From dba7e823fac146f506adfbbbb083e050c69de047 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Mon, 20 Apr 2020 15:59:21 +0200
Subject: [PATCH] Reformat all src files and handle change MsRunStatistics for
tdf format
---
src/core/automaticfilterparameters.h | 4 +-
.../identificationmascotdatfile.cpp | 4 +-
.../identificationmascotdatfile.h | 1 -
src/core/msrun.cpp | 2 +-
src/core/peptidextp.h | 2 +-
src/core/proteinxtp.cpp | 12 +++--
src/core/qvalue/computeqvalues.cpp | 7 +--
src/core/qvalue/computeqvalues.h | 9 ++--
src/core/tandem_run/tandembatchprocess.cpp | 2 +-
src/core/tandem_run/tandembatchprocess.h | 3 +-
src/core/tandem_run/tandemcondorprocess.cpp | 5 +-
src/core/tandem_run/tandemparameters.cpp | 2 +-
src/grouping/groupinggroup.cpp | 3 +-
src/grouping/ptm/ptmgroupingexperiment.cpp | 6 ++-
src/grouping/ptm/ptmisland.cpp | 15 ++++--
src/grouping/ptm/ptmislandgroup.cpp | 6 ++-
src/grouping/ptm/ptmislandsubgroup.cpp | 6 ++-
src/grouping/ptm/ptmsamplescan.cpp | 3 +-
src/gui/about_dialog/aboutdialog.h | 2 +-
.../choosemodificationdialog.cpp | 18 +++++--
.../choosemodificationdialog.h | 2 +-
.../edit_label_methods/editlabelmethods.h | 2 +-
.../edit_modifications/editmodifications.h | 2 +-
.../exportmasschroqdialog.h | 1 -
.../msidlistworkerstatus.cpp | 52 ++++++++++++++++---
.../msidlistworkerstatus.h | 3 ++
.../msidentificationtablemodel.cpp | 40 ++++++++++++--
.../msidentificationtablemodel.h | 1 +
.../load_results_dialog/loadresultsdialog.cpp | 3 +-
.../load_results_dialog/loadresultsdialog.h | 2 +-
.../peptidetableproxymodel.h | 4 +-
.../identificationgroupwidget.h | 2 +-
src/gui/protein_list_view/proteinlistwindow.h | 4 +-
.../protein_list_view/proteintablemodel.cpp | 3 +-
src/gui/protein_list_view/proteintablemodel.h | 6 +--
.../proteintableproxymodel.h | 4 +-
.../ptmislandlistwindow.cpp | 36 +++++++++----
.../ptmislandlistwindow.h | 2 +-
.../ptmislandtablemodel.cpp | 3 +-
.../ptmislandtablemodel.h | 4 +-
.../ptmpeptidelistwindow.cpp | 18 ++++---
.../ptmpeptidelistwindow.h | 2 +-
.../ptmpeptidetablemodel.cpp | 3 +-
.../ptmpeptidetablemodel.h | 4 +-
.../ptmpeptidetableproxymodel.cpp | 26 ++++++----
.../ptmpeptidetableproxymodel.h | 14 +++--
.../ptmsequencedelegate.h | 3 +-
src/gui/tandem_run_dialog/tandemrundialog.cpp | 6 ++-
src/gui/tandem_run_dialog/tandemrundialog.h | 2 +-
.../alignmentgroupmenu.cpp | 9 ++--
.../automaticfilterwidget.cpp | 5 +-
src/gui/widgets/decoy_widget/decoywidget.cpp | 4 +-
src/gui/widgets/decoy_widget/decoywidget.h | 2 +-
.../xicextractionmethodwidget.h | 3 +-
src/gui/xic_view/xic_widgets/zivywidget.cpp | 8 +--
src/gui/xic_view/xicworkerthread.cpp | 3 +-
src/gui/xic_view/xicworkerthread.h | 3 +-
src/input/condorqxmlsaxhandler.cpp | 33 +++++++-----
src/input/condorqxmlsaxhandler.h | 9 ++--
src/input/identificationpwizreader.cpp | 3 +-
src/input/identificationpwizreader.h | 11 ++--
src/input/pepxmlsaxhandler.cpp | 2 +-
src/input/pepxmlsaxhandler.h | 9 ++--
src/input/xpipsaxhandler.h | 9 ++--
src/input/xtpxpipsaxhandler.cpp | 4 +-
src/output/masschroqprm.h | 1 -
src/output/mcqr/mcqrscpeptide.cpp | 15 ++++--
src/output/mcqr/mcqrscpeptide.h | 3 +-
src/output/mcqr/mcqrscprotein.cpp | 3 +-
src/output/mcqrspectralcount.cpp | 27 ++++++----
src/output/mcqrspectralcount.h | 3 +-
src/output/ods/comparbasesheet.cpp | 10 ++--
src/output/ods/comparbasesheet.h | 6 ++-
src/output/ods/comparspecificspectrasheet.cpp | 18 ++++---
src/output/ods/comparspecificspectrasheet.h | 6 ++-
src/output/ods/comparspectrabypeptide.cpp | 21 +++++---
src/output/ods/comparspectrabypeptide.h | 9 ++--
src/output/ods/comparspectrasheet.cpp | 12 +++--
src/output/ods/comparspectrasheet.h | 30 +++++++----
src/output/ods/groupingsheet.h | 3 +-
src/output/ods/infosheet.cpp | 31 ++++++-----
src/output/ods/peptidesheet.cpp | 3 +-
src/output/ods/peptidesheet.h | 3 +-
src/output/ods/proteinsheet.h | 3 +-
src/output/ods/ptm/ptmislandsheet.cpp | 3 +-
src/output/ods/ptm/ptmislandsheet.h | 3 +-
src/output/ods/ptm/ptmspectrasheet.h | 9 ++--
src/output/ods/qvaluessheet.cpp | 4 +-
src/output/ods/samplesheet.cpp | 18 ++++---
src/output/ods/samplesheet.h | 3 +-
src/output/ods/spectrasheet.h | 10 ++--
src/utils/msrunstore.h | 1 -
src/utils/peptidestore.h | 1 -
src/utils/utils.h | 3 +-
94 files changed, 488 insertions(+), 257 deletions(-)
diff --git a/src/core/automaticfilterparameters.h b/src/core/automaticfilterparameters.h
index ee02f445..6c0e7e8d 100644
--- a/src/core/automaticfilterparameters.h
+++ b/src/core/automaticfilterparameters.h
@@ -51,12 +51,12 @@ class AutomaticFilterParameters
unsigned int getFilterMinimumPeptidePerMatch() const;
bool getFilterCrossSamplePeptideNumber() const;
unsigned int getFilterPeptideObservedInLessSamplesThan() const;
-
+
bool useFDR() const;
private:
- double m_filterFDR = -1;
+ double m_filterFDR = -1;
pappso::pappso_double _filter_minimum_peptide_evalue = 1;
pappso::pappso_double _filter_minimum_protein_evalue = 1;
unsigned int _filter_minimum_peptide_per_match = 1;
diff --git a/src/core/identification_sources/identificationmascotdatfile.cpp b/src/core/identification_sources/identificationmascotdatfile.cpp
index 8964d524..a97947fc 100644
--- a/src/core/identification_sources/identificationmascotdatfile.cpp
+++ b/src/core/identification_sources/identificationmascotdatfile.cpp
@@ -36,8 +36,8 @@
IdentificationMascotDatFile::IdentificationMascotDatFile(
const QFileInfo &mascot_dat_file)
- : IdentificationDataSource(mascot_dat_file.absoluteFilePath())
- , _mascot_dat_file(mascot_dat_file)
+ : IdentificationDataSource(mascot_dat_file.absoluteFilePath()),
+ _mascot_dat_file(mascot_dat_file)
{
_engine = IdentificationEngine::mascot;
}
diff --git a/src/core/identification_sources/identificationmascotdatfile.h b/src/core/identification_sources/identificationmascotdatfile.h
index 88cd8050..12293798 100644
--- a/src/core/identification_sources/identificationmascotdatfile.h
+++ b/src/core/identification_sources/identificationmascotdatfile.h
@@ -51,4 +51,3 @@ class IdentificationMascotDatFile : public IdentificationDataSource
private:
const QFileInfo _mascot_dat_file;
};
-
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index b0cad14f..e7ceae2b 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -52,7 +52,7 @@ MsRun::MsRun(const QString &location) : pappso::MsRunId(location)
MsRun::MsRun(const MsRun &other) : pappso::MsRunId(other)
{
- _param_stats = other._param_stats;
+ _param_stats = other._param_stats;
m_centroidOptions = other.m_centroidOptions;
}
diff --git a/src/core/peptidextp.h b/src/core/peptidextp.h
index 6bd6d03d..e485b8e4 100644
--- a/src/core/peptidextp.h
+++ b/src/core/peptidextp.h
@@ -58,7 +58,7 @@ class PeptideXtp : public pappso::Peptide
/** @brief human readable string that contains modifications
* @param without_label get modifications without existing labels
* */
- const QString getModifString(bool without_label =false) const;
+ const QString getModifString(bool without_label = false) const;
/** @brief replace modification in peptide
*/
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index 2be7f7b6..9282dcd6 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -185,9 +185,13 @@ class DigestionHandler : public pappso::EnzymeProductInterface
public:
void
setPeptide(std::int8_t sequence_database_id,
- const pappso::ProteinSp &protein_sp, bool is_decoy,
- const QString &peptide, unsigned int start, bool is_nter,
- unsigned int missed_cleavage_number, bool semi_enzyme) override
+ const pappso::ProteinSp &protein_sp,
+ bool is_decoy,
+ const QString &peptide,
+ unsigned int start,
+ bool is_nter,
+ unsigned int missed_cleavage_number,
+ bool semi_enzyme) override
{
_peptide_list.append(peptide);
};
@@ -237,7 +241,7 @@ ProteinXtp::countTrypticPeptidesForPAI() const
void
ProteinXtp::parseAccession2dbxref()
{
- //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
QStringList access_list = getAccession().split("|");
// if (access.length == 1)
QRegExp atg("^[Aa][Tt][MmCc1-5][Gg]\\d{5}\\.?\\d?$");
diff --git a/src/core/qvalue/computeqvalues.cpp b/src/core/qvalue/computeqvalues.cpp
index 901ab302..f6dab8ad 100644
--- a/src/core/qvalue/computeqvalues.cpp
+++ b/src/core/qvalue/computeqvalues.cpp
@@ -216,13 +216,14 @@ ComputeQvalues::writeDistributionsByEngines(CalcWriterInterface *p_writer) const
}
// double qvalue = Utils::computeFdr(count_decoy, count_target);
// pep->setParam(PeptideEvidenceParam::pappso_qvalue, QVariant(qvalue));
- p_writer->writeCell((int) count_target);
+ p_writer->writeCell((int)count_target);
- p_writer->writeCell((int) count_decoy);
+ p_writer->writeCell((int)count_decoy);
p_writer->writeCell(pep->getEvalue());
- p_writer->writeCell(pep->getParam(PeptideEvidenceParam::pappso_qvalue).toDouble());
+ p_writer->writeCell(
+ pep->getParam(PeptideEvidenceParam::pappso_qvalue).toDouble());
p_writer->writeLine();
}
}
diff --git a/src/core/qvalue/computeqvalues.h b/src/core/qvalue/computeqvalues.h
index 58b6987f..b98733e3 100644
--- a/src/core/qvalue/computeqvalues.h
+++ b/src/core/qvalue/computeqvalues.h
@@ -46,8 +46,8 @@ class ComputeQvalues
* Destructor
*/
~ComputeQvalues();
-
- void writeDistributionsByEngines(CalcWriterInterface * p_writer) const;
+
+ void writeDistributionsByEngines(CalcWriterInterface *p_writer) const;
private:
void computeTandemPeptideEvidenceQvalues(
@@ -60,7 +60,6 @@ class ComputeQvalues
private:
std::set<const PeptideEvidence *> m_falsePeptideEvidenceList;
-
- std::vector<PeptideEvidence *> m_tandemPeptideEvidenceList;
-
+
+ std::vector<PeptideEvidence *> m_tandemPeptideEvidenceList;
};
diff --git a/src/core/tandem_run/tandembatchprocess.cpp b/src/core/tandem_run/tandembatchprocess.cpp
index 2527eb1d..32fdeb9e 100644
--- a/src/core/tandem_run/tandembatchprocess.cpp
+++ b/src/core/tandem_run/tandembatchprocess.cpp
@@ -375,7 +375,7 @@ TandemBatchProcess::runOne(const QString &mz_file)
try
{
- //QProcess::ExitStatus Status = xt_process->exitStatus();
+ // QProcess::ExitStatus Status = xt_process->exitStatus();
const QDateTime dt_begin = QDateTime::currentDateTime();
