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/**
* \file gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
* \date 30/9/2017
* \author Olivier Langella
* \brief edit tandem preset dialog
*/
/*******************************************************************************
* 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 "edittandempresetdialog.h"
#include <QDebug>
#include <pappsomspp/exception/exceptionnotfound.h>
#include "ui_edit_tandem_preset_dialog.h"
EditTandemPresetDialog::EditTandemPresetDialog(QWidget * parent):
QDialog(parent),
ui(new Ui::EditTandemPresetView)
{
qDebug() << "EditTandemPresetDialog::EditTandemPresetDialog begin";
ui->setupUi(this);
this->setModal(true);
#if QT_VERSION >= 0x050000
// Qt5 code
#else
// Qt4 code
#endif
qDebug() << "EditTandemPresetDialog::EditTandemPresetDialog end";
}
EditTandemPresetDialog::~EditTandemPresetDialog()
{
delete ui;
if (_p_tandem_preset_file != nullptr) {
delete _p_tandem_preset_file;
}
}
void EditTandemPresetDialog::setTandemParametersFile(const TandemParametersFile & tandem_preset_file) {
if (tandem_preset_file.exists()) {
_p_tandem_preset_file = new TandemParametersFile( tandem_preset_file);
_preset_directory = _p_tandem_preset_file->getAbsoluteDir().absolutePath();
_p_tandem_preset_file = new TandemParametersFile(":/tandem/ressources/model/QExactive_analysis_FDR_nosemi.xml");
QSettings settings;
_preset_directory = settings.value("path/tandemrun_preset_directory", "").toString();
_tandem_params = _p_tandem_preset_file->getTandemParameters();
void EditTandemPresetDialog::doCopy() {
ui->method_name_line_edit->setText("untitled");
readUi();
if (_p_tandem_preset_file == nullptr) {
throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
}
else {
delete _p_tandem_preset_file;
}
_p_tandem_preset_file = new TandemParametersFile(QString("%1/untitled.xml").arg(_preset_directory));
void EditTandemPresetDialog::doSelectDir() {
try {
QString directory = QFileDialog::getExistingDirectory(this,tr("Choose preset directory"),_preset_directory );
if (!directory.isEmpty() && ! directory.isNull()) {
fillPresetComboBox();
}
}
catch (pappso::PappsoException & error) {
//QMessageBox::warning(this,
// tr("Error choosing identification result files : %1").arg(error.qwhat()), error);
}
}
void EditTandemPresetDialog::doSave() {
readUi();
if (_p_tandem_preset_file == nullptr) {
throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
}
_p_tandem_preset_file->setTandemParameters(_tandem_params);
}
void EditTandemPresetDialog::doLoad() {
int index = ui->preset_combo_box->currentIndex();
if (_p_tandem_preset_file == nullptr) {
throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
}
else {
delete _p_tandem_preset_file;
}
_p_tandem_preset_file = new TandemParametersFile(
ui->preset_combo_box->itemData(index).value<QString>());
_tandem_params = _p_tandem_preset_file->getTandemParameters();
populate();
const TandemParametersFile & EditTandemPresetDialog::getTandemParametersFile() const {
if (_p_tandem_preset_file == nullptr) {
throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
}
if (!_p_tandem_preset_file->exists()) {
throw pappso::PappsoException(QObject::tr("preset file %1 does not exists").arg(_p_tandem_preset_file->getAbsoluteFilePath()));
}
return *_p_tandem_preset_file;
}
void EditTandemPresetDialog::fillPresetComboBox() {
ui->preset_combo_box->clear();
QString default_preset_name = _tandem_params.getMethodName();
QStringList filters;
filters << "*.xml";
preset_dir.setNameFilters(filters);
for (QFileInfo file_info: preset_dir.entryInfoList() ) {
ui->preset_combo_box->addItem(file_info.baseName(), QVariant(file_info.absoluteFilePath()));
}
int index = ui->preset_combo_box->findText(default_preset_name);
if ( index != -1 ) { // -1 for not found
ui->preset_combo_box->setCurrentIndex(index);
}
}
void EditTandemPresetDialog::doEdit(QString value) {
QObject *senderObj = sender();
QString senderObjName = senderObj->objectName();
qDebug() << "EditTandemPresetDialog::doEdit begin " << senderObjName << " " << value;
qDebug() << "EditTandemPresetDialog::doEdit end " << senderObjName;
}
void EditTandemPresetDialog::doHelp() {
QObject *senderObj = sender();
QString senderObjName = senderObj->objectName();
qDebug() << "EditTandemPresetDialog::doHelp begin " << senderObjName;
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html_doc.setFileName(":/tandem/resources/html_doc/spmmeu.html");
}
if(senderObjName == "smpc_push_button")
{
//spmmeu.html
html_doc.setFileName(":/tandem/resources/html_doc/smpc.html");
}
if(senderObjName == "spmmem_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/spmmem.html");
}
if(senderObjName == "spmmep_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/spmmep.html");
}
