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// ==========================================================================
// 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: Jonathan Goeke <goeke@molgen.mpg.de>
// ==========================================================================
// This file contains the function that calls alignment free sequence
// comparisons algorithms (see AFScore):
// alignmentFreeComparison()
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_COMPARISON_H_
#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_COMPARISON_H_
namespace seqan {
/*!
* @fn alignmentFreeComparison
* @headerfile <seqan/alignment_free.h>
* @brief Computes the pairwise similarity scores for a set of sequences.
*
* @signature void alignmentFreeComparison(scoreMatrix, sequenceSet, score);
*
* @param[out] scoreMatrix A two-dimensional @link Matrix @endlink, used to store all pairwise scores.
* @param[in] sequenceSet @link StringSet @endlink containing all sequences for which pairwise scores will be
* computed.
* @param[in] score The @link AFScore @endlink object to be used for computing the alignment.
*
* @section Examples
*
* Calculate the alignment free sequence similarity of two masked DNA sequences.
*
* @code{.cpp}
* using namespace seqan;
* StringSet<Dna5String> sequences;
* Dna5String seq1 =
* "TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG"
* "TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG"
* "AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC"
* "GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTTATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT"
* "CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA"
* "CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT"
* "CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG";
* Dna5String seq2 =
* "ACCGACGATTAGCTTTGTCCGAGTTACAACGGTTCAATAATACAAAGGATGGCATAAACCCATTTGTGTGAA"
* "AGTGCCCATCACATTATGATTCTGTCTACTATGGTTAATTCCCAATATACTCTCGAAAAGAGGGTATGCTCC"
* "CACGGCCATTTACGTCACTAAAAGATAAGATTGCTCAAANNNNNNNNNACTGCCAACTTGCTGGTAGCTTCA"
* "GGGGTTGTCCACAGCGGGGGGTCGTATGCCTTTGTGGTATACCTTACTAGCCGCGCCATGGTGCCTAAGAAT"
* "GAAGTAAAACAATTGATGTGAGACTCGACAGCCAGGCTTCGCGCTAAGGACGCAAAGAAATTCCCTACATCA"
* "GACGGCCGCGNNNAACGATGCTATCGGTTAGGACATTGTGCCCTAGTATGTACATGCCTAATACAATTGGAT"
* "CAAACGTTATTCCCACACACGGGTAGAAGAACNNNNATTACCCGTAGGCACTCCCCGATTCAAGTAGCCGCG";
*
* clear(sequences);
* appendValue(sequences, seq1);
* appendValue(sequences, seq2);
*
* Matrix<double, 2> myMatrix;
*
* unsigned kmerSize = 5;
* unsigned bgModelOrder = 1;
* String<char> revCom = "both_strands";
* unsigned mismatches = 1;
* double mismatchWeight = 0.5;
* AFScore<N2> myScoreN2(kmerSize, bgModelOrder, revCom, mismatches, mismatchWeight);
*
* alignmentFreeComparison(myMatrix, sequences, myScoreN2);
* std::cout << myMatrix;
* @endcode
*/
template <typename TStringSet, typename TValue, typename TComparisonMethod>
void alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, TStringSet const & sequenceSet, TComparisonMethod const & comparisonMethod)
{
_alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod);
}
} // namespace seqan
#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_COMPARISON_H_
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