From 1d45b982b8eba70c78eef9cd47b4d0cd654348a1 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sat, 2 Feb 2019 23:27:46 +0100
Subject: [PATCH] WIP: adapt code to the new pappsoMS++ code policy
---
src/config.h.cmake | 2 -
.../identificationdatasource.cpp | 8 +--
.../identificationdatasource.h | 5 +-
.../identificationmascotdatfile.cpp | 13 ++---
.../identificationmascotdatfile.h | 4 +-
.../identificationpepxmlfile.cpp | 12 ++---
.../identificationpepxmlfile.h | 4 +-
.../identificationpwizfile.cpp | 12 ++---
.../identificationpwizfile.h | 4 +-
.../identificationxtandemfile.cpp | 13 ++---
.../identificationxtandemfile.h | 4 +-
src/core/identificationgroup.cpp | 2 +-
src/core/peptideevidence.cpp | 8 +--
src/core/peptideevidence.h | 6 +--
src/core/peptidextp.cpp | 12 ++---
src/core/peptidextp.h | 2 +-
src/core/project.cpp | 8 +--
src/core/project.h | 3 +-
src/core/proteinxtp.cpp | 2 +-
src/core/tandem_run/tandembatchprocess.cpp | 4 +-
src/core/tandem_run/tandembatchprocess.h | 3 +-
src/grouping/groupingpeptidemass.cpp | 3 +-
src/grouping/ptm/ptmgroupingexperiment.cpp | 6 ++-
src/grouping/ptm/ptmgroupingexperiment.h | 2 +-
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 | 25 +++++++---
.../choosemodificationdialog.h | 6 +--
.../edit_label_methods/editlabelmethods.cpp | 16 +++---
src/gui/edit_label_methods/editlabelmethods.h | 2 +-
.../edit_modifications/editmodifications.cpp | 35 +++++++++----
.../edit_modifications/editmodifications.h | 2 +-
.../edittandempresetdialog.cpp | 12 +++--
.../edittandempresetdialog.h | 2 +-
.../masschroqfileparameters.cpp | 2 +-
.../masschroqfileparameters.h | 14 +++---
.../exportspreadsheetdialog.h | 4 +-
.../load_results_dialog/loadresultsdialog.cpp | 9 ++--
.../load_results_dialog/loadresultsdialog.h | 2 +-
src/gui/mainwindow.h | 6 ++-
.../peptide_detail_view.ui | 6 +--
src/gui/peptide_detail_view/peptidewindow.cpp | 39 +++++++--------
src/gui/peptide_detail_view/peptidewindow.h | 16 +++---
.../peptide_list_view/peptidelistwindow.cpp | 39 +++++++++++----
src/gui/peptide_list_view/peptidelistwindow.h | 2 +-
src/gui/peptide_list_view/peptidetablemodel.h | 4 +-
.../peptidetableproxymodel.cpp | 3 +-
.../peptidetableproxymodel.h | 4 +-
.../identificationgroupwidget.cpp | 10 ++--
.../identificationgroupwidget.h | 2 +-
src/gui/project_view/projectwindow.cpp | 3 +-
src/gui/protein_list_view/proteinlistwindow.h | 2 +-
.../protein_list_view/proteintablemodel.cpp | 3 +-
src/gui/protein_list_view/proteintablemodel.h | 4 +-
.../proteintableproxymodel.h | 4 +-
src/gui/protein_view/proteinwindow.cpp | 33 +++++++-----
src/gui/protein_view/proteinwindow.h | 2 +-
.../ptmislandlistwindow.cpp | 36 +++++++++----
.../ptmislandlistwindow.h | 2 +-
.../ptmislandtablemodel.cpp | 3 +-
.../ptmislandtablemodel.h | 4 +-
.../ptmpeptidelistwindow.cpp | 16 ++++--
.../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 | 8 +--
.../waitingmessagedialog.h | 2 +-
.../automaticfilterwidget.h | 2 +-
.../contaminant_widget/contaminantwidget.h | 2 +-
src/gui/workerthread.cpp | 6 ++-
src/gui/workerthread.h | 7 ++-
src/gui/xic_view/xic_box/xicbox.cpp | 35 +++++++------
src/gui/xic_view/xic_box/xicbox.h | 30 +++++------
src/gui/xic_view/xic_widgets/zivywidget.h | 1 -
src/gui/xic_view/xicwindow.cpp | 11 ++--
src/gui/xic_view/xicwindow.h | 6 +--
src/gui/xic_view/xicworkerthread.cpp | 16 +++---
src/gui/xic_view/xicworkerthread.h | 10 ++--
src/input/condorqxmlsaxhandler.cpp | 33 +++++++-----
src/input/condorqxmlsaxhandler.h | 9 ++--
src/input/identificationpwizreader.cpp | 2 +-
src/input/identificationpwizreader.h | 11 ++--
src/input/pepxmlsaxhandler.cpp | 38 ++++++++------
src/input/pepxmlsaxhandler.h | 9 ++--
src/input/xpipsaxhandler.cpp | 44 ++++++++--------
src/input/xpipsaxhandler.h | 11 ++--
src/input/xtandemparamsaxhandler.cpp | 36 +++++++------
src/input/xtandemparamsaxhandler.h | 9 ++--
src/input/xtandemsaxhandler.cpp | 50 +++++++++++--------
src/input/xtandemsaxhandler.h | 9 ++--
src/input/xtpxpipsaxhandler.cpp | 26 ++++++----
src/input/xtpxpipsaxhandler.h | 9 ++--
src/main.cpp | 15 +++---
src/output/exportfastafile.h | 3 +-
src/output/masschroqml.cpp | 10 ++--
src/output/mcqr/mcqrscpeptide.cpp | 4 +-
src/output/mcqr/mcqrscprotein.cpp | 3 +-
src/output/mcqrspectralcount.h | 6 ++-
src/output/ods/comparspecificspectrasheet.h | 1 -
src/output/ods/groupingsheet.cpp | 15 ++++--
src/output/ods/groupingsheet.h | 3 +-
src/output/ods/infosheet.cpp | 31 +++++++-----
src/output/ods/infosheet.h | 3 +-
src/output/ods/peptidepossheet.cpp | 6 ++-
src/output/ods/peptidepossheet.h | 3 +-
src/output/ods/peptidesheet.cpp | 3 +-
src/output/ods/peptidesheet.h | 3 +-
src/output/ods/proteinsheet.cpp | 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/samplesheet.cpp | 18 ++++---
src/output/ods/samplesheet.h | 3 +-
src/output/ods/spectrasheet.cpp | 10 ++--
src/output/ods/spectrasheet.h | 9 ++--
src/output/proticdbml.cpp | 23 +++++----
src/output/xpip.cpp | 18 ++++---
src/utils/httpversion.h | 4 +-
src/utils/msrunstatisticshandler.cpp | 8 +--
src/utils/msrunstatisticshandler.h | 4 +-
src/utils/msrunstore.cpp | 11 ++--
src/utils/peptideevidencestore.cpp | 4 +-
src/utils/peptideevidencestore.h | 3 +-
src/utils/peptidestore.cpp | 2 +-
src/utils/types.h | 4 +-
src/utils/utils.cpp | 28 +++++------
src/utils/utils.h | 2 +-
134 files changed, 779 insertions(+), 534 deletions(-)
diff --git a/src/config.h.cmake b/src/config.h.cmake
index cf5e13174..4bfd4ce1f 100644
--- a/src/config.h.cmake
+++ b/src/config.h.cmake
@@ -10,6 +10,4 @@
#include <QDebug>
-
-
#endif /* _CONFIG_H */
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index 9ef578db6..aa21e177a 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -191,8 +191,8 @@ IdentificationDataSource::getIdentificationEngineStatistics(
}
}
-pappso::SpectrumSp
-IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const
+pappso::MassSpectrumCstSPtr
+IdentificationDataSource::getMassSpectrumCstSPtr(unsigned int scan_number) const
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -222,8 +222,8 @@ IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ <<
// _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumListSize();
- pappso::SpectrumSp spectrum_sp =
- msrun_reader_sp.get()->getSpectrumSp(scan_number);
+ pappso::MassSpectrumCstSPtr spectrum_sp =
+ msrun_reader_sp.get()->massSpectrumCstSPtr(scan_number);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
return spectrum_sp;
}
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index 519225b5f..69a26c70c 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -25,7 +25,7 @@
#define IDENTIFICATIONDATASOURCE_H
-#include <pappsomspp/spectrum/spectrum.h>
+#include <pappsomspp/spectrum/massspectrum.h>
#include <memory>
#include <QVariant>
#include "../msrun.h"
@@ -63,7 +63,8 @@ class IdentificationDataSource
MsRunSp getMsRunSp() const;
/** @brief get the spectrum with scan number
* */
- virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const;
+ virtual pappso::MassSpectrumCstSPtr
+ getMassSpectrumCstSPtr(unsigned int scan_number) const;
/** \brief read source content to store it in project
diff --git a/src/core/identification_sources/identificationmascotdatfile.cpp b/src/core/identification_sources/identificationmascotdatfile.cpp
index 01e804a3d..aacb8ea51 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;
}
@@ -59,11 +59,12 @@ operator==(const IdentificationMascotDatFile &other) const
{
}
-pappso::SpectrumSp
-IdentificationMascotDatFile::getSpectrumSp(unsigned int scan_number) const
+pappso::MassSpectrumCstSPtr
+IdentificationMascotDatFile::getMassSpectrumCstSPtr(
+ unsigned int scan_number) const
{
- pappso::SpectrumSp spectrum_sp =
- IdentificationDataSource::getSpectrumSp(scan_number);
+ pappso::MassSpectrumCstSPtr spectrum_sp =
+ IdentificationDataSource::getMassSpectrumCstSPtr(scan_number);
return spectrum_sp;
}
diff --git a/src/core/identification_sources/identificationmascotdatfile.h b/src/core/identification_sources/identificationmascotdatfile.h
index a1d856f03..e80602fae 100644
--- a/src/core/identification_sources/identificationmascotdatfile.h
+++ b/src/core/identification_sources/identificationmascotdatfile.h
@@ -42,8 +42,8 @@ class IdentificationMascotDatFile : public IdentificationDataSource
~IdentificationMascotDatFile();
bool operator==(const IdentificationMascotDatFile &other) const;
- virtual pappso::SpectrumSp
- getSpectrumSp(unsigned int scan_number) const override;
+ virtual pappso::MassSpectrumCstSPtr
+ getMassSpectrumCstSPtr(unsigned int scan_number) const override;
virtual void parseTo(Project *p_project) override;
// virtual const bool isValid(const PeptideEvidence * p_peptide_evidence,
diff --git a/src/core/identification_sources/identificationpepxmlfile.cpp b/src/core/identification_sources/identificationpepxmlfile.cpp
index 464a691b8..563aea5cb 100644
--- a/src/core/identification_sources/identificationpepxmlfile.cpp
+++ b/src/core/identification_sources/identificationpepxmlfile.cpp
@@ -33,8 +33,8 @@
IdentificationPepXmlFile::IdentificationPepXmlFile(
const QFileInfo &mascot_dat_file)
- : IdentificationDataSource(mascot_dat_file.absoluteFilePath())
