/usr/include/OpenMS/DATASTRUCTURES/SuffixArrayTrypticSeqan.h is in libopenms-dev 1.11.1-5.
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// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * 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 any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// 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 ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS 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,
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Clemens Groepl,Andreas Bertsch$
// $Authors: Chris Bauer $
// --------------------------------------------------------------------------
#ifndef OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICSEQAN_H
#define OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICSEQAN_H
#include <OpenMS/DATASTRUCTURES/SuffixArraySeqan.h>
namespace OpenMS
{
/**
@brief Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum
This class uses SEQAN suffix array. It can just be used for finding peptide Candidates for a given MS Spectrum within a certain mass tolerance. The suffix array can be saved to disc for reused so it has to be build just once.
*/
class OPENMS_DLLAPI SuffixArrayTrypticSeqan :
public SuffixArraySeqan
{
public:
/** @brief constructor for tryptic seqan array with a specially optimized implementation
@param st the suffix array string, which is used to build the suffix array
@param filename filename of fasta file
@param weight_mode if not monoistopic weight should be used, this parameters can be set to AVERAGE
@throw InvalidValue is thrown if string st if invalid
@throw FileNotFound is thrown if given file is not found
*/
SuffixArrayTrypticSeqan(const String & st, const String & filename, const WeightWrapper::WEIGHTMODE weight_mode = WeightWrapper::MONO);
/**
@brief returns if an enzyme will cut after first character
@param aa1 const char as first aminoacid
@param aa2 const char as second aminoacid
@return bool descibing if it is a digesting site
*/
bool isDigestingEnd(const char aa1, const char aa2) const;
};
}
#endif //OPENMS_DATASTRUCTURES_SUFFIXARRAYTRYPTICSEQAN_H
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