QSettings settings;
diff --git a/src/core/tandem_run/tandembatchprocess.h b/src/core/tandem_run/tandembatchprocess.h
index 9596d455..f440ada5 100644
--- a/src/core/tandem_run/tandembatchprocess.h
+++ b/src/core/tandem_run/tandembatchprocess.h
@@ -35,7 +35,8 @@
class TandemBatchProcess
{
public:
- TandemBatchProcess(MainWindow *p_main_window, WorkMonitorInterface *p_monitor,
+ TandemBatchProcess(MainWindow *p_main_window,
+ WorkMonitorInterface *p_monitor,
const TandemRunBatch &tandem_run_batch);
virtual ~TandemBatchProcess();
diff --git a/src/core/tandem_run/tandemcondorprocess.cpp b/src/core/tandem_run/tandemcondorprocess.cpp
index 7aab8476..0bbf77b7 100644
--- a/src/core/tandem_run/tandemcondorprocess.cpp
+++ b/src/core/tandem_run/tandemcondorprocess.cpp
@@ -262,9 +262,8 @@ TandemCondorProcess::run()
<< " -t "
<< settings.value("timstof/tmp_dir_path", QDir::tempPath())
.toString()
- << "--tandem" << _tandem_run_batch._tandem_bin_path
- << "--centroid" << centroidOption
- << endl;
+ << "--tandem" << _tandem_run_batch._tandem_bin_path
+ << "--centroid" << centroidOption << endl;
}
*p_out << "Queue" << endl;
}
diff --git a/src/core/tandem_run/tandemparameters.cpp b/src/core/tandem_run/tandemparameters.cpp
index c15f8753..47b972f8 100644
--- a/src/core/tandem_run/tandemparameters.cpp
+++ b/src/core/tandem_run/tandemparameters.cpp
@@ -266,7 +266,7 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(label == "residue, potential modification mass 3") ||
(label == "residue, potential modification motif 1") ||
(label == "residue, potential modification motif 2") ||
- (label == "residue, potential modification motif 3")||
+ (label == "residue, potential modification motif 3") ||
(label == "spectrum, timstof MS2 centroid parameters"))
{
// string
diff --git a/src/grouping/groupinggroup.cpp b/src/grouping/groupinggroup.cpp
index f86ef82f..cfcf224e 100644
--- a/src/grouping/groupinggroup.cpp
+++ b/src/grouping/groupinggroup.cpp
@@ -275,7 +275,8 @@ unsigned int
GroupingGroup::countProteinInSubgroup(unsigned int subgroup_number) const
{
return std::count_if(
- _protein_match_list.begin(), _protein_match_list.end(),
+ _protein_match_list.begin(),
+ _protein_match_list.end(),
[subgroup_number](const ProteinMatch *p_protein_match) {
if(p_protein_match->getGrpProteinSp().get()->getSubGroupNumber() ==
subgroup_number)
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index 903b2622..dc25f640 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -99,7 +99,8 @@ PtmGroupingExperiment::getPtmIslandList() const
void
PtmGroupingExperiment::numbering()
{
- std::sort(_ptm_island_group_list.begin(), _ptm_island_group_list.end(),
+ std::sort(_ptm_island_group_list.begin(),
+ _ptm_island_group_list.end(),
[](const PtmIslandGroupSp a, const PtmIslandGroupSp b) {
return *(a.get()) < *(b.get());
});
@@ -192,7 +193,8 @@ PtmGroupingExperiment::mergePeptideMatchPtmIslandList(
for(PtmIslandSp ptm_island_sp : ptm_island_list)
{
// http://en.cppreference.com/w/cpp/algorithm/all_any_none_of
- if(std::none_of(new_ptm_island_list.begin(), new_ptm_island_list.end(),
+ if(std::none_of(new_ptm_island_list.begin(),
+ new_ptm_island_list.end(),
[ptm_island_sp](PtmIslandSp element) {
return element.get()->merge(ptm_island_sp);
}))
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 98c15f4a..17cc60d3 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -152,7 +152,8 @@ bool
PtmIsland::containsPeptideMatch(const PeptideMatch &peptide_match) const
{
- return std::any_of(_peptide_match_list.begin(), _peptide_match_list.end(),
+ return std::any_of(_peptide_match_list.begin(),
+ _peptide_match_list.end(),
[peptide_match](const PeptideMatch &element) {
return (peptide_match == element);
});
@@ -199,7 +200,8 @@ PtmIsland::getProteinStartPosition() const
bool
PtmIsland::merge(PtmIslandSp ptm_island_sp)
{
- if(std::none_of(_peptide_match_list.begin(), _peptide_match_list.end(),
+ if(std::none_of(_peptide_match_list.begin(),
+ _peptide_match_list.end(),
[ptm_island_sp](const PeptideMatch &element) {
return ptm_island_sp.get()->containsPeptideMatch(element);
}))
@@ -213,7 +215,8 @@ PtmIsland::merge(PtmIslandSp ptm_island_sp)
_peptide_match_list.begin(),
ptm_island_sp.get()->_peptide_match_list.begin(),
ptm_island_sp.get()->_peptide_match_list.end());
- std::sort(_peptide_match_list.begin(), _peptide_match_list.end(),
+ std::sort(_peptide_match_list.begin(),
+ _peptide_match_list.end(),
[](const PeptideMatch &a, const PeptideMatch &b) {
return (a.operator<(b));
});
@@ -231,14 +234,16 @@ PtmIsland::merge(PtmIslandSp ptm_island_sp)
std::vector<PeptideMatch>::const_iterator it_result =
- std::max_element(_peptide_match_list.begin(), _peptide_match_list.end(),
+ std::max_element(_peptide_match_list.begin(),
+ _peptide_match_list.end(),
[](const PeptideMatch &a, const PeptideMatch &b) {
return (a.getStop() < b.getStop());
});
_protein_stop = it_result->getStop();
it_result =
- std::min_element(_peptide_match_list.begin(), _peptide_match_list.end(),
+ std::min_element(_peptide_match_list.begin(),
+ _peptide_match_list.end(),
[](const PeptideMatch &a, const PeptideMatch &b) {
return a.getStart() < b.getStart();
});
diff --git a/src/grouping/ptm/ptmislandgroup.cpp b/src/grouping/ptm/ptmislandgroup.cpp
index 0f3a2b38..ca793c67 100644
--- a/src/grouping/ptm/ptmislandgroup.cpp
+++ b/src/grouping/ptm/ptmislandgroup.cpp
@@ -80,7 +80,8 @@ PtmIslandGroup::setGroupNumber(unsigned int number)
{
ptm_island_subgroup.get()->setPtmIslandGroup(this);
}
- std::sort(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(),
+ std::sort(_ptm_island_subgroup_list.begin(),
+ _ptm_island_subgroup_list.end(),
[](const PtmIslandSubgroupSp &a, const PtmIslandSubgroupSp &b) {
return (a.get()->getFirstPtmIsland()->getProteinStartPosition() <
b.get()->getFirstPtmIsland()->getProteinStartPosition());
@@ -116,7 +117,8 @@ unsigned int
PtmIslandGroup::maxCountSampleScan() const
{
std::vector<PtmIslandSubgroupSp>::const_iterator it_result = std::max_element(
- _ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(),
+ _ptm_island_subgroup_list.begin(),
+ _ptm_island_subgroup_list.end(),
[](const PtmIslandSubgroupSp &a, const PtmIslandSubgroupSp &b) {
return (a.get()->countSampleScan() < b.get()->countSampleScan());
});
diff --git a/src/grouping/ptm/ptmislandsubgroup.cpp b/src/grouping/ptm/ptmislandsubgroup.cpp
index d43c016a..7a5c334e 100644
--- a/src/grouping/ptm/ptmislandsubgroup.cpp
+++ b/src/grouping/ptm/ptmislandsubgroup.cpp
@@ -73,7 +73,8 @@ PtmIslandSubgroup::setSubgroupNumber(unsigned int number)
ptm_island.get()->setPtmIslandSubgroup(this);
}
std::sort(
- _ptm_island_list.begin(), _ptm_island_list.end(),
+ _ptm_island_list.begin(),
+ _ptm_island_list.end(),
[](const PtmIslandSp &a, const PtmIslandSp &b) {
return (
a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() <
@@ -92,7 +93,8 @@ PtmIslandSubgroup::setPtmIslandGroup(PtmIslandGroup *p_ptm_island_group)
{
_ptm_island_group_p = p_ptm_island_group;
std::sort(
- _ptm_island_list.begin(), _ptm_island_list.end(),
+ _ptm_island_list.begin(),
+ _ptm_island_list.end(),
[](const PtmIslandSp &a, const PtmIslandSp &b) {
return (
a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() <
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
index 623eb6d9..3837399f 100644
--- a/src/grouping/ptm/ptmsamplescan.cpp
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -95,7 +95,8 @@ PtmSampleScan::add(const PeptideMatch &peptide_match)
// qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__ ;
// sort list
- std::sort(_peptide_match_list.begin(), _peptide_match_list.end(),
+ std::sort(_peptide_match_list.begin(),
+ _peptide_match_list.end(),
[](const PeptideMatch &first, const PeptideMatch &second) {
return (first.getPeptideEvidence()->getEvalue() <
second.getPeptideEvidence()->getEvalue());
diff --git a/src/gui/about_dialog/aboutdialog.h b/src/gui/about_dialog/aboutdialog.h
index fe2b90f2..260a0435 100644
--- a/src/gui/about_dialog/aboutdialog.h
+++ b/src/gui/about_dialog/aboutdialog.h
@@ -30,7 +30,7 @@
namespace Ui
{
- class AboutDialog;
+class AboutDialog;
}
class AboutDialog : public QDialog
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.cpp b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
index e1d4d90a..1a9fd625 100644
--- a/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.cpp
@@ -48,17 +48,25 @@ ChooseModificationDialog::ChooseModificationDialog(QWidget *parent)
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(ui->modification_listview, &QListView::clicked, this,
+ connect(ui->modification_listview,
+ &QListView::clicked,
+ this,
&ChooseModificationDialog::ItemClicked);
- connect(ui->modification_listview, &QListView::doubleClicked, this,
+ connect(ui->modification_listview,
+ &QListView::doubleClicked,
+ this,
&ChooseModificationDialog::ItemDoubleClicked);
#else
// Qt4 code
- connect(ui->modification_listview, SIGNAL(clicked(const QModelIndex)), this,
+ connect(ui->modification_listview,
+ SIGNAL(clicked(const QModelIndex)),
+ this,
SLOT(ItemClicked(QModelIndex)));
- connect(ui->modification_listview, SIGNAL(doubleClicked(const QModelIndex)),
- this, SLOT(ItemDoubleClicked(QModelIndex)));
+ connect(ui->modification_listview,
+ SIGNAL(doubleClicked(const QModelIndex)),
+ this,
+ SLOT(ItemDoubleClicked(QModelIndex)));
#endif
}
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.h b/src/gui/choose_modification_dialog/choosemodificationdialog.h
index 2b5e42b2..c641196f 100644
--- a/src/gui/choose_modification_dialog/choosemodificationdialog.h
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.h
@@ -33,7 +33,7 @@
namespace Ui
{
- class ChooseModificationDialog;
+class ChooseModificationDialog;
}
class ChooseModificationDialog : public QDialog
diff --git a/src/gui/edit/edit_label_methods/editlabelmethods.h b/src/gui/edit/edit_label_methods/editlabelmethods.h
index 0a3d3dbd..4d5bcd12 100644
--- a/src/gui/edit/edit_label_methods/editlabelmethods.h
+++ b/src/gui/edit/edit_label_methods/editlabelmethods.h
