From f6af7221c5bedacf40517782fad836fd98ea0317 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 2 Oct 2018 13:50:01 +0200
Subject: [PATCH] indentation
---
src/core/msrun.h | 2 +-
src/core/tandem_run/tandembatchprocess.cpp | 14 +-
src/core/tandem_run/tandemparameters.cpp | 4 +-
src/files/tandemparametersfile.cpp | 4 +-
.../edittandempresetdialog.cpp | 50 ++--
src/gui/protein_view/proteinwindow.cpp | 33 +--
.../ptmpeptidelistwindow.cpp | 4 +-
.../ptmpeptidetableproxymodel.cpp | 2 +-
src/gui/tandem_run_dialog/tandemrundialog.cpp | 6 +-
src/gui/workerthread.cpp | 256 +++++-------------
src/input/mascot/mascotdatparser.cpp | 18 +-
src/input/mascot/mascotdatparser.h | 3 +-
src/input/pepxmlsaxhandler.cpp | 2 +-
src/input/xpipsaxhandler.cpp | 2 +-
src/output/masschroqml.cpp | 10 +-
src/output/ods/peptidepossheet.cpp | 4 +-
src/output/ods/peptidesheet.cpp | 6 +-
src/output/ods/ptm/ptmislandsheet.cpp | 4 +-
src/output/ods/samplesheet.cpp | 18 +-
src/output/ods/spectrasheet.cpp | 3 +-
src/output/proticdbml.cpp | 2 +-
src/output/xpip.cpp | 6 +-
22 files changed, 161 insertions(+), 292 deletions(-)
diff --git a/src/core/msrun.h b/src/core/msrun.h
index 5420e9d81..3a5399c4a 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -70,7 +70,7 @@ class MsRun : public pappso::MsRunId
bool findMsRunFile();
pappso::MsRunReaderSp &getMsRunReaderSp();
-
+
/** @brief release shared pointer on MSrun reader
*/
void freeMsRunReaderSp();
diff --git a/src/core/tandem_run/tandembatchprocess.cpp b/src/core/tandem_run/tandembatchprocess.cpp
index ba9be3d7d..f2c3142b9 100644
--- a/src/core/tandem_run/tandembatchprocess.cpp
+++ b/src/core/tandem_run/tandembatchprocess.cpp
@@ -86,10 +86,10 @@ TandemBatchProcess::writeXmlDatabaseFile(QXmlStreamWriter *p_out)
p_out->writeStartElement("taxon");
p_out->writeAttribute("label", "usedefined");
//<file format="peptide"
- //URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/contaminants_standards.fasta"></file>
+ // URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/contaminants_standards.fasta"></file>
//<file format="peptide"
- //URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/Escherichia
- //coli 27J42_WGS_ECOLI_1.fasta"></file>
+ // URL="/gorgone/pappso/jouy/users/Didier/fasta/20170608_Delastours/Escherichia
+ // coli 27J42_WGS_ECOLI_1.fasta"></file>
for(QString fasta_file : _tandem_run_batch._fasta_file_list)
{
p_out->writeStartElement("file");
@@ -198,7 +198,7 @@ TandemBatchProcess::writeXmlInputFile(QXmlStreamWriter *p_out,
p_out->writeEndElement();
//<note type="input" label="list path, default
- //parameters">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/QExactive_IAM_4CPU_Classic_ClassicAvecReversed..xml</note>
+ // parameters">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/QExactive_IAM_4CPU_Classic_ClassicAvecReversed..xml</note>
p_out->writeStartElement("note");
p_out->writeAttribute("type", "input");
p_out->writeAttribute("label", "list path, default parameters");
@@ -206,7 +206,7 @@ TandemBatchProcess::writeXmlInputFile(QXmlStreamWriter *p_out,
p_out->writeEndElement();
//<note type="input" label="list path, taxonomy
- //information">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/database.xml</note>
+ // information">/gorgone/pappso/tmp/temp_condor_job93294001891239208719639434471283743/database.xml</note>
p_out->writeStartElement("note");
p_out->writeAttribute("type", "input");
p_out->writeAttribute("label", "list path, taxonomy information");
@@ -215,7 +215,7 @@ TandemBatchProcess::writeXmlInputFile(QXmlStreamWriter *p_out,
//<note type="input" label="spectrum,
- //path">/gorgone/pappso/jouy/raw/2017_Qex/20170405_Delastours/20170405_Delastour_11.mzXML</note>
+ // path">/gorgone/pappso/jouy/raw/2017_Qex/20170405_Delastours/20170405_Delastour_11.mzXML</note>
p_out->writeStartElement("note");
p_out->writeAttribute("type", "input");
@@ -242,7 +242,7 @@ TandemBatchProcess::writeXmlInputFile(QXmlStreamWriter *p_out,
p_out->writeEndElement();
//<note type="input" label="output,
- //path">/gorgone/pappso/jouy/users/Didier/Xcal2017/2017_05_04_Delastours/Interrogation_souches_sequencees/Patient27/J42/20170405_Delastour_11.xml</note>
+ // path">/gorgone/pappso/jouy/users/Didier/Xcal2017/2017_05_04_Delastours/Interrogation_souches_sequencees/Patient27/J42/20170405_Delastour_11.xml</note>
p_out->writeStartElement("note");
p_out->writeAttribute("type", "input");
diff --git a/src/core/tandem_run/tandemparameters.cpp b/src/core/tandem_run/tandemparameters.cpp
index b20665b01..e558e51b3 100644
--- a/src/core/tandem_run/tandemparameters.cpp
+++ b/src/core/tandem_run/tandemparameters.cpp
@@ -105,9 +105,9 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
{
// list path
//<note type="input" label="list path, default
- //parameters">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/QExactive_analysis_FDR_nosemi.xml</note>
+ // parameters">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/QExactive_analysis_FDR_nosemi.xml</note>
