/usr/include/OpenMS/CHEMISTRY/PepIterator.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,
// 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: Chris Bauer $
// --------------------------------------------------------------------------
#ifndef OPENMS_CHEMISTRY_PEPITERATOR_H
#define OPENMS_CHEMISTRY_PEPITERATOR_H
#include <OpenMS/DATASTRUCTURES/String.h>
namespace OpenMS
{
/**
@brief Abstract base class for different peptide iterators
@note every derived class has to implement the static functions "PepIterator * create()" and "const String getProductName()" (see Factory for details)
*/
class OPENMS_DLLAPI PepIterator
{
public:
typedef std::pair<String, String> FASTAEntry;
/**
@brief constructor
*/
PepIterator();
/**
@brief destructor
*/
virtual ~PepIterator();
/**
@brief copy constructor
*/
PepIterator(const PepIterator & source);
/**
@brief * operator for accessing the value of the iterator
@return FASTAEntry representing a peptide
@throw InvalidIterator if iterator has not been initialized
*/
virtual FASTAEntry operator*() = 0;
/**
@brief operator ++ for pre-increment
@return Reference to PepIterator
@throw InvalidIterator if iterator has not been initialized
*/
virtual PepIterator & operator++() = 0;
/**
@brief operator ++ for post-increment
@return pointer to PepIterator
@throw Exception::InvalidIterator if iterator has not been initialized
*/
virtual PepIterator * operator++(int) = 0;
/**
@brief setter for FASTA file
@param f const String reference representing file location
@throw Exception::FileNotFound
@throw Exception::ParseError
*/
virtual void setFastaFile(const String & f) = 0;
/**
@brief getter for FASTA file
@return String with file location
*/
virtual String getFastaFile() = 0;
/**
@brief setter for spectrum
@param s ms spectrum given as vector of DoubleReals
@throw Exception::InvalidValue if spectrum is not sorted acendingly
*/
virtual void setSpectrum(const std::vector<DoubleReal> & s) = 0;
/**
@brief getter for spectrum
@return the used spectrum
*/
virtual const std::vector<DoubleReal> & getSpectrum() = 0;
/**
@brief setter for tolerance
@param t tolerance value
@throw Exception::InvalidValue if tolerance is negative
*/
virtual void setTolerance(DoubleReal t) = 0;
/**
@brief getter for tolerance
@return tolerance
*/
virtual DoubleReal getTolerance() = 0;
/**
@brief initializing iterator
*/
virtual bool begin() = 0;
/**
@brief idicator where iterator is at end
*/
virtual bool isAtEnd() = 0;
/**
@brief all children has to be registered here
@see Factory
*/
static void registerChildren();
};
}
#endif // OPENMS_CHEMISTRY_PEPITERATOR_H
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