str);
}
// --------------------------------------------------------------------------
// comparable
// --------------------------------------------------------------------------
// Test operator<().
template <typename TString>
void testSequenceLess(TString & /*Tag*/)
{
// Nothing is smaller than something.
{
TString string1;
TString string2;
assign(string2, "A");
SEQAN_ASSERT(string1 < string2);
}
// Equal is not smaller
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "A");
SEQAN_ASSERT_NOT(string1 < string2);
}
// Sequences with lex. smaller characters and equal length are smaller.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "C");
SEQAN_ASSERT(string1 < string2);
}
// Sequences with lex. smaller characters but larger length are smaller.
{
TString string1;
assign(string1, "AA");
TString string2;
assign(string2, "C");
SEQAN_ASSERT(string1 < string2);
}
// Sequences with equal characters but smaller length are smaller.
{
TString string1;
assign(string1, "AA");
TString string2;
assign(string2, "AAA");
SEQAN_ASSERT(string1 < string2);
}
}
SEQAN_TYPED_TEST(StringTestCommon, LessOperator)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceLess(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceLess(constStr);
testConstructDeconstruct(str);
}
// Test operator<=().
template <typename TString>
void testSequenceLessEqual(TString & /*Tag*/)
{
// Nothing is equal to nothing.
{
TString string1;
TString string2;
SEQAN_ASSERT(string1 <= string2);
}
// Nothing is smaller than something.
{
TString string1;
TString string2;
assign(string2, "A");
SEQAN_ASSERT(string1 <= string2);
}
// Sequences of equal characters and length are equal.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "A");
SEQAN_ASSERT(string1 <= string2);
}
// Sequences with lex. smaller characters and equal length are smaller.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "C");
SEQAN_ASSERT(string1 <= string2);
}
// Sequences with lex. smaller characters but larger length are smaller.
{
TString string1;
assign(string1, "AA");
TString string2;
assign(string2, "C");
SEQAN_ASSERT(string1 <= string2);
}
// Sequences with equal characters but smaller length are smaller.
{
TString string1;
assign(string1, "AA");
TString string2;
assign(string2, "AAA");
SEQAN_ASSERT(string1 <= string2);
}
// Sequences with equal characters but smaller length are smaller.
{
TString string1;
assign(string1, "AAA");
TString string2;
assign(string2, "AA");
SEQAN_ASSERT_NOT(string1 <= string2);
}
}
SEQAN_TYPED_TEST(StringTestCommon, LessEqualOperator)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceLessEqual(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceLessEqual(constStr);
testConstructDeconstruct(str);
}
// Test operator>().
template <typename TString>
void testSequenceGreater(TString & /*Tag*/)
{
// Something is greater than nothing.
{
TString string1;
assign(string1, "A");
TString string2;
SEQAN_ASSERT(string1 > string2);
}
// Equal is not greater
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "A");
SEQAN_ASSERT_NOT(string1 > string2);
}
// Sequences with lex. greater characters and equal length are greater.
{
TString string1;
assign(string1, "C");
TString string2;
assign(string2, "A");
SEQAN_ASSERT(string1 > string2);
}
// Sequences with equal characters but larger length are larger.
{
TString string1;
assign(string1, "AA");
TString string2;
assign(string2, "A");
SEQAN_ASSERT(string1 > string2);
}
// Sequences with lex. greater characters are greater.
{
TString string1;
assign(string1, "C");
TString string2;
assign(string2, "AA");
SEQAN_ASSERT(string1 > string2);
}
}
SEQAN_TYPED_TEST(StringTestCommon, GreaterOperator)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceGreater(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceGreater(constStr);
testConstructDeconstruct(str);
}
// Test operator>=().
template <typename TString>
void testSequenceGreaterEqual(TString & /*Tag*/)
{
// Nothing is equal to nothing.
{
TString string1;
TString string2;
SEQAN_ASSERT(string1 >= string2);
}
// Something is greater than nothing.
{
TString string1;
assign(string1, "A");
TString string2;
SEQAN_ASSERT(string1 >= string2);
}
// Sequences of equal characters and length are equal.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "A");
SEQAN_ASSERT(string1 >= string2);
}
// Sequences with lex. greater characters and equal length are greater.
