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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: Jonathan Goeke <goeke@molgen.mpg.de>
// ==========================================================================
// This header contains the implementation of the D2 score for alignment free
// sequence comparison (inner product of kmer counts).
//
// These functions can be called with alignmentFreeComparison().
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2_H_
#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2_H_
namespace seqan2 {
/*
* _alignmentFreeComparison is called by alignmentFreeComparison() (see alignment_free_comparison.h)
*/
template <typename TStringSet, typename TValue>
void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix,
TStringSet const & sequenceSet,
AFScore<D2> const & score)
{
//typedef typename Value<TStringSet>::Type TString;
//typedef typename Value<TString>::Type TAlphabet;
typedef typename Iterator<TStringSet const>::Type TIteratorSet;
typedef typename Iterator<StringSet<String<unsigned> > >::Type TIteratorSetInt;
//typedef Matrix<TValue, 2> TMatrix;
unsigned seqNumber = length(sequenceSet);
// Resize the scoreMatrix
setLength(scoreMatrix, 0, seqNumber);
setLength(scoreMatrix, 1, seqNumber);
resize(scoreMatrix, (TValue) 0);
StringSet<String<unsigned> > kmerCounts;
resize(kmerCounts, seqNumber);
// Count all kmers
TIteratorSetInt itKmerCounts = begin(kmerCounts);
TIteratorSet itSeqSet = begin(sequenceSet);
for (; itSeqSet < end(sequenceSet); ++itSeqSet)
{
countKmers(value(itKmerCounts), value(itSeqSet), score.kmerSize);
++itKmerCounts;
}
if(score.verbose)
{
std::cout << "\ncounted words";
}
// Calculate all pairwise scores and store them in scoreMatrix
for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex)
{
if(score.verbose)
{
std::cout << "\nSequence number " << rowIndex;
}
for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex)
{
_alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex], kmerCounts[colIndex], score);
value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetric entries
}
}
}
/*
* Calculate pairwise score given the counts of all kmers
*/
template <typename TValue>
void
_alignmentFreeCompareCounts(TValue & result,
String<unsigned> const & kmerCounts1,
String<unsigned> const & kmerCounts2,
AFScore<D2> const & /*score*/)
{
typedef typename Iterator<String<unsigned> const>::Type TIteratorInt;
TIteratorInt it1 = begin(kmerCounts1);
TIteratorInt it2 = begin(kmerCounts2);
result = 0;
for (; it1 < end(kmerCounts1); ++it1)
{
result += value(it1) * value(it2);
++it2;
}
}
} // namespace seqan2
#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2_H_
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