- , _pep_xml_file(mascot_dat_file)
+ : IdentificationDataSource(mascot_dat_file.absoluteFilePath()),
+ _pep_xml_file(mascot_dat_file)
{
_engine = IdentificationEngine::unknown;
}
@@ -56,11 +56,11 @@ operator==(const IdentificationPepXmlFile &other) const
{
}
-pappso::SpectrumSp
-IdentificationPepXmlFile::getSpectrumSp(unsigned int scan_number) const
+pappso::MassSpectrumCstSPtr
+IdentificationPepXmlFile::getMassSpectrumCstSPtr(unsigned int scan_number) const
{
- pappso::SpectrumSp spectrum_sp =
- IdentificationDataSource::getSpectrumSp(scan_number);
+ pappso::MassSpectrumCstSPtr spectrum_sp =
+ IdentificationDataSource::getMassSpectrumCstSPtr(scan_number);
return spectrum_sp;
}
diff --git a/src/core/identification_sources/identificationpepxmlfile.h b/src/core/identification_sources/identificationpepxmlfile.h
index 2a66e24c6..0075de6f3 100644
--- a/src/core/identification_sources/identificationpepxmlfile.h
+++ b/src/core/identification_sources/identificationpepxmlfile.h
@@ -39,8 +39,8 @@ class IdentificationPepXmlFile : public IdentificationDataSource
~IdentificationPepXmlFile();
bool operator==(const IdentificationPepXmlFile &other) const;
- virtual pappso::SpectrumSp
- getSpectrumSp(unsigned int scan_number) const override;
+ virtual pappso::MassSpectrumCstSPtr
+ getMassSpectrumCstSPtr(unsigned int scan_number) const override;
virtual void parseTo(Project *p_project) override;
// virtual const bool isValid(const PeptideEvidence * p_peptide_evidence,
diff --git a/src/core/identification_sources/identificationpwizfile.cpp b/src/core/identification_sources/identificationpwizfile.cpp
index 2ee2672f2..e86cdda76 100644
--- a/src/core/identification_sources/identificationpwizfile.cpp
+++ b/src/core/identification_sources/identificationpwizfile.cpp
@@ -34,8 +34,8 @@
#include <pappsomspp/pappsoexception.h>
IdentificationPwizFile::IdentificationPwizFile(const QFileInfo &ident_file)
- : IdentificationDataSource(ident_file.absoluteFilePath())
- , _ident_file(ident_file)
+ : IdentificationDataSource(ident_file.absoluteFilePath()),
+ _ident_file(ident_file)
{
//_engine = IdentificationEngine::XTandem;
_engine = IdentificationEngine::peptider;
@@ -57,11 +57,11 @@ IdentificationPwizFile::operator==(const IdentificationPwizFile &other) const
{
}
-pappso::SpectrumSp
-IdentificationPwizFile::getSpectrumSp(unsigned int scan_number) const
+pappso::MassSpectrumCstSPtr
+IdentificationPwizFile::getMassSpectrumCstSPtr(unsigned int scan_number) const
{
- pappso::SpectrumSp spectrum_sp =
- IdentificationDataSource::getSpectrumSp(scan_number);
+ pappso::MassSpectrumCstSPtr spectrum_sp =
+ IdentificationDataSource::getMassSpectrumCstSPtr(scan_number);
return spectrum_sp;
}
diff --git a/src/core/identification_sources/identificationpwizfile.h b/src/core/identification_sources/identificationpwizfile.h
index 183041351..25712c79c 100644
--- a/src/core/identification_sources/identificationpwizfile.h
+++ b/src/core/identification_sources/identificationpwizfile.h
@@ -43,8 +43,8 @@ class IdentificationPwizFile : public IdentificationDataSource
~IdentificationPwizFile();
bool operator==(const IdentificationPwizFile &other) const;
- virtual pappso::SpectrumSp
- getSpectrumSp(unsigned int scan_number) const override;
+ virtual pappso::MassSpectrumCstSPtr
+ getMassSpectrumCstSPtr(unsigned int scan_number) const override;
virtual void parseTo(Project *p_project) override;
private:
diff --git a/src/core/identification_sources/identificationxtandemfile.cpp b/src/core/identification_sources/identificationxtandemfile.cpp
index 74d631386..adc0ce556 100644
--- a/src/core/identification_sources/identificationxtandemfile.cpp
+++ b/src/core/identification_sources/identificationxtandemfile.cpp
@@ -28,8 +28,8 @@
IdentificationXtandemFile::IdentificationXtandemFile(
const QFileInfo &xtandem_file)
- : IdentificationDataSource(xtandem_file.absoluteFilePath())
- , _xtandem_file(xtandem_file)
+ : IdentificationDataSource(xtandem_file.absoluteFilePath()),
+ _xtandem_file(xtandem_file)
{
_engine = IdentificationEngine::XTandem;
}
@@ -51,11 +51,12 @@ operator==(const IdentificationXtandemFile &other) const
{
}
-pappso::SpectrumSp
-IdentificationXtandemFile::getSpectrumSp(unsigned int scan_number) const
+pappso::MassSpectrumCstSPtr
+IdentificationXtandemFile::getMassSpectrumCstSPtr(
+ unsigned int scan_number) const
{
- pappso::SpectrumSp spectrum_sp =
- IdentificationDataSource::getSpectrumSp(scan_number);
+ pappso::MassSpectrumCstSPtr spectrum_sp =
+ IdentificationDataSource::getMassSpectrumCstSPtr(scan_number);
return spectrum_sp;
}
diff --git a/src/core/identification_sources/identificationxtandemfile.h b/src/core/identification_sources/identificationxtandemfile.h
index 751eb6c9c..06e28cd67 100644
--- a/src/core/identification_sources/identificationxtandemfile.h
+++ b/src/core/identification_sources/identificationxtandemfile.h
@@ -35,8 +35,8 @@ class IdentificationXtandemFile : public IdentificationDataSource
~IdentificationXtandemFile();
bool operator==(const IdentificationXtandemFile &other) const;
- virtual pappso::SpectrumSp
- getSpectrumSp(unsigned int scan_number) const override;
+ virtual pappso::MassSpectrumCstSPtr
+ getMassSpectrumCstSPtr(unsigned int scan_number) const override;
virtual void parseTo(Project *p_project) override;
private:
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 13178ddf3..e668b13ef 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -445,7 +445,7 @@ IdentificationGroup::getTabName() const
pappso::pappso_double
IdentificationGroup::getPsmFdr(ValidationState state) const
{
-
+
pappso::pappso_double total_peptide = countPeptideEvidence(state);
pappso::pappso_double false_peptide = countDecoyPeptideEvidence(state);
diff --git a/src/core/peptideevidence.cpp b/src/core/peptideevidence.cpp
index be909da73..29c335e4a 100644
--- a/src/core/peptideevidence.cpp
+++ b/src/core/peptideevidence.cpp
@@ -62,7 +62,7 @@ PeptideEvidence::PeptideEvidence(const PeptideEvidence &other)
_identification_engine = other._identification_engine;
}
-pappso::mz
+pappso::pappso_double
PeptideEvidence::getTheoreticalMz() const
{
return (getPeptideXtpSp().get()->getMz(getCharge()));
@@ -166,7 +166,7 @@ PeptideEvidence::getExperimentalMhplus() const
pappso::pappso_double
PeptideEvidence::getExperimentalMz() const
{
- pappso::mz mz = _exp_mass;
+ pappso::pappso_double mz = _exp_mass;
for(unsigned int i = 0; i < _charge; i++)
{
mz += pappso::MHPLUS;
@@ -179,12 +179,12 @@ PeptideEvidence::setExperimentalMass(pappso::pappso_double exp_mass)
{
_exp_mass = exp_mass;
}
-pappso::mz
+pappso::pappso_double
PeptideEvidence::getDeltaMass() const
{
return ((_exp_mass + pappso::MHPLUS) - _peptide_sp.get()->getMz(1));
}
-pappso::mz
+pappso::pappso_double
PeptideEvidence::getPpmDeltaMass() const
{
// return (_peptide_sp.get()->getMz(1) - (_exp_mass+pappso::MHPLUS));
diff --git a/src/core/peptideevidence.h b/src/core/peptideevidence.h
index 490aec2b7..b532c3360 100644
--- a/src/core/peptideevidence.h
+++ b/src/core/peptideevidence.h
@@ -135,19 +135,19 @@ class PeptideEvidence
/** @brief get delta between theoretical mhplus mass and mhplus experimental
* mass mhplus experimental mass - theoretical mhplus mass
*/
- pappso::mz getDeltaMass() const;
+ pappso::pappso_double getDeltaMass() const;
/** @brief get delta in ppm between theoretical mhplus mass and mhplus
* experimental mass
* @return mhplus experimental mass - theoretical mhplus mass
*/
- pappso::mz getPpmDeltaMass() const;
+ pappso::pappso_double getPpmDeltaMass() const;
/** @brief get theoretical (not observed) m/z based on peptide composition and
* charge
* @return theoretical mz mass
*/
- pappso::mz getTheoreticalMz() const;
+ pappso::pappso_double getTheoreticalMz() const;
ValidationState getValidationState() const;
diff --git a/src/core/peptidextp.cpp b/src/core/peptidextp.cpp
index 598a1222f..7330913b0 100644
--- a/src/core/peptidextp.cpp
+++ b/src/core/peptidextp.cpp
@@ -44,7 +44,7 @@ PeptideXtp::getModifString() const
{
QStringList modif_list;
unsigned int i = 1;
- for(const pappso::Aa &amino_acid : _aa_vec)
+ for(const pappso::Aa &amino_acid : m_aaVec)
{
std::list<pappso::AaModificationP> aa_modif_list =
amino_acid.getModificationList();
@@ -79,7 +79,7 @@ PeptideXtp::makePeptideXtpSp() const
}
-pappso::mz
+pappso::pappso_double
PeptideXtp::getGroupingMass() const
{
return getNativePeptideP()->getMass();
@@ -117,16 +117,16 @@ void
PeptideXtp::applyLabelingMethod(LabelingMethodSp labeling_method_sp)
{
std::list<pappso::AaModificationP> modification_set;
- for(const pappso::Aa &amino_acid : _aa_vec)
+ for(const pappso::Aa &amino_acid : m_aaVec)
{
std::list<pappso::AaModificationP> aa_modif_list =
amino_acid.getModificationList();
- modification_set.insert(modification_set.begin(), aa_modif_list.begin(),
- aa_modif_list.end());
+ modification_set.insert(
+ modification_set.begin(), aa_modif_list.begin(), aa_modif_list.end());
}
modification_set.unique();
- _p_label = nullptr;
+ _p_label = nullptr;
const Label *p_label = labeling_method_sp.get()->getLabel(modification_set);
if(p_label != nullptr)
