/usr/include/libpwiz/pwiz/data/identdata/IdentDataFile.hpp is in libpwiz-dev 3.0.9393-1+b2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// $Id: IdentDataFile.hpp 2824 2011-06-29 18:37:47Z chambm $
//
//
// Original author: Robert Burke <robert.burke@proteowizard.org>
//
// Copyright 2009 Spielberg Family Center for Applied Proteomics
// University of Southern California, Los Angeles, California 90033
//
// 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 _IDENTDATAFILE_HPP_
#define _IDENTDATAFILE_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include "IdentData.hpp"
#include "Reader.hpp"
#include "pwiz/utility/misc/IterationListener.hpp"
namespace pwiz {
namespace identdata {
/// IdentData object plus file I/O
struct PWIZ_API_DECL IdentDataFile : public IdentData
{
/// constructs IdentData object backed by file;
/// reader==0 -> use DefaultReaderList
IdentDataFile(const std::string& filename,
const Reader* reader = 0,
const pwiz::util::IterationListenerRegistry* iterationListenerRegistry = 0,
bool ignoreSequenceCollectionAndAnalysisData = false);
/// data format for write()
enum PWIZ_API_DECL Format {Format_Text, Format_MzIdentML, Format_pepXML};
/// configuration for write()
struct PWIZ_API_DECL WriteConfig
{
Format format;
WriteConfig(Format format = Format_MzIdentML)
: format(format)
{}
};
/// static write function for any IdentData object;
static void write(const IdentData& mzid,
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 IdentData object;
static void write(const IdentData& mzid,
const std::string& filename,
std::ostream& os,
const WriteConfig& config = WriteConfig(),
const pwiz::util::IterationListenerRegistry* iterationListenerRegistry = 0);
/// member write function
void write(std::ostream& os,
const std::string& filename,
const WriteConfig& config = WriteConfig(),
const pwiz::util::IterationListenerRegistry* iterationListenerRegistry = 0);
};
PWIZ_API_DECL std::ostream& operator<<(std::ostream& os, IdentDataFile::Format format);
PWIZ_API_DECL std::ostream& operator<<(std::ostream& os, const IdentDataFile::WriteConfig& config);
} // namespace identdata
} // namespace pwiz
#endif // _IDENTDATAFILE_HPP_
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