//<note type="input" label="list path, taxonomy
- //information">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/database.xml</note>
+ // information">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/database.xml</note>
if(getLabelCategory(label) == "list path")
{
return;
diff --git a/src/files/tandemparametersfile.cpp b/src/files/tandemparametersfile.cpp
index 498ce27ee..68c82d692 100644
--- a/src/files/tandemparametersfile.cpp
+++ b/src/files/tandemparametersfile.cpp
@@ -216,8 +216,8 @@ TandemParametersFile::writeXmlParametersFile(
//<?xml version="1.0" encoding="UTF-8"?>
//<bioml label="example api document">
//<note type="input" label="spectrum, parent monoisotopic mass error
- //units">ppm</note> <note type="input" label="spectrum, parent monoisotopic
- //mass error minus">10</note>
+ // units">ppm</note> <note type="input" label="spectrum, parent monoisotopic
+ // mass error minus">10</note>
p_out->writeStartElement("bioml");
p_out->writeAttribute("label", "example api document");
for(const QString &label : parameters.getMapLabelValue().keys())
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
index 0f08ef9f3..598e3a75e 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -849,15 +849,15 @@ EditTandemPresetDialog::populate()
ui->spmmeu_ppm_radio_button->setChecked(true);
}
//<note type="input" label="spectrum, parent monoisotopic mass error
- //minus">10</note>
+ // 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>
+ // 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>
+ // error">yes</note>
ui->spmmie_yes_radio_button->setChecked(true);
ui->spmmie_no_radio_button->setChecked(false);
if(_tandem_params.getValue(
@@ -871,14 +871,14 @@ EditTandemPresetDialog::populate()
_tandem_params.getValue("spectrum, maximum parent charge"));
//<note type="input" label="spectrum, fragment mass
- //type">monoisotopic</note>
+ // 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>
+ // units">Daltons</note>
ui->sfmmeu_daltons_radio_button->setChecked(true);
ui->sfmmeu_ppm_radio_button->setChecked(false);
if(_tandem_params.getValue(
@@ -889,7 +889,7 @@ EditTandemPresetDialog::populate()
}
//<note type="input" label="spectrum, fragment monoisotopic mass
- //error">0.02</note>
+ // error">0.02</note>
ui->sfmme_edit->setText(
_tandem_params.getValue("spectrum, fragment monoisotopic mass error"));
@@ -965,20 +965,20 @@ EditTandemPresetDialog::populate()
//<note type="input" label="protein, cleavage C-terminal mass
- //change">+17.00305</note>
+ // 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>
+ // 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>
+ // 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>
+ // mass">0.0</note>
ui->pntrmm_edit->setText(_tandem_params.getValue(
"protein, N-terminal residue modification mass"));
@@ -1027,26 +1027,26 @@ EditTandemPresetDialog::populate()
//<note type="input" label="residue, potential modification
- //mass">15.99491@M</note>
+ // 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>
+ // 1"></note>
ui->rpmm1_edit->setText(
_tandem_params.getValue("residue, potential modification mass 1"));
//<note type="input" label="residue, potential modification mass
- //2"></note>
+ // 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>
+ // 1"></note>
ui->rpmmotif1_edit->setText(
_tandem_params.getValue("residue, potential modification motif 1"));
//<note type="input" label="residue, potential modification motif
- //2"></note>
+ // 2"></note>
ui->rpmmotif2_edit->setText(
_tandem_params.getValue("residue, potential modification motif 2"));
@@ -1054,7 +1054,7 @@ EditTandemPresetDialog::populate()
ui->smic_edit->setText(
_tandem_params.getValue("scoring, minimum ion count"));
//<note type="input" label="scoring, maximum missed cleavage
- //sites">1</note>
+ // sites">1</note>
ui->smmcs_edit->setText(
_tandem_params.getValue("scoring, maximum missed cleavage sites"));
//<note type="input" label="scoring, cyclic permutation">yes</note>
@@ -1132,16 +1132,16 @@ EditTandemPresetDialog::populate()
ui->refine_no_radio_button->setChecked(true);
}
//<note type="input" label="refine, maximum valid expectation
- //value">0.01</note>
+ // 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>
+ // 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>
+ // 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>
@@ -1154,7 +1154,7 @@ EditTandemPresetDialog::populate()
ui->refmm2_edit->setText(
_tandem_params.getValue("refine, modification mass 2"));
//<note type="input" label="refine, potential modification
- //mass">15.99491@M</note>
+ // 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>
@@ -1167,15 +1167,15 @@ EditTandemPresetDialog::populate()
ui->refpmmotif_edit->setText(
_tandem_params.getValue("refine, potential modification motif"));
//<note type="input" label="refine, potential modification motif
- //1"></note>
+ // 1"></note>
ui->refpmmotif1_edit->setText(
_tandem_params.getValue("refine, potential modification motif 1"));
