identificationgroup.cpp

/*******************************************************************************
* 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/>.
*
* Contributors:
*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
******************************************************************************/

#include "identificationgroup.h"
#include "project.h"
#include "../utils/groupstore.h"
#include <pappsomspp/pappsoexception.h>


IdentificationGroup::IdentificationGroup(Project * project)
{
    _p_project = project;
}

IdentificationGroup::~IdentificationGroup()
{
    auto it = _protein_match_list.begin();
    while (it != _protein_match_list.end()) {
        delete (*it);
        it++;
    }
}

const PtmGroupingExperiment * IdentificationGroup::getPtmGroupingExperiment() const {
    return _p_grp_ptm_experiment;
}
const GroupStore & IdentificationGroup::getGroupStore() const {
    return _group_store;
}

unsigned int IdentificationGroup::countPeptideMass(ValidationState state) const {

    std::vector<pappso::GrpPeptide *> count_peptide_mass;
    for (auto & p_protein_match : _protein_match_list) {
        if (p_protein_match->getValidationState() >= state) {
            p_protein_match->countPeptideMass(count_peptide_mass, state);
        }
    }
    std::sort(count_peptide_mass.begin(), count_peptide_mass.end());
    auto last = std::unique(count_peptide_mass.begin(),count_peptide_mass.end());
    return std::distance(count_peptide_mass.begin(),last);
}

unsigned int IdentificationGroup::countPeptideMassSample(ValidationState state) const {

    std::vector<std::size_t> count_peptide_mass_sample;
    for (auto & p_protein_match : _protein_match_list) {
        if (p_protein_match->getValidationState() >= state) {
            p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
        }
    }
    std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
    auto last = std::unique(count_peptide_mass_sample.begin(),count_peptide_mass_sample.end());
    return std::distance(count_peptide_mass_sample.begin(),last);
}

unsigned int IdentificationGroup::countDecoyPeptideMassSample(ValidationState state) const {
    std::vector<std::size_t> count_peptide_mass_sample;
    for (auto & p_protein_match : _protein_match_list) {
        if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
            if (p_protein_match->getValidationState() >= state) {
                p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
            }
        }
    }
    std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
    auto last = std::unique(count_peptide_mass_sample.begin(),count_peptide_mass_sample.end());
    return std::distance(count_peptide_mass_sample.begin(),last);
}


unsigned int IdentificationGroup::countDecoyProteinMatch(ValidationState state) const {
    return std::count_if (_protein_match_list.begin(), _protein_match_list.end(), [state](const ProteinMatch * p_protein_match) {
        if ((p_protein_match->getProteinXtpSp().get()->isDecoy()) && (p_protein_match->getValidationState() >= state)) {
            return true;
        }
        else              {
            return false;
        }
    });
}

unsigned int IdentificationGroup::countPeptideEvidence(ValidationState state) const {
    std::set<const PeptideEvidence *> peptide_evidence_set;
    for (auto & p_protein_match : _protein_match_list) {
        if (p_protein_match->getValidationState() >= state) {
            p_protein_match->collectPeptideEvidences(peptide_evidence_set,state);
        }
    }
    return peptide_evidence_set.size();
}

unsigned int IdentificationGroup::countDecoyPeptideEvidence(ValidationState state) const {
    std::set<const PeptideEvidence *> peptide_evidence_set;
    for (auto & p_protein_match : _protein_match_list) {
        if (p_protein_match->getValidationState() >= state) {
            if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
                p_protein_match->collectPeptideEvidences(peptide_evidence_set,state);
            }
        }
    }
    return peptide_evidence_set.size();
}

unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const {
    unsigned int i=0;
    for (auto & p_protein_match : _protein_match_list) {
        if (p_protein_match->getValidationState() >= state) {
            i+=p_protein_match->countPeptideMatch(state);
        }
    }
    return i;
}

unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const {
    unsigned int i=0;
    for (auto & p_protein_match : _protein_match_list) {
        if (p_protein_match->getValidationState() >= state) {
            if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
                i+=p_protein_match->countPeptideMatch(state);
            }
        }
    }
    return i;
}
unsigned int IdentificationGroup::countProteinMatch(ValidationState state) const {
    return std::count_if (_protein_match_list.begin(), _protein_match_list.end(), [state](const ProteinMatch * p_protein_match) {
        if (p_protein_match->getValidationState() >= state) {
            return true;
        }
        else              {
            return false;
        }
    });
}

void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
    qDebug() << "IdentificationGroup::updateAutomaticFilters begin" ;
    for (IdentificationDataSource * p_identification_source_list:_id_source_list) {
        p_identification_source_list->getPeptideEvidenceStore().updateAutomaticFilters(automatic_filter_parameters);
    }
    for (auto & p_protein_match : _protein_match_list) {
        p_protein_match->updateAutomaticFilters(automatic_filter_parameters);
    }

    if (_p_grp_experiment != nullptr) {
    }
    qDebug() << "IdentificationGroup::updateAutomaticFilters end" ;