@@ -35,7 +35,7 @@ class ProjectWindow;
namespace Ui
{
- class EditLabelMethodView;
+class EditLabelMethodView;
}
class EditLabelMethods : public QDialog
diff --git a/src/gui/edit/edit_modifications/editmodifications.h b/src/gui/edit/edit_modifications/editmodifications.h
index 8a57d416..08f50afe 100644
--- a/src/gui/edit/edit_modifications/editmodifications.h
+++ b/src/gui/edit/edit_modifications/editmodifications.h
@@ -34,7 +34,7 @@ class ProjectWindow;
// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
namespace Ui
{
- class EditModificationView;
+class EditModificationView;
}
class EditModifications : public QMainWindow
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
index 26f0d1e6..4e695133 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
@@ -80,5 +80,4 @@ class ExportMasschroqDialog : public QDialog
private:
void fillMsrunListComboBox();
-
};
diff --git a/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp b/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp
index 103a1784..dc17389a 100644
--- a/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp
+++ b/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp
@@ -153,6 +153,51 @@ MsIdListWorkerStatus::getStatus(
void
MsIdListWorkerStatus::doComputeMsNumber(
IdentificationDataSourceSp identificationDataSource)
+{
+ if(QFileInfo(identificationDataSource.get()->getMsRunSp()->getFileName())
+ .completeSuffix() == "tdf")
+ {
+ doComputeMsNumberForTDF(identificationDataSource);
+ }
+ else
+ {
+ doComputeMsNumberForMzXML(identificationDataSource);
+ }
+}
+
+void
+MsIdListWorkerStatus::changeWaitingQueue(int row)
+{
+ m_waitingComputing.clear();
+ qDebug() << m_waitingComputing.size();
+}
+
+void
+MsIdListWorkerStatus::doComputeMsNumberForTDF(
+ IdentificationDataSourceSp identificationDataSource)
+{
+ if(identificationDataSource->getMsRunSp()->findMsRunFile())
+ {
+ try
+ {
+ }
+ catch(pappso::PappsoException &error)
+ {
+ // error while computing
+ qDebug() << error.qwhat();
+ m_identificationError.push_back(identificationDataSource.get());
+ }
+ }
+ else
+ {
+ // file not found
+ m_identificationFileNotFound.push_back(identificationDataSource.get());
+ }
+}
+
+void
+MsIdListWorkerStatus::doComputeMsNumberForMzXML(
+ IdentificationDataSourceSp identificationDataSource)
{
pappso::MsRunReaderSPtr msrun_reader_sp =
identificationDataSource->getMsRunSp().get()->getMsRunReaderSPtr();
@@ -209,10 +254,3 @@ MsIdListWorkerStatus::doComputeMsNumber(
m_identificationFileNotFound.push_back(identificationDataSource.get());
}
}
-
-void
-MsIdListWorkerStatus::changeWaitingQueue(int row)
-{
- m_waitingComputing.clear();
- qDebug() << m_waitingComputing.size();
-}
diff --git a/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.h b/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.h
index 92661506..2eb70ea9 100644
--- a/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.h
+++ b/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.h
@@ -63,6 +63,7 @@ enum class WorkerStatus : std::int8_t
Ready = 3,
NotReady = 4,
Error = 5,
+ NotAvailable = 6,
};
class MsIdentificationListWindow;
class MsIdListWorkerStatus
@@ -77,6 +78,8 @@ class MsIdListWorkerStatus
*/
WorkerStatus getStatus(IdentificationDataSourceSp identificationDataSource);
void doComputeMsNumber(IdentificationDataSourceSp identificationDataSource);
+ void doComputeMsNumberForTDF(IdentificationDataSourceSp identificationDataSource);
+ void doComputeMsNumberForMzXML(IdentificationDataSourceSp identificationDataSource);
void changeWaitingQueue(int row);
diff --git a/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp b/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp
index 337da3be..9280959d 100644
--- a/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp
+++ b/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp
@@ -400,8 +400,18 @@ MsIdentificationTableModel::data(const QModelIndex &index, int role) const
}
if(col == (std::int8_t)msIdentificationListColumn::nb_tic_1)
{
+ // if(QFileInfo(m_identificationDataSourceSpList.at(row)
+ // ->getMsRunSp()
+ // ->getFileName())
+ // .completeSuffix() == "tdf")
+ // {
+ // return QVariant("NA");
+ // }
+ // else
+ // {
return getMsRunStatisticsNumber(row,
MsRunStatistics::tic_spectra_ms1);
+ // }
}
if(col == (std::int8_t)msIdentificationListColumn::nb_tic_2)
{
@@ -551,9 +561,8 @@ MsIdentificationTableModel::getMsRunStatisticsNumber(
switch(temp)
{
case WorkerStatus::Ready:
- var_return = m_identificationDataSourceSpList.at(row)
- ->getMsRunSp()
- ->getMsRunStatistics(column);
+ var_return = getMsRunStatisticsFollowingFormat(
+ m_identificationDataSourceSpList.at(row)->getMsRunSp(), column);
emit projectStatusChanged();
break;
case WorkerStatus::NotReady:
@@ -618,3 +627,28 @@ MsIdentificationTableModel::stopThreads()
{
msp_workerStatus.get()->stopThreads();
}
+
+QVariant
+MsIdentificationTableModel::getMsRunStatisticsFollowingFormat(
+ MsRunSp msrun_sp, MsRunStatistics column) const
+{
+ QString raw_format = QFileInfo(msrun_sp->getFileName()).completeSuffix();
+
+ if(raw_format != "tdf")
+ {
+ return msrun_sp->getMsRunStatistics(column);
+ }
+ else
+ {
+ if(column == MsRunStatistics::tic_spectra_ms1 ||
+ column == MsRunStatistics::tic_spectra_ms2 ||
+ column == MsRunStatistics::tic_spectra_ms3)
+ {
+ return QVariant("NA");
+ }
+ else
+ {
+ return msrun_sp->getMsRunStatistics(column);
+ }
+ }
+}
diff --git a/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.h b/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.h
index 38ed79dc..c43fb920 100644
--- a/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.h
+++ b/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.h
@@ -109,6 +109,7 @@ class MsIdentificationTableModel : public QAbstractTableModel
private:
static int getColumnWidth(int column);
+ QVariant getMsRunStatisticsFollowingFormat(MsRunSp msrun_sp, MsRunStatistics column) const;
private:
std::vector<IdentificationDataSourceSp> m_identificationDataSourceSpList;
diff --git a/src/gui/load_results_dialog/loadresultsdialog.cpp b/src/gui/load_results_dialog/loadresultsdialog.cpp
index 97990c18..167008e6 100644
--- a/src/gui/load_results_dialog/loadresultsdialog.cpp
+++ b/src/gui/load_results_dialog/loadresultsdialog.cpp
@@ -53,7 +53,8 @@ LoadResultsDialog::LoadResultsDialog(QWidget *parent)
settings.value("automatic_filter/protein_evalue", "0.01").toDouble());
ui->automatic_filter_widget->setAutomaticFilterParameters(param);
- setMinimumWidth(ui->automatic_filter_widget->getAutomaticFilterWindowWidth() + 200);
+ setMinimumWidth(ui->automatic_filter_widget->getAutomaticFilterWindowWidth() +
+ 200);
#if QT_VERSION >= 0x050000
// Qt5 code
diff --git a/src/gui/load_results_dialog/loadresultsdialog.h b/src/gui/load_results_dialog/loadresultsdialog.h
index 613e058c..6ba44e42 100644
--- a/src/gui/load_results_dialog/loadresultsdialog.h
+++ b/src/gui/load_results_dialog/loadresultsdialog.h
@@ -33,7 +33,7 @@
namespace Ui
{
- class LoadResultsDialog;
+class LoadResultsDialog;
}
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.h b/src/gui/peptide_list_view/peptidetableproxymodel.h
index 569bc201..123ce4b4 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.h
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.h
@@ -47,8 +47,8 @@ class PeptideTableProxyModel : public QSortFilterProxyModel
bool filterAcceptsColumn(int source_column,
const QModelIndex &source_parent) const override;
- QVariant headerData(int section, Qt::Orientation orientation,
- int role) const override;
+ QVariant
+ headerData(int section, Qt::Orientation orientation, int role) const override;
QVariant data(const QModelIndex &index,
int role = Qt::DisplayRole) const override;
bool lessThan(const QModelIndex &left,
diff --git a/src/gui/project_view/identification_group_widget/identificationgroupwidget.h b/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
index 14da2a05..764eb254 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
@@ -28,7 +28,7 @@
namespace Ui
{
- class IdentificationGroupWidget;
+class IdentificationGroupWidget;
}
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index d3e5665e..246e3d0c 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -85,8 +85,8 @@ class ProteinListWindow : public QMainWindow
signals:
void identificationGroupEdited(IdentificationGroup *p_identification_group);
void proteinDataChanged();
- void projectStatusChanged();
-
+ void projectStatusChanged();
+
protected slots:
void doNotValidHide(bool hide);
void doNotCheckedHide(bool hide);
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 490f40bb..cbe0d4ec 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -209,7 +209,8 @@ ProteinTableModel::getDescription(std::int8_t column)
return "";
}
QVariant
-ProteinTableModel::headerData(int section, Qt::Orientation orientation,
+ProteinTableModel::headerData(int section,
+ Qt::Orientation orientation,
int role) const
{
if(_p_identification_group == nullptr)
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index 1a38de15..a55106b1 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -61,8 +61,8 @@ class ProteinTableModel : public QAbstractTableModel
rowCount(const QModelIndex &parent = QModelIndex()) const override;
virtual int
columnCount(const QModelIndex &parent = QModelIndex()) const override;
- virtual QVariant headerData(int section, Qt::Orientation orientation,
- int role) const override;
+ virtual QVariant
+ headerData(int section, Qt::Orientation orientation, int role) const override;
virtual QVariant data(const QModelIndex &index,
int role = Qt::DisplayRole) const override;
@@ -75,7 +75,7 @@ class ProteinTableModel : public QAbstractTableModel
void setIdentificationGroup(IdentificationGroup *p_identification_group);
IdentificationGroup *getIdentificationGroup();
-
+
public slots:
void onProteinDataChanged();
diff --git a/src/gui/protein_list_view/proteintableproxymodel.h b/src/gui/protein_list_view/proteintableproxymodel.h
index adefbcb0..d4f68770 100644
--- a/src/gui/protein_list_view/proteintableproxymodel.h
