tandemrundialog.cpp

/**
 * \file /gui/tandem_run_dialog/tandem_run_dialog.cpp
 * \date 31/8/2017
 * \author Olivier Langella
 * \brief dialog window to launch tandem process
 */

/*******************************************************************************
* 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 "tandemrundialog.h"

#include "ui_tandem_run_dialog.h"
#include <QDebug>
#include <QSettings>
#include <QFileDialog>
#include <QMessageBox>
#include <pappsomspp/pappsoexception.h>
#include "../../files/tandemparametersfile.h"

//Q_DECLARE_METATYPE(QFileInfo)

TandemRunDialog::TandemRunDialog(QWidget * parent):
    QDialog(parent),
    ui(new Ui::TandemRunDialog)
{
    qDebug() << "TandemRunDialog::TandemRunDialog begin";
    ui->setupUi(this);
    this->setModal(true);
    _p_fasta_file_list = new QStringListModel();
    _p_mz_file_list = new QStringListModel();
    ui->fasta_file_listview->setModel(_p_fasta_file_list);
    ui->mz_file_listview->setModel(_p_mz_file_list);

#if QT_VERSION >= 0x050000
    // Qt5 code
#else
// Qt4 code

#endif
    reset();
    fillPresetComboBox();
    qDebug() << "TandemRunDialog::TandemRunDialog end";
}

TandemRunDialog::~TandemRunDialog()
{
    delete ui;
    delete _p_fasta_file_list;
    delete _p_mz_file_list;
}
void TandemRunDialog::setPresetName(QString preset_name) {
    QSettings settings;
    settings.setValue("tandem/preset_name", preset_name);
    
    
    //get presets :
    TandemParametersFile param_file(ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QString>());
    
    ui->thread_spin_box->setValue(param_file.getTandemParameters().getValue("spectrum, threads").toInt());
    
}
void TandemRunDialog::fillPresetComboBox() {
    ui->preset_combobox->clear();
    QSettings settings;
    QString default_preset_location = settings.value("path/tandemrun_preset_directory", "").toString();
    QString default_preset_name = settings.value("tandem/preset_name", "").toString();

    QDir preset_dir(default_preset_location);
    QStringList filters;
    filters << "*.xml";
    preset_dir.setNameFilters(filters);
    for (QFileInfo file_info: preset_dir.entryInfoList() ) {
        ui->preset_combobox->addItem(file_info.baseName(), QVariant(file_info.absoluteFilePath()));
    }
    int index = ui->preset_combobox->findText(default_preset_name);
    if ( index != -1 ) { // -1 for not found
        ui->preset_combobox->setCurrentIndex(index);
    }

}
void TandemRunDialog::reset() {
    QSettings settings;
    QString default_output_location = settings.value("path/identificationfiles", "").toString();
    QString tandem_bin_path = settings.value("path/tandem_bin", "/usr/bin/tandem").toString();

    ui->output_directory_label->setText(default_output_location);
    ui->tandem_bin_label->setText(tandem_bin_path);

    _p_fasta_file_list->stringList().clear();
    _p_mz_file_list->stringList().clear();
    /*
    if (filenames.size() > 0) {
        settings.setValue("path/identificationfiles", QFileInfo(filenames[0]).absolutePath());
    }*/
}

void TandemRunDialog::selectPresetDirectory() {
    try {
        QSettings settings;
        QString default_preset_location = settings.value("path/tandemrun_preset_directory", "").toString();

        QString directory = QFileDialog::getExistingDirectory(this,tr("Choose preset directory"),default_preset_location );

        if (!directory.isEmpty()) {
            settings.setValue("path/tandemrun_preset_directory", directory);
            fillPresetComboBox();
        }

    }
    catch (pappso::PappsoException & error) {
        //QMessageBox::warning(this,
        //                  tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
    }
}
void TandemRunDialog::selectOutputDirectory() {
    try {
        QSettings settings;
        QString default_output_location = settings.value("path/identificationfiles", "").toString();

        QString directory = QFileDialog::getExistingDirectory(this,tr("Choose output directory"),default_output_location );

        if (!directory.isEmpty()) {
            settings.setValue("path/identificationfiles", directory);
            ui->output_directory_label->setText(directory);
        }


    }
    catch (pappso::PappsoException & error) {
        //QMessageBox::warning(this,
        //                  tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
    }
}

void TandemRunDialog::selectFastaFiles() {
    try {
        QSettings settings;
        QString default_fasta_location = settings.value("path/tandemrun_fastafiles_directory", "").toString();

        QStringList filenames = QFileDialog::getOpenFileNames(this,tr("FASTA files"),default_fasta_location,
                                tr("FASTA files (*.fasta);;all files (*)") );

        if (filenames.size() > 0) {
            settings.setValue("path/tandemrun_fastafiles_directory", QFileInfo(filenames[0]).absolutePath());
        }
        QStringList file_list = _p_fasta_file_list->stringList();
        file_list.append(filenames);
        _p_fasta_file_list->setStringList(file_list);

    }
    catch (pappso::PappsoException & error) {
        //QMessageBox::warning(this,
        //                  tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
    }
}

void TandemRunDialog::selectMzFiles() {
    try {
        QSettings settings;
        QString default_mz_location = settings.value("path/tandemrun_mzfiles_directory", "").toString();

        QStringList filenames = QFileDialog::getOpenFileNames(this,tr("select peak list files"),default_mz_location,
                                tr("mz files (*.mzXML *.mzML *.mgf);;all files (*)") );

        if (filenames.size() > 0) {
            settings.setValue("path/tandemrun_mzfiles_directory", QFileInfo(filenames[0]).absolutePath());
        }
        QStringList file_list = _p_mz_file_list->stringList();
        file_list.append(filenames);
        _p_mz_file_list->setStringList(file_list);

    }
    catch (pappso::PappsoException & error) {
        //QMessageBox::warning(this,
        //                  tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
    }
}

TandemRunBatch TandemRunDialog::getTandemRunBatch() const {
    TandemRunBatch tandem_run_batch;
    tandem_run_batch._tandem_bin_path = ui->tandem_bin_label->text();
    tandem_run_batch._mz_file_list = _p_mz_file_list->stringList();
    tandem_run_batch._fasta_file_list = _p_fasta_file_list->stringList();
    //tandem_run_batch._preset_file = ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QFileInfo>().absoluteFilePath();
    tandem_run_batch._preset_file = ui->preset_combobox->itemData(ui->preset_combobox->currentIndex()).value<QString>();
    tandem_run_batch._output_directory = ui->output_directory_label->text();
    tandem_run_batch._number_of_threads = ui->thread_spin_box->value();
    return tandem_run_batch;
}