/usr/include/libpwiz/pwiz/data/msdata/MSDataFile.hpp is in libpwiz-dev 3.0.9393-1+b2.
This file is owned by root:root, with mode 0o644.
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// $Id: MSDataFile.hpp 4009 2012-10-17 18:40:44Z kaipot $
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2007 Spielberg Family Center for Applied Proteomics
// Cedars-Sinai Medical Center, Los Angeles, California 90048
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
#ifndef _MSDATAFILE_HPP_
#define _MSDATAFILE_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include "MSData.hpp"
#include "Reader.hpp"
#include "BinaryDataEncoder.hpp"
#include "pwiz/utility/misc/IterationListener.hpp"
namespace pwiz {
namespace msdata {
/// MSData object plus file I/O
struct PWIZ_API_DECL MSDataFile : public MSData
{
/// constructs MSData object backed by file;
/// reader==0 -> use DefaultReaderList
MSDataFile(const std::string& filename,
const Reader* reader = 0,
bool calculateSourceFileChecksum = false);
/// data format for write()
enum PWIZ_API_DECL Format {Format_Text, Format_mzML, Format_mzXML, Format_MGF, Format_MS1, Format_CMS1, Format_MS2, Format_CMS2, Format_MZ5};
/// configuration for write()
struct PWIZ_API_DECL WriteConfig
{
Format format;
BinaryDataEncoder::Config binaryDataEncoderConfig;
bool indexed;
bool gzipped; // if true, file is written as .gz
WriteConfig(Format _format = Format_mzML,bool _gzipped = false)
: format(_format), indexed(true), gzipped(_gzipped)
{}
};
/// static write function for any MSData object;
/// iterationListenerRegistry may be used for progress updates
static void write(const MSData& msd,
const std::string& filename,
const WriteConfig& config = WriteConfig(),
const pwiz::util::IterationListenerRegistry* iterationListenerRegistry = 0);
/// member write function
void write(const std::string& filename,
const WriteConfig& config = WriteConfig(),
const pwiz::util::IterationListenerRegistry* iterationListenerRegistry = 0);
/// static write function for any MSData object;
/// iterationListenerRegistry may be used for progress updates
static void write(const MSData& msd,
std::ostream& os,
const WriteConfig& config = WriteConfig(),
const pwiz::util::IterationListenerRegistry* iterationListenerRegistry = 0);
/// member write function
void write(std::ostream& os,
const WriteConfig& config = WriteConfig(),
const pwiz::util::IterationListenerRegistry* iterationListenerRegistry = 0);
};
/// calculates and adds a CV term for the SHA1 checksum of a source file element
PWIZ_API_DECL void calculateSourceFileSHA1(SourceFile& sourceFile);
/// Iterate and calculate SHA-1 for all source files
PWIZ_API_DECL void calculateSHA1Checksums(const MSData& msd);
PWIZ_API_DECL std::ostream& operator<<(std::ostream& os, MSDataFile::Format format);
PWIZ_API_DECL std::ostream& operator<<(std::ostream& os, const MSDataFile::WriteConfig& config);
} // namespace msdata
} // namespace pwiz
#endif // _MSDATAFILE_HPP_
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