+++ b/src/gui/protein_list_view/proteintableproxymodel.h
@@ -48,8 +48,8 @@ class ProteinTableProxyModel : public QSortFilterProxyModel
bool filterAcceptsColumn(int source_column,
const QModelIndex &source_parent) const override;
- QVariant headerData(int section, Qt::Orientation orientation,
- int role) const override;
+ QVariant
+ headerData(int section, Qt::Orientation orientation, int role) const override;
QVariant data(const QModelIndex &index,
int role = Qt::DisplayRole) const override;
bool lessThan(const QModelIndex &left,
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 53328632..b9a80f64 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -63,30 +63,46 @@ PtmIslandListWindow::PtmIslandListWindow(ProjectWindow *parent)
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(this, &PtmIslandListWindow::ptmIslandDataChanged, _ptm_table_model_p,
+ connect(this,
+ &PtmIslandListWindow::ptmIslandDataChanged,
+ _ptm_table_model_p,
&PtmIslandTableModel::onPtmIslandDataChanged);
- connect(_project_window, &ProjectWindow::identificationPtmGroupGrouped, this,
+ connect(_project_window,
+ &ProjectWindow::identificationPtmGroupGrouped,
+ this,
&PtmIslandListWindow::doIdentificationPtmGroupGrouped);
- connect(_project_window, &ProjectWindow::identificationGroupGrouped, this,
+ connect(_project_window,
+ &ProjectWindow::identificationGroupGrouped,
+ this,
&PtmIslandListWindow::doIdentificationGroupGrouped);
- connect(ui->ptm_island_tableview, &QTableView::clicked, _ptm_proxy_model_p,
+ connect(ui->ptm_island_tableview,
+ &QTableView::clicked,
+ _ptm_proxy_model_p,
&PtmIslandProxyModel::onTableClicked);
- connect(_ptm_table_model_p, &PtmIslandTableModel::layoutChanged, this,
+ connect(_ptm_table_model_p,
+ &PtmIslandTableModel::layoutChanged,
+ this,
&PtmIslandListWindow::updateStatusBar);
#else
// Qt4 code
- connect(this, SIGNAL(ptmIslandDataChanged()), _ptm_table_model_p,
+ connect(this,
+ SIGNAL(ptmIslandDataChanged()),
+ _ptm_table_model_p,
SLOT(onPtmIslandDataChanged()));
connect(_project_window,
- SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)), this,
+ SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)),
+ this,
SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *)));
connect(_project_window,
- SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
+ this,
SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
- connect(ui->ptm_island_tableview, SIGNAL(clicked(const QModelIndex &)),
- _ptm_proxy_model_p, SLOT(onTableClicked(const QModelIndex &)));
+ connect(ui->ptm_island_tableview,
+ SIGNAL(clicked(const QModelIndex &)),
+ _ptm_proxy_model_p,
+ SLOT(onTableClicked(const QModelIndex &)));
#endif
}
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index 70cb8e16..e5f49d37 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -42,7 +42,7 @@ class PtmPeptideListWindow;
// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
namespace Ui
{
- class PtmIslandListWindow;
+class PtmIslandListWindow;
}
class PtmIslandListWindow : public QMainWindow
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index d039db1f..9057339b 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -178,7 +178,8 @@ PtmIslandTableModel::columnCount(const QModelIndex &parent) const
return 0;
}
QVariant
-PtmIslandTableModel::headerData(int section, Qt::Orientation orientation,
+PtmIslandTableModel::headerData(int section,
+ Qt::Orientation orientation,
int role) const
{
if(getPtmGroupingExperiment() == nullptr)
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index 2cee9bc6..da20d0d4 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -70,8 +70,8 @@ class PtmIslandTableModel : public QAbstractTableModel
rowCount(const QModelIndex &parent = QModelIndex()) const override;
virtual int
columnCount(const QModelIndex &parent = QModelIndex()) const override;
- virtual QVariant headerData(int section, Qt::Orientation orientation,
- int role) const override;
+ virtual QVariant
+ headerData(int section, Qt::Orientation orientation, int role) const override;
virtual QVariant data(const QModelIndex &index,
int role = Qt::DisplayRole) const override;
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index 2eb2a838..6113bd9e 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -55,7 +55,7 @@ PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow *parent)
ui->ptm_peptide_tableview->setSortingEnabled(true);
ui->ptm_peptide_tableview->setAlternatingRowColors(true);
ui->ptm_peptide_tableview->horizontalHeader()->setSectionsMovable(true);
-
+
PtmSequenceDelegate *p_sequence_delegate =
new PtmSequenceDelegate(_p_ptm_island_list_window, this);
ui->ptm_peptide_tableview->setItemDelegateForColumn(
@@ -64,9 +64,12 @@ PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow *parent)
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(ui->ptm_peptide_tableview, &QTableView::clicked, _ptm_proxy_model_p,
+ connect(ui->ptm_peptide_tableview,
+ &QTableView::clicked,
+ _ptm_proxy_model_p,
&PtmPeptideTableProxyModel::onTableClicked);
- connect(this, &PtmPeptideListWindow::requestPeptideDetailView,
+ connect(this,
+ &PtmPeptideListWindow::requestPeptideDetailView,
_p_ptm_island_list_window->getProjectWindowP(),
&ProjectWindow::doViewPeptideDetail);
#else
@@ -79,9 +82,12 @@ PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow *parent)
// this,SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *))); connect
// (_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 *)),
+ connect(ui->ptm_peptide_tableview,
+ SIGNAL(clicked(const QModelIndex &)),
+ _ptm_proxy_model_p,
+ SLOT(onTableClicked(const QModelIndex &)));
+ connect(this,
+ SIGNAL(requestPeptideDetailView(PeptideMatch *)),
_p_ptm_island_list_window->getProjectWindowP(),
SLOT(doViewPeptideDetail(PeptideMatch *)));
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
index d49489ef..b4bcc15c 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
@@ -40,7 +40,7 @@ class PtmIslandListWindow;
namespace Ui
{
- class PtmPeptideListWindow;
+class PtmPeptideListWindow;
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
index ba001ecf..9ccc8b59 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
@@ -188,7 +188,8 @@ PtmPeptideTableModel::columnCount(const QModelIndex &parent) const
return 15;
}
QVariant
-PtmPeptideTableModel::headerData(int section, Qt::Orientation orientation,
+PtmPeptideTableModel::headerData(int section,
+ Qt::Orientation orientation,
int role) const
{
if(orientation == Qt::Horizontal)
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
index 76c02ce6..59ae2434 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
@@ -71,8 +71,8 @@ class PtmPeptideTableModel : public QAbstractTableModel
rowCount(const QModelIndex &parent = QModelIndex()) const override;
virtual int
columnCount(const QModelIndex &parent = QModelIndex()) const override;
- virtual QVariant headerData(int section, Qt::Orientation orientation,
- int role) const override;
+ virtual QVariant
+ headerData(int section, Qt::Orientation orientation, int role) const override;
virtual QVariant data(const QModelIndex &index,
int role = Qt::DisplayRole) const override;
static const QString getTitle(PtmPeptideListColumn column);
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
index 4a15cc54..e3705641 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
@@ -35,7 +35,8 @@
PtmPeptideMenuQicon::PtmPeptideMenuQicon(
const PtmGroupingExperiment *p_ptm_grouping_experiment,
- const PtmSampleScan *p_ptm_sample, const PeptideMatch *p_peptide_match)
+ const PtmSampleScan *p_ptm_sample,
+ const PeptideMatch *p_peptide_match)
: QIcon(), _peptide_match(*p_peptide_match)
{
_p_ptm_sample_scan = p_ptm_sample;
@@ -45,8 +46,10 @@ PtmPeptideMenuQicon::~PtmPeptideMenuQicon()
{
}
void
-PtmPeptideMenuQicon::paint(QPainter *painter, const QRect &rect,
- Qt::Alignment alignment, Mode mode,
+PtmPeptideMenuQicon::paint(QPainter *painter,
+ const QRect &rect,
+ Qt::Alignment alignment,
+ Mode mode,
State state) const
{
@@ -69,14 +72,15 @@ PtmPeptideMenuQicon::paint(QPainter *painter, const QRect &rect,
PtmPeptideMenuQaction::PtmPeptideMenuQaction(
PtmPeptideTableProxyModel *parent,
const PtmGroupingExperiment *p_ptm_grouping_experiment,
- const PtmSampleScan *p_ptm_sample, PeptideMatch *p_peptide_match)
+ const PtmSampleScan *p_ptm_sample,
+ PeptideMatch *p_peptide_match)
: QAction(parent)
{
_p_ptm_peptide_table_proxy_model = parent;
_peptide_match = *p_peptide_match;
- this->setIcon(PtmPeptideMenuQicon(p_ptm_grouping_experiment, p_ptm_sample,
- p_peptide_match));
+ this->setIcon(PtmPeptideMenuQicon(
+ p_ptm_grouping_experiment, p_ptm_sample, p_peptide_match));
// this->setText(p_peptide_match->getPeptideXtpSp().get()->getSequence());
QStringList position_list;
@@ -97,7 +101,9 @@ PtmPeptideMenuQaction::PtmPeptideMenuQaction(
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(this, &PtmPeptideMenuQaction::triggered, this,
+ connect(this,
+ &PtmPeptideMenuQaction::triggered,
+ this,
&PtmPeptideMenuQaction::doTriggered);
#else
// Qt4 code
@@ -187,8 +193,10 @@ PtmPeptideTableProxyModel::showContextMenu(const QModelIndex &index)
for(auto p_peptide_match : sp_ptm_sample_scan.get()->getPeptideMatchList())
{
p_action = new PtmPeptideMenuQaction(
- this, _p_ptm_table_model->getPtmGroupingExperiment(),
- sp_ptm_sample_scan.get(), &p_peptide_match);
+ this,
+ _p_ptm_table_model->getPtmGroupingExperiment(),
+ sp_ptm_sample_scan.get(),
+ &p_peptide_match);
_p_context_menu->addAction(p_action);
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
index 3b458883..fc1211ec 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
@@ -46,12 +46,15 @@ class PtmPeptideMenuQicon : public QIcon
public:
explicit PtmPeptideMenuQicon(
const PtmGroupingExperiment *p_ptm_grouping_experiment,
- const PtmSampleScan *p_ptm_sample, const PeptideMatch *p_peptide_match);
+ const PtmSampleScan *p_ptm_sample,
+ const PeptideMatch *p_peptide_match);
~PtmPeptideMenuQicon();
- void paint(QPainter *painter, const QRect &rect,