//<note type="input" label="refine, potential modification motif
- //2"></note>
+ // 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>
+ // refinement">yes</note>
ui->rupmffr_yes_radio_button->setChecked(true);
ui->rupmffr_no_radio_button->setChecked(false);
if(_tandem_params.getValue(
@@ -1219,11 +1219,11 @@ EditTandemPresetDialog::populate()
//<note type="input" label="output, maximum valid expectation
- //value">0.05</note>
+ // 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>
+ // 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>
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 9b17a7741..397c5aea1 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -39,8 +39,8 @@ DbXrefButton::DbXrefButton(QWidget *parent, DbXref dbxref) : QPushButton(parent)
_dbxref = dbxref;
#if QT_VERSION >= 0x050000
// Qt5 code
- QObject::connect(
- this, &DbXrefButton::clicked, this, &DbXrefButton::clickedSlot);
+ QObject::connect(this, &DbXrefButton::clicked, this,
+ &DbXrefButton::clickedSlot);
#else
// Qt4 code
QObject::connect(this, SIGNAL(clicked()), this, SLOT(clickedSlot()));
@@ -67,23 +67,16 @@ ProteinWindow::ProteinWindow(ProjectWindow *parent)
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(_p_project_window,
- &ProjectWindow::identificationGroupGrouped,
- this,
+ connect(_p_project_window, &ProjectWindow::identificationGroupGrouped, this,
&ProteinWindow::doIdentificationGroupGrouped);
- connect(_p_project_window,
- &ProjectWindow::peptideEvidenceSelected,
- this,
+ connect(_p_project_window, &ProjectWindow::peptideEvidenceSelected, this,
&ProteinWindow::doPeptideEvidenceSelected);
#else
// Qt4 code
connect(_p_project_window,
- SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
- this,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
- connect(_p_project_window,
- SIGNAL(peptideMatchSelected(PeptideMatch *)),
- this,
+ connect(_p_project_window, SIGNAL(peptideMatchSelected(PeptideMatch *)), this,
SLOT(doPeptideMatchSelected(PeptideMatch *)));
// connect(_protein_table_model_p, SIGNAL(layoutChanged()), this,
@@ -150,10 +143,9 @@ ProteinWindow::updateDisplay()
_p_protein_match->getProteinXtpSp().get()->getDbxrefList())
{
QString accession = ui->accession_label->text().replace(
- dbxref.accession,
- QString("<span style=\"color:%2;\">%1</span>")
- .arg(dbxref.accession)
- .arg("blue"));
+ dbxref.accession, QString("<span style=\"color:%2;\">%1</span>")
+ .arg(dbxref.accession)
+ .arg("blue"));
ui->accession_label->setText(accession);
qDebug() << "ProteinWindow::updateDisplay " << accession;
@@ -179,14 +171,13 @@ ProteinWindow::updateDisplay()
}
catch(pappso::PappsoException exception_pappso)
{
- QMessageBox::warning(this,
- tr("Unable to display protein details :"),
+ QMessageBox::warning(this, tr("Unable to display protein details :"),
exception_pappso.qwhat());
}
catch(std::exception exception_std)
{
- QMessageBox::warning(
- this, tr("Unable to display protein details :"), exception_std.what());
+ QMessageBox::warning(this, tr("Unable to display protein details :"),
+ exception_std.what());
}
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index f2b0b68b5..5fb53774e 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -75,8 +75,8 @@ PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow *parent)
// connect (_project_window,
// SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)),
// this,SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *))); connect
- // (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
- // this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+ // (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup
+ // *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
connect(ui->ptm_peptide_tableview, SIGNAL(clicked(const QModelIndex &)),
_ptm_proxy_model_p, SLOT(onTableClicked(const QModelIndex &)));
connect(this, SIGNAL(requestPeptideDetailView(PeptideMatch *)),
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
index 2d4e4368c..4a15cc548 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
@@ -195,7 +195,7 @@ PtmPeptideTableProxyModel::showContextMenu(const QModelIndex &index)
_p_context_menu->exec(QCursor::pos());
//_p_context_menu->exec(_p_ptm_peptide_list_window->
- //mapToGlobal(QCursor::pos()));
+ // mapToGlobal(QCursor::pos()));
_p_context_menu->show();
}
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index 3337ec9fb..3c9472054 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -439,11 +439,11 @@ TandemRunDialog::done(int r)
// QString("%1/xtpcpp").arg(settings.value("condor/tmp_dir",
// "/tmp").toString()); _p_tmp_dir = new QTemporaryDir(condor_tmp_dir);
//_p_tmp_dir->setAutoRemove(settings.value("condor/tmp_dir_autoremove",
- //true).toBool()); _condor_submit_command =
- //settings.value("condor/submit", "/usr/bin/condor_submit").toString();
+ // true).toBool()); _condor_submit_command =
+ // settings.value("condor/submit", "/usr/bin/condor_submit").toString();
