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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: Stephan Aiche <stephan.aiche@fu-berlin.de>
// ==========================================================================
// TODO(holtgrew): Should be called _globalAlignmentScore()!
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// When using different alphabets, we will internally use the pattern alphabet
// for the comparison. This means that the text character is converted to the
// pattern alphabet. Here, the "pattern" is the shorter source sequence.
template <typename TAlphabetH, typename TSpecH, typename TAlphabetV, typename TSpecV>
int
_globalAlignmentScore(String<TAlphabetH, TSpecH> const & seqH,
String<TAlphabetV, TSpecV> const & seqV,
MyersBitVector const & algorithmTag)
{
// Switch horizontal and vertical gap roles, gapsV should be the shorter one
// to fit into less words.
if (length(seqH) < length(seqV))
return _globalAlignmentScore(seqV, seqH, algorithmTag);
// Use size of unsigned int as blocksize for bit-vectors.
const unsigned int BLOCK_SIZE = BitsPerValue<unsigned int>::VALUE;
typedef String<TAlphabetH, TSpecH> const TSequenceH;
typedef String<TAlphabetV, TSpecV> const TSequenceV;
typedef typename Value<TSequenceV>::Type TPatternAlphabet;
typedef typename Size<TSequenceH>::Type TSourceSize;
TSequenceH const & x = seqH;
TSequenceV const & y = seqV;
TSourceSize len_x = length(x);
unsigned int pos = 0;
// init variables
unsigned int len_y = length(y);
int score = (-1)*len_y;
unsigned int patternAlphabetSize = ValueSize<TPatternAlphabet>::VALUE;
unsigned int blockCount = (len_y + BLOCK_SIZE - 1) / BLOCK_SIZE;
unsigned int scoreMask = 1 << ((len_y % BLOCK_SIZE) - 1); // the mask with a bit set at the position of the last active cell
String<unsigned> VP;
resize(VP, blockCount, std::numeric_limits<unsigned>::max());
String<unsigned> VN;
resize(VN, blockCount, 0);
String<unsigned> bitMask;
resize(bitMask, patternAlphabetSize * blockCount, 0);
// encoding the letters as bit-vectors
for (unsigned int j = 0; j < len_y; j++)
bitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] = bitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE);
// compute score
unsigned int X, D0, HN, HP;
if(blockCount == 1)
{
while (pos < len_x) {
X = bitMask[ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)))] | VN[0];
D0 = ((VP[0] + (X & VP[0])) ^ VP[0]) | X;
HN = VP[0] & D0;
HP = VN[0] | ~(VP[0] | D0);
// customized to compute edit distance
X = (HP << 1) | 1;
VN[0] = X & D0;
VP[0] = (HN << 1) | ~(X | D0);
if (HP & scoreMask)
score--;
else if (HN & scoreMask)
score++;
++pos;
}
} // end compute score - short pattern
else
{
unsigned int temp, shift, currentBlock;
unsigned int carryD0, carryHP, carryHN;
while (pos < len_x)
{
// set vars
carryD0 = carryHP = carryHN = 0;
shift = blockCount * ordValue(static_cast<TPatternAlphabet>(getValue(x,pos)));
// computing first the top most block
X = bitMask[shift] | VN[0];
temp = VP[0] + (X & VP[0]);
carryD0 = temp < VP[0];
D0 = (temp ^ VP[0]) | X;
HN = VP[0] & D0;
HP = VN[0] | ~(VP[0] | D0);
// customized to compute edit distance
X = (HP << 1) | 1;
carryHP = HP >> (BLOCK_SIZE - 1);
VN[0] = X & D0;
temp = (HN << 1);
carryHN = HN >> (BLOCK_SIZE - 1);
VP[0] = temp | ~(X | D0);
// computing the necessary blocks, carries between blocks following one another are stored
for (currentBlock = 1; currentBlock < blockCount; currentBlock++) {
X = bitMask[shift + currentBlock] | VN[currentBlock];
temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0;
carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]);
D0 = (temp ^ VP[currentBlock]) | X;
HN = VP[currentBlock] & D0;
HP = VN[currentBlock] | ~(VP[currentBlock] | D0);
X = (HP << 1) | carryHP;
carryHP = HP >> (BLOCK_SIZE-1);
VN[currentBlock] = X & D0;
temp = (HN << 1) | carryHN;
carryHN = HN >> (BLOCK_SIZE - 1);
VP[currentBlock] = temp | ~(X | D0);
}
// update score with the HP and HN values of the last block the last block
if (HP & scoreMask)
score--;
else if (HN & scoreMask)
score++;
++pos;
}
} // end compute score - long pattern
return score;
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_
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