// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, 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: Stephan Aiche <stephan.aiche@fu-berlin.de>
// ==========================================================================
#include <stack>
// TODO(holtgrew): Get rid of this?
//#define SEQAN_HIRSCHBERG_DEBUG_CUT
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
struct Hirschberg_;
typedef Tag<Hirschberg_> Hirschberg;
// ----------------------------------------------------------------------------
// Helper Class HirschbergSet_
// ----------------------------------------------------------------------------
// State for the implementation of Hirschberg's algorithm.
class HirschbergSet_
{
public:
unsigned x1;
unsigned x2;
unsigned y1;
unsigned y2;
int score;
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _begin1()
// ----------------------------------------------------------------------------
inline unsigned &
_begin1(HirschbergSet_ & me) {
return me.x1;
}
inline unsigned const &
_begin1(HirschbergSet_ const & me) {
return me.x1;
}
// ----------------------------------------------------------------------------
// Function _setBegin1()
// ----------------------------------------------------------------------------
inline void
_setBegin1(HirschbergSet_ & me, unsigned const & new_begin) {
me.x1 = new_begin;
}
// ----------------------------------------------------------------------------
// Function _end1()
// ----------------------------------------------------------------------------
inline unsigned &
_end1(HirschbergSet_ & me) {
return me.x2;
}
inline unsigned const &
_end1(HirschbergSet_ const & me) {
return me.x2;
}
// ----------------------------------------------------------------------------
// Function _setEnd1()
// ----------------------------------------------------------------------------
inline void
_setEnd1(HirschbergSet_ & me, unsigned const & new_end) {
me.x2 = new_end;
}
// ----------------------------------------------------------------------------
// Function _begin2()
// ----------------------------------------------------------------------------
inline unsigned &
_begin2(HirschbergSet_ & me) {
return me.y1;
}
inline unsigned const &
_begin2(HirschbergSet_ const & me) {
return me.y1;
}
// ----------------------------------------------------------------------------
// Function _setBegin2()
// ----------------------------------------------------------------------------
inline void
_setBegin2(HirschbergSet_ & me, unsigned const & new_begin) {
me.y1 = new_begin;
}
// ----------------------------------------------------------------------------
// Function _end2()
// ----------------------------------------------------------------------------
inline unsigned &
_end2(HirschbergSet_ & me) {
return me.y2;
}
inline unsigned const &
_end2(HirschbergSet_ const & me) {
return me.y2;
}
// ----------------------------------------------------------------------------
// Function _setEnd2()
// ----------------------------------------------------------------------------
inline void
_setEnd2(HirschbergSet_ & me, unsigned const & new_end) {
me.y2 = new_end;
}
// ----------------------------------------------------------------------------
// Function _score()
// ----------------------------------------------------------------------------
inline int &
_score(HirschbergSet_ & me) {
return me.score;
}
// ----------------------------------------------------------------------------
// Function _score()
// ----------------------------------------------------------------------------
inline int const &
_score(HirschbergSet_ const & me)
{
return me.score;
}
// ----------------------------------------------------------------------------
// Function _setScore()
// ----------------------------------------------------------------------------
inline void