//_condor_q_command = settings.value("condor/condor_q",
//"/usr/bin/condor_q").toString(); _condor_rm_command =
- //settings.value("condor/condor_rm", "/usr/bin/condor_rm").toString();
+ // settings.value("condor/condor_rm", "/usr/bin/condor_rm").toString();
settings.setValue("tandem/condor_request_memory",
ui->request_memory_edit->text());
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 5a6fc5fa9..3fefbddb3 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -57,177 +57,103 @@ WorkerThread::WorkerThread(MainWindow *p_main_window)
#if QT_VERSION >= 0x050000
// Qt5 code
// worker message
- connect(_p_work_monitor,
- &WorkMonitor::workerMessage,
- p_main_window,
+ connect(_p_work_monitor, &WorkMonitor::workerMessage, p_main_window,
&MainWindow::doDisplayLoadingMessage);
- connect(_p_work_monitor,
- &WorkMonitor::workerMessagePercent,
- p_main_window,
+ connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_main_window,
&MainWindow::doDisplayLoadingMessagePercent);
- connect(_p_work_monitor,
- &WorkMonitor::workerAppendText,
- p_main_window,
+ connect(_p_work_monitor, &WorkMonitor::workerAppendText, p_main_window,
&MainWindow::doWorkerAppendText);
- connect(_p_work_monitor,
- &WorkMonitor::workerSetText,
- p_main_window,
+ connect(_p_work_monitor, &WorkMonitor::workerSetText, p_main_window,
&MainWindow::doWorkerSetText);
- connect(_p_work_monitor,
- &WorkMonitor::workerJobFinished,
- p_main_window,
+ connect(_p_work_monitor, &WorkMonitor::workerJobFinished, p_main_window,
&MainWindow::doDisplayJobFinished);
- connect(p_main_window,
- &MainWindow::operateXpipFile,
- this,
+ connect(p_main_window, &MainWindow::operateXpipFile, this,
&WorkerThread::doXpipFileLoad);
- connect(p_main_window,
- &MainWindow::operateWritingXpipFile,
- this,
+ connect(p_main_window, &MainWindow::operateWritingXpipFile, this,
&WorkerThread::doWritingXpipFile);
- connect(this,
- &WorkerThread::projectReady,
- p_main_window,
+ connect(this, &WorkerThread::projectReady, p_main_window,
&MainWindow::doProjectReady);
- connect(this,
- &WorkerThread::loadingResultsFinished,
- p_main_window,
+ connect(this, &WorkerThread::loadingResultsFinished, p_main_window,
&MainWindow::doLoadingResultsReady);
- connect(p_main_window,
- &MainWindow::operateLoadingResults,
- this,
+ connect(p_main_window, &MainWindow::operateLoadingResults, this,
&WorkerThread::doLoadingResults);
- connect(p_main_window,
- &MainWindow::operateRunningXtandem,
- this,
+ connect(p_main_window, &MainWindow::operateRunningXtandem, this,
&WorkerThread::doRunningXtandem);
- connect(this,
- &WorkerThread::loadingMessage,
- p_main_window,
+ connect(this, &WorkerThread::loadingMessage, p_main_window,
&MainWindow::doDisplayLoadingMessage);
- connect(this,
- &WorkerThread::projectNotReady,
- p_main_window,
+ connect(this, &WorkerThread::projectNotReady, p_main_window,
&MainWindow::doProjectNotReady);
// grouping
- connect(p_main_window,
- &MainWindow::operateGrouping,
- this,
+ connect(p_main_window, &MainWindow::operateGrouping, this,
&WorkerThread::doGrouping);
- connect(this,
- &WorkerThread::groupingFinished,
- p_main_window,
+ connect(this, &WorkerThread::groupingFinished, p_main_window,
&MainWindow::doGroupingFinished);
// masschroq write
- connect(p_main_window,
- &MainWindow::operateWritingMassChroqFile,
- this,
+ connect(p_main_window, &MainWindow::operateWritingMassChroqFile, this,
&WorkerThread::doWritingMassChroqFile);
- connect(p_main_window,
- &MainWindow::operateWritingMassChroqPrmFile,
- this,
+ connect(p_main_window, &MainWindow::operateWritingMassChroqPrmFile, this,
&WorkerThread::doWritingMassChroqPrmFile);
- connect(p_main_window,
- &MainWindow::operateWritingMcqrSpectralCountFile,
- this,
+ connect(p_main_window, &MainWindow::operateWritingMcqrSpectralCountFile, this,
&WorkerThread::doWritingMcqrSpectralCountFile);
// protic write
- connect(p_main_window,
- &MainWindow::operateWritingProticFile,
- this,
+ connect(p_main_window, &MainWindow::operateWritingProticFile, this,
&WorkerThread::doWritingProticFile);
// writing ODS file :
- connect(p_main_window,
- &MainWindow::operateWritingOdsFile,
- this,
+ connect(p_main_window, &MainWindow::operateWritingOdsFile, this,
&WorkerThread::doWritingOdsFile);
- connect(this,
- &WorkerThread::operationFailed,
- p_main_window,
+ connect(this, &WorkerThread::operationFailed, p_main_window,
&MainWindow::doOperationFailed);
- connect(this,
- &WorkerThread::operationFinished,
- p_main_window,
+ connect(this, &WorkerThread::operationFinished, p_main_window,
&MainWindow::doOperationFinished);
#else
// Qt4 code
// worker message
- connect(_p_work_monitor,
- SIGNAL(workerMessage(QString)),
- p_main_window,
+ connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_main_window,
SLOT(doDisplayLoadingMessage(QString)));
- connect(_p_work_monitor,
- SIGNAL(workerMessage(QString, int)),
- p_main_window,
+ connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)), p_main_window,
