/**
* \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/pappsoexception.h>
#include <pappsomspp/exception/exceptionnotfound.h>
#include "ui_edit_tandem_preset_dialog.h"
#include <QSettings>
#include <QDir>
#include <QFileDialog>
#include <QMessageBox>
EditTandemPresetDialog::EditTandemPresetDialog(QWidget *parent)
: QDialog(parent), ui(new Ui::EditTandemPresetView)
{
qDebug() << "EditTandemPresetDialog::EditTandemPresetDialog begin";
ui->setupUi(this);
this->setModal(true);
ui->splitter->setStretchFactor(0, 1);
#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)
{
try
{
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();
}
else
{
_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));
}
}
catch(pappso::PappsoException &error)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
QMessageBox::warning(
this, tr("Error"), tr("Error :\n %1").arg(error.qwhat()));
}
fillPresetComboBox();
populate();
}
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);
QFileInfo my_dir(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()));
}
_preset_directory = directory;
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);
fillPresetComboBox();
populate();
}
void
EditTandemPresetDialog::doLoad()
{
int index = ui->preset_combo_box->currentIndex();
if(index != -1)
{ // -1 for not found
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
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;
try
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_tandem_params = _p_tandem_preset_file->getTandemParameters();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
populate();
}
catch(pappso::PappsoException &error)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
QMessageBox::warning(
this,
tr("Error :"),
tr("Error reading %1 X!Tandem parameter file:\n %2")
.arg(p_tandem_preset_file->getAbsoluteFilePath())
.arg(error.qwhat()));
}
}
else
{
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();
QDir preset_dir(_preset_directory);
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;
QFile html_doc;
if(senderObjName == "spmmeu_push_button")
{
// spmmeu.html
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 == "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")
{
html_doc.setFileName(":/tandem/resources/html_doc/rpmm.html");
}
if(senderObjName == "rpmmotif_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");
}
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");
}
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(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, 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 motif",
ui->rpmmotif_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());
}
catch(pappso::PappsoException &error)
{
QMessageBox::warning(this, tr("Error in parameters :"), error.qwhat());
}
}
void
EditTandemPresetDialog::populate()
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
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);
try
{
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);
}
}
catch(pappso::ExceptionNotFound &error)
{
ui->sunlw_yes_radio_button->setChecked(false);
ui->sunlw_no_radio_button->setChecked(true);
}
try
{
//<note type="input" label="spectrum, neutral loss
// mass">18.01057</note>
ui->snlm_edit->setText(
_tandem_params.getValue("spectrum, neutral loss mass"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->snlm_edit->setText("18.01057");
}
try
{
//<note type="input" label="spectrum, neutral loss window">0.02</note>
ui->snlw_edit->setText(
_tandem_params.getValue("spectrum, neutral loss window"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->snlm_edit->setText("0.02");
}
//<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);
}
//<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);
try
{
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);
}
}
catch(pappso::ExceptionNotFound &error)
{
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);
}
try
{
//<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"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->pcctmc_edit->setText("+17.00305");
}
try
{
//<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"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->pcntmc_edit->setText("+1.00794");
}
//<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);
try
{
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);
}
}
catch(pappso::ExceptionNotFound &error)
{
}
//<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"));
try
{
//<note type="input" label="residue, modification mass 1"></note>
ui->rmm1_edit->setText(
_tandem_params.getValue("residue, modification mass 1"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->rmm1_edit->setText("");
}
try
{
//<note type="input" label="residue, modification mass 2"></note>
ui->rmm2_edit->setText(
_tandem_params.getValue("residue, modification mass 2"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->rmm2_edit->setText("");
}
//<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 motif"></note>
ui->rpmmotif_edit->setText(
_tandem_params.getValue("residue, potential modification motif"));
//<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"));
try
{
//<note type="input" label="refine, modification mass 1"></note>
ui->refmm1_edit->setText(
_tandem_params.getValue("refine, modification mass 1"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->refmm1_edit->setText("");
}
try
{
//<note type="input" label="refine, modification mass 2"></note>
ui->refmm2_edit->setText(
_tandem_params.getValue("refine, modification mass 2"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->refmm2_edit->setText("");
}
//<note type="input" label="refine, potential modification
// mass">15.99491@M</note>
ui->refpmm_edit->setText(
_tandem_params.getValue("refine, potential modification mass"));
try
{
//<note type="input" label="refine, potential modification mass
// 1"></note>
ui->refpmm1_edit->setText(
_tandem_params.getValue("refine, potential modification mass 1"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->refpmm1_edit->setText("");
}
try
{
//<note type="input" label="refine, potential modification mass
// 2"></note>
ui->refpmm2_edit->setText(
_tandem_params.getValue("refine, potential modification mass 2"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->refpmm2_edit->setText("");
}
//<note type="input" label="refine, potential modification motif"></note>
ui->refpmmotif_edit->setText(
_tandem_params.getValue("refine, potential modification motif"));
try
{
//<note type="input" label="refine, potential modification motif
// 1"></note>
ui->refpmmotif1_edit->setText(
_tandem_params.getValue("refine, potential modification motif 1"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->refpmmotif1_edit->setText("");
}
try
{
//<note type="input" label="refine, potential modification motif
// 2"></note>
ui->refpmmotif2_edit->setText(
_tandem_params.getValue("refine, potential modification motif 2"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->refpmmotif2_edit->setText("");
}
//<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);
try
{
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);
}
}
catch(pappso::ExceptionNotFound &error)
{
}
//<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);
}
try
{
//<note type="input" label="output, maximum valid expectation
// value">0.05</note>
ui->omvev_edit->setText(
_tandem_params.getValue("output, maximum valid expectation value"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->omvev_edit->setText("0.01");
}
try
{
//<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"));
}
catch(pappso::ExceptionNotFound &error)
{
ui->omvpev_edit->setText("0.01");
}
//<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);
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"));
}
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());
}
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
EditTandemPresetDialog::done(int r)
{
if(QDialog::Accepted == r) // ok was pressed
{
readUi();
if(!_p_tandem_preset_file->exists())
{
QMessageBox::warning(
this,
tr("Save parameters"),
tr("Parameters file does not exists.\nPlease save it before "
"pressing ok or cancel edition"));
return;
}
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;
}
}