{
diff --git a/src/core/peptidextp.h b/src/core/peptidextp.h
index dc545559a..3d92e6e1f 100644
--- a/src/core/peptidextp.h
+++ b/src/core/peptidextp.h
@@ -48,7 +48,7 @@ class PeptideXtp : public pappso::Peptide
* tagged peptide with taget modification is a light, inter or heavy version
* of the same peptide
*/
- pappso::mz getGroupingMass() const;
+ pappso::pappso_double getGroupingMass() const;
const pappso::Peptide *getNativePeptideP() const;
diff --git a/src/core/project.cpp b/src/core/project.cpp
index effd7a3af..fb5ee702a 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -281,11 +281,13 @@ Project::hasPtmExperiment() const
void
Project::getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
+ unsigned int charge) const
{
for(const IdentificationGroup *p_ident_group : _identification_goup_list)
{
- p_ident_group->getSameXicPeptideEvidenceList(peptide_evidence_list,
- p_msrun, p_peptide, charge);
+ p_ident_group->getSameXicPeptideEvidenceList(
+ peptide_evidence_list, p_msrun, p_peptide, charge);
}
}
diff --git a/src/core/project.h b/src/core/project.h
index 3fbbdd7ae..6db5c633b 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -98,7 +98,8 @@ class Project
*/
void getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide,
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
unsigned int charge) const;
private:
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index bca7524ce..c46f92ebb 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -218,7 +218,7 @@ ProteinXtp::countTrypticPeptidesForPAI() const
for(const QString &peptide_str : digestion._peptide_list)
{
pappso::Peptide peptide(peptide_str);
- pappso::mz mass = peptide.getMass();
+ pappso::pappso_double mass = peptide.getMass();
if((mass > 800) && (mass < 2500))
{
count++;
diff --git a/src/core/tandem_run/tandembatchprocess.cpp b/src/core/tandem_run/tandembatchprocess.cpp
index b1f6b7067..6683cb5a2 100644
--- a/src/core/tandem_run/tandembatchprocess.cpp
+++ b/src/core/tandem_run/tandembatchprocess.cpp
@@ -93,7 +93,9 @@ TandemBatchProcess::writeXmlDatabaseFile(QXmlStreamWriter *p_out)
if(!QFileInfo(fasta_file).isWritable())
{
throw pappso::PappsoException(
- QObject::tr("error : Fasta file %1 is not writable.\n\"tandem.exe\" requires write permission on fasta files to run correctly.")
+ QObject::tr(
+ "error : Fasta file %1 is not writable.\n\"tandem.exe\" requires "
+ "write permission on fasta files to run correctly.")
.arg(_tmp_database_file.fileName()));
}
p_out->writeStartElement("file");
diff --git a/src/core/tandem_run/tandembatchprocess.h b/src/core/tandem_run/tandembatchprocess.h
index 0c1029745..dbd7ca8f0 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/grouping/groupingpeptidemass.cpp b/src/grouping/groupingpeptidemass.cpp
index 4e8e373f2..d2d75064d 100644
--- a/src/grouping/groupingpeptidemass.cpp
+++ b/src/grouping/groupingpeptidemass.cpp
@@ -113,7 +113,8 @@ GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp proteinSp,
{
return _p_grp_experiment->setGrpPeptide(
- proteinSp, p_peptide_evidence->getPeptideXtpSp().get()->getSequence(),
+ proteinSp,
+ p_peptide_evidence->getPeptideXtpSp().get()->getSequence(),
p_peptide_evidence->getPeptideXtpSp().get()->getGroupingMass());
}
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index 903b26226..dc25f640c 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/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index 686889bfd..84442a060 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/src/grouping/ptm/ptmgroupingexperiment.h
@@ -82,7 +82,7 @@ class PtmGroupingExperiment
getPtmPositions(const ProteinMatch *protein_match) const;
std::vector<PtmIslandSp>
- mergePeptideMatchPtmIslandList(vector<PtmIslandSp> ptm_island_list);
+ mergePeptideMatchPtmIslandList(std::vector<PtmIslandSp> ptm_island_list);
void addPtmIsland(PtmIslandSp ptm_island);
void numbering();
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 98c15f4a2..17cc60d32 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 0f3a2b384..ca793c67f 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 d43c016a8..7a5c334e4 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 623eb6d9d..3837399f2 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 fe2b90f2b..260a04352 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 9d682cdc9..1a9fd6256 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
}
@@ -72,7 +80,7 @@ ChooseModificationDialog::~ChooseModificationDialog()
}
void
-ChooseModificationDialog::setMassRange(const pappso::MassRange &massrange)
+ChooseModificationDialog::setMassRange(const pappso::MzRange &massrange)
{
qDebug() << "ChooseModificationDialog::setMassRange " << massrange.toString();
@@ -93,10 +101,11 @@ ChooseModificationDialog::setMassRange(const pappso::MassRange &massrange)
QStandardItem *item;
item = new QStandardItem(
- QString("[%1] %2").arg(term._accession).arg(term._name));
+ QString("[%1] %2").arg(term.m_accession).arg(term.m_name));
item->setEditable(false);
_p_modification_str_li->appendRow(item);
- item->setData(QVariant(QString("%1").arg(term._accession)), Qt::UserRole);
+ item->setData(QVariant(QString("%1").arg(term.m_accession)),
+ Qt::UserRole);
}
}
diff --git a/src/gui/choose_modification_dialog/choosemodificationdialog.h b/src/gui/choose_modification_dialog/choosemodificationdialog.h
index 32479c43f..c641196ff 100644
--- a/src/gui/choose_modification_dialog/choosemodificationdialog.h
+++ b/src/gui/choose_modification_dialog/choosemodificationdialog.h
@@ -27,13 +27,13 @@
#include <QDialog>
#include <QStandardItemModel>
-#include <pappsomspp/mass_range.h>
+#include <pappsomspp/mzrange.h>
#include <pappsomspp/amino_acid/aamodification.h>
namespace Ui
{
- class ChooseModificationDialog;
+class ChooseModificationDialog;
}
class ChooseModificationDialog : public QDialog
@@ -44,7 +44,7 @@ class ChooseModificationDialog : public QDialog
explicit ChooseModificationDialog(QWidget *parent);
~ChooseModificationDialog();
- void setMassRange(const pappso::MassRange &massrange);
+ void setMassRange(const pappso::MzRange &massrange);
public slots:
void ItemClicked(QModelIndex index);
void ItemDoubleClicked(QModelIndex index);
diff --git a/src/gui/edit_label_methods/editlabelmethods.cpp b/src/gui/edit_label_methods/editlabelmethods.cpp
index 738841833..b965d07c9 100644
--- a/src/gui/edit_label_methods/editlabelmethods.cpp
+++ b/src/gui/edit_label_methods/editlabelmethods.cpp
@@ -40,11 +40,15 @@ EditLabelMethods::EditLabelMethods(ProjectWindow *parent)
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(ui->method_list_view, &QListView::clicked, this,
+ connect(ui->method_list_view,
+ &QListView::clicked,
+ this,
&EditLabelMethods::ItemClicked);
#else
- connect(ui->method_list_view, SIGNAL(clicked(const QModelIndex)), this,
+ connect(ui->method_list_view,
+ SIGNAL(clicked(const QModelIndex)),
+ this,
SLOT(ItemClicked(QModelIndex)));
@@ -70,15 +74,15 @@ EditLabelMethods::setProjectSp(ProjectSp project_sp)
if(!xml_doc.open(QIODevice::ReadOnly))
{
// error
- QMessageBox::warning(this, tr("error"),
- tr("error opening catalog_label resource file"));
+ QMessageBox::warning(
+ this, tr("error"), tr("error opening catalog_label resource file"));
return;
}
if(!dom->setContent(&xml_doc))
{
xml_doc.close();
- QMessageBox::warning(this, tr("error"),
- tr("error setting catalog_label xml content"));
+ QMessageBox::warning(
+ this, tr("error"), tr("error setting catalog_label xml content"));
return;
}
diff --git a/src/gui/edit_label_methods/editlabelmethods.h b/src/gui/edit_label_methods/editlabelmethods.h
index 5b05b7b32..4bfb8a5f0 100644
--- a/src/gui/edit_label_methods/editlabelmethods.h
+++ b/src/gui/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_modifications/editmodifications.cpp b/src/gui/edit_modifications/editmodifications.cpp
index 8cfacd24f..f5064ff99 100644
--- a/src/gui/edit_modifications/editmodifications.cpp
+++ b/src/gui/edit_modifications/editmodifications.cpp
@@ -42,21 +42,33 @@ EditModifications::EditModifications(ProjectWindow *parent)
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(ui->modification_list_view, &QListView::clicked, this,
+ connect(ui->modification_list_view,
+ &QListView::clicked,
+ this,
&EditModifications::ItemClicked);
- connect(ui->modification_list_view, &QListView::doubleClicked, this,
+ connect(ui->modification_list_view,
+ &QListView::doubleClicked,
+ this,
&EditModifications::ItemDoubleClicked);
- connect(_p_browse_modification_dialog, &ChooseModificationDialog::accepted,
- this, &EditModifications::doAcceptedBrowseDialog);
+ connect(_p_browse_modification_dialog,
+ &ChooseModificationDialog::accepted,
+ this,
+ &EditModifications::doAcceptedBrowseDialog);
#else
- connect(ui->modification_list_view, SIGNAL(clicked(const QModelIndex)), this,
+ connect(ui->modification_list_view,
+ SIGNAL(clicked(const QModelIndex)),
+ this,
SLOT(ItemClicked(QModelIndex)));
- connect(ui->modification_list_view, SIGNAL(doubleClicked(const QModelIndex)),
- this, SLOT(ItemDoubleClicked(QModelIndex)));
-
- connect(_p_browse_modification_dialog, SIGNAL(accepted()), this,