- Qt::Alignment alignment = Qt::AlignCenter, Mode mode = Normal,
- State state = Off) const;
+ void paint(QPainter *painter,
+ const QRect &rect,
+ Qt::Alignment alignment = Qt::AlignCenter,
+ Mode mode = Normal,
+ State state = Off) const;
private:
const PtmSampleScan *_p_ptm_sample_scan;
@@ -66,7 +69,8 @@ class PtmPeptideMenuQaction : public QAction
explicit PtmPeptideMenuQaction(
PtmPeptideTableProxyModel *parent,
const PtmGroupingExperiment *p_ptm_grouping_experiment,
- const PtmSampleScan *p_ptm_sample, PeptideMatch *p_peptide_match);
+ const PtmSampleScan *p_ptm_sample,
+ PeptideMatch *p_peptide_match);
~PtmPeptideMenuQaction();
public slots:
diff --git a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h b/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h
index e9b786bc..fef38bde 100644
--- a/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h
+++ b/src/gui/ptm_peptide_list_view/ptmsequencedelegate.h
@@ -41,7 +41,8 @@ class PtmSequenceDelegate : public QStyledItemDelegate
PtmSequenceDelegate(PtmIslandListWindow *p_ptm_island_list_window,
QWidget *parent = 0);
- void paint(QPainter *painter, const QStyleOptionViewItem &option,
+ void paint(QPainter *painter,
+ const QStyleOptionViewItem &option,
const QModelIndex &index) const override;
// QSize sizeHint(const QStyleOptionViewItem &option,
// const QModelIndex &index) const override;
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index d95cf3e2..a48debfe 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -389,8 +389,10 @@ TandemRunDialog::selectMzFiles()
this,
tr("select peak list files"),
default_mz_location,
- tr("any mz files (*.mzXML *.mzxml *.mzML *.mzml *.mgf *.tdf);;mzXML (*.mzXML "
- "*.mzxml);;mzML (*.mzML *.mzml);;MGF (*.mgf);; tdf (*.tdf);;all files (*)"));
+ tr("any mz files (*.mzXML *.mzxml *.mzML *.mzml *.mgf *.tdf);;mzXML "
+ "(*.mzXML "
+ "*.mzxml);;mzML (*.mzML *.mzml);;MGF (*.mgf);; tdf (*.tdf);;all "
+ "files (*)"));
if(filenames.size() > 0)
{
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.h b/src/gui/tandem_run_dialog/tandemrundialog.h
index 08ad6463..f2497ae6 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.h
+++ b/src/gui/tandem_run_dialog/tandemrundialog.h
@@ -33,7 +33,7 @@
namespace Ui
{
- class TandemRunDialog;
+class TandemRunDialog;
}
diff --git a/src/gui/widgets/Alignment_group_menu/alignmentgroupmenu.cpp b/src/gui/widgets/Alignment_group_menu/alignmentgroupmenu.cpp
index 7e486abd..50c9f139 100644
--- a/src/gui/widgets/Alignment_group_menu/alignmentgroupmenu.cpp
+++ b/src/gui/widgets/Alignment_group_menu/alignmentgroupmenu.cpp
@@ -47,7 +47,8 @@ AlignmentGroupsQMenu::AlignmentGroupsQMenu(MsIdentificationListWindow *parent,
QIcon *remove_reference_icon =
new QIcon(":/icons/resources/icons/icon_remove_reference.svg");
- mp_removeReference = new QAction(*remove_reference_icon, tr("&Remove reference"));
+ mp_removeReference =
+ new QAction(*remove_reference_icon, tr("&Remove reference"));
this->addAction(mp_removeReference);
mp_ungroup = new QAction(
@@ -95,9 +96,9 @@ AlignmentGroupsQMenu::createGroupsSubMenu()
mp_subMenuGroup->addAction(mp_newGroup);
mp_subMenuGroup->addSeparator();
foreach(MsRunAlignmentGroupSp group, mp_project->getMsRunAlignmentGroupList())
- {
- mp_subMenuGroup->addAction(group->getMsRunAlignmentGroupName());
- }
+ {
+ mp_subMenuGroup->addAction(group->getMsRunAlignmentGroupName());
+ }
}
void
diff --git a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
index 337d3348..acd18feb 100644
--- a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
+++ b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.cpp
@@ -164,7 +164,7 @@ AutomaticFilterWidget::doSetParameters()
{
if(ui->fdr_radio_button->isChecked())
{
- _parameters.setFilterPeptideFDR(ui->peptide_fdr_spinbox->value()/100);
+ _parameters.setFilterPeptideFDR(ui->peptide_fdr_spinbox->value() / 100);
ui->peptide_evalue_spinbox->setDisabled(true);
ui->peptide_fdr_spinbox->setEnabled(true);
}
@@ -179,7 +179,8 @@ AutomaticFilterWidget::doSetParameters()
}
-int AutomaticFilterWidget::getAutomaticFilterWindowWidth() const
+int
+AutomaticFilterWidget::getAutomaticFilterWindowWidth() const
{
return ui->gridLayout_2->minimumSize().width();
}
diff --git a/src/gui/widgets/decoy_widget/decoywidget.cpp b/src/gui/widgets/decoy_widget/decoywidget.cpp
index d627f397..b2289982 100644
--- a/src/gui/widgets/decoy_widget/decoywidget.cpp
+++ b/src/gui/widgets/decoy_widget/decoywidget.cpp
@@ -224,7 +224,9 @@ DecoyWidget::doSelectFastaFile()
settings.value("path/fastafiles_directory", "").toString();
QStringList filenames = QFileDialog::getOpenFileNames(
- this, tr("FASTA files"), default_fasta_location,
+ this,
+ tr("FASTA files"),
+ default_fasta_location,
tr("FASTA files (*.fasta);;all files (*)"));
if(filenames.size() > 0)
diff --git a/src/gui/widgets/decoy_widget/decoywidget.h b/src/gui/widgets/decoy_widget/decoywidget.h
index 4406058d..9cd64c78 100644
--- a/src/gui/widgets/decoy_widget/decoywidget.h
+++ b/src/gui/widgets/decoy_widget/decoywidget.h
@@ -36,7 +36,7 @@
namespace Ui
{
- class DecoyWidget;
+class DecoyWidget;
}
class DecoyWidget : public QWidget
diff --git a/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h b/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h
index 962543d9..63d8bf35 100644
--- a/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h
+++ b/src/gui/widgets/xic_extraction_method_widget/xicextractionmethodwidget.h
@@ -49,8 +49,7 @@ class XicExtractionMethodWidget : public QWidget
XicExtractionMethodWidget(QWidget *parent = 0);
~XicExtractionMethodWidget();
pappso::XicExtractMethod getXicExtractionMethod() const;
-
+
signals:
void xicExtractionMethodChanged(pappso::XicExtractMethod method) const;
};
-
diff --git a/src/gui/xic_view/xic_widgets/zivywidget.cpp b/src/gui/xic_view/xic_widgets/zivywidget.cpp
index afc675f6..b23fa95d 100644
--- a/src/gui/xic_view/xic_widgets/zivywidget.cpp
+++ b/src/gui/xic_view/xic_widgets/zivywidget.cpp
@@ -37,10 +37,10 @@ std::shared_ptr<pappso::TraceDetectionInterface>
ZivyParams::newTraceDetectionZivySPtr() const
{
return std::make_shared<pappso::TraceDetectionZivy>(_smoothing_half_window,
- _minmax_half_window,
- _maxmin_half_window,
- _minmax_threshold,
- _maxmin_threshold);
+ _minmax_half_window,
+ _maxmin_half_window,
+ _minmax_threshold,
+ _maxmin_threshold);
}
void
diff --git a/src/gui/xic_view/xicworkerthread.cpp b/src/gui/xic_view/xicworkerthread.cpp
index e038f058..910dbf49 100644
--- a/src/gui/xic_view/xicworkerthread.cpp
+++ b/src/gui/xic_view/xicworkerthread.cpp
@@ -98,7 +98,8 @@ XicWorkerThread::doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
isotope_mass_list = isotope_list.getByIntensityRatio(
charge, precision, minimum_isotope_pattern_ratio);
- std::sort(isotope_mass_list.begin(), isotope_mass_list.end(),
+ std::sort(isotope_mass_list.begin(),
+ isotope_mass_list.end(),
[](const pappso::PeptideNaturalIsotopeAverageSp &m,
const pappso::PeptideNaturalIsotopeAverageSp &n) -> bool {
unsigned int mn(m.get()->getIsotopeNumber()),
diff --git a/src/gui/xic_view/xicworkerthread.h b/src/gui/xic_view/xicworkerthread.h
index 4285d840..3b699a7f 100644
--- a/src/gui/xic_view/xicworkerthread.h
+++ b/src/gui/xic_view/xicworkerthread.h
@@ -43,7 +43,8 @@ class XicWorkerThread : public QObject
XicWorkerThread(XicBox *parent);
virtual ~XicWorkerThread();
public slots:
- void doXicLoad(MsRunSp p_msrun, std::vector<pappso::pappso_double> mz_list,
+ void doXicLoad(MsRunSp p_msrun,
+ std::vector<pappso::pappso_double> mz_list,
pappso::PrecisionPtr precision,
pappso::XicExtractMethod method);
void doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
diff --git a/src/input/condorqxmlsaxhandler.cpp b/src/input/condorqxmlsaxhandler.cpp
index 0b7081d3..726e9b8b 100644
--- a/src/input/condorqxmlsaxhandler.cpp
+++ b/src/input/condorqxmlsaxhandler.cpp
@@ -72,16 +72,18 @@ CondorQxmlSaxHandler::startElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::startElement tag "
- "%1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in CondorQxmlSaxHandler::startElement tag "
+ "%1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
}
catch(std::exception exception_std)
{
- _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::startElement tag "
- "%1, std exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in CondorQxmlSaxHandler::startElement tag "
+ "%1, std exception:\n%2")
.arg(qName)
.arg(exception_std.what());
return false;
@@ -91,7 +93,8 @@ CondorQxmlSaxHandler::startElement(const QString &namespaceURI,
bool
CondorQxmlSaxHandler::endElement(const QString &namespaceURI,
- const QString &localName, const QString &qName)
+ const QString &localName,
+ const QString &qName)
{
bool is_ok = true;
@@ -118,16 +121,18 @@ CondorQxmlSaxHandler::endElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::endElement tag "
- "%1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in CondorQxmlSaxHandler::endElement tag "
+ "%1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
}
catch(std::exception exception_std)
{
- _errorStr = QObject::tr("ERROR in CondorQxmlSaxHandler::endElement tag "
- "%1, std exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in CondorQxmlSaxHandler::endElement tag "
+ "%1, std exception:\n%2")
.arg(qName)
.arg(exception_std.what());
return false;
@@ -143,8 +148,9 @@ CondorQxmlSaxHandler::endElement(const QString &namespaceURI,
bool
CondorQxmlSaxHandler::error(const QXmlParseException &exception)
{
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3")
+ _errorStr = QObject::tr(
+ "Parse error at line %1, column %2 :\n"
+ "%3")
.arg(exception.lineNumber())
.arg(exception.columnNumber())
.arg(exception.message());
@@ -156,8 +162,9 @@ CondorQxmlSaxHandler::error(const QXmlParseException &exception)
bool
CondorQxmlSaxHandler::fatalError(const QXmlParseException &exception)
{
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3")
+ _errorStr = QObject::tr(
+ "Parse error at line %1, column %2 :\n"
+ "%3")
.arg(exception.lineNumber())
.arg(exception.columnNumber())
.arg(exception.message());