SLOT(doDisplayLoadingMessage(QString, int)));
- connect(_p_work_monitor,
- SIGNAL(workerAppendText(char *)),
- p_main_window,
+ connect(_p_work_monitor, SIGNAL(workerAppendText(char *)), p_main_window,
SLOT(doWorkerAppendText(char *)));
- connect(p_main_window,
- SIGNAL(operateXpipFile(QString)),
- this,
+ connect(p_main_window, SIGNAL(operateXpipFile(QString)), this,
SLOT(doXpipFileLoad(QString)));
- connect(this,
- SIGNAL(projectReady(ProjectSp)),
- p_main_window,
+ connect(this, SIGNAL(projectReady(ProjectSp)), p_main_window,
SLOT(doProjectReady(ProjectSp)));
connect(
p_main_window,
SIGNAL(operateLoadingResults(bool, AutomaticFilterParameters, QStringList)),
- this,
- SLOT(doLoadingResults(bool, AutomaticFilterParameters, QStringList)));
+ this, SLOT(doLoadingResults(bool, AutomaticFilterParameters, QStringList)));
- connect(p_main_window,
- SIGNAL(operateRunningXtandem(TandemRunBatch)),
- this,
+ connect(p_main_window, SIGNAL(operateRunningXtandem(TandemRunBatch)), this,
SLOT(doRunningXtandem(TandemRunBatch)));
- connect(this,
- SIGNAL(loadingMessage(QString)),
- p_main_window,
+ connect(this, SIGNAL(loadingMessage(QString)), p_main_window,
SLOT(doDisplayLoadingMessage(QString)));
- connect(this,
- SIGNAL(projectNotReady(QString)),
- p_main_window,
+ connect(this, SIGNAL(projectNotReady(QString)), p_main_window,
SLOT(doProjectNotReady(QString)));
// grouping
- connect(p_main_window,
- SIGNAL(operateGrouping(ProjectSp)),
- this,
+ connect(p_main_window, SIGNAL(operateGrouping(ProjectSp)), this,
SLOT(doGrouping(ProjectSp)));
- connect(this,
- SIGNAL(groupingFinished()),
- p_main_window,
+ connect(this, SIGNAL(groupingFinished()), p_main_window,
SLOT(doGroupingFinished()));
// masschroq write
connect(p_main_window,
- SIGNAL(operateWritingMassChroqFile(QString, ProjectSp)),
- this,
+ SIGNAL(operateWritingMassChroqFile(QString, ProjectSp)), this,
SLOT(doWritingMassChroqFile(QString, ProjectSp)));
// protic write
- connect(p_main_window,
- SIGNAL(operateWritingProticFile(QString, ProjectSp)),
- this,
- SLOT(doWritingProticFile(QString, ProjectSp)));
+ connect(p_main_window, SIGNAL(operateWritingProticFile(QString, ProjectSp)),
+ this, SLOT(doWritingProticFile(QString, ProjectSp)));
// writing ODS file :
- connect(p_main_window,
- SIGNAL(operateWritingOdsFile(QString, ProjectSp)),
- this,
- SLOT(doWritingOdsFile(QString, ProjectSp)));
- connect(this,
- SIGNAL(operationFailed(QString)),
- p_main_window,
+ connect(p_main_window, SIGNAL(operateWritingOdsFile(QString, ProjectSp)),
+ this, SLOT(doWritingOdsFile(QString, ProjectSp)));
+ connect(this, SIGNAL(operationFailed(QString)), p_main_window,
SLOT(doOperationFailed(QString)));
- connect(this,
- SIGNAL(operationFinished()),
- p_main_window,
+ connect(this, SIGNAL(operationFinished()), p_main_window,
SLOT(doOperationFinished()));
#endif
@@ -244,56 +170,34 @@ WorkerThread::WorkerThread(ProjectWindow *p_project_window)
// Qt5 code
// worker message
- connect(_p_work_monitor,
- &WorkMonitor::workerMessage,
- p_project_window,
+ connect(_p_work_monitor, &WorkMonitor::workerMessage, p_project_window,
&ProjectWindow::doDisplayLoadingMessage);
- connect(_p_work_monitor,
- &WorkMonitor::workerMessagePercent,
- p_project_window,
+ connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_project_window,
&ProjectWindow::doDisplayLoadingMessagePercent);
- connect(this,
- &WorkerThread::loadingMessage,
- p_project_window,
+ connect(this, &WorkerThread::loadingMessage, p_project_window,
&ProjectWindow::doDisplayLoadingMessage);
// grouping
- connect(p_project_window,
- &ProjectWindow::operateGrouping,
- this,
+ connect(p_project_window, &ProjectWindow::operateGrouping, this,
&WorkerThread::doGrouping);
- connect(this,
- &WorkerThread::groupingFinished,
- p_project_window,
+ connect(this, &WorkerThread::groupingFinished, p_project_window,
&ProjectWindow::doGroupingFinished);
// PTM grouping on IdentificationGroup
- connect(p_project_window,
- &ProjectWindow::operatePtmGroupingOnIdentification,
- this,
- &WorkerThread::doPtmGroupingOnIdentification);
- connect(this,
- &WorkerThread::ptmGroupingOnIdentificationFinished,
- p_project_window,
- &ProjectWindow::refreshPtmGroup);
+ connect(p_project_window, &ProjectWindow::operatePtmGroupingOnIdentification,
+ this, &WorkerThread::doPtmGroupingOnIdentification);
+ connect(this, &WorkerThread::ptmGroupingOnIdentificationFinished,
+ p_project_window, &ProjectWindow::refreshPtmGroup);
// grouping on IdentificationGroup
- connect(p_project_window,
- &ProjectWindow::operateGroupingOnIdentification,
- this,
- &WorkerThread::doGroupingOnIdentification);
- connect(this,
- &WorkerThread::groupingOnIdentificationFinished,
- p_project_window,
- &ProjectWindow::refreshGroup);
+ connect(p_project_window, &ProjectWindow::operateGroupingOnIdentification,
+ this, &WorkerThread::doGroupingOnIdentification);
+ connect(this, &WorkerThread::groupingOnIdentificationFinished,
+ p_project_window, &ProjectWindow::refreshGroup);
