msrun.cpp

/**
 * \filed core/msrun.cpp
 * \date 5/4/2017
 * \author Olivier Langella
 * \brief describes an MS run (chemical sample injected in a mass spectrometer)
 */


/*******************************************************************************
* 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 "msrun.h"
#include <QFileInfo>
#include <QSettings>
#include <QDebug>
#include <QDir>
#include <pappsomspp/msrun/msrunreaderfactory.h>
#include <pappsomspp/exception/exceptionnotfound.h>

MsRun::MsRun(const QString & location):pappso::MsRunId(location) {
    QFileInfo fileinfo(location);
}

MsRun::MsRun(const MsRun& other):pappso::MsRunId(other) {
    _param_stats = other._param_stats;
}

MsRun::~MsRun() {
}
pappso::MsRunReaderSp & MsRun::getMsRunReaderSp() {
    return _msrun_reader_sp;
}

void MsRun::setMsRunStatistics(MsRunStatistics param, const QVariant& value) {
    _param_stats.insert(std::pair<MsRunStatistics, QVariant>(param, value));
}

const std::map<MsRunStatistics, QVariant> & MsRun::getMsRunStatisticsMap() const {
    return _param_stats;
}

const QVariant MsRun::getMsRunStatistics(MsRunStatistics param) const {
    try {
        return _param_stats.at(param);
    }
    catch (std::out_of_range) {
        return QVariant();
    }
}

bool MsRun::findMsRunFile() {

    QFileInfo file(this->getFilename());
    bool file_ok = false;

    if (file.exists()) {
        file_ok = true;
    }

    QString basename = file.baseName();
    QString onlyfilename = file.fileName();
    QSettings settings;
    QString path = settings.value("path/mzdatadir", "").toString();

    QDir dir_search(path);

    QFileInfoList files = dir_search.entryInfoList();
    foreach (QFileInfo file, files) {
        if (file.isDir()) {
            qDebug() << "DIR: " << file.fileName();
        } else {
            qDebug() << "FILE: " << file.fileName();
            if (onlyfilename == file.fileName()) {
                this->setFilename(file.absoluteFilePath());
                file_ok = true;
            }
            if (file.fileName().contains(onlyfilename)) {
                this->setFilename(file.absoluteFilePath());
                file_ok =  true;
            }
        }
    }
    if (file_ok) {
        if (_msrun_reader_sp == nullptr) {
            _msrun_reader_sp = pappso::MsRunReaderFactory::getInstance().buildPwizMsRunReaderSp(*this);
        }
    }
    return file_ok;
}

void MsRun::checkMsRunStatistics() {
       QVariant msrun_var = getMsRunStatistics(MsRunStatistics::total_spectra);
    if (msrun_var.isNull()) {
        try {
            pappso::MsRunSimpleStatistics stats;
            _msrun_reader_sp.get()->readSpectrumCollection(stats);

            setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) stats.getTotalCount());
            setMsRunStatistics(MsRunStatistics::total_spectra_ms1, (unsigned int) stats.getMsLevelCount(1));
            setMsRunStatistics(MsRunStatistics::total_spectra_ms2, (unsigned int) stats.getMsLevelCount(2));
            setMsRunStatistics(MsRunStatistics::total_spectra_ms3, (unsigned int) stats.getMsLevelCount(3));
        }
        catch (pappso::ExceptionNotFound& error) {
            //no file found, no statistics
        }
    }
}