diff --git a/src/input/condorqxmlsaxhandler.h b/src/input/condorqxmlsaxhandler.h
index 4fd269c6..9b2e05b9 100644
--- a/src/input/condorqxmlsaxhandler.h
+++ b/src/input/condorqxmlsaxhandler.h
@@ -55,10 +55,13 @@ class CondorQxmlSaxHandler : public QXmlDefaultHandler
CondorQxmlSaxHandler(TandemCondorProcess *tandem_condor_process);
~CondorQxmlSaxHandler();
- bool startElement(const QString &namespaceURI, const QString &localName,
- const QString &qName, const QXmlAttributes &attributes);
+ bool startElement(const QString &namespaceURI,
+ const QString &localName,
+ const QString &qName,
+ const QXmlAttributes &attributes);
- bool endElement(const QString &namespaceURI, const QString &localName,
+ bool endElement(const QString &namespaceURI,
+ const QString &localName,
const QString &qName);
bool startDocument();
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 9cc1dafc..73b85475 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -252,7 +252,8 @@ getQVariantDoubleParam(pwiz::data::ParamContainer *item, pwiz::cv::CVID param)
void
IdentificationPwizReader::read(
- IdentificationDataSource *p_identification_data_source, Project *p_project,
+ IdentificationDataSource *p_identification_data_source,
+ Project *p_project,
IdentificationGroup *p_identification_group)
{
qDebug() << "IdentificationPwizReader::read begin";
diff --git a/src/input/identificationpwizreader.h b/src/input/identificationpwizreader.h
index 4738d65f..bba10d61 100644
--- a/src/input/identificationpwizreader.h
+++ b/src/input/identificationpwizreader.h
@@ -42,10 +42,10 @@
namespace pwiz
{
- namespace identdata
- {
- class IdentDataFile;
- }
+namespace identdata
+{
+class IdentDataFile;
+}
} // namespace pwiz
class IdentificationPwizReader
@@ -57,7 +57,8 @@ class IdentificationPwizReader
IdentificationEngine getIdentificationEngine() const;
void read(IdentificationDataSource *p_identification_data_source,
- Project *p_project, IdentificationGroup *p_identification_group);
+ Project *p_project,
+ IdentificationGroup *p_identification_group);
private:
IdentificationEngine getIdentificationEngine(const QString &xml_id) const;
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index bdc252be..4d3b8432 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -332,7 +332,7 @@ 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/pepxmlsaxhandler.h b/src/input/pepxmlsaxhandler.h
index 8856408c..ac42d018 100644
--- a/src/input/pepxmlsaxhandler.h
+++ b/src/input/pepxmlsaxhandler.h
@@ -46,10 +46,13 @@ class PepXmlSaxHandler : public QXmlDefaultHandler
IdentificationDataSource *p_identification_data_source);
~PepXmlSaxHandler();
- bool startElement(const QString &namespaceURI, const QString &localName,
- const QString &qName, const QXmlAttributes &attributes);
+ bool startElement(const QString &namespaceURI,
+ const QString &localName,
+ const QString &qName,
+ const QXmlAttributes &attributes);
- bool endElement(const QString &namespaceURI, const QString &localName,
+ bool endElement(const QString &namespaceURI,
+ const QString &localName,
const QString &qName);
bool startDocument();
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index 4a4731c2..cc692ecd 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -39,10 +39,13 @@ class XpipSaxHandler : public QXmlDefaultHandler
XpipSaxHandler(WorkMonitorInterface *p_monitor, Project *p_project);
~XpipSaxHandler();
- bool startElement(const QString &namespaceURI, const QString &localName,
- const QString &qName, const QXmlAttributes &attributes);
+ bool startElement(const QString &namespaceURI,
+ const QString &localName,
+ const QString &qName,
+ const QXmlAttributes &attributes);
- bool endElement(const QString &namespaceURI, const QString &localName,
+ bool endElement(const QString &namespaceURI,
+ const QString &localName,
const QString &qName);
bool startDocument();
diff --git a/src/input/xtpxpipsaxhandler.cpp b/src/input/xtpxpipsaxhandler.cpp
index 3f44fcef..a755348d 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -589,8 +589,8 @@ XtpXpipSaxHandler::startElement_msrun(QXmlAttributes attributes)
bool
XtpXpipSaxHandler::startElement_alignmentGroup(QXmlAttributes attributes)
{
- msp_alignment_group = std::make_shared<MsRunAlignmentGroup>(_p_project,
- attributes.value("name").simplified());
+ msp_alignment_group = std::make_shared<MsRunAlignmentGroup>(
+ _p_project, attributes.value("name").simplified());
_p_project->addMsRunAlignmentGroupToList(msp_alignment_group);
QString reference_id = attributes.value("reference").simplified();
if(reference_id != "")
diff --git a/src/output/masschroqprm.h b/src/output/masschroqprm.h
index 0ad73cbb..754b9437 100644
--- a/src/output/masschroqprm.h
+++ b/src/output/masschroqprm.h
@@ -54,4 +54,3 @@ class MassChroqPrm
ProjectSp _sp_project;
IdentificationGroup *_p_identification_group;
};
-
diff --git a/src/output/mcqr/mcqrscpeptide.cpp b/src/output/mcqr/mcqrscpeptide.cpp
index a855c9dd..8d9bca9b 100644
--- a/src/output/mcqr/mcqrscpeptide.cpp
+++ b/src/output/mcqr/mcqrscpeptide.cpp
@@ -98,7 +98,8 @@ McqRscPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
std::vector<const ProteinMatch *> protein_match_list =
group_pair.second.get()->getProteinMatchList();
- std::sort(protein_match_list.begin(), protein_match_list.end(),
+ std::sort(protein_match_list.begin(),
+ protein_match_list.end(),
[](const ProteinMatch *a, const ProteinMatch *b) {
return a->getGrpProteinSp().get()->getSubGroupNumber() <
b->getGrpProteinSp().get()->getSubGroupNumber();
@@ -125,8 +126,10 @@ McqRscPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
std::vector<PeptideMatch> peptide_match_in_msrun =
protein_match->getPeptideMatchList(validation_state,
msrun_sp.get());
- writePeptidesInMsrun(protein_match, msrun_sp.get(),
- peptide_match_in_msrun, count_scan_zero);
+ writePeptidesInMsrun(protein_match,
+ msrun_sp.get(),
+ peptide_match_in_msrun,
+ count_scan_zero);
}
}
}
@@ -136,7 +139,8 @@ McqRscPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
void
McqRscPeptide::writePeptidesInMsrun(
- const ProteinMatch *p_protein_match, const MsRun *p_msrun,
+ const ProteinMatch *p_protein_match,
+ const MsRun *p_msrun,
const std::vector<PeptideMatch> &peptide_match_in_msrun,
const std::map<ScPeptideLabel, std::size_t> &count_scan_zero)
{
@@ -194,7 +198,8 @@ McqRscPeptide::writePeptidesInMsrun(
(unsigned int)p_protein_match->getGroupingGroupSp()
.get()
->countSpecificSequenceLi(p_protein_match,
- ValidationState::grouped, p_msrun,
+ ValidationState::grouped,
+ p_msrun,
pair_count.first._p_label));
}
qDebug() << "McqRscPeptide::writePeptidesInMsrun end";
diff --git a/src/output/mcqr/mcqrscpeptide.h b/src/output/mcqr/mcqrscpeptide.h
index 977a478f..76984f83 100644
--- a/src/output/mcqr/mcqrscpeptide.h
+++ b/src/output/mcqr/mcqrscpeptide.h
@@ -55,7 +55,8 @@ class McqRscPeptide
void writeIdentificationGroup(IdentificationGroup *p_ident);
void writeHeaders(IdentificationGroup *p_ident);
void writePeptidesInMsrun(
- const ProteinMatch *p_protein_match, const MsRun *p_msrun,
+ const ProteinMatch *p_protein_match,
+ const MsRun *p_msrun,
const std::vector<PeptideMatch> &peptide_match_in_msrun,
const std::map<ScPeptideLabel, std::size_t> &count_scan_zero);
diff --git a/src/output/mcqr/mcqrscprotein.cpp b/src/output/mcqr/mcqrscprotein.cpp
index b77b4830..c6c34ce3 100644
--- a/src/output/mcqr/mcqrscprotein.cpp
+++ b/src/output/mcqr/mcqrscprotein.cpp
@@ -87,7 +87,8 @@ McqRscProtein::writeIdentificationGroup(IdentificationGroup *p_ident)
std::vector<const ProteinMatch *> protein_match_list =
group_pair.second.get()->getProteinMatchList();
- std::sort(protein_match_list.begin(), protein_match_list.end(),
+ std::sort(protein_match_list.begin(),
+ protein_match_list.end(),
[](const ProteinMatch *a, const ProteinMatch *b) {
return a->getGrpProteinSp().get()->getSubGroupNumber() <
b->getGrpProteinSp().get()->getSubGroupNumber();
diff --git a/src/output/mcqrspectralcount.cpp b/src/output/mcqrspectralcount.cpp
index 60c8e45c..77fc580f 100644
--- a/src/output/mcqrspectralcount.cpp
+++ b/src/output/mcqrspectralcount.cpp
@@ -102,7 +102,8 @@ McqrSpectralCount::writeIdentificationGroup(IdentificationGroup *p_ident)
std::vector<const ProteinMatch *> protein_match_list =
group_pair.second.get()->getProteinMatchList();
- std::sort(protein_match_list.begin(), protein_match_list.end(),
+ std::sort(protein_match_list.begin(),
+ protein_match_list.end(),
[](const ProteinMatch *a, const ProteinMatch *b) {
return a->getGrpProteinSp().get()->getSubGroupNumber() <
b->getGrpProteinSp().get()->getSubGroupNumber();
@@ -139,15 +140,21 @@ McqrSpectralCount::writeOneProtein(const GroupingGroup *p_group,
if(_label_list.size() == 0)
{
- writeOneProteinLabel(p_grp_protein, msrun_sp.get(), nullptr,
- p_protein, p_protein_match);
+ writeOneProteinLabel(p_grp_protein,
+ msrun_sp.get(),
+ nullptr,
+ p_protein,
+ p_protein_match);
}
else
{
for(auto &p_label : _label_list)
{
- writeOneProteinLabel(p_grp_protein, msrun_sp.get(), p_label,
- p_protein, p_protein_match);
+ writeOneProteinLabel(p_grp_protein,
+ msrun_sp.get(),
+ p_label,
+ p_protein,
+ p_protein_match);
}
}
}
@@ -194,9 +201,9 @@ McqrSpectralCount::writeOneProteinLabel(const pappso::GrpProtein *p_grp_protein,
_p_writer->writeCell(p_protein_match->countSampleScan(
ValidationState::grouped, p_msrun, p_label));
- _p_writer->writeCell((unsigned int)p_protein_match->getGroupingGroupSp()
- .get()
- ->countSpecificSampleScan(p_protein_match,
- ValidationState::grouped,
- p_msrun, p_label));
+ _p_writer->writeCell(
+ (unsigned int)p_protein_match->getGroupingGroupSp()
+ .get()
+ ->countSpecificSampleScan(
+ p_protein_match, ValidationState::grouped, p_msrun, p_label));
}
diff --git a/src/output/mcqrspectralcount.h b/src/output/mcqrspectralcount.h
index bf26cfd8..d6a40133 100644
--- a/src/output/mcqrspectralcount.h
+++ b/src/output/mcqrspectralcount.h
@@ -47,7 +47,8 @@ class McqrSpectralCount
void writeOneProtein(const GroupingGroup *p_group,
const ProteinMatch *p_protein_match);