{
TString string1;
assign(string1, "C");
TString string2;
assign(string2, "A");
SEQAN_ASSERT(string1 >= string2);
}
// Sequences with equal characters but larger length are greater.
{
TString string1;
assign(string1, "AA");
TString string2;
assign(string2, "A");
SEQAN_ASSERT(string1 >= string2);
}
// Sequences with lex. greater characters are greater.
{
TString string1;
assign(string1, "C");
TString string2;
assign(string2, "AA");
SEQAN_ASSERT(string1 > string2);
}
}
SEQAN_TYPED_TEST(StringTestCommon, GreaterEqualOperator)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceGreaterEqual(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceGreaterEqual(constStr);
testConstructDeconstruct(str);
}
// Test operator==().
template <typename TString>
void testSequenceEqual(TString & /*Tag*/)
{
// // Nothing is equal to nothing.
{
TString string1;
TString string2;
SEQAN_ASSERT(string1 == string2);
}
// Something is greater than nothing.
{
TString string1;
assign(string1, "A");
TString string2;
SEQAN_ASSERT_NOT(string1 == string2);
}
{
TString string1;
TString string2;
assign(string2, "A");
SEQAN_ASSERT_NOT(string1 == string2);
}
// Sequences of equal characters and length are equal.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "A");
SEQAN_ASSERT(string1 == string2);
}
// Sequences of equal characters but different length are not equal.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "AA");
SEQAN_ASSERT_NOT(string1 == string2);
}
{
TString string1;
assign(string1, "AA");
TString string2;
assign(string2, "A");
SEQAN_ASSERT_NOT(string1 == string2);
}
// Sequences of different characters are not equal.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "C");
SEQAN_ASSERT_NOT(string1 == string2);
}
{
TString string1;
assign(string1, "C");
TString string2;
assign(string2, "A");
SEQAN_ASSERT_NOT(string1 == string2);
}
}
SEQAN_TYPED_TEST(StringTestCommon, EqualOperator)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceEqual(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceEqual(constStr);
testConstructDeconstruct(str);
}
// Test operator!=().
template <typename TString>
void testSequenceUnequal(TString & /*Tag*/)
{
// Nothing is equal to nothing.
{
TString string1;
TString string2;
SEQAN_ASSERT_NOT(string1 != string2);
}
// Something is greater than nothing.
{
TString string1;
assign(string1, "A");
TString string2;
SEQAN_ASSERT_NOT(string1 == string2);
}
{
TString string1;
TString string2;
assign(string2, "A");
SEQAN_ASSERT_NOT(string1 == string2);
}
// Sequences of equal characters and length are equal.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "A");
SEQAN_ASSERT_NOT(string1 != string2);
}
// Sequences of equal characters but different length are not equal.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "AA");
SEQAN_ASSERT_NOT(string1 == string2);
}
{
TString string1;
assign(string1, "AA");
TString string2;
assign(string2, "A");
SEQAN_ASSERT_NOT(string1 == string2);
}
// Sequences of different characters are not equal.
{
TString string1;
assign(string1, "A");
TString string2;
assign(string2, "C");
SEQAN_ASSERT_NOT(string1 == string2);
}
{
TString string1;
assign(string1, "C");
TString string2;
assign(string2, "A");
SEQAN_ASSERT_NOT(string1 == string2);
}
}
SEQAN_TYPED_TEST(StringTestCommon, UnequalOperator)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceUnequal(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceEqual(constStr);
testConstructDeconstruct(str);
}
// --------------------------------------------------------------------------
// Assignable
// --------------------------------------------------------------------------
// Test whether sequences are assignable.
template <typename TString>
void testSequenceAssign(TString & /*Tag*/)
{
{
// Test on an empty string.
TString string1;
assign(string1, "");
TString string2;
assign(string2, string1);
SEQAN_ASSERT(string1 == string2);
}
{
// Test the basic concept on a non empty string.