+ connect(ui->modification_list_view,
+ SIGNAL(doubleClicked(const QModelIndex)),
+ this,
+ SLOT(ItemDoubleClicked(QModelIndex)));
+
+ connect(_p_browse_modification_dialog,
+ SIGNAL(accepted()),
+ this,
SLOT(doAcceptedBrowseDialog()));
#endif
@@ -165,8 +177,9 @@ EditModifications::doActionBrowse()
qDebug() << "EditModifications::doActionBrowse begin";
if(_selected_modification != nullptr)
{
- pappso::MassRange massrange(_selected_modification->getMass(),
- pappso::Precision::getDaltonInstance(0.05));
+ pappso::MzRange massrange(
+ _selected_modification->getMass(),
+ pappso::PrecisionFactory::getDaltonInstance(0.05));
_p_browse_modification_dialog->setMassRange(massrange);
_p_browse_modification_dialog->show();
_p_browse_modification_dialog->raise();
diff --git a/src/gui/edit_modifications/editmodifications.h b/src/gui/edit_modifications/editmodifications.h
index 36f0b1416..3758ea3f2 100644
--- a/src/gui/edit_modifications/editmodifications.h
+++ b/src/gui/edit_modifications/editmodifications.h
@@ -36,7 +36,7 @@ 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/edit_tandem_preset_dialog/edittandempresetdialog.cpp b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
index 598e3a75e..2ef02ef41 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -140,7 +140,8 @@ EditTandemPresetDialog::doSelectDir()
catch(pappso::PappsoException &error)
{
QMessageBox::warning(
- this, tr("Error :"),
+ this,
+ tr("Error :"),
tr("Error choosing preset directory : %1").arg(error.qwhat()));
}
}
@@ -187,7 +188,8 @@ EditTandemPresetDialog::doLoad()
else
{
QMessageBox::warning(
- this, tr("Error :"),
+ this,
+ tr("Error :"),
tr("%1 is not an X!Tandem parameter file")
.arg(p_tandem_preset_file->getAbsoluteFilePath()));
}
@@ -1290,7 +1292,8 @@ EditTandemPresetDialog::done(int r)
if(!_p_tandem_preset_file->exists())
{
QMessageBox::warning(
- this, tr("Save parameters"),
+ this,
+ tr("Save parameters"),
tr("Parameters file does not exists.\nPlease save it before "
"pressing ok or cancel edition"));
return;
@@ -1305,7 +1308,8 @@ EditTandemPresetDialog::done(int r)
else
{
QMessageBox::warning(
- this, tr("Save parameters"),
+ this,
+ tr("Save parameters"),
tr("Parameters modified but not saved.\nPlease save it before "
"pressing ok or cancel edition"));
return;
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h
index fffcef167..871142793 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.h
@@ -36,7 +36,7 @@
namespace Ui
{
- class EditTandemPresetView;
+class EditTandemPresetView;
}
class EditTandemPresetDialog : public QDialog
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
index 533c3b97a..e8e28f2f0 100644
--- a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
@@ -120,7 +120,7 @@ MasschroqFileParameters::load()
settings.value("export_masschroqml/ms1_smoothing_half_window", "0")
.toUInt();
- xic_extraction_range = pappso::Precision::fromString(
+ xic_extraction_range = pappso::PrecisionFactory::fromString(
settings.value("export_masschroqml/xic_extraction_range", "10 ppm")
.toString());
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
index fb01242da..a4dda270b 100644
--- a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
@@ -32,7 +32,7 @@
#include "../../../utils/types.h"
#include <QString>
-#include <pappsomspp/mass_range.h>
+#include <pappsomspp/mzrange.h>
struct MasschroqFileParameters
{
@@ -48,15 +48,15 @@ struct MasschroqFileParameters
bool export_compar_file = false;
QString compar_file_name;
TableFileFormat compar_file_format = TableFileFormat::ods;
-
+
bool write_alignment_times;
QString alignment_times_directory;
-
+
unsigned int ms2_tendency_half_window;
unsigned int ms2_smoothing_half_window;
unsigned int ms1_smoothing_half_window;
-
- pappso::PrecisionP xic_extraction_range;
-
- QString xic_extraction_method; //sum or max
+
+ pappso::PrecisionPtr xic_extraction_range;
+
+ QString xic_extraction_method; // sum or max
};
diff --git a/src/gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.h b/src/gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.h
index a95b8e5e8..d13ee34e2 100644
--- a/src/gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.h
+++ b/src/gui/export/export_spreadsheet_dialog/exportspreadsheetdialog.h
@@ -39,7 +39,7 @@
namespace Ui
{
- class ExportSpreadsheetDialog;
+class ExportSpreadsheetDialog;
}
class ExportSpreadsheetDialog : public QDialog
@@ -49,7 +49,7 @@ class ExportSpreadsheetDialog : public QDialog
public:
explicit ExportSpreadsheetDialog(QWidget *parent);
~ExportSpreadsheetDialog();
-
+
QString getExportFormat() const;
void setProject(const Project *p_project);
diff --git a/src/gui/load_results_dialog/loadresultsdialog.cpp b/src/gui/load_results_dialog/loadresultsdialog.cpp
index efcbf6104..8e9d1f8fe 100644
--- a/src/gui/load_results_dialog/loadresultsdialog.cpp
+++ b/src/gui/load_results_dialog/loadresultsdialog.cpp
@@ -104,9 +104,12 @@ LoadResultsDialog::chooseFiles()
settings.value("path/identificationfiles", "").toString();
QStringList filenames = QFileDialog::getOpenFileNames(
- this, tr("identification files"), default_location,
- tr("X!Tandem, Mascot DAT, pepXML or mzIdentML files (*.xml *.mzid *.dat "
- "*.pepxml *.pepXML);;all files (*)"));
+ this,
+ tr("identification files"),
+ default_location,
+ tr(
+ "X!Tandem, Mascot DAT, pepXML or mzIdentML files (*.xml *.mzid *.dat "
+ "*.pepxml *.pepXML);;all files (*)"));
if(filenames.size() > 0)
{
diff --git a/src/gui/load_results_dialog/loadresultsdialog.h b/src/gui/load_results_dialog/loadresultsdialog.h
index 613e058c2..6ba44e428 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/mainwindow.h b/src/gui/mainwindow.h
index c93a4cc32..e55123a45 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -31,7 +31,7 @@
#include <QCloseEvent>
#include <pappsomspp/types.h>
#include <pappsomspp/peptide/peptide.h>
-#include <pappsomspp/spectrum/spectrum.h>
+#include <pappsomspp/spectrum/massspectrum.h>
#include "core/project.h"
#include "project_view/projectwindow.h"
#include "load_results_dialog/loadresultsdialog.h"
@@ -108,7 +108,9 @@ class MainWindow : public QMainWindow
void operateWritingXpipFile(QString filename, ProjectSp project_sp);
void
operateWritingOdsFile(QString filename, QString format, ProjectSp project_sp);
- void operateWritingMassChroqFile(QString filename, ProjectSp project_sp, MasschroqFileParameters params);
+ void operateWritingMassChroqFile(QString filename,
+ ProjectSp project_sp,
+ MasschroqFileParameters params);
void operateWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
void operateWritingProticFile(QString filename, ProjectSp project_sp);
void operateWritingMcqrSpectralCountFile(QString filename,
diff --git a/src/gui/peptide_detail_view/peptide_detail_view.ui b/src/gui/peptide_detail_view/peptide_detail_view.ui
index e4a10ea88..409568153 100644
--- a/src/gui/peptide_detail_view/peptide_detail_view.ui
+++ b/src/gui/peptide_detail_view/peptide_detail_view.ui
@@ -165,7 +165,7 @@
<item>
<layout class="QHBoxLayout" name="horizontalLayout_4">
<item>
- <widget class="pappso::SpectrumWidget" name="spectrum_widget" native="true">
+ <widget class="pappso::MassSpectrumWidget" name="spectrum_widget" native="true">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Expanding">
<horstretch>0</horstretch>
@@ -372,9 +372,9 @@
</widget>
<customwidgets>
<customwidget>
- <class>pappso::SpectrumWidget</class>
+ <class>pappso::MassSpectrumWidget</class>
<extends>QWidget</extends>
- <header>pappsomspp/widget/spectrumwidget/spectrumwidget.h</header>
+ <header>pappsomspp/widget/massspectrumwidget/massspectrumwidget.h</header>
<container>1</container>
<slots>
<signal>mzChanged(double)</signal>
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 979b4b78c..4172be076 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -27,7 +27,7 @@
#include "../../config.h"
#include "ui_peptide_detail_view.h"
#include <pappsomspp/exception/exceptionnotfound.h>
-#include <pappsomspp/spectrum/qualifiedspectrum.h>
+#include <pappsomspp/spectrum/qualifiedmassspectrum.h>
#include <QMessageBox>
#include <QFileDialog>
#include <QSettings>
@@ -42,12 +42,11 @@ void
SpectrumSpLoaderThread::doLoadSpectrumSp(PeptideEvidence *p_peptide_evidence)
{
qDebug() << "SpectrumSpLoaderThread::doLoadSpectrumSp begin";
- pappso::SpectrumSp spectrum;
+ pappso::MassSpectrumCstSPtr spectrum;
try
{
- spectrum =
- p_peptide_evidence->getIdentificationDataSource()->getSpectrumSp(
- p_peptide_evidence->getScan());
+ spectrum = p_peptide_evidence->getIdentificationDataSource()
+ ->getMassSpectrumCstSPtr(p_peptide_evidence->getScan());
emit spectrumSpReady(spectrum, QString(""), QString(""));
}
@@ -91,7 +90,7 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent)
QString precision_str =
settings.value("peptideview/precision", "0.2 dalton").toString();
- _p_precision = pappso::Precision::fromString(precision_str);
+ _p_precision = pappso::PrecisionFactory::fromString(precision_str);
ui->file_not_found->setVisible(false);
@@ -133,7 +132,6 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent)
&pappso::SpectrumWidget::mzChanged,
this,
&PeptideWindow::setMz);
- */
