/usr/include/OpenMS/FORMAT/SpecArrayFile.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: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
#ifndef OPENMS_FORMAT_SPECARRAYFILE_H
#define OPENMS_FORMAT_SPECARRAYFILE_H
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <fstream>
#include <vector>
namespace OpenMS
{
/**
@brief File adapter for SpecArray (.pepList) files.
The first line is the header and contains the column names:<br>
m/z rt(min) snr charge intensity
Every subsequent line is a feature.
Entries are separated by Tab (\\t).
@ingroup FileIO
*/
class OPENMS_DLLAPI SpecArrayFile
{
public:
/// Default constructor
SpecArrayFile();
/// Destructor
virtual ~SpecArrayFile();
/**
@brief Loads a SpecArray file into a featureXML.
The content of the file is stored in @p features.
@exception Exception::FileNotFound is thrown if the file could not be opened
@exception Exception::ParseError is thrown if an error occurs during parsing
*/
template <typename FeatureMapType>
void load(const String & filename, FeatureMapType & feature_map)
{
// load input
TextFile input(filename, false);
// reset map
FeatureMapType fmap;
feature_map = fmap;
for (Size i = 1; i < input.size(); ++i)
{
String line = input[i];
std::vector<String> parts;
line.split('\t', parts);
if (parts.size() < 5)
{
throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, "", String("Failed to convert line") + String(i + 1) + "not enough columns (expected 5 or more, got " + String(parts.size()) + ")");
}
Feature f;
try
{
f.setMZ(parts[0].toDouble());
f.setRT(parts[1].toDouble() * 60.0);
f.setMetaValue("s/n", parts[2].toDouble());
f.setCharge(parts[3].toInt());
f.setIntensity(parts[4].toDouble());
}
catch (Exception::BaseException /*&e*/)
{
throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, "", String("Failed to convert value into a number (line '") + (i + 1) + ")");
}
feature_map.push_back(f);
}
}
/**
@brief Stores a featureXML as a SpecArray file.
NOT IMPLEMENTED
@exception Exception::UnableToCreateFile is thrown if the file could not be created
*/
template <typename SpectrumType>
void store(const String & filename, const SpectrumType & spectrum) const
{
std::cerr << "Store() for SpecArrayFile not implemented. Filename was: " << filename << ", spec of size " << spectrum.size() << "\n";
throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
}
};
} // namespace OpenMS
#endif // OPENMS_FORMAT_SPECARRAYFILE_H
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