TString string1;
assign(string1, "ACGTACGTACGT");
TString string2;
assign(string2, string1);
SEQAN_ASSERT(string1 == string2);
}
}
// TODO(singer): error: no viable conversion from
template <typename TValue>
void testSequenceAssign(String<TValue, Block<> > & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, Assign)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceAssign(str);
testConstructDeconstruct(str);
}
// Test whether sequences are assignable.
template <typename TString>
void testSequenceOperatorAssign(TString & /*Tag*/)
{
{
// Test on an empty string.
TString string1;
assign(string1, "");
TString string2; // Separate definition and assignment on purpose.
assign(string2, string1);
SEQAN_ASSERT(string1 == string2);
}
{
// Test the basic concept on a non empty string.
TString string1;
assign(string1, "ACGTACGTACGT");
TString string2; // Separate definition and assignment on purpose.
assign(string2, string1);
SEQAN_ASSERT(string1 == string2);
assign(value(string2, 0), 'C');
SEQAN_ASSERT(string1 != string2);
}
}
SEQAN_TYPED_TEST(StringTestCommon, OperatorAssign)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceOperatorAssign(str);
testConstructDeconstruct(str);
}
// Test of swap().
template <typename TString>
void testSequenceSwap(TString & /*Tag*/)
{
using namespace seqan2;
{
TString string1;
assign(string1, "");
TString string2;
assign(string2, "");
TString string3 = string1;
TString string4 = string2;
swap(string1, string2);
SEQAN_ASSERT(string1 == string4);
SEQAN_ASSERT(string2 == string3);
}
{
TString string1;
assign(string1, "ACGT");
TString string2;
assign(string2, "");
TString string3 = string1;
TString string4 = string2;
swap(string1, string2);
SEQAN_ASSERT(string1 == string4);
SEQAN_ASSERT(string2 == string3);
}
{
TString string1;
assign(string1, "");
TString string2;
assign(string2, "ACGT");
TString string3 = string1;
TString string4 = string2;
swap(string1, string2);
SEQAN_ASSERT(string1 == string4);
SEQAN_ASSERT(string2 == string3);
}
{
TString string1;
assign(string1, "ACAC");
TString string2;
assign(string2, "GTGT");
TString string3 = string1;
TString string4 = string2;
swap(string1, string2);
SEQAN_ASSERT(string1 == string4);
SEQAN_ASSERT(string2 == string3);
}
}
template <typename TValue>
void testSequenceSwap(String<TValue, External<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceSwap(String<TValue, MMap<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceSwap(String<TValue, Block<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceSwap(String<TValue, Array<100> > & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, Swap)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceSwap(str);
testConstructDeconstruct(str);
}
// workaround for weird bug in clang
#if defined(__clang__)
template <typename TChar, typename TAlloc>
void testSequenceReverse(std::deque<TChar, TAlloc> & ) {}
#endif
// Test of reverse().
template <typename TString>
void testSequenceReverse(TString & /*Tag*/)
{
using namespace seqan2;
{
TString string1;
assign(string1, "");
TString string2;
assign(string2, "");
reverse(string1);
SEQAN_ASSERT(string1 == string2);
}
{
TString string1;
assign(string1, "ACGT");
TString string2;
assign(string2, "TGCA");
reverse(string1);
SEQAN_ASSERT(string1 == string2);
}
{
TString string1;
assign(string1, "ACAGT");
TString string2;
assign(string2, "TGACA");
reverse(string1);
SEQAN_ASSERT(string1 == string2);
}
}
template <typename TChar, typename TAlloc>
void testSequenceReverse(std::forward_list<TChar, TAlloc> & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, Reverse)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceReverse(str);
testConstructDeconstruct(str);
}
// Test of assignValue().