- connect(this,
- &WorkerThread::operationFailed,
- p_project_window,
+ connect(this, &WorkerThread::operationFailed, p_project_window,
&ProjectWindow::doOperationFailed);
- connect(this,
- &WorkerThread::operationFinished,
- p_project_window,
+ connect(this, &WorkerThread::operationFinished, p_project_window,
&ProjectWindow::doOperationFinished);
#else
@@ -301,39 +205,27 @@ WorkerThread::WorkerThread(ProjectWindow *p_project_window)
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
// worker message
- connect(_p_work_monitor,
- SIGNAL(workerMessage(QString)),
- p_project_window,
+ connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_project_window,
SLOT(doDisplayLoadingMessage(QString)));
- connect(_p_work_monitor,
- SIGNAL(workerMessage(QString, int)),
- p_project_window,
- SLOT(doDisplayLoadingMessage(QString, int)));
+ connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)),
+ p_project_window, SLOT(doDisplayLoadingMessage(QString, int)));
- connect(this,
- SIGNAL(loadingMessage(QString)),
- p_project_window,
+ connect(this, SIGNAL(loadingMessage(QString)), p_project_window,
SLOT(doDisplayLoadingMessage(QString)));
// grouping
- connect(p_project_window,
- SIGNAL(operateGrouping(ProjectSp)),
- this,
+ connect(p_project_window, SIGNAL(operateGrouping(ProjectSp)), this,
SLOT(doGrouping(ProjectSp)));
- connect(this,
- SIGNAL(groupingFinished()),
- p_project_window,
+ connect(this, SIGNAL(groupingFinished()), p_project_window,
SLOT(doGroupingFinished()));
// PTM grouping on IdentificationGroup
connect(p_project_window,
SIGNAL(operatePtmGroupingOnIdentification(IdentificationGroup *)),
- this,
- SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
+ this, SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
connect(this,
SIGNAL(ptmGroupingOnIdentificationFinished(IdentificationGroup *)),
- p_project_window,
- SLOT(refreshPtmGroup(IdentificationGroup *)));
+ p_project_window, SLOT(refreshPtmGroup(IdentificationGroup *)));
// grouping on IdentificationGroup
connect(
@@ -342,18 +234,12 @@ WorkerThread::WorkerThread(ProjectWindow *p_project_window)
operateGroupingOnIdentification(IdentificationGroup *, GroupingType)),
this,
SLOT(doGroupingOnIdentification(IdentificationGroup *, GroupingType)));
- connect(this,
- SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)),
- p_project_window,
- SLOT(refreshGroup(IdentificationGroup *)));
+ connect(this, SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)),
+ p_project_window, SLOT(refreshGroup(IdentificationGroup *)));
- connect(this,
- SIGNAL(operationFailed(QString)),
- p_project_window,
+ connect(this, SIGNAL(operationFailed(QString)), p_project_window,
SLOT(doOperationFailed(QString)));
- connect(this,
- SIGNAL(operationFinished()),
- p_project_window,
+ connect(this, SIGNAL(operationFinished()), p_project_window,
SLOT(doOperationFinished()));
#endif
@@ -693,14 +579,14 @@ WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch)
if(use_htcondor)
{
- TandemCondorProcess xt_process(
- _p_main_window, _p_work_monitor, tandem_run_batch);
+ TandemCondorProcess xt_process(_p_main_window, _p_work_monitor,
+ tandem_run_batch);
xt_process.run();
}
else
{
- TandemBatchProcess xt_process(
- _p_main_window, _p_work_monitor, tandem_run_batch);
+ TandemBatchProcess xt_process(_p_main_window, _p_work_monitor,
+ tandem_run_batch);
xt_process.run();
}
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index 681ce9448..8308eaa53 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -38,8 +38,7 @@
#include "../../core/peptideevidence.h"
MascotDatParser::MascotDatParser(
- Project *p_project,
- IdentificationGroup *p_identification_group,
+ Project *p_project, IdentificationGroup *p_identification_group,
IdentificationDataSource *p_identification_data_source)
{
_p_project = p_project;
@@ -416,9 +415,8 @@ MascotDatParser::parsePeptidesLine(const QString &peptide_line)
catch(pappso::PappsoException exception_pappso)
{
- _error_str = QObject::tr(
- "ERROR in MascotDatParser::parsePeptidesLine "
- "%1, PAPPSO exception:\n%2")
+ _error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine "
+ "%1, PAPPSO exception:\n%2")
.arg(peptide_line)
.arg(exception_pappso.qwhat());
qDebug() << _error_str;
@@ -635,10 +633,9 @@ MascotDatParser::savePeptideList(std::vector<PeptideLine> &peptide_list,
if(is_decoy)
{
- peptide_evidence.setEvalue(
- getEvalue(ion_score,
- _decoy_summary_list.at(_current_query.query_index - 1),
- 0.05));
+ peptide_evidence.setEvalue(getEvalue(
+ ion_score, _decoy_summary_list.at(_current_query.query_index - 1),
+ 0.05));
}
else
{
@@ -770,8 +767,7 @@ MascotDatParser::getEvalue(pappso::pappso_double ion_score,
pappso::pappso_double
MascotDatParser::getEvalueExperimental(
- pappso::pappso_double ion_score,
- SummaryLine &summary_line,
+ pappso::pappso_double ion_score, SummaryLine &summary_line,
pappso::pappso_double confidence_interval) const
{
// Evalue experimental Homology threshold (QPlughole value from .dat file).
