Commit 533c6688 authored by Langella Olivier's avatar Langella Olivier
Browse files

Merge branch 'master' of forgemia.inra.fr:pappso/xtpcpp

parents f8043b04 7ff56874
......@@ -17,3 +17,7 @@ License: MIT
Files: */src/resources/icons/mit/jamicons
Copyright: Michael Amprimo <https://github.com/michaelampr/jam>
License: MIT
Files: */src/resources/html_doc
Copyright: The Global Proteome Machine Organization <https://www.thegpm.org/TANDEM/>
License: Artistic
......@@ -385,6 +385,36 @@ IdentificationGroup::collectMhDelta(
}
}
}
void
IdentificationGroup::collectTargetDecoyMhDelta(
std::vector<pappso::pappso_double> &delta_list,
pappso::PrecisionUnit unit,
ValidationState state) const
{
std::set<const PeptideEvidence *> peptide_evidence_list;
for(auto &p_protein_match : _protein_match_list)
{
if(p_protein_match->getValidationState() == state)
{
p_protein_match->collectPeptideEvidences(peptide_evidence_list,
state);
}
}
for(const PeptideEvidence *p_peptide_evidence : peptide_evidence_list)
{
if(unit == pappso::PrecisionUnit::ppm)
{
delta_list.push_back(p_peptide_evidence->getPpmDeltaMass());
}
else
{
delta_list.push_back(p_peptide_evidence->getDeltaMass());
}
}
}
void
IdentificationGroup::startGrouping(
ContaminantRemovalMode contaminantRemovalMode,
......
......@@ -157,14 +157,33 @@ class IdentificationGroup
bool containSample(const QString &sample) const;
/** @brief collect mass delta between theoretical mass and observed mass
* each peptide evidence is only counted once
/** @brief collect mass delta between theoretical mass and observed mass for
* target sequences
*
* each peptide evidence is only counted once it counts only
* peptide evidence for target Sequences
* @param delta_list list of mass delta
* @param unit precision unit, ppm or dalton
* @param state validation state of the peptides to collect
*/
void collectMhDelta(std::vector<pappso::pappso_double> &delta_list,
pappso::PrecisionUnit unit,
ValidationState state) const;
/** @brief collect mass delta between theoretical mass and observed mass
*
* each peptide evidence is only counted once it counts target or decoy
* peptide evidence
* @param delta_list list of mass delta
* @param unit precision unit, ppm or dalton
* @param state validation state of the peptides to collect
*/
void collectTargetDecoyMhDelta(std::vector<pappso::pappso_double> &delta_list,
pappso::PrecisionUnit unit,
ValidationState state) const;
/** @brief look for a peptide in the same XIC
* @param peptide_evidence_list the peptide evidence list to build
* @param p_msrun MSrun to look for
......
/*******************************************************************************
* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
* Copyright (c) 2015 Olivier Langella <olivier.langella@u-psud.fr>.
*
* This file is part of PAPPSOms-tools.
* This file is part of XTPcpp.
*
* PAPPSOms-tools is free software: you can redistribute it and/or modify
* XTPcpp is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms-tools is distributed in the hope that it will be useful,
* XTPcpp is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
#include "config.h"
......
/*******************************************************************************
* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
*
* This file is part of XTPcpp.
*
* XTPcpp is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* XTPcpp is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#include "utils.h"
#include <pappsomspp/exception/exceptionnotfound.h>
#include <pappsomspp/mzrange.h>
......
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