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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.
//
// ==========================================================================
#ifndef TESTS_ALIGN_TEST_ALIGN_ALIGN_H_
#define TESTS_ALIGN_TEST_ALIGN_ALIGN_H_
#include <iostream>
#include <cstdio>
#include <vector>
#include <seqan/sequence.h>
#include <seqan/stream.h>
#include <seqan/align.h>
using namespace std;
using namespace seqan2;
template <typename TAlign>
void testAlignBasics()
{
TAlign ali1; //default C'tor
TAlign const & c_ali1 = ali1; //const version
resize(rows(ali1), 2); //rows
//add some rows to ali1
assignSource(row(ali1, 0), "abcdef");
insertGaps(row(ali1, 0), 2, 3);
assignSource(row(ali1, 1), "xyz");
//test copy C'tor
TAlign ali2(ali1);
SEQAN_ASSERT(row(ali1, 0) == row(ali2, 0)); //is the same as ali1
SEQAN_ASSERT(row(ali1, 1) == row(ali2, 1));
// it is a real copy
// SEQAN_ASSERT(getObjectId(row(ali1, 0)); == getObjectId(row(ali2, 0));) //(its not a real copy)
// SEQAN_ASSERT(getObjectId(row(ali1, 1)) == getObjectId(row(ali2, 1));)
TAlign ali3;
ali3 = ali1; //operator =
SEQAN_ASSERT(row(ali1, 0) == row(ali3, 0)); //is the same as ali1
SEQAN_ASSERT(row(ali1, 1) == row(ali3, 1));
// it is a real copy
// SEQAN_ASSERT(getObjectId(row(ali1, 0)) == getObjectId(row(ali3, 0))) //(its not a real copy)
// SEQAN_ASSERT(getObjectId(row(ali1, 1)) == getObjectId(row(ali3, 1)))
detach(ali3); //detach
SEQAN_ASSERT(row(ali1, 0) == row(ali3, 0)); //is the same as ali1
SEQAN_ASSERT(row(ali1, 1) == row(ali3, 1));
// it is a real copy
// SEQAN_ASSERT(getObjectId(row(ali1, 0)) != getObjectId(row(ali3, 0))) //ali3 is not dependent anymore
// SEQAN_ASSERT(getObjectId(row(ali1, 1)) != getObjectId(row(ali3, 1)))
SEQAN_ASSERT_NOT(dependentSource(row(ali3, 0))); //dependent
SEQAN_ASSERT_NOT(dependentSource(row(ali3, 1)));
//____________________________________________________________________________
// Test Column Access
typedef typename Cols<TAlign>::Type TCols;
typedef typename Cols<TAlign const>::Type TConstCols;
TCols cols1 = cols(ali1); //cols
TConstCols cols2 = cols(c_ali1); //const version
typename Col<TAlign>::Type col1 = col(ali1, 0); //col
SEQAN_ASSERT(col1 == cols1[0]);
typename Col<TAlign const>::Type c_col1 = col(c_ali1, 0);
SEQAN_ASSERT(c_col1 == col1);
//____________________________________________________________________________
// Test Rows Access
typename Rows<TAlign>::Type rows1 = rows(ali1); //rows
typename Rows<TAlign const>::Type rows2 = rows(c_ali1); //rows
typename Row<TAlign>::Type row1 = row(ali1, 0); //row
typename Row<TAlign>::Type row2 = rows1[0]; //rows::operator[]
typename Row<TAlign const>::Type row3 = rows2[0];
//____________________________________________________________________________
}
//////////////////////////////////////////////////////////////////////////////
template <typename TAlign>
void testAlignColsBase()
{
//____________________________________________________________________________
TAlign ali1;
TAlign const & c_ali1 = ali1;
resize(rows(ali1), 2);
assignSource(row(ali1, 0), "abcdef");
insertGaps(row(ali1, 0), 2, 3);
assignSource(row(ali1, 1), "xyz");
typedef typename Cols<TAlign>::Type TCols;
TCols cols1(ali1); //special c'tor
TCols const & c_cols1 = cols1; //(const version)
TCols cols2; //default c'tor
TCols cols3 = cols1; //copy c'tor
cols2 = cols1; //operator =
typedef typename Cols<TAlign const>::Type TConstCols;
