identificationdatasource.cpp

/*******************************************************************************
* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and implementation
******************************************************************************/
#include "identificationdatasource.h"
#include "identificationxtandemfile.h"
#include <pappsomspp/pappsoexception.h>
#include <QFileInfo>
#include "../../utils/readspectrum.h"

FastaFileStore IdentificationDataSource::_fasta_file_store;

IdentificationDataSource::IdentificationDataSource(const QString resource_name)
{
    _resource_name = resource_name;
}

IdentificationDataSource::IdentificationDataSource(const IdentificationDataSource& other)
{
    _ms_run_sp = other._ms_run_sp;
    _resource_name = other._resource_name;
}

IdentificationDataSource::~IdentificationDataSource()
{

}

bool IdentificationDataSource::operator==(const IdentificationDataSource& other) const
{

}

const QString & IdentificationDataSource::getResourceName () const {
    return _resource_name;
}

const QString IdentificationDataSource::getSampleName () const {
    QFileInfo file(_ms_run_sp.get()->getFilename());
    return file.baseName();
}

void IdentificationDataSource::setMsRunSp (MsRunSp ms_run_sp) {
    _ms_run_sp = ms_run_sp;
}
MsRunSp IdentificationDataSource::getMsRunSp () const {
    return (_ms_run_sp);
}

IdentificationEngine IdentificationDataSource::getIdentificationEngine() const {
    return _engine;
}
const QString& IdentificationDataSource::getIdentificationEngineVersion() const {
    return _version;
}
void IdentificationDataSource::setIdentificationEngineVersion(const QString& version) {
    _version = version;
}
void IdentificationDataSource::setIdentificationEngineParam(IdentificationEngineParam param, const QString& value) {
    _params.insert(std::pair<IdentificationEngineParam, QString>(param, value));
}

pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const {
    pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunSp(_ms_run_sp, scan_number);
    return spectrum_sp;
}

void IdentificationDataSource::addFastaFile (FastaFile file) {
    _fastafile_list.push_back(IdentificationDataSource::_fasta_file_store.getInstance(file));
}
const std::vector<FastaFileSp> & IdentificationDataSource::getFastaFileList() const {
    qDebug()<<  "IdentificationDataSource::getFastaFileList begin" << _fastafile_list.size();
    return _fastafile_list;
}