void writeOneProteinLabel(const pappso::GrpProtein *p_grp_protein,
- const MsRun *p_msrun, const Label *p_label,
+ const MsRun *p_msrun,
+ const Label *p_label,
const ProteinXtp *p_protein,
const ProteinMatch *p_protein_match);
diff --git a/src/output/ods/comparbasesheet.cpp b/src/output/ods/comparbasesheet.cpp
index 88e1115b..3c7bfaa5 100644
--- a/src/output/ods/comparbasesheet.cpp
+++ b/src/output/ods/comparbasesheet.cpp
@@ -164,8 +164,8 @@ ComparBaseSheet::writeProteinMatch(const ProteinMatch *p_protein_match)
{
if(_label_list.size() == 0)
{
- writeComparValue(p_protein_match, ValidationState::validAndChecked,
- msrun_sp.get());
+ writeComparValue(
+ p_protein_match, ValidationState::validAndChecked, msrun_sp.get());
if(_first_cell_coordinate.isEmpty())
{
_first_cell_coordinate = _p_writer->getOdsCellCoordinate();
@@ -176,7 +176,8 @@ ComparBaseSheet::writeProteinMatch(const ProteinMatch *p_protein_match)
for(const Label *p_label : _label_list)
{
writeComparValue(p_protein_match,
- ValidationState::validAndChecked, msrun_sp.get(),
+ ValidationState::validAndChecked,
+ msrun_sp.get(),
p_label);
if(_first_cell_coordinate.isEmpty())
{
@@ -211,7 +212,8 @@ ComparBaseSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
}
std::sort(
- protein_match_list.begin(), protein_match_list.end(),
+ protein_match_list.begin(),
+ protein_match_list.end(),
[](const ProteinMatch *a, const ProteinMatch *b) {
unsigned int agroup = a->getGrpProteinSp().get()->getGroupNumber();
unsigned int asubgroup = a->getGrpProteinSp().get()->getSubGroupNumber();
diff --git a/src/output/ods/comparbasesheet.h b/src/output/ods/comparbasesheet.h
index 4b85ab7d..c5871f86 100644
--- a/src/output/ods/comparbasesheet.h
+++ b/src/output/ods/comparbasesheet.h
@@ -39,7 +39,8 @@
class ComparBaseSheet
{
public:
- ComparBaseSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ ComparBaseSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
private:
@@ -51,7 +52,8 @@ class ComparBaseSheet
protected:
virtual void writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label = nullptr) = 0;
void writeProteinMatch(const ProteinMatch *p_protein_match);
diff --git a/src/output/ods/comparspecificspectrasheet.cpp b/src/output/ods/comparspecificspectrasheet.cpp
index 5ad6c4fe..20e6923a 100644
--- a/src/output/ods/comparspecificspectrasheet.cpp
+++ b/src/output/ods/comparspecificspectrasheet.cpp
@@ -32,7 +32,8 @@
ComparSpecificSpectraSheet::ComparSpecificSpectraSheet(
- OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project)
: ComparBaseSheet(p_ods_export, p_writer, p_project)
{
@@ -42,8 +43,10 @@ ComparSpecificSpectraSheet::ComparSpecificSpectraSheet(
void
ComparSpecificSpectraSheet::writeComparValue(
- const ProteinMatch *p_protein_match, ValidationState state,
- const MsRun *p_msrun, const Label *p_label)
+ const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun,
+ const Label *p_label)
{
qDebug() << "ComparSpecificSpectraSheet::writeComparValue begin";
_p_writer->writeCell(
@@ -55,7 +58,8 @@ ComparSpecificSpectraSheet::writeComparValue(
ComparSpecificSequenceSheet::ComparSpecificSequenceSheet(
- OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project)
: ComparBaseSheet(p_ods_export, p_writer, p_project)
{
@@ -64,8 +68,10 @@ ComparSpecificSequenceSheet::ComparSpecificSequenceSheet(
void
ComparSpecificSequenceSheet::writeComparValue(
- const ProteinMatch *p_protein_match, ValidationState state,
- const MsRun *p_msrun, const Label *p_label)
+ const ProteinMatch *p_protein_match,
+ ValidationState state,
+ const MsRun *p_msrun,
+ const Label *p_label)
{
qDebug() << "ComparSpecificSequenceSheet::writeComparValue begin";
_p_writer->writeCell(
diff --git a/src/output/ods/comparspecificspectrasheet.h b/src/output/ods/comparspecificspectrasheet.h
index 90398835..e677f28f 100644
--- a/src/output/ods/comparspecificspectrasheet.h
+++ b/src/output/ods/comparspecificspectrasheet.h
@@ -41,7 +41,8 @@ class ComparSpecificSpectraSheet : public ComparBaseSheet
protected:
virtual void writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label = nullptr) override;
};
@@ -54,7 +55,8 @@ class ComparSpecificSequenceSheet : public ComparBaseSheet
protected:
virtual void writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label = nullptr) override;
};
diff --git a/src/output/ods/comparspectrabypeptide.cpp b/src/output/ods/comparspectrabypeptide.cpp
index 1649ee15..2898bbe1 100644
--- a/src/output/ods/comparspectrabypeptide.cpp
+++ b/src/output/ods/comparspectrabypeptide.cpp
@@ -132,7 +132,8 @@ ComparSpectraByPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
std::vector<const PeptideEvidence *> peptide_evidence_list =
group_pair.second.get()->getPeptideEvidenceList();
- std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
+ std::sort(peptide_evidence_list.begin(),
+ peptide_evidence_list.end(),
[](const PeptideEvidence *a, const PeptideEvidence *b) {
return a->getGrpPeptideSp().get()->getRank() <
b->getGrpPeptideSp().get()->getRank();
@@ -198,8 +199,8 @@ ComparSpectraByPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
if(p_best_peptide_evidence != nullptr)
{
- writeBestPeptideEvidence(group_pair.second.get(),
- p_best_peptide_evidence, sample_scan_list);
+ writeBestPeptideEvidence(
+ group_pair.second.get(), p_best_peptide_evidence, sample_scan_list);
sample_scan_list.clear();
}
}
@@ -221,7 +222,8 @@ ComparSpectraByPeptide::writeIdentificationGroup(IdentificationGroup *p_ident)
void
ComparSpectraByPeptide::writeBestPeptideEvidence(
- const GroupingGroup *p_group, const PeptideEvidence *p_peptide_evidence,
+ const GroupingGroup *p_group,
+ const PeptideEvidence *p_peptide_evidence,
const std::map<QString, std::vector<size_t>> &sample_scan_list)
{
@@ -255,8 +257,8 @@ ComparSpectraByPeptide::writeBestPeptideEvidence(
{
if(_label_list.size() == 0)
{
- writeComparValue(sample_scan_list, ValidationState::validAndChecked,
- msrun_sp.get());
+ writeComparValue(
+ sample_scan_list, ValidationState::validAndChecked, msrun_sp.get());
if(_first_cell_coordinate.isEmpty())
{
_first_cell_coordinate = _p_writer->getOdsCellCoordinate();
@@ -267,7 +269,8 @@ ComparSpectraByPeptide::writeBestPeptideEvidence(
for(const Label *p_label : _label_list)
{
writeComparValue(sample_scan_list,
- ValidationState::validAndChecked, msrun_sp.get(),
+ ValidationState::validAndChecked,
+ msrun_sp.get(),
p_label);
if(_first_cell_coordinate.isEmpty())
{
@@ -282,7 +285,9 @@ ComparSpectraByPeptide::writeBestPeptideEvidence(
void
ComparSpectraByPeptide::writeComparValue(
const std::map<QString, std::vector<size_t>> &sample_scan_list,
- ValidationState state, const MsRun *p_msrun, const Label *p_label)
+ ValidationState state,
+ const MsRun *p_msrun,
+ const Label *p_label)
{
/*
std::sort(sample_scan_list.begin(), sample_scan_list.end());
diff --git a/src/output/ods/comparspectrabypeptide.h b/src/output/ods/comparspectrabypeptide.h
index 97436247..a566384d 100644
--- a/src/output/ods/comparspectrabypeptide.h
+++ b/src/output/ods/comparspectrabypeptide.h
@@ -50,15 +50,18 @@ class ComparSpectraByPeptide
void writeIdentificationGroup(IdentificationGroup *p_ident);
void writeHeaders(IdentificationGroup *p_ident);
void writeBestPeptideEvidence(
- const GroupingGroup *p_group, const PeptideEvidence *p_peptide_evidence,
+ const GroupingGroup *p_group,
+ const PeptideEvidence *p_peptide_evidence,
const std::map<QString, std::vector<size_t>> &sample_scan_list);
void writeComparValue(
const std::map<QString, std::vector<size_t>> &sample_scan_list,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label = nullptr);
public:
- ComparSpectraByPeptide(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ ComparSpectraByPeptide(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
void writeSheet();
};
diff --git a/src/output/ods/comparspectrasheet.cpp b/src/output/ods/comparspectrasheet.cpp
index 184ee49a..b9ee4cc3 100644
--- a/src/output/ods/comparspectrasheet.cpp
+++ b/src/output/ods/comparspectrasheet.cpp
@@ -46,7 +46,8 @@ ComparSpectraSheet::ComparSpectraSheet(OdsExport *p_ods_export,
void
ComparSpectraSheet::writeComparValue(const ProteinMatch *p_protein_match,
ValidationState state,
- const MsRun *p_msrun, const Label *p_label)
+ const MsRun *p_msrun,
+ const Label *p_label)
{
qDebug() << "ComparSpectraSheet::writeComparValue begin";
_p_writer->writeCell(
@@ -85,7 +86,8 @@ ComparPaiSheet::ComparPaiSheet(OdsExport *p_ods_export,
void
ComparPaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label)
{
qDebug() << "ComparPaiSheet::writeComparValue begin";
@@ -103,7 +105,8 @@ ComparEmpaiSheet::ComparEmpaiSheet(OdsExport *p_ods_export,
void
ComparEmpaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label)
{
qDebug() << "ComparEmpaiSheet::writeComparValue begin";
@@ -121,7 +124,8 @@ ComparNsafSheet::ComparNsafSheet(OdsExport *p_ods_export,
void
ComparNsafSheet::writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label)
{
qDebug() << "ComparNsafSheet::writeComparValue begin";
diff --git a/src/output/ods/comparspectrasheet.h b/src/output/ods/comparspectrasheet.h
index 04b0df80..d129f71f 100644
--- a/src/output/ods/comparspectrasheet.h
+++ b/src/output/ods/comparspectrasheet.h
@@ -36,12 +36,14 @@
class ComparSpectraSheet : public ComparBaseSheet
{
public:
- ComparSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ ComparSpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
protected:
virtual void writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label = nullptr) override;
};
@@ -49,48 +51,56 @@ class ComparSpectraSheet : public ComparBaseSheet
class ComparSequenceSheet : public ComparBaseSheet
{
public:
- ComparSequenceSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ ComparSequenceSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
protected:
virtual void writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label = nullptr) override;
};
class ComparPaiSheet : public ComparBaseSheet
{
public:
- ComparPaiSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ ComparPaiSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