connect(ui->spectrum_widget,
qOverload<const pappso::Peak *>(&pappso::SpectrumWidget::peakChanged),
this,
@@ -144,6 +142,7 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent)
this,
&PeptideWindow::setIon);
+ */
#else
// Qt4 code
connect(_p_project_window,
@@ -178,26 +177,26 @@ PeptideWindow::~PeptideWindow()
void
-PeptideWindow::setIon(pappso::PeakIonIsotopeMatch ion)
+PeptideWindow::setIon(pappso::PeakIonIsotopeMatchCstSPtr ion)
{
QString plusstr = "+";
- plusstr = plusstr.repeated(ion.getCharge());
+ plusstr = plusstr.repeated(ion->getCharge());
_ion_label->setText(
QString("%1%2%3 (+%4) - th. isotope ratio %5%")
- .arg(ion.getPeptideFragmentIonSp().get()->getPeptideIonName())
- .arg(ion.getPeptideFragmentIonSp().get()->size())
+ .arg(ion->getPeptideFragmentIonSp().get()->getPeptideIonName())
+ .arg(ion->getPeptideFragmentIonSp().get()->size())
.arg(plusstr)
- .arg(ion.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
- .arg((int)(ion.getPeptideNaturalIsotopeAverageSp()
+ .arg(ion->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
+ .arg((int)(ion->getPeptideNaturalIsotopeAverageSp()
.get()
->getIntensityRatio() *
100)));
}
void
-PeptideWindow::setPeak(const pappso::Peak *p_peak_match)
+PeptideWindow::setPeak(pappso::DataPointCstSPtr p_peak_match)
{
- qDebug() << "PeptideWindow::setPeak begin" << p_peak_match;
+ qDebug() << "PeptideWindow::setPeak begin";
if(p_peak_match == nullptr)
{
_peak_label->setText(QString("no peak"));
@@ -206,8 +205,8 @@ PeptideWindow::setPeak(const pappso::Peak *p_peak_match)
else
{
_peak_label->setText(QString("peak mz=%1 intensity=%2")
- .arg(QString::number(p_peak_match->mz, 'g', 10))
- .arg(p_peak_match->intensity));
+ .arg(QString::number(p_peak_match->x, 'g', 10))
+ .arg(p_peak_match->y));
}
}
@@ -339,7 +338,7 @@ PeptideWindow::openInXicViewer()
}
void
-PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp,
+PeptideWindow::doSpectrumSpReady(pappso::MassSpectrumCstSPtr spectrum_sp,
QString error,
QString fatal_error)
{
@@ -353,7 +352,7 @@ PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp,
ui->xic_button->setEnabled(true);
ui->spectrum_widget->setMsLevel(2);
- ui->spectrum_widget->setSpectrumSp(spectrum_sp);
+ ui->spectrum_widget->setMassSpectrumCstSPtr(spectrum_sp);
qDebug() << "PeptideWindow::doSpectrumSpReady plot";
ui->spectrum_widget->plot();
qDebug() << "PeptideWindow::doSpectrumSpReady rescale";
@@ -427,7 +426,7 @@ PeptideWindow::setPeptideEvidence(PeptideEvidence *p_peptide_evidence)
}
void
-PeptideWindow::doMsmsPrecisionChanged(pappso::PrecisionP precision)
+PeptideWindow::doMsmsPrecisionChanged(pappso::PrecisionPtr precision)
{
qDebug() << "PeptideWindow::doMsmsPrecisionChanged begin "
diff --git a/src/gui/peptide_detail_view/peptidewindow.h b/src/gui/peptide_detail_view/peptidewindow.h
index 97e30f8d1..f5629040a 100644
--- a/src/gui/peptide_detail_view/peptidewindow.h
+++ b/src/gui/peptide_detail_view/peptidewindow.h
@@ -27,8 +27,8 @@
#include <QTextDocument>
#include <QThread>
#include <QLabel>
-#include <pappsomspp/mass_range.h>
-#include <pappsomspp/spectrum/spectrum.h>
+#include <pappsomspp/mzrange.h>
+#include <pappsomspp/spectrum/massspectrum.h>
#include <pappsomspp/psm/peakionisotopematch.h>
#include "../../core/peptidematch.h"
#include "../../core/identificationgroup.h"
@@ -49,7 +49,7 @@ class SpectrumSpLoaderThread : public QObject
void doLoadSpectrumSp(PeptideEvidence *p_peptide_evidence);
signals:
- void spectrumSpReady(pappso::SpectrumSp spectrum_sp,
+ void spectrumSpReady(pappso::MassSpectrumCstSPtr spectrum_sp,
QString error,
QString fatal_error);
@@ -71,17 +71,17 @@ class PeptideWindow : public QMainWindow
void
doIdentificationGroupGrouped(IdentificationGroup *p_identification_group);
void setMz(double);
- void setPeak(const pappso::Peak *p_peak_match);
- void setIon(pappso::PeakIonIsotopeMatch ion);
+ void setPeak(pappso::DataPointCstSPtr p_peak_match);
+ void setIon(pappso::PeakIonIsotopeMatchCstSPtr ion);
signals:
void loadSpectrumSp(PeptideEvidence *p_peptide_evidence);
protected slots:
- void doSpectrumSpReady(pappso::SpectrumSp spectrum_sp,
+ void doSpectrumSpReady(pappso::MassSpectrumCstSPtr spectrum_sp,
QString error,
QString fatal_error);
- void doMsmsPrecisionChanged(pappso::PrecisionP);
+ void doMsmsPrecisionChanged(pappso::PrecisionPtr);
void doSaveSvg();
void chooseDefaultMzDataDir();
void openInPeptideViewer();
@@ -99,7 +99,7 @@ class PeptideWindow : public QMainWindow
Ui::PeptideDetailView *ui;
ProjectWindow *_p_project_window;
PeptideEvidence *_p_peptide_evidence = nullptr;
- pappso::PrecisionP _p_precision;
+ pappso::PrecisionPtr _p_precision;
bool _spectrum_is_ready = false;
};
diff --git a/src/gui/peptide_list_view/peptidelistwindow.cpp b/src/gui/peptide_list_view/peptidelistwindow.cpp
index 533afa4a0..f3cd586a0 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.cpp
+++ b/src/gui/peptide_list_view/peptidelistwindow.cpp
@@ -47,7 +47,9 @@ PeptideListQactionColumn::PeptideListQactionColumn(PeptideListWindow *parent,
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(this, &PeptideListQactionColumn::toggled, this,
+ connect(this,
+ &PeptideListQactionColumn::toggled,
+ this,
&PeptideListQactionColumn::doToggled);
#else
// Qt4 code
@@ -119,30 +121,47 @@ PeptideListWindow::PeptideListWindow(ProjectWindow *parent)
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(_project_window, &ProjectWindow::identificationGroupGrouped, this,
+ connect(_project_window,
+ &ProjectWindow::identificationGroupGrouped,
+ this,
&PeptideListWindow::doIdentificationGroupGrouped);
- connect(this, &PeptideListWindow::peptideDataChanged, _peptide_table_model_p,
+ connect(this,
+ &PeptideListWindow::peptideDataChanged,
+ _peptide_table_model_p,
&PeptideTableModel::onPeptideDataChanged);
- connect(ui->tableView, &QTableView::clicked, _p_proxy_model,
+ connect(ui->tableView,
+ &QTableView::clicked,
+ _p_proxy_model,
&PeptideTableProxyModel::onTableClicked);
- connect(_peptide_table_model_p, &PeptideTableModel::layoutChanged, this,
+ connect(_peptide_table_model_p,
+ &PeptideTableModel::layoutChanged,
+ this,
&PeptideListWindow::updateStatusBar);
- connect(ui->centralwidget, &QWidget::customContextMenuRequested, this,
+ connect(ui->centralwidget,
+ &QWidget::customContextMenuRequested,
+ this,
&PeptideListWindow::showContextMenu);
#else
// Qt4 code
connect(_project_window,
- SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
+ this,
SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
- connect(this, SIGNAL(peptideDataChanged()), _peptide_table_model_p,
+ connect(this,
+ SIGNAL(peptideDataChanged()),
+ _peptide_table_model_p,
SLOT(onPeptideDataChanged()));
- connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model,
+ connect(ui->tableView,
+ SIGNAL(clicked(const QModelIndex &)),
+ _p_proxy_model,
SLOT(onTableClicked(const QModelIndex &)));
- connect(_peptide_table_model_p, SIGNAL(layoutChanged()), this,
+ connect(_peptide_table_model_p,
+ SIGNAL(layoutChanged()),
+ this,
SLOT(updateStatusBar()));
/*
diff --git a/src/gui/peptide_list_view/peptidelistwindow.h b/src/gui/peptide_list_view/peptidelistwindow.h
index 3aecc9243..ffea46d7a 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.h
+++ b/src/gui/peptide_list_view/peptidelistwindow.h
@@ -36,7 +36,7 @@ class ProjectWindow;
// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
namespace Ui
{
- class PeptideView;
+class PeptideView;
}
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index 82addadd8..eeee8485f 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -88,8 +88,8 @@ class PeptideTableModel : public QAbstractTableModel
PeptideTableModel(PeptideListWindow *parent);
int rowCount(const QModelIndex &parent = QModelIndex()) const override;
int columnCount(const QModelIndex &parent = QModelIndex()) 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;
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.cpp b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
index 3993cd412..3c0ec4d7c 100644
--- a/src/gui/peptide_list_view/peptidetableproxymodel.cpp
+++ b/src/gui/peptide_list_view/peptidetableproxymodel.cpp
@@ -317,7 +317,8 @@ PeptideTableProxyModel::lessThan(const QModelIndex &left,
QVariant
-PeptideTableProxyModel::headerData(int section, Qt::Orientation orientation,
+PeptideTableProxyModel::headerData(int section,
+ Qt::Orientation orientation,
int role) const
{
int col = mapToSource(index(0, section)).column();
diff --git a/src/gui/peptide_list_view/peptidetableproxymodel.h b/src/gui/peptide_list_view/peptidetableproxymodel.h
index 569bc2016..123ce4b4f 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.cpp b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
index ac279cfd1..d95594793 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
@@ -52,13 +52,16 @@ IdentificationGroupWidget::setIdentificationGroup(
_p_project_window = parent;
#if QT_VERSION >= 0x050000
// Qt5 code
- connect(_p_project_window, &ProjectWindow::identificationGroupGrouped, this,
+ connect(_p_project_window,
+ &ProjectWindow::identificationGroupGrouped,
+ this,
&IdentificationGroupWidget::doIdentificationGroupGrouped);