template <typename TString>
void testSequenceAssignValue(TString & /*Tag*/)
{
typedef typename Value<TString>::Type TValue;
TString string;
assign(string, "AA");
assignValue(string, 1, TValue('G'));
SEQAN_ASSERT_EQ(value(string, 1), TValue('G'));
}
SEQAN_TYPED_TEST(StringTestCommon, AssignValue)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceAssignValue(str);
testConstructDeconstruct(str);
}
// --------------------------------------------------------------------------
// Function append
// --------------------------------------------------------------------------
template <typename TString>
void testSequenceAppend(TString & /*Tag*/)
{
// Test the append function on empty strings
{
TString string1;
assign(string1, "");
TString string2;
assign(string2, "");
append(string1, string2);
SEQAN_ASSERT(empty(string1));
}
// Test the append function on one empty and one non empty string
{
TString string1;
assign(string1, "ACGTACGTACGT");
TString string0 = string1;
TString string2;
assign(string2, "");
append(string1, string2);
SEQAN_ASSERT(string1 == string0);
}
// Test the append function on one empty and one non empty string
{
TString string1;
assign(string1, "");
TString string2;
assign(string2, "TTGGATTAACC");
TString string0 = string2;
append(string1, string2);
SEQAN_ASSERT(string1 == string0);
}
// Test the append function on two non empty strings.
{
TString string1;
assign(string1, "ACGTACGTACGT");
TString string2;
assign(string2, "TTGGATTAACCC");
append(string1, string2);
TString string0;
assign(string0, "ACGTACGTACGTTTGGATTAACCC");
SEQAN_ASSERT(string1 == string0);
}
}
SEQAN_TYPED_TEST(StringTestCommon, Append)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceAppend(str);
testConstructDeconstruct(str);
}
// Test of appendValue().
template <typename TString>
void testSequenceAppendValue(TString & /*Tag*/)
{
typedef typename Value<TString>::Type TValue;
TString string;
assign(string, "");
// Test the appendValue function
TString string2;
assign(string2, "A");
TValue value = 'A';
appendValue(string, value);
SEQAN_ASSERT(string == string2);
// Test the appendValue function
TString string3;
assign(string3, "AA");
appendValue(string, 'A');
SEQAN_ASSERT(string == string3);
}
// TODO(singer): error: no matching function for call to '_setLength'
template <typename TValue>
void testSequenceAppendValue(String<TValue, External<> > & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, AppendValue)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceAppendValue(str);
testConstructDeconstruct(str);
}
// We need two back() tests, since back() returns a reference or a copy
// (depending on TString). We check whether we can modify the reference.
// Test of back() for non const strings.
template <typename TString>
void testSequenceBack(TString & /*Tag*/)
{
typedef typename Reference<TString>::Type TReference;
TString string;
assign(string, "ACGT");
// val is a reference in contrast to the const version of back().
TReference val = back(string);
val = 'A';
SEQAN_ASSERT_EQ(val, value(string, length(string) - 1));
}
// Test of back() for const strings.
template <typename TString>
void testSequenceBack(TString const & /*Tag*/)
{
typedef typename Reference<TString const>::Type TReference;
TString const string;
assign(string, "ACGT");
// val is not a reference in contrast to the non const version of back().
TReference val = back(string);
SEQAN_ASSERT_EQ(val, value(string, length(string) - 1));
}
SEQAN_TYPED_TEST(StringTestCommon, Back)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceBack(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceEqual(constStr);
testConstructDeconstruct(str);
}
// Test of seqan2::begin().
template <typename TString>
void testSequenceBegin(TString & /*Tag*/)
{
typedef typename Value<TString>::Type TValue;
TString string;
assign(string, "ACGT");
SEQAN_ASSERT_EQ(*seqan2::begin(string), TValue('A'));
SEQAN_ASSERT_EQ(*seqan2::begin(string, Standard()), TValue('A'));
// SEQAN_ASSERT_EQ(*seqan2::begin(string, Rooted()), TValue('A'));
}
// template <typename TValue>
// void testSequenceBegin(String<TValue, MMap<> > & /*Tag*/) {}
// template <typename TValue>
// void testSequenceBegin(String<TValue, MMap<> > const & /*Tag*/) {}
//
SEQAN_TYPED_TEST(StringTestCommon, Begin)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceBegin(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceEqual(constStr);
testConstructDeconstruct(str);
}
// Test of beginPosition().
template <typename TString>
void testSequenceBeginPosition(TString & /*Tag*/)
{
// Test on an empty string.
TString string1;
assign(string1, "");
SEQAN_ASSERT_EQ(beginPosition(string1), 0u);
// Test on a non empty string.
