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// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) 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 Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS 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: David Alexander
#pragma once
#include <string>
#include <vector>
namespace ConsensusCore {
/// \brief A pairwise alignment
class PairwiseAlignment {
private:
std::string target_;
std::string query_;
std::string transcript_;
public:
// target string, including gaps; usually the "reference"
std::string Target() const;
// query string, including gaps; usually the "read"
std::string Query() const;
// transcript as defined by Gusfield pg 215.
std::string Transcript() const;
public:
float Accuracy() const;
int Matches() const;
int Errors() const;
int Mismatches() const;
int Insertions() const;
int Deletions() const;
int Length() const;
public:
PairwiseAlignment(const std::string& target,
const std::string& query);
};
//
// We provide a crude Needleman-Wunsch implementations
// - no suppport for a subsitution matrix,
// - no support for affine gap penalties.
struct NeedlemanWunschParams {
float MatchScore;
float MismatchScore;
float InsertScore;
float DeleteScore;
NeedlemanWunschParams(float matchScore,
float mismatchScore,
float insertScore,
float deleteScore);
};
NeedlemanWunschParams DefaultNeedlemanWunschParams();
PairwiseAlignment* Align(const std::string& target,
const std::string& query,
NeedlemanWunschParams params = DefaultNeedlemanWunschParams()); // NOLINT
// These calls return an array, same len as target, containing indices into the query string.
std::vector<int> TargetToQueryPositions(const std::string& transcript);
std::vector<int> TargetToQueryPositions(const PairwiseAlignment& aln);
}
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