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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: Andreas Bertsch $
// $Authors: $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/OMSSACSVFile.h>
#include <fstream>
#include <algorithm>
using namespace std;
namespace OpenMS
{
OMSSACSVFile::OMSSACSVFile()
{
}
OMSSACSVFile::~OMSSACSVFile()
{
}
void OMSSACSVFile::load(const String & filename, ProteinIdentification & /* protein_identification */, vector<PeptideIdentification> & id_data) const
{
ifstream is(filename.c_str());
if (!is)
{
throw Exception::FileNotFound(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);
}
String line;
getline(is, line, '\n');
if (!line.hasPrefix("Spectrum"))
{
throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, "first line does not contain a description", "");
}
// line number counter
Size line_number = 0;
// ignore first line
Int actual_spectrum_number(-1);
while (getline(is, line, '\n'))
{
++line_number;
// Spectrum number, Filename/id, Peptide, E-value, Mass, gi, Accession, Start, Stop, Defline, Mods, Charge, Theo Mass, P-value
// 1,,MSHHWGYGK,0.00336754,1101.49,0,6599,1,9,CRHU2 carbonate dehydratase (EC 4.2.1.1) II [validated] - human,,1,1101.48,1.30819e-08
line.trim();
// replace ',' in protein name
String::ConstIterator it = find(line.begin(), line.end(), '"');
UInt offset(0);
if (it != line.end())
{
while (*(++it) != '"')
{
if (*it == ',')
{
offset++;
}
}
}
vector<String> split;
line.split(',', split);
if (split.size() != 14 && split.size() != 14 + offset)
{
throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, line, "number of columns should be 14 in line " + String(line_number));
}
PeptideHit p;
p.setSequence(split[2].trim());
p.setScore(split[13 + offset].trim().toDouble());
p.setCharge(split[11 + offset].trim().toInt());
if (actual_spectrum_number != split[0].trim().toInt())
{
// new id
//id_data.push_back(IdentificationData());
id_data.push_back(PeptideIdentification());
id_data.back().setScoreType("OMSSA");
actual_spectrum_number = (UInt)split[0].trim().toInt();
}
id_data.back().insertHit(p);
}
}
} // namespace OpenMS
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