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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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: Petra Gutenbrunner $
// $Authors: Petra Gutenbrunner $
// --------------------------------------------------------------------------
//! [Identification]
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <iostream>
using namespace OpenMS;
using namespace std;
int main()
{
// Create new protein identification object corresponding to a single search
vector<ProteinIdentification> protein_ids;
ProteinIdentification protein_id;
protein_id.setIdentifier("Identifier");
// Each ProteinIdentification object stores a vector of protein hits
vector<ProteinHit> protein_hits;
ProteinHit protein_hit = ProteinHit();
protein_hit.setAccession("MyAccession");
protein_hit.setSequence("PEPTIDEPEPTIDEPEPTIDEPEPTIDER");
protein_hit.setScore(1.0);
protein_hits.push_back(protein_hit);
protein_id.setHits(protein_hits);
DateTime now = DateTime::now();
String date_string = now.getDate();
protein_id.setDateTime(now);
// Example of possible search parameters
ProteinIdentification::SearchParameters search_parameters;
search_parameters.db = "database";
search_parameters.charges = "+2";
protein_id.setSearchParameters(search_parameters);
// Some search engine meta data
protein_id.setSearchEngineVersion("v1.0.0");
protein_id.setSearchEngine("SearchEngine");
protein_id.setScoreType("HyperScore");
protein_ids.push_back(protein_id);
// Iterate over protein identifications and protein hits
for (auto it = protein_ids.begin(); it != protein_ids.end(); ++it)
{
for (auto hit = it->getHits().begin(); hit < it->getHits().end(); ++hit)
{
cout << "Protein hit accession: " << hit->getAccession() << endl;
cout << "Protein hit sequence: " << hit->getSequence() << endl;
cout << "Protein hit score: " << hit->getScore() << endl;
}
}
// Create new peptide identifications
vector<PeptideIdentification> peptide_ids;
PeptideIdentification peptide_id;
peptide_id.setRT(1243.56);
peptide_id.setMZ(440.0);
peptide_id.setScoreType("ScoreType");
peptide_id.setHigherScoreBetter(false);
peptide_id.setIdentifier("Identifier");
// define additional meta value for the peptide identification
peptide_id.setMetaValue("AdditionalMetaValue", "Value");
// add PeptideHit to a PeptideIdentification
vector<PeptideHit> peptide_hits;
PeptideHit peptide_hit;
peptide_hit.setScore(1.0);
peptide_hit.setRank(1);
peptide_hit.setCharge(2);
peptide_hit.setSequence(AASequence::fromString("DLQM(Oxidation)TQSPSSLSVSVGDR"));
peptide_hits.push_back(peptide_hit);
// add second best PeptideHit to the PeptideIdentification
peptide_hit.setScore(1.5);
peptide_hit.setRank(2);
peptide_hit.setCharge(2);
peptide_hit.setSequence(AASequence::fromString("QLDM(Oxidation)TQSPSSLSVSVGDR"));
peptide_hits.push_back(peptide_hit);
// add PeptideHit to PeptideIdentification
peptide_id.setHits(peptide_hits);
// add PeptideIdentification
peptide_ids.push_back(peptide_id);
// We could now store the identification data in an idXML file
// IdXMLFile().store(outfile, protein_ids, peptide_ids);
// And load it back with
// IdXMLFile().load(outfile, protein_ids, peptide_ids);
// Iterate over PeptideIdentification
for (const auto& peptide_id : peptide_ids)
{
// Peptide identification values
cout << "Peptide ID m/z: " << peptide_id.getMZ() << endl;
cout << "Peptide ID rt: " << peptide_id.getRT() << endl;
cout << "Peptide ID score type: " << peptide_id.getScoreType() << endl;
// PeptideHits
for (const auto& scored_hit : peptide_id.getHits())
{
cout << " - Peptide hit rank: " << scored_hit.getRank() << endl;
cout << " - Peptide hit sequence: " << scored_hit.getSequence().toString() << endl;
cout << " - Peptide hit score: " << scored_hit.getScore() << endl;
}
}
// ...
return 0;
}
//! [Identification]
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