_setScore(HirschbergSet_ & me,int new_score) {
me.score = new_score;
}
// ----------------------------------------------------------------------------
// Function _setBegin2()
// ----------------------------------------------------------------------------
// //////////////////////////////////////////////////////////////////////////////////////////////
// Debug Methods
// functions are only used for debugging or verbose output, therefore they
// are only active in SEQAN_DEBUG
// //////////////////////////////////////////////////////////////////////////////////////////////
#ifdef SEQAN_DEBUG
inline
void
print(HirschbergSet_ const & me)
{
std::cout << me.x1 << " " << me.x2 << "\t" << me.y1 << " " << me.y2 << std::endl;
}
#endif
// ----------------------------------------------------------------------------
// Function operator==()
// ----------------------------------------------------------------------------
inline bool
operator==(HirschbergSet_ const & lhs,
HirschbergSet_ const & rhs)
{
return ((_begin1(lhs) == _begin1(rhs)) && (_end1(lhs) == _end1(rhs)) &&
(_begin2(lhs) == _begin2(rhs)) && (_end2(lhs) == _end2(rhs)));
}
// ----------------------------------------------------------------------------
// Function _writeDebugMatrix()
// ----------------------------------------------------------------------------
#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
template<typename TSource>
void _writeDebugMatrix(TSource s1,TSource s2)
{
int l1 = length(s1);
int l2 = length(s2);
int i,j,sg,sd;
String<String<int> > fMatrix,rMatrix,tMatrix;
resize(fMatrix,l1 + 1);
resize(rMatrix,l1 + 1);
resize(tMatrix,l1 + 1);
for(i = 0;i <= l1;++i)
{
resize(fMatrix[i],l2 + 1);
resize(rMatrix[i],l2 + 1);
resize(tMatrix[i],l2 + 1);
}
for(i = 0;i <= l1;++i)
fMatrix[i][0] = i * (-1);
for(i = l1;i >= 0;--i)
rMatrix[i][l2] = (l1 - i) * (-1);
// calculate forward matrix
for(j = 1;j <= l2;++j)
{
fMatrix[0][j] = j*(-1);
for(i = 1;i <= l1;++i)
{
sg = -1 + ((fMatrix[i-1][j] > fMatrix[i][j-1]) ? fMatrix[i-1][j] : fMatrix[i][j-1]);
sd = fMatrix[i-1][j-1] + ((s1[i - 1] == s2[j-1]) ? 0 : -1 );
fMatrix[i][j] = ((sg > sd) ? sg : sd);
}
}
// calculate reverse matrix
for(j = l2 - 1;j >= 0;--j)
{
rMatrix[l1][j] = (l2 - j)*(-1);
for(i = l1 - 1;i >= 0;--i)
{
sg = -1 + ((rMatrix[i+1][j] > rMatrix[i][j+1]) ? rMatrix[i+1][j] : rMatrix[i][j+1]);
sd = rMatrix[i+1][j+1] + ((s1[i] == s2[j]) ? 0 : -1 );
rMatrix[i][j] = ((sg > sd) ? sg : sd);
}
}
// print fMatrix
std::cout << ";-;";
for(i = 0;i < l1;++i)
std::cout << s1[i] << ";";
std::cout << std::endl << "-;";
for(j = 0;j <= l2;++j)
{
if(j != 0) std::cout << s2[j-1] << ";";
for(i = 0;i <= l1;++i)
{
std::cout << fMatrix[i][j] << ";";
}
std::cout << std::endl;
}
// print rMatrix
std::cout << ";";
for(i = 0;i < l1;++i)
std::cout << s1[i] << ";";
std::cout << "-;" << std::endl;
for(j = 0;j <= l2;++j)
{
if(j != l2) std::cout << s2[j] << ";";
else std::cout << "-;";
for(i = 0;i <= l1;++i)
{
std::cout << rMatrix[i][j] << ";";
}
std::cout << std::endl;
}
// fill and print target matrix
std::cout << ";-;";
for(i = 0;i < l1;++i)
std::cout << s1[i] << ";";
std::cout << std::endl << "-;";
for(j = 0;j <= l2;++j)
{
if(j != 0) std::cout << s2[j-1] << ";";
for(i = 0;i <= l1;++i)
{
tMatrix[i][j] = fMatrix[i][j] + rMatrix[i][j];
std::cout << tMatrix[i][j] << ";";
}
std::cout << std::endl;
}
}
#endif
// debug flag .. define to see where Hirschberg cuts the sequences
//#define SEQAN_HIRSCHBERG_DEBUG_CUT
// ----------------------------------------------------------------------------
// Function globalAlignment()
// ----------------------------------------------------------------------------
template <typename TSequenceH, typename TGapsSpecH, typename TSequenceV, typename TGapsSpecV,
typename TScoreValue, typename TScoreSpec>
TScoreValue
_globalAlignment(Gaps<TSequenceH, TGapsSpecH> & gapsH,
