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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: Sandro Andreotti $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_FASTAFILE_H
#define OPENMS_FORMAT_FASTAFILE_H
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <vector>
namespace OpenMS
{
/**
@brief This class serves for reading in FASTA files
*/
class OPENMS_DLLAPI FASTAFile
{
public:
/**
@brief FASTA entry type (identifier, description and sequence)
The first String corresponds to the identifier that is
written after the > in the FASTA file. The part after the
first whitespace is stored in description and the text
from the next line until the next > (exclusive) is stored
in sequence.
*/
struct FASTAEntry
{
String identifier;
String description;
String sequence;
FASTAEntry() :
identifier(""),
description(""),
sequence("")
{
}
FASTAEntry(String id, String desc, String seq) :
identifier(id),
description(desc),
sequence(seq)
{
}
bool operator==(const FASTAEntry& rhs) const
{
return identifier == rhs.identifier
&& description == rhs.description
&& sequence == rhs.sequence;
}
};
/// Copy constructor
FASTAFile();
/// Destructor
virtual ~FASTAFile();
/**
@brief loads a FASTA file given by 'filename' and stores the information in 'data'
@exception Exception::FileNotFound is thrown if the file does not exists.
@exception Exception::ParseError is thrown if the file does not suit to the standard.
*/
void load(const String& filename, std::vector<FASTAEntry>& data);
/**
@brief stores the data given by 'data' at the file 'filename'
@exception Exception::UnableToCreateFile is thrown if the process is not able to write the file.
*/
void store(const String& filename, const std::vector<FASTAEntry>& data) const;
};
} // namespace OpenMS
#endif // OPENMS_FORMAT_FASTAFILE_H
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