if(senderObjName == "spmmie_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/spmmie.html");
}
if(senderObjName == "sfmt_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sfmt.html");
}
if(senderObjName == "sfmmeu_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sfmmeu.html");
}
if(senderObjName == "sfmme_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sfmme.html");
}
if(senderObjName == "sunlw_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sunlw.html");
}
if(senderObjName == "sdr_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sdr.html");
}
if(senderObjName == "stp_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/stp.html");
}
if(senderObjName == "smp_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/smp.html");
}
if(senderObjName == "smfmz_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/smfmz.html");
}
if(senderObjName == "smpmh_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/smpmh.html");
}
if(senderObjName == "spsbs_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/spsbs.html");
}
if(senderObjName == "suca_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/suca.html");
}
if(senderObjName == "st_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/st.html");
}
if(senderObjName == "pcs_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pcs.html");
}
if(senderObjName == "pcsemi_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pcsemi.html");
}
if(senderObjName == "pcctmc_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pcctmc.html");
}
if(senderObjName == "pcntmc_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pcntmc.html");
}
if(senderObjName == "pctrmm_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pctrmm.html");
}
if(senderObjName == "pntrmm_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pntrmm.html");
}
if(senderObjName == "pqa_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pqa.html");
}
if(senderObjName == "pqp_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pqp.html");
}
if(senderObjName == "pstpb_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pstpb.html");
}
if(senderObjName == "pmrmf_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/pmrmf.html");
}
if ((senderObjName == "rmm_push_button") || (senderObjName == "rmm1_push_button") || (senderObjName == "rmm2_push_button"))
{
html_doc.setFileName(":/tandem/resources/html_doc/rmm.html");
}
if ((senderObjName == "rpmm_push_button") || (senderObjName == "rpmm1_push_button") || (senderObjName == "rpmm2_push_button"))
{
html_doc.setFileName(":/tandem/resources/html_doc/rpmm.html");
}
if ((senderObjName == "rpmmotif_push_button") || (senderObjName == "rpmmotif1_push_button") || (senderObjName == "rpmmotif2_push_button"))
{
html_doc.setFileName(":/tandem/resources/html_doc/rpmmotif.html");
}
if(senderObjName == "smic_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/smic.html");
}
if(senderObjName == "smmcs_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/smmcs.html");
}
if(senderObjName == "scp_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/scp.html");
}
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if(senderObjName == "sir_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sir.html");
}
if(senderObjName == "syi_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/syi.html");
}
if(senderObjName == "sbi_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sbi.html");
}
if(senderObjName == "sci_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sci.html");
}
if(senderObjName == "szi_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/szi.html");
}
if(senderObjName == "sai_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sai.html");
}
if(senderObjName == "sxi_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sxi.html");
}
if(senderObjName == "refine_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/refine.html");
}
if(senderObjName == "rmvev_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/rmvev.html");
}
if(senderObjName == "refpntm_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/refpntm.html");
}
if(senderObjName == "refpctm_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/refpctm.html");
}
if ((senderObjName == "refmm_push_button")|| (senderObjName == "refmm1_push_button")|| (senderObjName == "refmm2_push_button"))
{
html_doc.setFileName(":/tandem/resources/html_doc/refmm.html");
}
if ((senderObjName == "refpmm_push_button")|| (senderObjName == "refpmm1_push_button")|| (senderObjName == "refpmm2_push_button"))
{
html_doc.setFileName(":/tandem/resources/html_doc/refpmm.html");
}
if ((senderObjName == "refpmmotif_push_button")|| (senderObjName == "refpmmotif1_push_button")|| (senderObjName == "refpmmotif2_push_button"))
{
html_doc.setFileName(":/tandem/resources/html_doc/refpmmotif.html");
}
if(senderObjName == "rupmffr_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/rupmffr.html");