TString string2;
assign(string2, "ACGT");
SEQAN_ASSERT_EQ(beginPosition(string2), 0u);
}
SEQAN_TYPED_TEST(StringTestCommon, BeginPosition)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceBeginPosition(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceEqual(constStr);
testConstructDeconstruct(str);
}
// Test of capacity().
template <typename TString>
void testSequenceCapacity(TString & /*Tag*/)
{
// Test on an empty string.
TString string1;
assign(string1, "");
SEQAN_ASSERT_GEQ(capacity(string1), length(string1));
// Test on a non empty string.
TString string2;
assign(string2, "ACGTACGTACGT");
SEQAN_ASSERT_GEQ(capacity(string2), length(string2));
}
SEQAN_TYPED_TEST(StringTestCommon, Capacity)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceCapacity(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceEqual(constStr);
testConstructDeconstruct(str);
}
// Test of clear().
template <typename TString>
void testSequenceClear(TString & /*Tag*/)
{
{
// Test on an empty string.
TString string;
assign(string, "");
clear(string);
SEQAN_ASSERT(seqan2::begin(string) == seqan2::end(string));
SEQAN_ASSERT_EQ(length(string), 0u);
}
{
// Test on a non empty string.
TString string;
assign(string, "ACGTACGTACGT");
clear(string);
SEQAN_ASSERT(string == TString());
}
}
SEQAN_TYPED_TEST(StringTestCommon, Clear)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceClear(str);
testConstructDeconstruct(str);
}
// Test of seqan2::end().
template <typename TString>
void testSequenceEnd(TString & /*Tag*/)
{
typedef typename Value<TString>::Type TValue;
TString string;
assign(string, "ACGT");
typename Iterator<TString>::Type iter = seqan2::end(string);
--iter;
SEQAN_ASSERT_EQ(*iter, TValue('T'));
typename Iterator<TString, Standard>::Type standardIter = seqan2::end(string, Standard());
--standardIter;
SEQAN_ASSERT_EQ(*standardIter, TValue('T'));
// typename Iterator<TString, Rooted>::Type rootedIter = seqan2::end(string, Rooted());
// --rootedIter;
// SEQAN_ASSERT_EQ(*rootedIter, TValue('T'));
}
// // TODO(singer): Seg fault
// template <typename TValue>
// void testSequenceEnd(String<TValue, MMap<> > & /*Tag*/) {}
// template <typename TValue>
// void testSequenceEnd(String<TValue, MMap<> > const & /*Tag*/) {}
// cannot decrement fwd'lists iterator
template <typename TValue, typename TAlloc>
void testSequenceEnd(std::forward_list<TValue, TAlloc> & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, End)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceEnd(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceEqual(constStr);
testConstructDeconstruct(str);
}
// Test of endPosition().
template <typename TString>
void testSequenceEndPosition(TString & /*Tag*/)
{
// Test on an empty string.
TString string1;
assign(string1, "");
SEQAN_ASSERT_EQ(endPosition(string1), length(string1));
// Test on a non empty string.
TString string2;
assign(string2, "ACGT");
SEQAN_ASSERT_EQ(endPosition(string2), length(string2));
}
SEQAN_TYPED_TEST(StringTestCommon, EndPosition)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceEndPosition(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceEndPosition(constStr);
testConstructDeconstruct(str);
}
// Test of erase().
template <typename TString>
void testSequenceErase(TString & /*Tag*/)
{
// Test on a non empty string.
TString string, string0;
assign(string, "ACGTACGTACGT");
seqan2::erase(string, 1);
assign(string0, "AGTACGTACGT");
SEQAN_ASSERT(string == string0);
seqan2::erase(string, 2, 5);
assign(string0, "AGGTACGT");
SEQAN_ASSERT(string == string0);
}
template <typename TValue>
void testSequenceErase(String<TValue, External<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceErase(String<TValue, MMap<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceErase(String<TValue, Block<> > & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, Erase)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceErase(str);
testConstructDeconstruct(str);
}
// Test of eraseBack().
template <typename TString>
void testSequenceEraseBack(TString & /*Tag*/)
{
{
// Test on an empty string.
TString string;
assign(string, "");
// TODO (singer): eraseBack() on an empty string is not possible.
// Error message: "String must have more than 0 characters in eraseBack()!".
