Newer
Older
/**
* \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();
_tandem_params = _p_tandem_preset_file->getTandemParameters();
_p_tandem_preset_file = new TandemParametersFile(":/tandem/resources/model/QExactive_analysis_FDR_nosemi.xml");
_tandem_params = _p_tandem_preset_file->getTandemParameters();
QSettings settings;
_preset_directory = settings.value("path/tandemrun_preset_directory", "").toString();
_p_tandem_preset_file->setDirectory(QDir(_preset_directory));
Langella Olivier
committed
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()) {
if (!my_dir.isWritable()) {
throw pappso::PappsoException(QObject::tr("this directory is not writable, check permissions (%1)").arg(my_dir.absoluteFilePath()));
}
fillPresetComboBox();
}
}
catch (pappso::PappsoException & error) {
QMessageBox::warning(this,tr("Error :"), tr("Error choosing preset directory : %1").arg(error.qwhat()));
void EditTandemPresetDialog::doSave() {
readUi();
if (_p_tandem_preset_file == nullptr) {
throw pappso::PappsoException(QObject::tr("_p_tandem_preset_file == nullptr"));
}
_p_tandem_preset_file->setDirectory(QDir(_preset_directory));
_p_tandem_preset_file->setTandemParameters(_tandem_params);
}
void EditTandemPresetDialog::doLoad() {
int index = ui->preset_combo_box->currentIndex();
TandemParametersFile * p_tandem_preset_file = new TandemParametersFile(
ui->preset_combo_box->itemData(index).value<QString>());
if (p_tandem_preset_file->isTandemPresetFile()) {
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 = p_tandem_preset_file;
_tandem_params = _p_tandem_preset_file->getTandemParameters();
populate();
QMessageBox::warning(this,tr("Error :"), tr("%1 is not an X!Tandem parameter file").arg(p_tandem_preset_file->getAbsoluteFilePath()));
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;
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
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");
}
Langella Olivier
committed
if(senderObjName == "snlm_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/snlm.html");
}
if(senderObjName == "snlw_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/snlw.html");
}
if(senderObjName == "suns_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/suns.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");
}
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
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");
}
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
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");
}
Langella Olivier
committed
_tandem_params.setParamLabelValue("spectrum, neutral loss mass", ui->snlm_edit->text());
_tandem_params.setParamLabelValue("spectrum, neutral loss window", ui->snlw_edit->text());
_tandem_params.setParamLabelValue("spectrum, use noise suppression", "no");
if (ui->suns_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("spectrum, use noise suppression", "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);
}
Langella Olivier
committed
//<note type="input" label="spectrum, neutral loss mass">18.01057</note>
ui->snlm_edit->setText(_tandem_params.getValue("spectrum, neutral loss mass"));
//<note type="input" label="spectrum, neutral loss window">0.02</note>
ui->snlw_edit->setText(_tandem_params.getValue("spectrum, neutral loss window"));
//<note type="input" label="spectrum, use noise suppression">yes</note>
ui->suns_yes_radio_button->setChecked(true);
ui->suns_no_radio_button->setChecked(false);
if ( _tandem_params.getValue("spectrum, use noise suppression") == "no" ) { // -1 for not found
ui->suns_yes_radio_button->setChecked(false);
ui->suns_no_radio_button->setChecked(true);
}
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
//<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);
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
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);