}
if(senderObjName == "rcsemi_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/rcsemi.html");
}
if(senderObjName == "ruc_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/ruc.html");
}
if(senderObjName == "rss_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/rss.html");
}
if(senderObjName == "rpm_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/rpm.html");
}
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if ((senderObjName == "omvev_push_button") || (senderObjName == "omvpev_push_button"))
{
html_doc.setFileName(":/tandem/resources/html_doc/omvev.html");
}
if (senderObjName == "oresu_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/oresu.html");
}
if (senderObjName == "osrb_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/osrb.html");
}
if (senderObjName == "oprot_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/oprot.html");
}
if (senderObjName == "oseq_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/oseq.html");
}
if (senderObjName == "oosc_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/oosc.html");
}
if (senderObjName == "ospec_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/ospec.html");
}
if (senderObjName == "opara_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/opara.html");
}
if (senderObjName == "ohist_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/ohist.html");
}
if (senderObjName == "ohcw_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/ohcw.html");
}
if (senderObjName == "oph_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/oph.html");
}
if (senderObjName == "oxp_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/oxp.html");
}
if (senderObjName == "mzid_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/mzid.html");
}
if (html_doc.open(QFile::ReadOnly | QFile::Text)) {
QTextStream in(&html_doc);
ui->doc_plain_text_edit->setHtml(in.readAll());
qDebug() << "EditTandemPresetDialog::doHelp doc " << in.readAll();
}
else {
qDebug() << "EditTandemPresetDialog::doHelp doc not found";
}
qDebug() << "EditTandemPresetDialog::doHelp end " << senderObjName;
}
void EditTandemPresetDialog::readUi() {
try {
_tandem_params.setMethodName(ui->method_name_line_edit->text());
_tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error units", "Daltons");
if (ui->spmmeu_ppm_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error units", "ppm");
}
_tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error minus", ui->parent_ion_lower_window_edit->text());
_tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass error plus", ui->parent_ion_upper_window_edit->text());
_tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass isotope error", "no");
if (ui->spmmie_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("spectrum, parent monoisotopic mass isotope error", "yes");
}
_tandem_params.setParamLabelValue("spectrum, maximum parent charge", ui->smpc_edit->text());
_tandem_params.setParamLabelValue("spectrum, fragment mass type", ui->sfmt_combo_box->currentText());
_tandem_params.setParamLabelValue("spectrum, fragment monoisotopic mass error units", "Daltons");
if (ui->sfmmeu_ppm_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("spectrum, fragment monoisotopic mass error units", "ppm");
}
_tandem_params.setParamLabelValue("spectrum, fragment monoisotopic mass error", ui->sfmme_edit->text());
_tandem_params.setParamLabelValue("spectrum, use neutral loss window", "no");
if (ui->sunlw_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("spectrum, use neutral loss window", "yes");
}
_tandem_params.setParamLabelValue("spectrum, dynamic range", ui->sdr_edit->text());
_tandem_params.setParamLabelValue("spectrum, total peaks", ui->stp_edit->text());
_tandem_params.setParamLabelValue("spectrum, minimum peaks", ui->smp_edit->text());
_tandem_params.setParamLabelValue("spectrum, minimum fragment mz", ui->smfmz_edit->text());
_tandem_params.setParamLabelValue("spectrum, minimum parent m+h", ui->smpmh_edit->text());
_tandem_params.setParamLabelValue("spectrum, sequence batch size", ui->spsbs_edit->text());
_tandem_params.setParamLabelValue("spectrum, use contrast angle", "no");
if (ui->suca_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("spectrum, use contrast angle", "yes");
}
_tandem_params.setParamLabelValue("spectrum, threads", ui->st_edit->text());
_tandem_params.setParamLabelValue("protein, cleavage site", ui->pcs_edit->text());
_tandem_params.setParamLabelValue("protein, cleavage semi", "no");
if (ui->pcsemi_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("protein, cleavage semi", "yes");
}
_tandem_params.setParamLabelValue("protein, cleavage C-terminal mass change", ui->pcctmc_edit->text());
_tandem_params.setParamLabelValue("protein, cleavage N-terminal mass change", ui->pcntmc_edit->text());