// If erase() should work on empty strings than eraseBack() as well ???
// eraseBack(string);
// SEQAN_ASSERT_EQ(string, "");
}
{
// Test on a non empty string.
TString string;
assign(string, "ACGTACGTACGT");
TString string2;
assign(string2, "ACGTACGTACG");
eraseBack(string);
SEQAN_ASSERT(string == string2);
TString string3;
assign(string3, "A");
TString string4;
eraseBack(string3);
SEQAN_ASSERT(string3 == string4);
}
}
SEQAN_TYPED_TEST(StringTestCommon, EraseBack)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceEraseBack(str);
testConstructDeconstruct(str);
}
// Test of front() for non const strings.
template <typename TString>
void testSequenceFront(TString & /*Tag*/)
{
typedef typename Reference<TString>::Type TReference;
TString string;
assign(string, "ACGT");
// val is a reference in contrast to the const version of front()
TReference val = front(string);
val = 'A';
SEQAN_ASSERT_EQ(val, value(string, 0));
}
// Test of front() for const strings.
template <typename TString>
void testSequenceFront(TString const & /*Tag*/)
{
typedef typename Reference<TString const>::Type TReference;
TString const string;
assign(string, "ACGT"); // TODO(weese:) reenable non-const string here (need to fix Proxy vs. SimpleType comparison first)
// val is not a reference in contrast to the non const version of front()
TReference val = front(string);
SEQAN_ASSERT_EQ(val, value(string, 0));
}
SEQAN_TYPED_TEST(StringTestCommon, Front)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceFront(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceFront(constStr);
std::cout << __LINE__ << std::endl;
testConstructDeconstruct(str);
std::cout << __LINE__ << std::endl;
}
SEQAN_TYPED_TEST(StringTestCommon, GetValue)
{
SEQAN_SKIP_TEST; // getValue() is deprecated.
// CountingChar::clear();
//
// typename TestFixture::TString str;
// testSequenceGetValue(str);
//
// //TODO
//// typename TestFixture::TString const constStr;
//// testSequenceGetValue(constStr);
//
// testConstructDeconstruct(str);
}
// Test of insert().
template <typename TString>
void testSequenceInsert(TString & /*Tag*/)
{
//typedef typename Value<TString>::Type TValue;
{
// Test of inserting an empty string.
TString string1;
assign(string1, "");
TString string2;
assign(string2, "");
insert(string1, 0, string2);
SEQAN_ASSERT(empty(string1));
}
{
// Test of inserting an string.
TString string1, string0;
assign(string1, "A");
TString string2;
assign(string2, "ACGT");
insert(string1, 0, string2);
assign(string0, "ACGTA");
SEQAN_ASSERT(string1 == string0);
}
}
template <typename TValue>
void testSequenceInsert(String<TValue, External<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceInsert(String<TValue, Block<> > & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, Insert)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceInsert(str);
testConstructDeconstruct(str);
}
// Test of insertValue().
template <typename TString>
void testSequenceInsertValue(TString & /*Tag*/)
{
//typedef typename Value<TString>::Type TValue;
// Test of inserting into an empty string.
TString string, string0;
assign(string, "");
insertValue(string, 0, 'A');
assign(string0, "A");
SEQAN_ASSERT(string == string0);
// Test of inserting into a non empty string.
insertValue(string, 0, 'C');
assign(string0, "CA");
SEQAN_ASSERT(string == string0);
}
template <typename TValue>
void testSequenceInsertValue(String<TValue, External<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceInsertValue(String<TValue, Block<> > & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, InsertValue)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceInsertValue(str);
testConstructDeconstruct(str);
}
// Test of iter().
template <typename TString>
void testSequenceIter(TString & /*Tag*/)
{
typedef typename Iterator<TString>::Type TIterator;
typedef typename Iterator<TString, Standard>::Type TStandardIterator;
typedef typename Iterator<TString, Rooted>::Type TRootedIterator;
// Test on an empty string.
{
TString string;
TIterator iterator = iter(string, 0);
TStandardIterator standardIterator = iter(string, 0);
TRootedIterator rootedIterator = iter(string, 0);
SEQAN_ASSERT(iterator == seqan2::begin(string));
SEQAN_ASSERT(standardIterator == seqan2::begin(string));
SEQAN_ASSERT(rootedIterator == seqan2::begin(string));
}
// Test on a non empty string.