protected:
virtual void writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label = nullptr) override;
};
class ComparEmpaiSheet : public ComparBaseSheet
{
public:
- ComparEmpaiSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ ComparEmpaiSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
protected:
virtual void writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label = nullptr) override;
};
class ComparNsafSheet : public ComparBaseSheet
{
public:
- ComparNsafSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ ComparNsafSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
protected:
virtual void writeComparValue(const ProteinMatch *p_protein_match,
- ValidationState state, const MsRun *p_msrun,
+ ValidationState state,
+ const MsRun *p_msrun,
const Label *p_label = nullptr) override;
private:
diff --git a/src/output/ods/groupingsheet.h b/src/output/ods/groupingsheet.h
index 9202bc4f..ec253be6 100644
--- a/src/output/ods/groupingsheet.h
+++ b/src/output/ods/groupingsheet.h
@@ -38,7 +38,8 @@
class GroupingSheet
{
public:
- GroupingSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ GroupingSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
private:
diff --git a/src/output/ods/infosheet.cpp b/src/output/ods/infosheet.cpp
index 364bacfb..4b6699e6 100644
--- a/src/output/ods/infosheet.cpp
+++ b/src/output/ods/infosheet.cpp
@@ -34,7 +34,8 @@
#include <QSettings>
-InfoSheet::InfoSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+InfoSheet::InfoSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project)
: _p_project(p_project)
{
@@ -129,8 +130,9 @@ InfoSheet::InfoSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
if(settings.value("export_ods/groups", "true").toBool())
{
p_writer->writeCell("groups");
- p_writer->writeCell("simple statistics on the current grouping "
- "experiment (numbers of groups, subgroups...)");
+ p_writer->writeCell(
+ "simple statistics on the current grouping "
+ "experiment (numbers of groups, subgroups...)");
p_writer->writeLine();
}
@@ -144,26 +146,29 @@ InfoSheet::InfoSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
if(settings.value("export_ods/peptides", "true").toBool())
{
p_writer->writeCell("peptides");
- p_writer->writeCell("list of peptides used by the grouping algorithm. "
- "Beware : peptides are intended as unique pairs of "
- "sequence+mass, given that Leucine and Isoleucine as "
- "the same mass, all Leucines are considered as "
- "Isoleucines");
+ p_writer->writeCell(
+ "list of peptides used by the grouping algorithm. "
+ "Beware : peptides are intended as unique pairs of "
+ "sequence+mass, given that Leucine and Isoleucine as "
+ "the same mass, all Leucines are considered as "
+ "Isoleucines");
p_writer->writeLine();
}
if(settings.value("export_ods/spectra", "true").toBool())
{
p_writer->writeCell("spectra");
- p_writer->writeCell("list of all validated and checked spectrum match. "
- "Only the best assigned peptide (best Evalue) is "
- "reported ");
+ p_writer->writeCell(
+ "list of all validated and checked spectrum match. "
+ "Only the best assigned peptide (best Evalue) is "
+ "reported ");
p_writer->writeLine();
}
if(settings.value("export_ods/peptidepos", "true").toBool())
{
p_writer->writeCell("peptide pos");
- p_writer->writeCell("list of all *real* peptides identified on their "
- "proteins, with their position on the sequence.");
+ p_writer->writeCell(
+ "list of all *real* peptides identified on their "
+ "proteins, with their position on the sequence.");
p_writer->writeLine();
}
}
diff --git a/src/output/ods/peptidesheet.cpp b/src/output/ods/peptidesheet.cpp
index 8e97e737..c05710d4 100644
--- a/src/output/ods/peptidesheet.cpp
+++ b/src/output/ods/peptidesheet.cpp
@@ -101,7 +101,8 @@ PeptideSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
std::vector<const PeptideEvidence *> peptide_evidence_list =
group_pair.second.get()->getPeptideEvidenceList();
- std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
+ std::sort(peptide_evidence_list.begin(),
+ peptide_evidence_list.end(),
[](const PeptideEvidence *a, const PeptideEvidence *b) {
return a->getGrpPeptideSp().get()->getRank() <
b->getGrpPeptideSp().get()->getRank();
diff --git a/src/output/ods/peptidesheet.h b/src/output/ods/peptidesheet.h
index 7db49c45..1f64c4be 100644
--- a/src/output/ods/peptidesheet.h
+++ b/src/output/ods/peptidesheet.h
@@ -39,7 +39,8 @@
class PeptideSheet
{
public:
- PeptideSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ PeptideSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
private:
diff --git a/src/output/ods/proteinsheet.h b/src/output/ods/proteinsheet.h
index 66025624..a4e7347a 100644
--- a/src/output/ods/proteinsheet.h
+++ b/src/output/ods/proteinsheet.h
@@ -40,7 +40,8 @@
class ProteinSheet
{
public:
- ProteinSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ ProteinSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
private:
diff --git a/src/output/ods/ptm/ptmislandsheet.cpp b/src/output/ods/ptm/ptmislandsheet.cpp
index 87e15abe..e6d9489f 100644
--- a/src/output/ods/ptm/ptmislandsheet.cpp
+++ b/src/output/ods/ptm/ptmislandsheet.cpp
@@ -133,7 +133,8 @@ PtmIslandSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
ptm_island_list.push_back(ptm_island_sp);
}
qDebug() << "PtmIslandSheet::writeIdentificationGroup sort";
- std::sort(ptm_island_list.begin(), ptm_island_list.end(),
+ std::sort(ptm_island_list.begin(),
+ ptm_island_list.end(),
[](PtmIslandSp &a, PtmIslandSp &b) {
return a.get()->getGroupingId() < b.get()->getGroupingId();
});
diff --git a/src/output/ods/ptm/ptmislandsheet.h b/src/output/ods/ptm/ptmislandsheet.h
index b9e9071f..dcf46ad2 100644
--- a/src/output/ods/ptm/ptmislandsheet.h
+++ b/src/output/ods/ptm/ptmislandsheet.h
@@ -40,7 +40,8 @@
class PtmIslandSheet
{
public:
- PtmIslandSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ PtmIslandSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
private:
diff --git a/src/output/ods/ptm/ptmspectrasheet.h b/src/output/ods/ptm/ptmspectrasheet.h
index 6b589c04..4832ebee 100644
--- a/src/output/ods/ptm/ptmspectrasheet.h
+++ b/src/output/ods/ptm/ptmspectrasheet.h
@@ -40,12 +40,15 @@
class PtmSpectraSheet
{
public:
- PtmSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ PtmSpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
protected:
- PtmSpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
- const Project *p_project, const QString &sheet_name);
+ PtmSpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project,
+ const QString &sheet_name);
virtual void writeIdentificationGroup(IdentificationGroup *p_ident);
void writeHeaders(IdentificationGroup *p_ident);
void writeBestPeptideEvidence(
diff --git a/src/output/ods/qvaluessheet.cpp b/src/output/ods/qvaluessheet.cpp
index 2a99efd5..6a5ba666 100644
--- a/src/output/ods/qvaluessheet.cpp
+++ b/src/output/ods/qvaluessheet.cpp
@@ -40,9 +40,9 @@ QvaluesSheet::QvaluesSheet(OdsExport *p_ods_export,
table_settings.setVerticalSplit(1);
_p_writer->setCurrentOdsTableSettings(table_settings);
- // writeHeaders();
+ // writeHeaders();
ComputeQvalues qvalues(p_project);
-
+
qvalues.writeDistributionsByEngines(_p_writer);
}
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index 7f4f1570..48ad1acb 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -30,7 +30,8 @@
#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)
{
@@ -118,16 +119,19 @@ 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/samplesheet.h b/src/output/ods/samplesheet.h
index 12677f5f..ce018194 100644
--- a/src/output/ods/samplesheet.h
+++ b/src/output/ods/samplesheet.h
@@ -38,7 +38,8 @@
class SampleSheet
{
public:
- SampleSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ SampleSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
private:
diff --git a/src/output/ods/spectrasheet.h b/src/output/ods/spectrasheet.h
index 0f315547..09b5195e 100644
--- a/src/output/ods/spectrasheet.h
+++ b/src/output/ods/spectrasheet.h
@@ -39,12 +39,15 @@
class SpectraSheet
{
public:
- SpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ SpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
protected:
- SpectraSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
- const Project *p_project, const QString &sheet_name);
+ SpectraSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
+ const Project *p_project,
+ const QString &sheet_name);
virtual void writeIdentificationGroup(IdentificationGroup *p_ident);
void writeHeaders(IdentificationGroup *p_ident);
void writeBestPeptideEvidence(const GroupingGroup *p_group,
@@ -56,4 +59,3 @@ class SpectraSheet
const Project *_p_project;
CalcWriterInterface *_p_writer;
};
-
diff --git a/src/utils/msrunstore.h b/src/utils/msrunstore.h
index 4828d825..1e0003bc 100644
--- a/src/utils/msrunstore.h
+++ b/src/utils/msrunstore.h
@@ -50,4 +50,3 @@ class MsRunStore
private:
std::vector<MsRunSp> _map_msrun;
};
-
diff --git a/src/utils/peptidestore.h b/src/utils/peptidestore.h
index b815aed2..8c898925 100644
--- a/src/utils/peptidestore.h
+++ b/src/utils/peptidestore.h
@@ -72,4 +72,3 @@ class PeptideStore
std::unordered_map<std::size_t, PeptideXtpSp> _map_crc_peptide_list;
std::set<pappso::AaModificationP> _modification_collection;
};
-
diff --git a/src/utils/utils.h b/src/utils/utils.h
index 0262b211..e4ec72c5 100644
--- a/src/utils/utils.h
+++ b/src/utils/utils.h
@@ -36,7 +36,8 @@ class Utils
static const QString getDatabaseName(ExternalDatabase database);
static const QString getXmlDouble(pappso::pappso_double number);
static const QString checkXtandemVersion(const QString &tandem_bin_path);
- static const double computeFdr(std::size_t count_decoy, std::size_t count_target);
+ static const double computeFdr(std::size_t count_decoy,
+ std::size_t count_target);
static pappso::AaModificationP
guessAaModificationPbyMonoisotopicMassDelta(pappso::pappso_double mass);
static pappso::AaModificationP
--
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