}
ProteinMatch * IdentificationGroup::getProteinMatchInstance(const QString accession) {
    if (accession.isEmpty()) {
        throw pappso::PappsoException(QObject::tr("Error protein match not found : accession is empty"));
    }
    auto it_cache = _cache_accession_protein_match.find(accession);
    if (it_cache == _cache_accession_protein_match.end()) {
        //accession not found in cache
        ProteinMatch * p_protein_match = new ProteinMatch();
        _cache_accession_protein_match.insert(std::pair<QString, ProteinMatch *>(accession, p_protein_match));
        _protein_match_list.push_back(p_protein_match);
        return p_protein_match;
    }
    else {
        return it_cache->second;
    }
    return nullptr;
}
void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
    _protein_match_list.push_back(protein_match);
}

bool IdentificationGroup::contains (const MsRun * p_msrun) const {
    for (const MsRunSp & msrun: _ms_run_list) {
        if (msrun.get() == p_msrun) return true;
    }
    return false;
}

void IdentificationGroup::addIdentificationDataSourceP(IdentificationDataSource *  p_identification_source) {
    addMsRunSp(p_identification_source->getMsRunSp());
    auto it = std::find (_id_source_list.begin() ,_id_source_list.end(),p_identification_source);
    if (it == _id_source_list.end()) {
        _id_source_list.push_back(p_identification_source);
    }
}
void IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp) {
    auto it = std::find (_ms_run_list.begin() ,_ms_run_list.end(),ms_run_sp);
    if (it == _ms_run_list.end()) {
        _ms_run_list.push_back(ms_run_sp);
    }
}
const std::vector<MsRunSp> & IdentificationGroup::getMsRunSpList() const {
    return _ms_run_list;
}
const std::vector<IdentificationDataSource *> & IdentificationGroup::getIdentificationDataSourceList() const {
    return _id_source_list;
}
const std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() const {
    return _protein_match_list;
}
std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() {
    return _protein_match_list;
}

std::size_t IdentificationGroup::countGroup()const {
    return _group_store.countGroup();
}

std::size_t IdentificationGroup::countSubGroup()const {
    return _group_store.countSubGroup();
}

void IdentificationGroup::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
    std::set<const PeptideEvidence *> already_counted;
    for (auto & p_protein_match : _protein_match_list) {
        if (p_protein_match->getValidationState() >= state) {
            if (!p_protein_match->getProteinXtpSp().get()->isDecoy()) {
                p_protein_match->collectMhDelta(already_counted, delta_list, unit, state);
            }
        }
    }
}
void IdentificationGroup::startGrouping (const GroupingType & grouping_type, WorkMonitorInterface * p_work_monitor) {
    qDebug() << "IdentificationGroup::startGrouping begin ";
    if (_p_grp_experiment != nullptr) {
        delete _p_grp_experiment;
    }
    _p_grp_experiment = GroupingExperiment::newInstance(grouping_type, p_work_monitor);
    for (ProteinMatch * p_protein_match : _protein_match_list) {
        p_protein_match->setGroupingExperiment(_p_grp_experiment);
    }

    _p_grp_experiment->startGrouping();
    _group_store.clear();
    for (ProteinMatch * p_protein_match : _protein_match_list) {
        p_protein_match->setGroupInstance(_group_store);
    }

    if (_p_grp_ptm_experiment != nullptr) {
        delete _p_grp_ptm_experiment;
        _p_grp_ptm_experiment = nullptr;
    }
    qDebug() << "IdentificationGroup::startGrouping end ";
}

void IdentificationGroup::startPtmGrouping () {
    qDebug() << "IdentificationGroup::startPtmGrouping begin ";
    if (_p_grp_ptm_experiment != nullptr) {
        delete _p_grp_ptm_experiment;
        _p_grp_ptm_experiment = nullptr;
    }
    _p_grp_ptm_experiment = new PtmGroupingExperiment();
    _p_grp_ptm_experiment->setValidationState(ValidationState::grouped);
    for (ProteinMatch * p_protein_match : _protein_match_list) {
        _p_grp_ptm_experiment->addProteinMatch(p_protein_match);
    }

    _p_grp_ptm_experiment->startGrouping();

    qDebug() << "IdentificationGroup::startPtmGrouping end ";
}

const QString IdentificationGroup::getTabName() const {
    return _ms_run_list[0]->getFilename();
}



pappso::pappso_double IdentificationGroup::getPeptideMassFdr(ValidationState state) const {
    //ValidationState state = ValidationState::valid;
    pappso::pappso_double total_peptide=countPeptideMassSample(state);
    pappso::pappso_double false_peptide=countDecoyPeptideMassSample(state);

    return (false_peptide/total_peptide);
}

pappso::pappso_double IdentificationGroup::getProteinFdr(ValidationState state) const {
    //ValidationState state = ValidationState::valid;
    pappso::pappso_double total_prot=countProteinMatch(state);
    pappso::pappso_double false_prot=countDecoyProteinMatch(state);


    return (false_prot/total_prot);
}