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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: Nico Pfeifer $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/MascotXMLFile.h>
#include <OpenMS/SYSTEM/File.h>
using namespace xercesc;
using namespace std;
namespace OpenMS
{
MascotXMLFile::MascotXMLFile() :
Internal::XMLFile()
{
}
void MascotXMLFile::load(const String& filename,
ProteinIdentification& protein_identification,
vector<PeptideIdentification>& id_data,
const RTMapping& rt_mapping,
const String& scan_regex)
{
map<String, vector<AASequence> > peptides;
load(filename, protein_identification, id_data, peptides, rt_mapping,
scan_regex);
}
void MascotXMLFile::load(const String& filename,
ProteinIdentification& protein_identification,
vector<PeptideIdentification>& id_data,
map<String, vector<AASequence> >& peptides,
const RTMapping& rt_mapping,
const String& scan_regex)
{
//clear
protein_identification = ProteinIdentification();
id_data.clear();
Internal::MascotXMLHandler handler(protein_identification, id_data,
filename, peptides, rt_mapping,
scan_regex);
parse_(filename, &handler);
// since the mascotXML can contain "peptides" without sequences,
// the identifications without any real peptide hit are removed
vector<PeptideIdentification> filtered_hits;
filtered_hits.reserve(id_data.size());
for (vector<PeptideIdentification>::iterator id_it = id_data.begin();
id_it != id_data.end(); ++id_it)
{
const vector<PeptideHit>& peptide_hits = id_it->getHits();
if (!peptide_hits.empty() &&
(peptide_hits.size() > 1 || !peptide_hits[0].getSequence().empty()))
{
filtered_hits.push_back(*id_it);
}
}
Size diff = id_data.size() - filtered_hits.size();
if (diff)
{
LOG_WARN << "Warning: Removed " << diff
<< " peptide identifications without sequence." << endl;
}
id_data.swap(filtered_hits);
// check if we have (some) RT information:
Size no_rt_count = 0;
for (vector<PeptideIdentification>::iterator id_it = id_data.begin();
id_it != id_data.end(); ++id_it)
{
if (!id_it->metaValueExists("RT")) no_rt_count++;
}
if (no_rt_count)
{
LOG_WARN << "Warning: " << no_rt_count << " (of " << id_data.size()
<< ") peptide identifications have no retention time value."
<< endl;
}
// if we have a mapping, but couldn't find any RT values, that's an error:
if (!rt_mapping.empty() && (no_rt_count == id_data.size()))
{
throw Exception::MissingInformation(
__FILE__, __LINE__, __PRETTY_FUNCTION__,
"No retention time information for peptide identifications found");
}
// argh! Mascot 2.2 tends to repeat the first hit (yes it appears twice),
// so we delete one of them
for (vector<PeptideIdentification>::iterator it = id_data.begin();
it != id_data.end(); ++it)
{
vector<PeptideHit> peptide_hits = it->getHits();
// check if equal, except for rank
if (peptide_hits.size() > 1 &&
peptide_hits[0].getScore() == peptide_hits[1].getScore() &&
peptide_hits[0].getSequence() == peptide_hits[1].getSequence() &&
peptide_hits[0].getCharge() == peptide_hits[1].getCharge())
{
// erase first hit
peptide_hits.erase(peptide_hits.begin() + 1);
it->setHits(peptide_hits);
}
}
}
void MascotXMLFile::generateRTMapping(
const MSExperiment<>::ConstIterator begin,
const MSExperiment<>::ConstIterator end, RTMapping& rt_mapping)
{
rt_mapping.clear();
for (MSExperiment<>::ConstIterator it = begin; it != end; ++it)
{
String id = it->getNativeID(); // expected format: "... scan=#"
try
{
Int num_id = id.suffix('=').toInt();
if (num_id >= 0) rt_mapping[num_id] = it->getRT();
else throw Exception::ConversionError(__FILE__, __LINE__,
__PRETTY_FUNCTION__, "error");
}
catch (Exception::ConversionError)
{
LOG_ERROR << "Error: Could not create mapping of scan numbers to retention times." << endl;
rt_mapping.clear();
break;
}
}
}
} // namespace OpenMS
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