#else
// Qt4 code
connect(_p_project_window,
- SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,
+ SIGNAL(identificationGroupGrouped(IdentificationGroup *)),
+ this,
SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
#endif
}
@@ -90,7 +93,8 @@ IdentificationGroupWidget::doIdentificationGroupGrouped(
<< _p_identification_group << " " << p_identification_group;
if(_p_identification_group == p_identification_group)
{
- vector<MsRunSp> ms_run_list = _p_identification_group->getMsRunSpList();
+ std::vector<MsRunSp> ms_run_list =
+ _p_identification_group->getMsRunSpList();
ui->sample_number_display->setText(QString("%1").arg(ms_run_list.size()));
ui->group_number_display->setText(
diff --git a/src/gui/project_view/identification_group_widget/identificationgroupwidget.h b/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
index 94d03b4be..0e34d4b4d 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.h
@@ -29,7 +29,7 @@
namespace Ui
{
- class IdentificationGroupWidget;
+class IdentificationGroupWidget;
}
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 6a0aae86b..b4422aa6c 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -280,8 +280,7 @@ ProjectWindow::computeFdr()
total_prot += identification_group->countProteinMatch(state);
false_prot += identification_group->countDecoyProteinMatch(state);
total_psm += identification_group->countPeptideEvidence(state);
- false_psm +=
- identification_group->countDecoyPeptideEvidence(state);
+ false_psm += identification_group->countDecoyPeptideEvidence(state);
total_peptide += identification_group->countPeptideMassSample(state);
false_peptide +=
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index a1015a9a3..b7ed2a105 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -37,7 +37,7 @@ class ProjectWindow;
// http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
namespace Ui
{
- class ProteinView;
+class ProteinView;
}
class ProteinListWindow;
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 490f40bb9..cbe0d4ec5 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 6cdaa1ce2..86734bcf8 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -62,8 +62,8 @@ 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;
diff --git a/src/gui/protein_list_view/proteintableproxymodel.h b/src/gui/protein_list_view/proteintableproxymodel.h
index adefbcb08..d4f687700 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/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 397c5aea1..9b17a7741 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()));
@@ -67,16 +67,23 @@ 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,
@@ -143,9 +150,10 @@ 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;
@@ -171,13 +179,14 @@ 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/protein_view/proteinwindow.h b/src/gui/protein_view/proteinwindow.h
index 8bb6fcf33..1e2885b4f 100644
--- a/src/gui/protein_view/proteinwindow.h
+++ b/src/gui/protein_view/proteinwindow.h
@@ -46,7 +46,7 @@ class ProjectWindow;
namespace Ui
{
- class ProteinDetailView;
+class ProteinDetailView;
}
class ProteinWindow : public QMainWindow
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 5114d8f0d..880533bae 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 70cb8e168..e5f49d377 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 d039db1fe..9057339b4 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 2cee9bc62..da20d0d4a 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 5fb53774e..da29d9267 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -62,9 +62,12 @@ 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
@@ -77,9 +80,12 @@ 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 d49489ef7..b4bcc15c8 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 ca333c6a2..2f9fbd0e2 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 76c02ce65..59ae24348 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 4a15cc548..e37056413 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 3b458883b..fc1211ecc 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 e9b786bcc..fef38bde8 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 56569fa43..596819d18 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -473,16 +473,16 @@ TandemRunDialog::fillTandemBinPath(const QString &tandem_bin_path_in,
if(tandem_bin_path_in.isEmpty())
{
// try to find default X!Tandem, depending on platform
- ui->tandem_bin_label->setText(
- "");
+ ui->tandem_bin_label->setText("");
if(QFileInfo("/usr/bin/tandem").exists())
{
fillTandemBinPath("/usr/bin/tandem", false);
}
else
{
- ui->tandem_version_label->setText(
- "<font color=\"red\">Please select the tandem.exe file path</font>");
+ ui->tandem_version_label->setText(
+ "<font color=\"red\">Please select the tandem.exe file "
+ "path</font>");
ui->exe_groupbox->setChecked(true);
}
}
diff --git a/src/gui/waiting_message_dialog/waitingmessagedialog.h b/src/gui/waiting_message_dialog/waitingmessagedialog.h
index 50a73da76..a20c256b4 100644
--- a/src/gui/waiting_message_dialog/waitingmessagedialog.h
+++ b/src/gui/waiting_message_dialog/waitingmessagedialog.h
@@ -34,7 +34,7 @@
namespace Ui
{
- class WaitingMessageDialog;
+class WaitingMessageDialog;
}
diff --git a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h
index a01b80525..5b2fa39f1 100644
--- a/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h
+++ b/src/gui/widgets/automatic_filter_widget/automaticfilterwidget.h
@@ -31,7 +31,7 @@
namespace Ui
{
- class AutomaticFilterWidget;
+class AutomaticFilterWidget;
}
class AutomaticFilterWidget : public QWidget
diff --git a/src/gui/widgets/contaminant_widget/contaminantwidget.h b/src/gui/widgets/contaminant_widget/contaminantwidget.h
index ffea09bd5..0a79d0958 100644
--- a/src/gui/widgets/contaminant_widget/contaminantwidget.h
+++ b/src/gui/widgets/contaminant_widget/contaminantwidget.h
@@ -40,7 +40,7 @@
namespace Ui
{
- class ContaminantWidget;
+class ContaminantWidget;
}
class ContaminantWidget : public QWidget
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index be10ce490..f432d576d 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -547,7 +547,9 @@ WorkerThread::doWritingOdsFile(QString filename,
void
-WorkerThread::doWritingMassChroqFile(QString filename, ProjectSp project_sp, MasschroqFileParameters params)
+WorkerThread::doWritingMassChroqFile(QString filename,
+ ProjectSp project_sp,
+ MasschroqFileParameters params)
{
try
@@ -750,7 +752,7 @@ WorkerThread::doWritingFastaFile(QString filename,
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
emit loadingMessage(tr("writing FASTA file, please wait"));
-
+
ExportFastaFile output(filename, type);
output.write(project_sp);
output.close();
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index 686485d74..42c9ced2e 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -57,11 +57,14 @@ class WorkerThread : public QObject
public slots:
void doXpipFileLoad(QString filename);
- void doLoadingResults(bool is_individual, AutomaticFilterParameters param,
+ void doLoadingResults(bool is_individual,
+ AutomaticFilterParameters param,
QStringList file_list);
void doWritingXpipFile(QString filename, ProjectSp project_sp);
void doWritingOdsFile(QString filename, QString format, ProjectSp project_sp);
- void doWritingMassChroqFile(QString filename, ProjectSp project_sp, MasschroqFileParameters params);
+ void doWritingMassChroqFile(QString filename,
+ ProjectSp project_sp,
+ MasschroqFileParameters params);
void doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
void doWritingProticFile(QString filename, ProjectSp project_sp);
void doWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp);
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index ebf3711c3..b4e36d96c 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -38,9 +38,9 @@
bool
-XicBoxNaturalIsotope::contains(const pappso::XicPeakSp &peak) const
+XicBoxNaturalIsotope::contains(const pappso::XicPeakCstSPtr &peak) const
{
- for(const pappso::XicPeakSp &peak_i : detected_peak_list)
+ for(const pappso::XicPeakCstSPtr &peak_i : detected_peak_list)
{
if(peak_i.get() == peak.get())
{
@@ -69,7 +69,7 @@ class XicDetectionList : public pappso::XicDetectionSinkInterface
void
setXicPeak(pappso::XicPeak &xic_peak) override
{
- pappso::XicPeakSp peak_sp = xic_peak.makeXicPeakSp();
+ pappso::XicPeakCstSPtr peak_sp = xic_peak.makeXicPeakCstSPtr();
_peak_list.push_back(peak_sp);
for(pappso::pappso_double rt : _rt_list)
@@ -84,12 +84,12 @@ class XicDetectionList : public pappso::XicDetectionSinkInterface
}
}
};
- const pappso::XicPeakSp &
+ const pappso::XicPeakCstSPtr &
getMatchedPeak() const
{
return _max_peak;
}
- const std::vector<pappso::XicPeakSp> &
+ const std::vector<pappso::XicPeakCstSPtr> &
getXicPeakList() const
{
return _peak_list;
@@ -103,9 +103,9 @@ class XicDetectionList : public pappso::XicDetectionSinkInterface
private:
unsigned int _count = 0;
- std::vector<pappso::XicPeakSp> _peak_list;
+ std::vector<pappso::XicPeakCstSPtr> _peak_list;
std::vector<pappso::pappso_double> _rt_list;
- pappso::XicPeakSp _max_peak;
+ pappso::XicPeakCstSPtr _max_peak;