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
index 800383150..e5b000a8f 100644
--- a/src/input/mascot/mascotdatparser.h
+++ b/src/input/mascot/mascotdatparser.h
@@ -86,8 +86,7 @@ class MascotDatParser
};
void savePeptideList(std::vector<PeptideLine> &peptide_list, bool is_decoy);
pappso::pappso_double
- getEvalue(pappso::pappso_double ion_score,
- SummaryLine &summary_line,
+ getEvalue(pappso::pappso_double ion_score, SummaryLine &summary_line,
pappso::pappso_double confidence_interval = 0.05) const;
pappso::pappso_double
getEvalueExperimental(pappso::pappso_double ion_score,
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index a5667416d..5076fc346 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -326,7 +326,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
//<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
// ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-// \
+// \
//S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
// peptide_next_aa="N"/>
bool
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index b80e79862..9e921ab29 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -210,7 +210,7 @@ XpipSaxHandler::startElement_filter_params(QXmlAttributes attributes)
{
//<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="1"
- //filter_to_all="false" database_filter="contaminants_standarts.fasta"/>
+ // filter_to_all="false" database_filter="contaminants_standarts.fasta"/>
qDebug() << "startElement_filter_params ";
_automatic_filter_parameters.setFilterPeptideEvalue(
attributes.value("pep_evalue").simplified().toDouble());
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index 570c75c25..5c7fa74c5 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -121,11 +121,11 @@ MassChroQml::write(ProjectSp sp_project)
_output_stream->writeAttribute("type", "input");
_output_stream->writeAttribute("version", "2.2");
//_output_stream->writeAttribute("creationDate",
- //QDateTime::currentDateTime().toString( Qt::ISODate));
+ // QDateTime::currentDateTime().toString( Qt::ISODate));
//_output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
//_output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/masschroqml/2.2");
//_output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/masschroqml/2.2
- //http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
+ // http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
// <rawdata><!-- time_values_dir="directory" to read retention time
// corrections-->
@@ -155,7 +155,7 @@ MassChroQml::write(ProjectSp sp_project)
// <data_file id="samp2" format="mzml" path="/home/user/bsa3.mzml"
// type="profile" />
//<data_file id="samp3" format="mzml" path="/home/user/bsa4.mzml"
- //type="profile" />
+ // type="profile" />
// _output_stream.writeEndElement();
// </rawdata>
_output_stream->writeEndElement();
@@ -353,7 +353,7 @@ MassChroQml::writeAlignments()
_output_stream->writeAttribute("id", "my_ms2");
//<ms2><!-- write_time_values_output_dir="directory" to write retention time
- //corrections -->
+ // corrections -->
_output_stream->writeStartElement("ms2");
_output_stream->writeComment("write_time_values_output_dir=\"directory\" to "
@@ -504,7 +504,7 @@ MassChroQml::writePeptideListInGroup(const GroupingGroup *p_group)
_output_stream->writeAttribute("seq", mcq_peptide.seq);
//<modifications><!-- this tag is optional but gives an exact mass
- //computation -->
+ // computation -->
std::vector<McqPsimod> mod_list;
unsigned int pos = 1;
for(const pappso::Aa &aa : *(mcq_peptide.native_peptide))
diff --git a/src/output/ods/peptidepossheet.cpp b/src/output/ods/peptidepossheet.cpp
index 65279b1c7..9918513ab 100644
--- a/src/output/ods/peptidepossheet.cpp
+++ b/src/output/ods/peptidepossheet.cpp
@@ -60,8 +60,8 @@ PeptidePosSheet::PeptidePosSheet(OdsExport *p_ods_export,
void
PeptidePosSheet::writeHeaders(IdentificationGroup *p_ident)
{
- // Peptide ID Protein ID accession description Sequence Modifs Start Stop MH+
- // theo
+ // Peptide ID Protein ID accession description Sequence Modifs Start Stop
+ // MH+ theo
// MS Sample : 20120906_balliau_extract_1_A01_urnb-1
diff --git a/src/output/ods/peptidesheet.cpp b/src/output/ods/peptidesheet.cpp
index 847e6d7ef..8e97e737a 100644
--- a/src/output/ods/peptidesheet.cpp
+++ b/src/output/ods/peptidesheet.cpp
@@ -58,9 +58,9 @@ PeptideSheet::PeptideSheet(OdsExport *p_ods_export,
void
PeptideSheet::writeHeaders(IdentificationGroup *p_ident)
{
- // Group ID Peptide ID SequenceLI Modifs Charge MH+ theo Number of subgroups
- // Subgroup ids Number of spectra
- // MS Sample : 20120906_balliau_extract_1_A01_urnb-1
+ // Group ID Peptide ID SequenceLI Modifs Charge MH+ theo Number of
+ // subgroups Subgroup ids Number of spectra MS Sample :
+ // 20120906_balliau_extract_1_A01_urnb-1
const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