_tandem_params.setParamLabelValue("protein, quick acetyl", "no");
if (ui->pqa_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("protein, quick acetyl", "yes");
}
_tandem_params.setParamLabelValue("protein, quick pyrolidone", "no");
if (ui->pqp_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("protein, quick pyrolidone", "yes");
}
_tandem_params.setParamLabelValue("protein, stP bias", "no");
if (ui->pstpb_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("protein, stP bias", "yes");
}
_tandem_params.setParamLabelValue("protein, modified residue mass file", ui->pmrmf_edit->text());
_tandem_params.setParamLabelValue("residue, modification mass", ui->rmm_edit->text());
_tandem_params.setParamLabelValue("residue, modification mass 1", ui->rmm1_edit->text());
_tandem_params.setParamLabelValue("residue, modification mass 2", ui->rmm2_edit->text());
_tandem_params.setParamLabelValue("residue, potential modification mass", ui->rpmm_edit->text());
_tandem_params.setParamLabelValue("residue, potential modification mass 1", ui->rpmm1_edit->text());
_tandem_params.setParamLabelValue("residue, potential modification mass 2", ui->rpmm2_edit->text());
_tandem_params.setParamLabelValue("residue, potential modification motif", ui->rpmmotif_edit->text());
_tandem_params.setParamLabelValue("residue, potential modification motif 1", ui->rpmmotif1_edit->text());
_tandem_params.setParamLabelValue("residue, potential modification motif 2", ui->rpmmotif2_edit->text());
_tandem_params.setParamLabelValue("scoring, maximum missed cleavage sites", ui->smmcs_edit->text());
_tandem_params.setParamLabelValue("scoring, cyclic permutation", "no");
if (ui->scp_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("scoring, cyclic permutation", "yes");
}
_tandem_params.setParamLabelValue("scoring, include reverse", "no");
if (ui->sir_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("scoring, include reverse", "yes");
}
_tandem_params.setParamLabelValue("scoring, minimum ion count", ui->smic_edit->text());
_tandem_params.setParamLabelValue("scoring, y ions", "no");
if (ui->syi_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("scoring, y ions", "yes");
}
_tandem_params.setParamLabelValue("scoring, b ions", "no");
if (ui->sbi_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("scoring, b ions", "yes");
}
_tandem_params.setParamLabelValue("scoring, c ions", "no");
if (ui->sci_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("scoring, c ions", "yes");
}
_tandem_params.setParamLabelValue("scoring, z ions", "no");
if (ui->szi_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("scoring, z ions", "yes");
}
_tandem_params.setParamLabelValue("scoring, a ions", "no");
if (ui->sai_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("scoring, a ions", "yes");
}
_tandem_params.setParamLabelValue("scoring, x ions", "no");
if (ui->sxi_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("scoring, x ions", "yes");
}
_tandem_params.setParamLabelValue("refine", "no");
if (ui->refine_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("refine", "yes");
}
_tandem_params.setParamLabelValue("refine, maximum valid expectation value", ui->rmvev_edit->text());
_tandem_params.setParamLabelValue("refine, potential N-terminus modifications", ui->refpntm_edit->text());
_tandem_params.setParamLabelValue("refine, potential C-terminus modifications", ui->refpctm_edit->text());
_tandem_params.setParamLabelValue("refine, modification mass", ui->refmm_edit->text());
_tandem_params.setParamLabelValue("refine, modification mass 1", ui->refmm1_edit->text());
_tandem_params.setParamLabelValue("refine, modification mass 2", ui->refmm2_edit->text());
_tandem_params.setParamLabelValue("refine, potential modification mass", ui->refpmm_edit->text());
_tandem_params.setParamLabelValue("refine, potential modification mass 1", ui->refpmm1_edit->text());
_tandem_params.setParamLabelValue("refine, potential modification mass 2", ui->refpmm2_edit->text());
_tandem_params.setParamLabelValue("refine, potential modification motif", ui->refpmmotif_edit->text());
_tandem_params.setParamLabelValue("refine, potential modification motif 1", ui->refpmmotif1_edit->text());
_tandem_params.setParamLabelValue("refine, potential modification motif 2", ui->refpmmotif2_edit->text());
_tandem_params.setParamLabelValue("refine, use potential modifications for full refinement", "no");
if (ui->rupmffr_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("refine, use potential modifications for full refinement", "yes");
}
_tandem_params.setParamLabelValue("refine, cleavage semi", "no");
if (ui->rcsemi_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("refine, cleavage semi", "yes");
}