Gaps<TSequenceV, TGapsSpecV> & gapsV,
Score<TScoreValue, TScoreSpec> const & score_,
Hirschberg const & /*algorithmTag*/)
{
TSequenceH const & s1 = source(gapsH);
TSequenceV const & s2 = source(gapsV);
TScoreValue total_score = 0;
typedef typename Value<TSequenceV>::Type TValueV;
typedef typename Size<TSequenceH>::Type TStringSize;
typedef typename Iterator<TSequenceH const, Standard>::Type TSequenceHIter;
typedef typename Iterator<TSequenceV const, Standard>::Type TSequenceVIter;
typedef typename Iterator<Gaps<TSequenceH, TGapsSpecH> >::Type TGapsHIter;
typedef typename Iterator<Gaps<TSequenceV, TGapsSpecV> >::Type TGapsVIter;
TGapsHIter target_0 = begin(gapsH);
TGapsVIter target_1 = begin(gapsV);
typedef typename Iterator<Matrix<TScoreValue> >::Type TMatrixIterator;
TValueV v;
TStringSize len1 = length(s1);
TStringSize len2 = length(s2);
// string to store the score values for the currently active cell
String<TScoreValue> c_score;
resize(c_score,len2 + 1);
// string to strore the backpointers
String<unsigned> pointer;
resize(pointer,len2 + 1);
// scoring-scheme specific score values
TScoreValue score_match = scoreMatch(score_);
TScoreValue score_mismatch = scoreMismatch(score_);
TScoreValue score_gap = scoreGapExtend(score_);
TScoreValue border,s,sg,sd,sg1,sg2;
int dp;
std::stack<HirschbergSet_> to_process;
HirschbergSet_ target;
unsigned i,j;
HirschbergSet_ hs_complete{0, static_cast<unsigned>(len1), 0, static_cast<unsigned>(len2), 0};
to_process.push(hs_complete);
while(!to_process.empty())
{
target = to_process.top();
to_process.pop();
if(_begin2(target) == _end2(target))
{
for(i = 0;i < (_end1(target) - _begin1(target));++i)
{
insertGap(target_1);
++target_0;
++target_1;
}
}
if(_begin1(target) == _end1(target))
{
for(i = 0;i < (_end2(target) - _begin2(target));++i)
{
insertGap(target_0);
++target_0;
++target_1;
}
}
else if(_begin1(target) + 1 == _end1(target) || _begin2(target) + 1 == _end2(target))
{
/* ALIGN */
#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
std::cout << "align s1 " << _begin1(target) << " to " << _end1(target) << " and s2 " << _begin2(target) << " to " << _end2(target) << std::endl;
std::cout << "align " << infix(s1,_begin1(target),_end1(target)) << " and " << infix(s2,_begin2(target),_end2(target)) << std::endl << std::endl;
#endif
TStringSize len_1 = _end1(target) - _begin1(target);
TStringSize len_2 = _end2(target) - _begin2(target);
Matrix<TScoreValue> matrix_;
setDimension(matrix_, 2);
setLength(matrix_, 0, len_1 + 1);
setLength(matrix_, 1, len_2 + 1);
resize(matrix_);
/* init matrix */
TSequenceHIter x_begin = iter(s1, _begin1(target), Standard()) - 1;
TSequenceHIter x_end = iter(s1, _end1(target), Standard()) - 1;
TSequenceVIter y_begin = iter(s2, _begin2(target), Standard()) - 1;
TSequenceVIter y_end = iter(s2, _end2(target), Standard()) - 1;
TSequenceHIter x = x_end;
TSequenceVIter y;
TMatrixIterator col_ = end(matrix_) - 1;
TMatrixIterator finger1;
TMatrixIterator finger2;
TScoreValue h = 0;
TScoreValue border_ = score_gap;
TScoreValue v = border_;
//-------------------------------------------------------------------------
// init
finger1 = col_;
*finger1 = 0;
for (x = x_end; x != x_begin; --x)
{
goPrevious(finger1, 0);
*finger1 = border_;
border_ += score_gap;
}
//-------------------------------------------------------------------------
//fill matrix
border_ = 0;
for (y = y_end; y != y_begin; --y)
{
TValueV cy = *y;
h = border_;
border_ += score_gap;
v = border_;
finger2 = col_;
goPrevious(col_, 1);
finger1 = col_;
*finger1 = v;
for (x = x_end; x != x_begin; --x)
{
goPrevious(finger1, 0);
goPrevious(finger2, 0);
if (*x == cy)
{
v = h + score_match;
h = *finger2;
}
else
{
TScoreValue s1 = h + score_mismatch;
h = *finger2;
TScoreValue s2 = score_gap + ((h > v) ? h : v);
v = (s1 > s2) ? s1 : s2;
}
*finger1 = v;
}
}