{
TString string;
assign(string, "A");
TIterator iterator = iter(string, 0);
TStandardIterator standardIterator = iter(string, 0);
TRootedIterator rootedIterator = iter(string, 0);
SEQAN_ASSERT_EQ(*iterator, getValue(string, 0));
SEQAN_ASSERT_EQ(*standardIterator, getValue(string, 0));
SEQAN_ASSERT_EQ(*rootedIterator, getValue(string, 0));
}
// Test on a non empty string.
{
TString string;
assign(string, "ACGT");
TIterator iterator = iter(string, 3);
TStandardIterator standardIterator = iter(string, 3);
TRootedIterator rootedIterator = iter(string, 3);
SEQAN_ASSERT_EQ(*iterator, getValue(string, 3));
SEQAN_ASSERT_EQ(*standardIterator, getValue(string, 3));
SEQAN_ASSERT_EQ(*rootedIterator, getValue(string, 3));
}
}
SEQAN_TYPED_TEST(StringTestCommon, Iter)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceIter(str);
//TODO
// typename TestFixture::TString constStr;
// testSequenceIter(constStr);
testConstructDeconstruct(str);
}
// Test of length().
template <typename TString>
void testSequenceLength(TString & /*Tag*/)
{
// Test on an empty string.
TString string1;
SEQAN_ASSERT_EQ(length(string1), 0u);
// Test on a non empty string.
TString string2;
assign(string2, "CGTACGTATC");
SEQAN_ASSERT_EQ(length(string2), 10u);
}
SEQAN_TYPED_TEST(StringTestCommon, Length)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceLength(str);
//TODO
// typename TestFixture::TString constStr;
// testSequenceLength(constStr);
testConstructDeconstruct(str);
}
// Test of value().
template <typename TString>
void testSequenceMoveValue(TString & /*Tag*/)
{
typedef typename Value<TString>::Type TValue;
TString string;
assign(string, "");
resize(string, 2);
moveValue(string, 1, 'G');
SEQAN_ASSERT_EQ(value(string, 1), TValue('G'));
}
SEQAN_TYPED_TEST(StringTestCommon, MoveValue)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceMoveValue(str);
testConstructDeconstruct(str);
}
// Test of replace().
template <typename TString>
void testSequenceReplace(TString & /*Tag*/)
{
{
TString string1;
assign(string1, "");
TString string2;
assign(string2, "");
// TODO (singer): This is problematic according to the documentation.
// 0 can be a position or an iterator causing compiler errors.
replace(string1, 0, 0, string2);
SEQAN_ASSERT(empty(string1));
}
{
TString string1;
assign(string1, "ACACACAC");
TString string2;
assign(string2, "");
replace(string1, 4, 4, string2);
TString string0;
assign(string0, "ACACACAC");
SEQAN_ASSERT(string1 == string0);
}
{
TString string1;
assign(string1, "");
TString string2;
assign(string2, "GTGTGTGT");
replace(string1, 0, 0, string2);
TString string0;
assign(string0, "GTGTGTGT");
SEQAN_ASSERT(string1 == string0);
}
{
TString string1;
assign(string1, "ACACACAC");
TString string2;
assign(string2, "GTGTGTGT");
replace(string1, 4, 4, string2);
TString string0;
assign(string0, "ACACGTGTGTGTACAC");
SEQAN_ASSERT(string1 == string0);
}
}
template <typename TValue>
void testSequenceReplace(String<TValue, External<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceReplace(String<TValue, Block<> > & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, Replace)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceReplace(str);
testConstructDeconstruct(str);
}
// Test of reserve().
template <typename TString>
void testSequenceReserve(TString & /*Tag*/)
{
TString string;
assign(string, "");
reserve(string, 0u);
SEQAN_ASSERT_GEQ(capacity(string), 0u);
reserve(string, 1000u);
SEQAN_ASSERT_GEQ(capacity(string), 1000u);
// If the the new capacity is smaller than the current one
// the new capacity must be larger or equal to the current length.