_tandem_params.setParamLabelValue("refine, unanticipated cleavage", "no");
if (ui->ruc_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("refine, unanticipated cleavage", "yes");
}
_tandem_params.setParamLabelValue("refine, spectrum synthesis", "no");
if (ui->rss_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("refine, spectrum synthesis", "yes");
}
_tandem_params.setParamLabelValue("refine, point mutations", "no");
if (ui->rpm_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("refine, point mutations", "yes");
}
_tandem_params.setParamLabelValue("output, maximum valid expectation value", ui->omvev_edit->text());
_tandem_params.setParamLabelValue("output, maximum valid protein expectation value", ui->omvpev_edit->text());
_tandem_params.setParamLabelValue("output, results", "valid");
if (ui->oresu_all_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("output, results", "all");
}
if (ui->oresu_stochastic_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("output, results", "stochastic");
}
_tandem_params.setParamLabelValue("output, spectra", "no");
if (ui->ospec_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("output, spectra", "yes");
}
_tandem_params.setParamLabelValue("output, histogram column width", "30");
_tandem_params.setParamLabelValue("output, xsl path", ui->oxp_edit->text());
_tandem_params.setParamLabelValue("output, mzid", "no");
if (ui->mzid_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("output, mzid", "yes");
}
}
catch (pappso::PappsoException & error) {
QMessageBox::warning(this,tr("Error in parameters :"), error.qwhat());
}
}
void EditTandemPresetDialog::populate() {
try {
ui->method_name_line_edit->setText(_tandem_params.getMethodName());
/*
* <note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
* */
ui->spmmeu_daltons_radio_button->setChecked(true);
ui->spmmeu_ppm_radio_button->setChecked(false);
if ( _tandem_params.getValue("spectrum, parent monoisotopic mass error units") == "ppm" ) { // -1 for not found
ui->spmmeu_daltons_radio_button->setChecked(false);
ui->spmmeu_ppm_radio_button->setChecked(true);
}
//<note type="input" label="spectrum, parent monoisotopic mass error minus">10</note>
ui->parent_ion_lower_window_edit->setText(_tandem_params.getValue("spectrum, parent monoisotopic mass error minus"));
//<note type="input" label="spectrum, parent monoisotopic mass error plus">10</note>
ui->parent_ion_upper_window_edit->setText(_tandem_params.getValue("spectrum, parent monoisotopic mass error plus"));
//<note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note>
ui->spmmie_yes_radio_button->setChecked(true);
ui->spmmie_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("spectrum, parent monoisotopic mass isotope error") == "no" ) { // -1 for not found
ui->spmmie_yes_radio_button->setChecked(false);
ui->spmmie_no_radio_button->setChecked(true);
}
//<note type="input" label="spectrum, maximum parent charge">4</note>
ui->smpc_edit->setText(_tandem_params.getValue("spectrum, maximum parent charge"));
//<note type="input" label="spectrum, fragment mass type">monoisotopic</note>
auto index = ui->sfmt_combo_box->findText("monoisotopic");
if ( index != -1 ) { // -1 for not found
ui->sfmt_combo_box->setCurrentIndex(index);
}
//<note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>
ui->sfmmeu_daltons_radio_button->setChecked(true);
ui->sfmmeu_ppm_radio_button->setChecked(false);
if ( _tandem_params.getValue("spectrum, fragment monoisotopic mass error units") == "ppm" ) { // -1 for not found
ui->sfmmeu_daltons_radio_button->setChecked(false);
ui->sfmmeu_ppm_radio_button->setChecked(true);
}
//<note type="input" label="spectrum, fragment monoisotopic mass error">0.02</note>
ui->sfmme_edit->setText(_tandem_params.getValue("spectrum, fragment monoisotopic mass error"));
//<note type="input" label="spectrum, use neutral loss window">yes</note>
ui->sunlw_yes_radio_button->setChecked(true);
ui->sunlw_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("spectrum, use neutral loss window") == "no" ) { // -1 for not found
ui->sunlw_yes_radio_button->setChecked(false);
ui->sunlw_no_radio_button->setChecked(true);
}
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//<note type="input" label="spectrum, dynamic range">100.0</note>
ui->sdr_edit->setText(_tandem_params.getValue("spectrum, dynamic range"));
//<note type="input" label="spectrum, total peaks">100</note>
ui->stp_edit->setText(_tandem_params.getValue("spectrum, total peaks"));
ui->smp_edit->setText(_tandem_params.getValue("spectrum, minimum peaks"));
//<note type="input" label="spectrum, minimum fragment mz">150.0</note>
ui->smfmz_edit->setText(_tandem_params.getValue("spectrum, minimum fragment mz"));
//<note type="input" label="spectrum, minimum parent m+h">500.0</note>
ui->smpmh_edit->setText(_tandem_params.getValue("spectrum, minimum parent m+h"));