TConstCols cols4(c_ali1); //special c'tor
typename Col<TAlign>::Type col1 = cols1[0]; //operator[]
typename Col<TAlign>::Type const c_col1 = c_cols1[1];
typename Col<TAlign const>::Type col2 = cols4[1];
typedef typename Iterator<TCols, Rooted>::Type TColsIterator;
typedef typename Iterator<TCols const, Rooted>::Type TConstColsIterator;
TColsIterator col_it1 = begin(cols1); //begin
TConstColsIterator const_col_it1 = begin(c_cols1);
SEQAN_ASSERT(value(col_it1, 0) == row(ali1, 0)[beginPosition(cols1)]);
SEQAN_ASSERT(value(col_it1, 1) == row(ali1, 1)[beginPosition(cols1)]);
SEQAN_ASSERT(value(const_col_it1, 0) == row(ali1, 0)[beginPosition(cols1)]);
SEQAN_ASSERT(value(const_col_it1, 1) == row(ali1, 1)[beginPosition(cols1)]);
col_it1 = end(cols1); //end
const_col_it1 = end(c_cols1);
--col_it1; //operator --
--const_col_it1;
SEQAN_ASSERT(value(col_it1, 0) == row(ali1, 0)[endPosition(cols1) - 1]);
SEQAN_ASSERT(value(col_it1, 1) == row(ali1, 1)[endPosition(cols1) - 1]);
SEQAN_ASSERT(value(const_col_it1, 0) == row(ali1, 0)[endPosition(c_cols1) - 1]);
SEQAN_ASSERT(value(const_col_it1, 1) == row(ali1, 1)[endPosition(c_cols1) - 1]);
setBeginPosition(row(ali1, 0), 4);
setBeginPosition(row(ali1, 1), 2);
SEQAN_ASSERT_EQ(beginPosition(cols(ali1)), 2u); //beginPosition
//____________________________________________________________________________
// cols iterator
TColsIterator col_it2; //defaut c'tor
TColsIterator col_it3(ali1); //special c'tor
TColsIterator const & c_col_it1 = col_it1; // (const version, dont confuse with const_col_it1)
// Test copying, but do not use further.
TColsIterator const & c_col_it2 = col_it2;
(void)c_col_it2;
SEQAN_ASSERT(&host(col_it1) == &ali1); //host
SEQAN_ASSERT(&host(c_col_it1) == &ali1);
setHost(col_it2, ali1); //setHost
SEQAN_ASSERT(&host(col_it2) == &ali1);
SEQAN_ASSERT(&host(container(col_it1)) == &ali1); //container
SEQAN_ASSERT(&host(container(c_col_it1)) == &ali1); //container
col_it1 = begin(cols1); //begin
SEQAN_ASSERT(value(col_it1, 0) == row(ali1, 0)[beginPosition(cols1)]);
SEQAN_ASSERT(value(col_it1, 1) == row(ali1, 1)[beginPosition(cols1)]);
col_it2 = ++col_it1; //operator ++ (prefix)
SEQAN_ASSERT(value(col_it1, 0) == row(ali1, 0)[beginPosition(cols1) + 1]);
SEQAN_ASSERT(value(col_it1, 1) == row(ali1, 1)[beginPosition(cols1) + 1]);
SEQAN_ASSERT(value(col_it2, 0) == row(ali1, 0)[beginPosition(cols1) + 1]);
SEQAN_ASSERT(value(col_it2, 1) == row(ali1, 1)[beginPosition(cols1) + 1]);
col_it2 = col_it1++; //operator ++ (suffix)
SEQAN_ASSERT(value(col_it1, 0) == row(ali1, 0)[beginPosition(cols1) + 2]);
SEQAN_ASSERT(value(col_it1, 1) == row(ali1, 1)[beginPosition(cols1) + 2]);
SEQAN_ASSERT(value(col_it2, 0) == row(ali1, 0)[beginPosition(cols1) + 1]);
SEQAN_ASSERT(value(col_it2, 1) == row(ali1, 1)[beginPosition(cols1) + 1]);
col_it2 = --col_it1; //operator -- (prefix)
SEQAN_ASSERT(value(col_it1, 0) == row(ali1, 0)[beginPosition(cols1) + 1]);
SEQAN_ASSERT(value(col_it1, 1) == row(ali1, 1)[beginPosition(cols1) + 1]);
SEQAN_ASSERT(value(col_it2, 0) == row(ali1, 0)[beginPosition(cols1) + 1]);
SEQAN_ASSERT(value(col_it2, 1) == row(ali1, 1)[beginPosition(cols1) + 1]);
col_it2 = col_it1--; //operator -- (suffix)
SEQAN_ASSERT(value(col_it1, 0) == row(ali1, 0)[beginPosition(cols1)]);
SEQAN_ASSERT(value(col_it1, 1) == row(ali1, 1)[beginPosition(cols1)]);
SEQAN_ASSERT(value(col_it2, 0) == row(ali1, 0)[beginPosition(cols1) + 1]);