reserve(string, 1u);
SEQAN_ASSERT_GEQ(capacity(string), length(string));
}
template <typename TValue, size_t CAPACITY>
void testSequenceReserve(String<TValue, Array<CAPACITY> > & /*Tag*/) {}
template <typename TValue, size_t SPACE>
void testSequenceReserve(String<TValue, Block<SPACE> > & /*Tag*/) {}
// reserve is NOOP on list
template <typename TValue, typename TAlloc>
void testSequenceReserve(std::list<TValue, TAlloc> & /*Tag*/) {}
// reserve is NOOP on list
template <typename TValue, typename TAlloc>
void testSequenceReserve(std::deque<TValue, TAlloc> & /*Tag*/) {}
// reserve is NOOP on list
template <typename TValue, typename TAlloc>
void testSequenceReserve(std::forward_list<TValue, TAlloc> & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, Reserve)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceReserve(str);
testConstructDeconstruct(str, 0);
}
// Test of resize().
template <typename TString>
void testSequenceResize(TString & /*Tag*/)
{
typedef typename Value<TString>::Type TValue;
TString string;// = "");
resize(string, 0);
SEQAN_ASSERT_EQ(length(string), 0u);
resize(string, 10);
SEQAN_ASSERT_EQ(length(string), 10u);
// TODO (singer): resize should initialize newly allocated memory,
// which it does not at the moment!
//SEQAN_ASSERT_EQ(string[0], TValue());
//SEQAN_ASSERT_EQ(string[0], TValue());
resize(string, 0);
SEQAN_ASSERT_EQ(length(string), 0u);
resize(string, 5, TValue());
SEQAN_ASSERT_EQ(length(string), 5u);
resize(string, 10, TValue('C'));
// SEQAN_ASSERT_EQ(string[0], TValue());
// SEQAN_ASSERT_EQ(string[5], TValue('C'));
SEQAN_ASSERT_EQ(value(string, 5), TValue('C'));
}
template <typename TValue>
void testSequenceResize(String<TValue, External<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceResize(String<TValue, Block<> > & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, Resize)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceResize(str);
testConstructDeconstruct(str);
}
// Test of value().
template <typename TString>
void testSequenceValue(TString & /*Tag*/)
{
typedef typename Value<TString>::Type TValue;
typedef typename Reference<TString>::Type TReference;
// In contrast to getValue(), value() does not return a copy but a reference.
// We test this using the variable value_.
TString string;// = "ACAC");
assign(string, "ACAC");
TReference ref = value(string, 0);
SEQAN_ASSERT_EQ(ref, TValue('A'));
ref = 'G';
SEQAN_ASSERT_EQ(ref, TValue('G'));
TString string0;
assign(string0, "GCAC");
SEQAN_ASSERT(string == string0);
}
// Test of value().
template <typename TString>
void testSequenceValue(TString const & /*Tag*/)
{
typedef typename Reference<TString const>::Type TReference;
// In contrast to getValue(), value() does not return a copy but a reference.
// We test this using the variable value_.
TString const string("ACAC");
TReference value_ = value(string, 0);
SEQAN_ASSERT_EQ(value_, 'A');
}
template <typename TValue>
void testSequenceValue(String<TValue, External<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceValue(String<TValue, External<> > const & /*Tag*/) {}
template <typename TValue>
void testSequenceValue(String<TValue, MMap<> > & /*Tag*/) {}
template <typename TValue>
void testSequenceValue(String<TValue, MMap<> > const & /*Tag*/) {}
template <typename TValue>
void testSequenceValue(std::list<TValue> const & /*Tag*/) {}
template <typename TValue>
void testSequenceValue(std::vector<TValue> const & /*Tag*/) {}
template <typename TValue>
void testSequenceValue(std::basic_string<TValue> const & /*Tag*/) {}
SEQAN_TYPED_TEST(StringTestCommon, Value)
{
CountingChar::clear();
typename TestFixture::TString str;
testSequenceValue(str);
//TODO
// typename TestFixture::TString const constStr;
// testSequenceValue(constStr);
testConstructDeconstruct(str);
}
#endif // TESTS_SEQUENCE_TEST_SEQUENCE_H_
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