//<note type="input" label="spectrum, sequence batch size">1000</note>
ui->spsbs_edit->setText(_tandem_params.getValue("spectrum, sequence batch size"));
//<note type="input" label="spectrum, use contrast angle">no</note>
ui->suca_yes_radio_button->setChecked(true);
ui->suca_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("spectrum, use contrast angle") == "no" ) { // -1 for not found
ui->suca_yes_radio_button->setChecked(false);
ui->suca_no_radio_button->setChecked(true);
}
//<note type="input" label="spectrum, threads">1</note>
ui->st_edit->setText(_tandem_params.getValue("spectrum, threads"));
//<note type="input" label="protein, cleavage site">[RK]|{P}</note>
ui->pcs_edit->setText(_tandem_params.getValue("protein, cleavage site"));
//<note type="input" label="protein, cleavage semi">no</note>
ui->pcsemi_yes_radio_button->setChecked(true);
ui->pcsemi_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("protein, cleavage semi") == "no" ) { // -1 for not found
ui->pcsemi_yes_radio_button->setChecked(false);
ui->pcsemi_no_radio_button->setChecked(true);
}
//<note type="input" label="protein, cleavage C-terminal mass change">+17.00305</note>
ui->pcctmc_edit->setText(_tandem_params.getValue("protein, cleavage C-terminal mass change"));
//<note type="input" label="protein, cleavage N-terminal mass change">+1.00794</note>
ui->pcntmc_edit->setText(_tandem_params.getValue("protein, cleavage N-terminal mass change"));
//<note type="input" label="protein, C-terminal residue modification mass">0.0</note>
ui->pctrmm_edit->setText(_tandem_params.getValue("protein, C-terminal residue modification mass"));
//<note type="input" label="protein, N-terminal residue modification mass">0.0</note>
ui->pntrmm_edit->setText(_tandem_params.getValue("protein, N-terminal residue modification mass"));
//<note type="input" label="protein, quick acetyl">yes</note>
ui->pqa_yes_radio_button->setChecked(true);
ui->pqa_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("protein, quick acetyl") == "no" ) { // -1 for not found
ui->pqa_yes_radio_button->setChecked(false);
ui->pqa_no_radio_button->setChecked(true);
}
//<note type="input" label="protein, quick pyrolidone">yes</note>
ui->pqp_yes_radio_button->setChecked(true);
ui->pqp_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("protein, quick pyrolidone") == "no" ) { // -1 for not found
ui->pqp_yes_radio_button->setChecked(false);
ui->pqp_no_radio_button->setChecked(true);
}
//<note type="input" label="protein, stP bias">yes</note>
ui->pstpb_yes_radio_button->setChecked(true);
ui->pstpb_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("protein, stP bias") == "no" ) { // -1 for not found
ui->pstpb_yes_radio_button->setChecked(false);
ui->pstpb_no_radio_button->setChecked(true);
}
//<note type="input" label="protein, modified residue mass file"></note>
ui->pmrmf_edit->setText(_tandem_params.getValue("protein, modified residue mass file"));
//<note type="input" label="residue, modification mass">57.02146@C</note>
ui->rmm_edit->setText(_tandem_params.getValue("residue, modification mass"));
//<note type="input" label="residue, modification mass 1"></note>
ui->rmm1_edit->setText(_tandem_params.getValue("residue, modification mass 1"));
//<note type="input" label="residue, modification mass 2"></note>
ui->rmm2_edit->setText(_tandem_params.getValue("residue, modification mass 2"));
//<note type="input" label="residue, potential modification mass">15.99491@M</note>
ui->rpmm_edit->setText(_tandem_params.getValue("residue, potential modification mass"));
//<note type="input" label="residue, potential modification mass 1"></note>
ui->rpmm1_edit->setText(_tandem_params.getValue("residue, potential modification mass 1"));
//<note type="input" label="residue, potential modification mass 2"></note>
ui->rpmm2_edit->setText(_tandem_params.getValue("residue, potential modification mass 2"));
//<note type="input" label="residue, potential modification motif"></note>
ui->rpmmotif_edit->setText(_tandem_params.getValue("residue, potential modification motif"));
//<note type="input" label="residue, potential modification motif 1"></note>
ui->rpmmotif1_edit->setText(_tandem_params.getValue("residue, potential modification motif 1"));
//<note type="input" label="residue, potential modification motif 2"></note>
ui->rpmmotif2_edit->setText(_tandem_params.getValue("residue, potential modification motif 2"));
//<note type="input" label="scoring, minimum ion count">4</note>
ui->smic_edit->setText(_tandem_params.getValue("scoring, minimum ion count"));
//<note type="input" label="scoring, maximum missed cleavage sites">1</note>
ui->smmcs_edit->setText(_tandem_params.getValue("scoring, maximum missed cleavage sites"));
//<note type="input" label="scoring, cyclic permutation">yes</note>