total_score += value(matrix_, 0,0);
#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
std::cout << "alignment score is " << total_score << std::endl << std::endl;
#endif
/* TRACE BACK */
finger1 = begin(matrix_);
x = iter(s1,_begin1(target));
y = iter(s2,_begin2(target));
x_end = iter(s1,_end1(target));
y_end = iter(s2,_end2(target));
while ((x != x_end) && (y != y_end))
{
bool gv;
bool gh;
if (*x == *y)
{
gv = gh = true;
}
else
{
TMatrixIterator it_ = finger1;
goNext(it_, 0);
TScoreValue v = *it_;
goNext(it_, 1);
TScoreValue d = *it_;
it_ = finger1;
goNext(it_, 1);
TScoreValue h = *it_;
gv = (v >= h) | (d >= h);
gh = (h >= v) | (d >= v);
}
if (gv)
{
++x;
goNext(finger1, 0);
}
else
{
insertGap(target_0);
}
if (gh)
{
++y;
goNext(finger1, 1);
}
else
{
insertGap(target_1);
}
++target_0;
++target_1;
}
// if x or y did not reached there end position, fill the rest with gaps
while(x != x_end)
{
insertGap(target_1);
++target_0;
++target_1;
++x;
}
while(y != y_end)
{
insertGap(target_0);
++target_0;
++target_1;
++y;
}
/* END ALIGN */
}
else
{
/*
Calculate cut using the algorithm as proposed in the lecture of Clemens Gröpl
using a backpointer to remember the position where the optimal alignment passes
the mid column
*/
unsigned mid = static_cast<unsigned>(floor( static_cast<double>((_begin1(target) + _end1(target))/2) ));
#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
std::cout << "calculate cut for s1 " << _begin1(target) << " to " << _end1(target) << " and s2 " << _begin2(target) << " to " << _end2(target) << std::endl;
std::cout << "calculate cut for " << infix(s1,_begin1(target),_end1(target)) << " and " << infix(s2,_begin2(target),_end2(target)) << std::endl;
std::cout << "cut is in row " << mid << " symbol is " << getValue(s1,mid-1) << std::endl << std::endl;
_writeDebugMatrix(infix(s1,_begin1(target),_end1(target)),infix(s2,_begin2(target),_end2(target)));
#endif
border = 0;
for(i = _begin2(target);i <= _end2(target);++i)
{
c_score[i] = border;
border += score_gap;
pointer[i] = i;
}
// iterate over s1 until the mid column is reached
border = score_gap;
for(i = _begin1(target) + 1;i <= mid;++i)
{
s = c_score[_begin2(target)];
c_score[_begin2(target)] = border;
border += score_gap;
v = getValue(s1,i-1);
for(j = _begin2(target) + 1;j <= _end2(target);++j)
{
sg = score_gap + ((c_score[j] > c_score[j - 1]) ? c_score[j] : c_score[j - 1]);
sd = s + ((v == getValue(s2,j-1)) ? score_match : score_mismatch);
s = c_score[j];
c_score[j] = (sg > sd) ? sg : sd;
}
}
// from here, rememeber the cell of mid-column, where optimal alignment passed
for(i = mid + 1;i <= _end1(target);++i)
{
s = c_score[_begin2(target)];
c_score[_begin2(target)] = border;
border += score_gap;
v = getValue(s1,i-1);
dp = _begin2(target);
for(j = _begin2(target) + 1;j <= _end2(target);++j)
{
sg1 = score_gap + c_score[j];
sg2 = score_gap + c_score[j - 1];
sd = s + ((v == getValue(s2,j-1)) ? score_match : score_mismatch);
s = c_score[j];
sg = pointer[j];
if(sd >= _max(sg1,sg2))
{
c_score[j] = sd;
pointer[j] = dp;
}
else
{
if(sg2 > sg1)
{
c_score[j] = sg2;
pointer[j] = pointer[j-1];
}
else
{
// gap introduced from left
// no update for the pointer
c_score[j] = sg1;
}
}
dp = sg;
}
}
#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT
std::cout << "hirschberg calculates cut in column " << mid << " and row " << pointer[_end2(target)] << std::endl;
std::cout << "requested position in c_score and pointer is " << _end2(target) << std::endl;
std::cout << "alignment score is " << c_score[_end2(target)] << std::endl << std::endl;
#endif
to_process.push(HirschbergSet_{mid, _end1(target), pointer[_end2(target)], _end2(target), 0});
to_process.push(HirschbergSet_{_begin1(target), mid, _begin2(target), pointer[_end2(target)], 0});
}
/* END CUT */
}
return total_score;
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_