SEQAN_ASSERT(value(col_it2, 1) == row(ali1, 1)[beginPosition(cols1) + 1]);
SEQAN_ASSERT_NOT(col_it1 == col_it2); //operator !=
SEQAN_ASSERT_NOT(c_col_it1 == col_it2) ;
SEQAN_ASSERT_NOT(col_it2 == c_col_it1) ;
SEQAN_ASSERT_NOT(c_col_it1 == c_col_it2) ;
--col_it2;
SEQAN_ASSERT(col_it1 == col_it2); //operator ==
SEQAN_ASSERT(c_col_it1 == col_it2);
SEQAN_ASSERT(col_it2 == c_col_it1);
SEQAN_ASSERT(c_col_it1 == c_col_it2);
SEQAN_ASSERT(row(ali1, 0) == "ab---cdef");
SEQAN_ASSERT_EQ(beginPosition(row(ali1, 0)), 4u);
col_it1 = iter(cols1, 6); //iter
SEQAN_ASSERT(value(col_it1, 0) == '-'); //value
SEQAN_ASSERT(value(c_col_it1, 0) == '-');
--col_it1;
SEQAN_ASSERT(value(col_it1, 0) == 'b'); //value
SEQAN_ASSERT(value(c_col_it1, 0) == 'b');
SEQAN_ASSERT(getValue(col_it1, 0) == 'b'); //getValue
SEQAN_ASSERT(getValue(c_col_it1, 0) == 'b');
char c = 'X';
assignValue(col_it1, 0, 'x'); //assignValue
SEQAN_ASSERT(row(ali1, 0) == "ax---cdef");
assignValue(col_it1, 0, c);
SEQAN_ASSERT(row(ali1, 0) == "aX---cdef");
c = 'Y';
assignValue(c_col_it1, 0, 'y');
SEQAN_ASSERT(row(ali1, 0) == "ay---cdef");
assignValue(c_col_it1, 0, c);
SEQAN_ASSERT(row(ali1, 0) == "aY---cdef");
c = 'X';
moveValue(col_it1, 0, 'x'); //moveValue
SEQAN_ASSERT(row(ali1, 0) == "ax---cdef");
moveValue(col_it1, 0, c);
SEQAN_ASSERT(row(ali1, 0) == "aX---cdef");
c = 'Y';
moveValue(c_col_it1, 0, 'y');
SEQAN_ASSERT(row(ali1, 0) == "ay---cdef");
moveValue(c_col_it1, 0, c);
SEQAN_ASSERT(row(ali1, 0) == "aY---cdef");
SEQAN_ASSERT_EQ(length(cols(ali1)), 11u);
}
template <typename TAlign>
void testGotohAlign()
{
typedef typename Value<TAlign>::Type TValue;
//align two sequences using Smith-Waterman-algorithm
String<TValue> str0 = "atgt";
String<TValue> str1 = "atagat";
TAlign ali;
resize(rows(ali), 2);
assignSource(row(ali, 0), str0);
assignSource(row(ali, 1), str1);
Score<int> score_type = Score<int>(1,-1,-1,-1);
int score = globalAlignment(ali,score_type);
SEQAN_ASSERT(score == 2);
SEQAN_ASSERT(row(ali,0) == "at-g-t" );
SEQAN_ASSERT(row(ali,1) == "atagat" );
clearGaps(row(ali,0));
clearGaps(row(ali,1));
Score<int> score_type1 = Score<int>(1,-1,-1,-3) ;
score = globalAlignment(ali,score_type1);
SEQAN_ASSERT(score == -2);
SEQAN_ASSERT((row(ali,0) == "at--gt") || (row(ali,0) == "atg--t" ));
SEQAN_ASSERT(row(ali,1) == "atagat" );
}
template <typename TAlign>
void testAlignBasics2()
{
typedef typename Source<TAlign>::Type TSource;
StringSet<TSource> ss;
appendValue(ss, "accagtta");
appendValue(ss, "ccactagggg");
TAlign aa(ss);
cout << ss[0];
SEQAN_ASSERT(row(aa, 0) == "accagtta");
SEQAN_ASSERT(getObjectId(row(aa, 0)) == getObjectId(value(ss, 0)));
SEQAN_ASSERT(row(aa, 1) == "ccactagggg");
SEQAN_ASSERT(getObjectId(row(aa, 1)) == getObjectId(value(ss, 1)));
}
template <typename TAlign>
void TestAlign_()
{
testAlignBasics<TAlign>();
testAlignBasics2<TAlign>();
testAlignColsBase<TAlign>();
testGotohAlign<TAlign>();
}
SEQAN_DEFINE_TEST(test_align_align_char_string_array_gaps) {
TestAlign_<Align<String<char>, ArrayGaps> >();
}
SEQAN_DEFINE_TEST(test_align_align_dna_array_gaps) {
TestAlign_<Align<String<Dna>, ArrayGaps> >();
}
// SEQAN_DEFINE_TEST(test_align_align_char_string_sumlist_gaps) {
// TestAlign_<Align<String<char>, SumlistGaps> >();
// }
// SEQAN_DEFINE_TEST(test_align_align_dna_sumlist_gaps) {
// TestAlign_<Align<String<Dna>, SumlistGaps> >();
// }
#endif
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