ui->scp_yes_radio_button->setChecked(true);
ui->scp_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("scoring, cyclic permutation") == "no" ) { // -1 for not found
ui->scp_yes_radio_button->setChecked(false);
ui->scp_no_radio_button->setChecked(true);
}
//<note type="input" label="scoring, include reverse">yes</note>
ui->sir_yes_radio_button->setChecked(true);
ui->sir_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("scoring, include reverse") == "no" ) { // -1 for not found
ui->sir_yes_radio_button->setChecked(false);
ui->sir_no_radio_button->setChecked(true);
}
//<note type="input" label="scoring, y ions">yes</note>
ui->syi_yes_radio_button->setChecked(true);
ui->syi_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("scoring, y ions") == "no" ) { // -1 for not found
ui->syi_yes_radio_button->setChecked(false);
ui->syi_no_radio_button->setChecked(true);
}
//<note type="input" label="scoring, b ions">yes</note>
ui->sbi_yes_radio_button->setChecked(true);
ui->sbi_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("scoring, b ions") == "no" ) { // -1 for not found
ui->sbi_yes_radio_button->setChecked(false);
ui->sbi_no_radio_button->setChecked(true);
}
//<note type="input" label="scoring, c ions">no</note>
ui->sci_yes_radio_button->setChecked(true);
ui->sci_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("scoring, c ions") == "no" ) { // -1 for not found
ui->sci_yes_radio_button->setChecked(false);
ui->sci_no_radio_button->setChecked(true);
}
//<note type="input" label="scoring, z ions">no</note>
ui->szi_yes_radio_button->setChecked(true);
ui->szi_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("scoring, z ions") == "no" ) { // -1 for not found
ui->szi_yes_radio_button->setChecked(false);
ui->szi_no_radio_button->setChecked(true);
}
//<note type="input" label="scoring, a ions">no</note>
ui->sai_yes_radio_button->setChecked(true);
ui->sai_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("scoring, a ions") == "no" ) { // -1 for not found
ui->sai_yes_radio_button->setChecked(false);
ui->sai_no_radio_button->setChecked(true);
}
//<note type="input" label="scoring, x ions">no</note>
ui->sxi_yes_radio_button->setChecked(true);
ui->sxi_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("scoring, x ions") == "no" ) { // -1 for not found
ui->sxi_yes_radio_button->setChecked(false);
ui->sxi_no_radio_button->setChecked(true);
}
//<note type="input" label="refine">yes</note>
ui->refine_yes_radio_button->setChecked(true);
ui->refine_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("refine") == "no" ) { // -1 for not found
ui->refine_yes_radio_button->setChecked(false);
ui->refine_no_radio_button->setChecked(true);
}
//<note type="input" label="refine, maximum valid expectation value">0.01</note>
ui->rmvev_edit->setText(_tandem_params.getValue("refine, maximum valid expectation value"));
//<note type="input" label="refine, potential N-terminus modifications">+42.01056@[</note>
ui->refpntm_edit->setText(_tandem_params.getValue("refine, potential N-terminus modifications"));
//<note type="input" label="refine, potential C-terminus modifications"></note>
ui->refpctm_edit->setText(_tandem_params.getValue("refine, potential C-terminus modifications"));
//<note type="input" label="refine, modification mass">57.02146@C</note>
ui->refmm_edit->setText(_tandem_params.getValue("refine, modification mass"));
//<note type="input" label="refine, modification mass 1"></note>
ui->refmm1_edit->setText(_tandem_params.getValue("refine, modification mass 1"));
//<note type="input" label="refine, modification mass 2"></note>
ui->refmm2_edit->setText(_tandem_params.getValue("refine, modification mass 2"));
//<note type="input" label="refine, potential modification mass">15.99491@M</note>
ui->refpmm_edit->setText(_tandem_params.getValue("refine, potential modification mass"));
//<note type="input" label="refine, potential modification mass 1"></note>
ui->refpmm1_edit->setText(_tandem_params.getValue("refine, potential modification mass 1"));
//<note type="input" label="refine, potential modification mass 2"></note>
ui->refpmm2_edit->setText(_tandem_params.getValue("refine, potential modification mass 2"));
//<note type="input" label="refine, potential modification motif"></note>
ui->refpmmotif_edit->setText(_tandem_params.getValue("refine, potential modification motif"));
//<note type="input" label="refine, potential modification motif 1"></note>
ui->refpmmotif1_edit->setText(_tandem_params.getValue("refine, potential modification motif 1"));
//<note type="input" label="refine, potential modification motif 2"></note>
ui->refpmmotif2_edit->setText(_tandem_params.getValue("refine, potential modification motif 2"));
//<note type="input" label="refine, use potential modifications for full refinement">yes</note>