if(msrun_list.size() == 1)
{
diff --git a/src/output/ods/ptm/ptmislandsheet.cpp b/src/output/ods/ptm/ptmislandsheet.cpp
index 70fa50a75..87e15abec 100644
--- a/src/output/ods/ptm/ptmislandsheet.cpp
+++ b/src/output/ods/ptm/ptmislandsheet.cpp
@@ -90,7 +90,7 @@ PtmIslandSheet::writeHeaders(IdentificationGroup *p_ident)
_p_writer->writeCell("PTM sub-group ID");
writeCellHeader(PtmIslandListColumn::ptm_island_id);
//_p_writer->PtmIslandListColumn("unique protein identifier within this
- //grouping experiment"); _p_writer->writeCell("Protein ID");
+ // grouping experiment"); _p_writer->writeCell("Protein ID");
writeCellHeader(PtmIslandListColumn::accession);
writeCellHeader(PtmIslandListColumn::description);
@@ -101,7 +101,7 @@ PtmIslandSheet::writeHeaders(IdentificationGroup *p_ident)
writeCellHeader(PtmIslandListColumn::spectrum);
//_p_writer->setCellAnnotation("number of scans (spectra) attributed to this
- //protein");
+ // protein");
// _p_writer->writeCell("Spectra");
writeCellHeader(PtmIslandListColumn::sequence);
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index a3c78b2a6..5fe39259f 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -30,8 +30,7 @@
#include "samplesheet.h"
-SampleSheet::SampleSheet(OdsExport *p_ods_export,
- CalcWriterInterface *p_writer,
+SampleSheet::SampleSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
const Project *p_project)
: _p_project(p_project)
{
@@ -119,19 +118,16 @@ SampleSheet::writeHeaders()
"total number of MS level 3 during the MS run (from mz file)");
_p_writer->writeCell("Total MS3");
- _p_writer->setCellAnnotation(
- "total ion current in MS level 1 spectra "
- "during the MS run (from mz file)");
+ _p_writer->setCellAnnotation("total ion current in MS level 1 spectra "
+ "during the MS run (from mz file)");
_p_writer->writeCell("TIC MS1");
- _p_writer->setCellAnnotation(
- "total ion current in MS level 2 spectra "
- "during the MS run (from mz file)");
+ _p_writer->setCellAnnotation("total ion current in MS level 2 spectra "
+ "during the MS run (from mz file)");
_p_writer->writeCell("TIC MS2");
- _p_writer->setCellAnnotation(
- "total ion current in MS level 3 spectra "
- "during the MS run (from mz file)");
+ _p_writer->setCellAnnotation("total ion current in MS level 3 spectra "
+ "during the MS run (from mz file)");
_p_writer->writeCell("TIC MS3");
}
diff --git a/src/output/ods/spectrasheet.cpp b/src/output/ods/spectrasheet.cpp
index c56f6b1e6..c260028ca 100644
--- a/src/output/ods/spectrasheet.cpp
+++ b/src/output/ods/spectrasheet.cpp
@@ -75,7 +75,8 @@ SpectraSheet::writeCellHeader(PeptideListColumn column)
void
SpectraSheet::writeHeaders(IdentificationGroup *p_ident)
{
- // Group ID Peptide ID Sample Scan Rt (minutes) Sequence (top) Modifs (top)
+ // Group ID Peptide ID Sample Scan Rt (minutes) Sequence (top) Modifs
+ // (top)
// Number of subgroups Sub-groups Ids Best E-value Best hyperscore m/z Obs
// Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index 9648842e5..b6a7faafc 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -97,7 +97,7 @@ ProticdbMl::write(ProjectSp sp_project)
_output_stream->writeStartElement("PROTICdb");
//_output_stream->writeAttribute("xmlns","http://pappso.inra.fr/xsd/masschroqml/2.2");
//_output_stream->writeAttribute("http://www.w3.org/2001/XMLSchema-instance","schemaLocation","http://pappso.inra.fr/xsd/masschroqml/2.2
- //http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
+ // http://pappso.inra.fr/xsd/masschroq-2.2.xsd");
// writer.writeAttribute(xmlnsxsi, "noNamespaceSchemaLocation",
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 5cc8afa96..ad9205994 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -86,7 +86,7 @@ Xpip::write(ProjectSp sp_project)
_output_stream->writeStartElement("xpip");
_output_stream->writeAttribute("version", "4.0");
//_output_stream->writeAttribute("creationDate",
- //QDateTime::currentDateTime().toString( Qt::ISODate));
+ // QDateTime::currentDateTime().toString( Qt::ISODate));
_output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance",
"xsi");
//_output_stream->writeNamespace("http://www.w3.org/2001/XMLSchema-instance","xsi");
@@ -107,8 +107,8 @@ Xpip::write(ProjectSp sp_project)
writeCounts();
//<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="2"
- //filter_to_all="false"
- //database_filter="/gorgone/pappso/jouy/raw/2013_Orbitrap/2013_07_04_Chanat/contaminants_standarts.fasta"/>
+ // filter_to_all="false"
+ // database_filter="/gorgone/pappso/jouy/raw/2013_Orbitrap/2013_07_04_Chanat/contaminants_standarts.fasta"/>
// const AutomaticFilterParameters & getAutomaticFilterParameters() const;
writeFilterParameters(_sp_project.get()->getAutomaticFilterParameters());
writeFastaFileList(_sp_project.get()->getFastaFileStore());
--
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