/usr/include/OpenMS/DATASTRUCTURES/BigString.h is in libopenms-dev 1.11.1-5.
This file is owned by root:root, with mode 0o644.
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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,
// 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.
//
// --------------------------------------------------------------------------
// $Maintainer: Clemens Groepl,Andreas Bertsch$
// $Authors: $
// --------------------------------------------------------------------------
#ifndef OPENMS_DATASTRUCTURES_BIGSTRING_H
#define OPENMS_DATASTRUCTURES_BIGSTRING_H
#include <vector>
#include <OpenMS/DATASTRUCTURES/String.h>
namespace OpenMS
{
/**
@brief concatenates Proteins given as FASTAEntry to one big string separated by a unique character (by default $)
Concatenates the strings given as FASTAEntry separating them with a unique character and storing the headers of FASTAEntry as well as the position of separator characters. So a substring can be accessed easily and the corresponding header can be found fast by using bineary search.
*/
class OPENMS_DLLAPI BigString
{
public:
typedef std::pair<String, String> FASTAEntry;
/**
@brief constructor
*/
BigString();
/**
@brief copy constructor
*/
BigString(const BigString & bs);
/**
@brief desctructor
*/
virtual ~BigString();
/**
@brief add new string to bigString
@param new_entry FASTAEntry to be added to big_string
*/
void add(FASTAEntry const & new_entry);
/**
@brief setter for separator character by default $
@param sep separator character
*/
void setSeparator(const char sep);
/**
@brief getter for separator character
@return separator character
*/
char getSeparator();
/**
@brief returns the number of strings
@return int with number of strings
*/
Size size();
/**
@brief length of bigString
@return int with length of the created bigString
*/
Size length();
/**
@brief getPeptide from start position with given length this includes FASTAHeader
@param entry contains the entry of the given range after calling
@param start start index
@param length length of desired substring
@return FASTAEntry describing the protein
@throw InvalidValue if a peptide is part of two different fasta entrys
*/
void getPeptide(FASTAEntry & entry, Size start, Size length);
/**
@brief returns bigString
@return const reference to bigString
*/
const String & getBigString() const;
protected:
/**
@brief private function to implement binary search
@param index
@param start start index
@param end end inxed
@return int with index
*/
Size getIndex_(Size index, Size start, Size end);
/**
@brief retrieves index of inserted protein by bigStringPosition
@param index
@return int with index
*/
Size getIndex_(Size index);
String big_string_; ///< concatenated String
char separator_; ///< separator sign
Size count_; ///< number of Strings added to big_string
Size len_; ///< length of the big_string
std::vector<Size> sep_indices_; ///< indices of separators
std::vector<String> FASTA_header_; ///< vector with headers of FASTAEntry
};
}
#endif // OPENMS_DATASTRUCTURES_BIGSTRING_H
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