ui->rupmffr_yes_radio_button->setChecked(true);
ui->rupmffr_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("refine, use potential modifications for full refinement") == "no" ) { // -1 for not found
ui->rupmffr_yes_radio_button->setChecked(false);
ui->rupmffr_no_radio_button->setChecked(true);
}
//<note type="input" label="refine, cleavage semi">no</note>
ui->rcsemi_yes_radio_button->setChecked(true);
ui->rcsemi_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("refine, cleavage semi") == "no" ) { // -1 for not found
ui->rcsemi_yes_radio_button->setChecked(false);
ui->rcsemi_no_radio_button->setChecked(true);
}
//<note type="input" label="refine, unanticipated cleavage">no</note>
ui->ruc_yes_radio_button->setChecked(true);
ui->ruc_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("refine, unanticipated cleavage") == "no" ) { // -1 for not found
ui->ruc_yes_radio_button->setChecked(false);
ui->ruc_no_radio_button->setChecked(true);
}
//<note type="input" label="refine, spectrum synthesis">yes</note>
ui->rss_yes_radio_button->setChecked(true);
ui->rss_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("refine, spectrum synthesis") == "no" ) { // -1 for not found
ui->rss_yes_radio_button->setChecked(false);
ui->rss_no_radio_button->setChecked(true);
}
//<note type="input" label="refine, point mutations">no</note>
ui->rpm_yes_radio_button->setChecked(true);
ui->rpm_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("refine, point mutations") == "no" ) { // -1 for not found
ui->rpm_yes_radio_button->setChecked(false);
ui->rpm_no_radio_button->setChecked(true);
}
//<note type="input" label="output, maximum valid expectation value">0.05</note>
ui->omvev_edit->setText(_tandem_params.getValue("output, maximum valid expectation value"));
//<note type="input" label="output, maximum valid protein expectation value">0.05</note>
ui->omvpev_edit->setText(_tandem_params.getValue("output, maximum valid protein expectation value"));
//<note type="input" label="output, results">valid</note>
ui->oresu_all_radio_button->setChecked(false);
ui->oresu_valid_radio_button->setChecked(true);
ui->oresu_stochastic_radio_button->setChecked(false);
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if ( _tandem_params.getValue("output, results") == "all" ) { // -1 for not found
ui->oresu_all_radio_button->setChecked(true);
ui->oresu_valid_radio_button->setChecked(false);
ui->oresu_stochastic_radio_button->setChecked(false);
}
if ( _tandem_params.getValue("output, results") == "stochastic" ) { // -1 for not found
ui->oresu_all_radio_button->setChecked(false);
ui->oresu_valid_radio_button->setChecked(false);
ui->oresu_stochastic_radio_button->setChecked(true);
}
//<note type="input" label="output, sort results by">spectrum</note>
//<note type="input" label="output, proteins">yes</note>
//<note type="input" label="output, sequences">yes</note>
//<note type="input" label="output, one sequence copy">yes</note>
//<note type="input" label="output, spectra">yes</note>
ui->ospec_yes_radio_button->setChecked(true);
ui->ospec_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("output, spectra") == "no" ) { // -1 for not found
ui->ospec_yes_radio_button->setChecked(false);
ui->ospec_no_radio_button->setChecked(true);
}
//<note type="input" label="output, parameters">yes</note>
//<note type="input" label="output, performance">yes</note>
//<note type="input" label="output, histograms">yes</note>
//<note type="input" label="output, histogram column width">30</note>
//<note type="input" label="output, path hashing">no</note>
//<note type="input" label="output, xsl path">tandem-style.xsl</note>
ui->oxp_edit->setText(_tandem_params.getValue("output, xsl path"));
//<note type="input" label="output, mzid">no</note>
ui->mzid_yes_radio_button->setChecked(true);
ui->mzid_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("output, mzid") == "no" ) { // -1 for not found
ui->mzid_yes_radio_button->setChecked(false);
ui->mzid_no_radio_button->setChecked(true);
}
}
catch (pappso::ExceptionNotFound & error) {
QMessageBox::warning(this,tr("Parameter not found :"), error.qwhat());
catch (pappso::PappsoException & error) {
QMessageBox::warning(this,tr("Error in parameters :"), error.qwhat());
void EditTandemPresetDialog::done(int r)
{
if(QDialog::Accepted == r) // ok was pressed
{
readUi();
TandemParameters ref_params = _p_tandem_preset_file->getTandemParameters();
if(ref_params.equals(_tandem_params)) // validate the data somehow
{
QDialog::done(r);
return;
}
else
{
QMessageBox::warning(this,
tr("Save parameters"), tr("Parameters modified but not saved.\nPlease save it before pressing ok or cancel edition"));
return;
}
}
else // cancel, close or exc was pressed
{
QDialog::done(r);
return;
}
}