};
@@ -150,12 +150,11 @@ XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
connect(
_p_xic_window, &XicWindow::reExtractXicNeeded, this, &XicBox::reExtractXic);
- connect(ui->xic_widget,
- qOverload<std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>>>(
- &pappso::XicWidget::xicPeakListChanged),
- this,
+ /* connect(ui->xic_widget,
+ qOverload<std::vector<std::pair<pappso::XicCstSPtr,
+ pappso::XicPeakSp>>>( &pappso::XicWidget::xicPeakListChanged), this,
&XicBox::setXicPeakList);
- /*
+
connect(ui->xic_widget,
&pappso::XicWidget::clicked,
this,
@@ -201,7 +200,7 @@ XicBox::onXicWidgetClick(double rt, double intensity)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
ui->xic_widget->clearXicPeakBorders();
- std::vector<pappso::XicPeakSp> draw_peak_borders;
+ std::vector<pappso::XicPeakCstSPtr> draw_peak_borders;
for(XicBoxNaturalIsotope peak : _natural_isotope_list)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -318,7 +317,7 @@ XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
}
void
-XicBox::setXic(std::vector<pappso::XicSp> xic_sp_list)
+XicBox::setXic(std::vector<pappso::XicCstSPtr> xic_sp_list)
{
qDebug() << "XicBox::setXic begin " << xic_sp_list.size();
ui->xic_widget->clear();
@@ -384,7 +383,7 @@ XicBox::setXic(std::vector<pappso::XicSp> xic_sp_list)
XicDetectionList xic_list;
xic_list.setPeptideEvidenceList(_peptide_evidence_list);
- std::vector<pappso::XicPeakSp> draw_peak_borders;
+ std::vector<pappso::XicPeakCstSPtr> draw_peak_borders;
for(XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
{
@@ -412,7 +411,7 @@ XicBox::setXic(std::vector<pappso::XicSp> xic_sp_list)
void
XicBox::drawObservedAreaBars(
- const std::vector<pappso::XicPeakSp> &observed_peak_to_draw_list)
+ const std::vector<pappso::XicPeakCstSPtr> &observed_peak_to_draw_list)
{
if(_isotope_ratio_graph_observed_intensity == nullptr)
{
@@ -439,8 +438,8 @@ XicBox::drawObservedAreaBars(
qDebug() << "XicBox::setXic plot _isotope_mass_list";
for(const XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
{
- pappso::XicPeakSp peak_to_draw;
- for(pappso::XicPeakSp observed_peak : observed_peak_to_draw_list)
+ pappso::XicPeakCstSPtr peak_to_draw;
+ for(pappso::XicPeakCstSPtr observed_peak : observed_peak_to_draw_list)
{
if(xic_isotope.contains(observed_peak))
{
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index f675882ad..b7acc1f17 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/src/gui/xic_view/xic_box/xicbox.h
@@ -40,20 +40,20 @@
namespace Ui
{
- class XicBox;
+class XicBox;
}
struct XicBoxNaturalIsotope
{
- bool contains(const pappso::XicPeakSp &peak) const;
+ bool contains(const pappso::XicPeakCstSPtr &peak) const;
- pappso::XicSp xic_sp;
+ pappso::XicCstSPtr xic_sp;
pappso::PeptideNaturalIsotopeAverageSp peptide_natural_isotope_sp;
- pappso::XicPeakSp matched_peak_sp;
- pappso::XicPeakSp one_peak_sp;
- std::vector<pappso::XicPeakSp> detected_peak_list;
+ pappso::XicPeakCstSPtr matched_peak_sp;
+ pappso::XicPeakCstSPtr one_peak_sp;
+ std::vector<pappso::XicPeakCstSPtr> detected_peak_list;
};
class XicBox : public QWidget
@@ -67,28 +67,30 @@ class XicBox : public QWidget
MsRunSp msrun_sp);
signals:
- void loadXic(MsRunSp p_msrun, std::vector<pappso::mz> mz_list,
- pappso::PrecisionP precision, pappso::XicExtractMethod method);
- void computeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge,
- pappso::PrecisionP precision,
+ void loadXic(MsRunSp p_msrun,
+ std::vector<pappso::pappso_double> mz_list,
+ pappso::PrecisionPtr precision,
+ pappso::XicExtractMethod method);
+ void computeIsotopeMassList(pappso::PeptideSp peptide_sp,
+ unsigned int charge,
+ pappso::PrecisionPtr precision,
double minimum_isotope_pattern_ratio);
private slots:
void remove();
void reExtractXic();
- void setXic(std::vector<pappso::XicSp> xic_sp_list);
+ void setXic(std::vector<pappso::XicCstSPtr> xic_sp_list);
void setIsotopeMassList(
std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
void error(QString error_message);
void extractXicInOtherMsRun();
void setRetentionTime(double rt);
- void setXicPeakList(
- std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>> xic_peak_list);
+ void setXicPeakList(pappso::XicXicPeakPairList xic_peak_list);
void onRtUnitChanged();
void onXicWidgetClick(double rt, double intensity);
private:
void drawObservedAreaBars(
- const std::vector<pappso::XicPeakSp> &observed_peak_to_draw);
+ const std::vector<pappso::XicPeakCstSPtr> &observed_peak_to_draw);
private:
Ui::XicBox *ui;
diff --git a/src/gui/xic_view/xic_widgets/zivywidget.h b/src/gui/xic_view/xic_widgets/zivywidget.h
index 19560c1d2..bc48fe3fc 100644
--- a/src/gui/xic_view/xic_widgets/zivywidget.h
+++ b/src/gui/xic_view/xic_widgets/zivywidget.h
@@ -71,4 +71,3 @@ class ZivyWidget : public QWidget
private:
Ui::ZivyWidget *ui;
};
-
diff --git a/src/gui/xic_view/xicwindow.cpp b/src/gui/xic_view/xicwindow.cpp
index 039383fa5..e4ea18390 100644
--- a/src/gui/xic_view/xicwindow.cpp
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -43,7 +43,8 @@ XicWindow::XicWindow(ProjectWindow *parent)
QSettings settings;
QString precision_str = settings.value("xic/precision", "10 ppm").toString();
- ui->xic_precision->setPrecision(pappso::Precision::fromString(precision_str));
+ ui->xic_precision->setPrecision(
+ pappso::PrecisionFactory::fromString(precision_str));
ZivyParams zivy_params;
@@ -56,7 +57,9 @@ XicWindow::XicWindow(ProjectWindow *parent)
_p_zivy_dialog->setZivyParams(zivy_params);
- connect(_p_zivy_dialog, &ZivyDialog::accepted, this,
+ connect(_p_zivy_dialog,
+ &ZivyDialog::accepted,
+ this,
&XicWindow::doAcceptedZivyDialog);
#if QT_VERSION >= 0x050000
@@ -121,14 +124,14 @@ XicWindow::removeXicBox(XicBox *xic_box)
delete xic_box;
}
-pappso::PrecisionP
+pappso::PrecisionPtr
XicWindow::getXicExtractPrecision() const
{
return (ui->xic_precision->getPrecision());
}
void
-XicWindow::xicPrecisionChanged(pappso::PrecisionP precision)
+XicWindow::xicPrecisionChanged(pappso::PrecisionPtr precision)
{
qDebug() << "XicWindow::xicPrecisionChanged begin";
qDebug() << "XicWindow::xicPrecisionChanged emit";
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
index 1598c977b..a83ae03b3 100644
--- a/src/gui/xic_view/xicwindow.h
+++ b/src/gui/xic_view/xicwindow.h
@@ -43,7 +43,7 @@ class ProjectWindow;
namespace Ui
{
- class XicWindow;
+class XicWindow;
}
class XicBox;
@@ -61,13 +61,13 @@ class XicWindow : public QMainWindow
void addXicInMsRun(const PeptideEvidence *p_peptide_evidence,
MsRunSp msrun_sp);
- pappso::PrecisionP getXicExtractPrecision() const;
+ pappso::PrecisionPtr getXicExtractPrecision() const;
bool isRetentionTimeSeconds() const;
void clear();
public slots:
- void xicPrecisionChanged(pappso::PrecisionP precision);
+ void xicPrecisionChanged(pappso::PrecisionPtr precision);
void rtUnitChanged(QAbstractButton *button);
protected slots:
diff --git a/src/gui/xic_view/xicworkerthread.cpp b/src/gui/xic_view/xicworkerthread.cpp
index 9039b5eba..6aef044af 100644
--- a/src/gui/xic_view/xicworkerthread.cpp
+++ b/src/gui/xic_view/xicworkerthread.cpp
@@ -42,17 +42,17 @@ XicWorkerThread::~XicWorkerThread()
}
void
XicWorkerThread::doXicLoad(MsRunSp p_msrun,
- std::vector<pappso::mz> mz_list,
- pappso::PrecisionP precision,
+ std::vector<pappso::pappso_double> mz_list,
+ pappso::PrecisionPtr precision,
pappso::XicExtractMethod method)
{
try
{
- std::vector<pappso::MassRange> mass_list;
- for(pappso::mz mass : mz_list)
+ std::vector<pappso::MzRange> mass_list;
+ for(pappso::pappso_double mass : mz_list)
{
- mass_list.push_back(pappso::MassRange(mass, precision));
+ mass_list.push_back(pappso::MzRange(mass, precision));
}
// std::vector<pappso::XicSp> xic_sp_list =
// SpectrumStore::getXicSpFromMsRunSp(p_msrun.get(), mass_list, method);
@@ -66,8 +66,8 @@ XicWorkerThread::doXicLoad(MsRunSp p_msrun,
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- std::vector<pappso::XicSp> xic_sp_list =
- extractor.get()->getXicSpList(mass_list);
+ std::vector<pappso::XicCstSPtr> xic_sp_list =
+ extractor.get()->getXicCstSPtrList(mass_list);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
emit xicLoaded(xic_sp_list);
@@ -85,7 +85,7 @@ XicWorkerThread::doXicLoad(MsRunSp p_msrun,
void
XicWorkerThread::doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
unsigned int charge,
- pappso::PrecisionP precision,
+ pappso::PrecisionPtr precision,
double minimum_isotope_pattern_ratio)
{
qDebug() << "XicWorkerThread::doComputeIsotopeMassList "
diff --git a/src/gui/xic_view/xicworkerthread.h b/src/gui/xic_view/xicworkerthread.h
index 66081f2a3..bb9cffb8e 100644
--- a/src/gui/xic_view/xicworkerthread.h
+++ b/src/gui/xic_view/xicworkerthread.h
@@ -43,15 +43,17 @@ class XicWorkerThread : public QObject
XicWorkerThread(XicBox *parent);
virtual ~XicWorkerThread();
public slots:
- void doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list,
- pappso::PrecisionP precision, pappso::XicExtractMethod method);
+ void doXicLoad(MsRunSp p_msrun,
+ std::vector<pappso::pappso_double> mz_list,
+ pappso::PrecisionPtr precision,
+ pappso::XicExtractMethod method);
void doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
unsigned int charge,
- pappso::PrecisionP precision,
+ pappso::PrecisionPtr precision,
double minimum_isotope_pattern_ratio);
signals:
- void xicLoaded(std::vector<pappso::XicSp> xic_sp_list);
+ void xicLoaded(std::vector<pappso::XicCstSPtr> xic_sp_list);
void isotopeMassListComputed(
std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
void operationFailed(QString error);
diff --git a/src/input/condorqxmlsaxhandler.cpp b/src/input/condorqxmlsaxhandler.cpp
index 0b7081d37..726e9b8b6 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 4fd269c61..9b2e05b9f 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 85cc572bd..73b854753 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -472,7 +472,7 @@ IdentificationPwizReader::read(
.c_str())
.toULong();
}
- catch(runtime_error &pwiz_error)
+ catch(std::runtime_error &pwiz_error)
{
throw pappso::PappsoException(
QObject::tr("Pwiz runtime error :\n%1\n parsing "
diff --git a/src/input/identificationpwizreader.h b/src/input/identificationpwizreader.h
index 4738d65f6..7ed1fde50 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 5076fc346..bc0ad83d3 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -38,7 +38,8 @@
PepXmlSaxHandler::PepXmlSaxHandler(
- Project *p_project, IdentificationGroup *p_identification_group,
+ Project *p_project,
+ IdentificationGroup *p_identification_group,
IdentificationDataSource *p_identification_data_source)
: _p_project(p_project)
{
@@ -55,7 +56,8 @@ PepXmlSaxHandler::~PepXmlSaxHandler()
bool
PepXmlSaxHandler::startElement(const QString &namespaceURI,
- const QString &localName, const QString &qName,
+ const QString &localName,
+ const QString &qName,
const QXmlAttributes &attributes)
{
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -128,8 +130,9 @@ PepXmlSaxHandler::startElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::startElement tag "
- "%1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in PepXmlSaxHandler::startElement tag "
+ "%1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -148,7 +151,8 @@ PepXmlSaxHandler::startElement(const QString &namespaceURI,
bool
PepXmlSaxHandler::endElement(const QString &namespaceURI,
- const QString &localName, const QString &qName)
+ const QString &localName,
+ const QString &qName)
{
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -171,8 +175,9 @@ PepXmlSaxHandler::endElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::endElement tag %1, "
- "PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in PepXmlSaxHandler::endElement tag %1, "
+ "PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -304,9 +309,10 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
if(attributes.value("retention_time_sec").isEmpty())
{
QString message =
- QObject::tr("ERROR reading pepxml file :\n"
- "unable to read search results from '%1' as retention time "
- "is not given in spectrum_query elements")
+ QObject::tr(
+ "ERROR reading pepxml file :\n"
+ "unable to read search results from '%1' as retention time "
+ "is not given in spectrum_query elements")
.arg(_current_search_engine);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< message;
@@ -326,7 +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
@@ -690,8 +696,9 @@ PepXmlSaxHandler::endElement_modification_info()
bool
PepXmlSaxHandler::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());
@@ -703,8 +710,9 @@ PepXmlSaxHandler::error(const QXmlParseException &exception)
bool
PepXmlSaxHandler::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/pepxmlsaxhandler.h b/src/input/pepxmlsaxhandler.h
index 8856408c8..ac42d0184 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.cpp b/src/input/xpipsaxhandler.cpp
index 9e921ab29..275cc3d1d 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -50,7 +50,8 @@ XpipSaxHandler::isJavaXpip() const
bool
XpipSaxHandler::startElement(const QString &namespaceURI,
- const QString &localName, const QString &qName,
+ const QString &localName,
+ const QString &qName,
const QXmlAttributes &attributes)
{
qDebug() << "XpipSaxHandler::startElement begin" << namespaceURI << " "
@@ -137,7 +138,8 @@ XpipSaxHandler::startElement(const QString &namespaceURI,
bool
XpipSaxHandler::endElement(const QString &namespaceURI,
- const QString &localName, const QString &qName)
+ const QString &localName,
+ const QString &qName)
{
bool is_ok = true;
@@ -262,7 +264,7 @@ XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes)
*/
qDebug() << "startElement_modifs_mass ";
QString mass_str(attributes.value("modvalue").simplified());
- pappso::mz mass = mass_str.toDouble();
+ pappso::pappso_double mass = mass_str.toDouble();
pappso::AaModificationP mod = getAaModificationP(mass);
@@ -470,8 +472,9 @@ XpipSaxHandler::endElement_match()
bool
XpipSaxHandler::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());
@@ -483,8 +486,9 @@ XpipSaxHandler::error(const QXmlParseException &exception)
bool
XpipSaxHandler::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());
@@ -522,70 +526,70 @@ XpipSaxHandler::characters(const QString &str)
pappso::AaModificationP
-XpipSaxHandler::getAaModificationP(pappso::mz mass) const
+XpipSaxHandler::getAaModificationP(pappso::pappso_double mass) const
{
- pappso::PrecisionP precision = pappso::Precision::getDaltonInstance(0.01);
+ pappso::PrecisionPtr precision =
+ pappso::PrecisionFactory::getDaltonInstance(0.01);
pappso::AaModificationP oxidation =
pappso::AaModification::getInstance("MOD:00719");
- if(pappso::MassRange(oxidation->getMass(), precision).contains(mass))
+ if(pappso::MzRange(oxidation->getMass(), precision).contains(mass))
{
return oxidation;
}
pappso::AaModificationP iodoacetamide =
pappso::AaModification::getInstance("MOD:00397");
- if(pappso::MassRange(iodoacetamide->getMass(), precision).contains(mass))
+ if(pappso::MzRange(iodoacetamide->getMass(), precision).contains(mass))
{
return iodoacetamide;
}
pappso::AaModificationP acetylated =
pappso::AaModification::getInstance("MOD:00408");
- if(pappso::MassRange(acetylated->getMass(), precision).contains(mass))
+ if(pappso::MzRange(acetylated->getMass(), precision).contains(mass))
{
return acetylated;
}
pappso::AaModificationP phosphorylated =
pappso::AaModification::getInstance("MOD:00696");
- if(pappso::MassRange(phosphorylated->getMass(), precision).contains(mass))
+ if(pappso::MzRange(phosphorylated->getMass(), precision).contains(mass))
{
return phosphorylated;
}
pappso::AaModificationP ammonia =
pappso::AaModification::getInstance("MOD:01160");
- if(pappso::MassRange(ammonia->getMass(), precision).contains(mass))
+ if(pappso::MzRange(ammonia->getMass(), precision).contains(mass))
{
return ammonia;
}
pappso::AaModificationP dehydrated =
pappso::AaModification::getInstance("MOD:00704");
- if(pappso::MassRange(dehydrated->getMass(), precision).contains(mass))
+ if(pappso::MzRange(dehydrated->getMass(), precision).contains(mass))
{
return dehydrated;
}
pappso::AaModificationP dimethylated =
pappso::AaModification::getInstance("MOD:00429");
- if(pappso::MassRange(dimethylated->getMass(), precision).contains(mass))
+ if(pappso::MzRange(dimethylated->getMass(), precision).contains(mass))
{
return dimethylated;
}
pappso::AaModificationP dimethylated_medium =
pappso::AaModification::getInstance("MOD:00552");
- if(pappso::MassRange(dimethylated_medium->getMass(), precision)
- .contains(mass))
+ if(pappso::MzRange(dimethylated_medium->getMass(), precision).contains(mass))
{
return dimethylated_medium;
}
pappso::AaModificationP dimethylated_heavy =
pappso::AaModification::getInstance("MOD:00638");
- if(pappso::MassRange(dimethylated_heavy->getMass(), precision).contains(mass))
+ if(pappso::MzRange(dimethylated_heavy->getMass(), precision).contains(mass))
{
return dimethylated_heavy;
}
pappso::AaModificationP DimethylpyrroleAdduct =
pappso::AaModification::getInstance("MOD:00628");
- if(pappso::MassRange(DimethylpyrroleAdduct->getMass(), precision)
+ if(pappso::MzRange(DimethylpyrroleAdduct->getMass(), precision)
.contains(mass))
{
return DimethylpyrroleAdduct;
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index fdb335a17..cc692ecd2 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();
@@ -74,7 +77,7 @@ class XpipSaxHandler : public QXmlDefaultHandler
bool endElement_peptide();
bool endElement_match();
- pappso::AaModificationP getAaModificationP(pappso::mz mass) const;
+ pappso::AaModificationP getAaModificationP(pappso::pappso_double mass) const;
private:
WorkMonitorInterface *_p_monitor;
diff --git a/src/input/xtandemparamsaxhandler.cpp b/src/input/xtandemparamsaxhandler.cpp
index 08b9feed0..3d0e2f437 100644
--- a/src/input/xtandemparamsaxhandler.cpp
+++ b/src/input/xtandemparamsaxhandler.cpp
@@ -67,10 +67,10 @@ XtandemParamSaxHandler::startElement(const QString &namespaceURI,
{
if(qName != "bioml")
{
- _errorStr =
- QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::startElement "
"root tag %1 is not <bioml>")
- .arg(qName);
+ .arg(qName);
return false;
}
}
@@ -84,16 +84,18 @@ XtandemParamSaxHandler::startElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::startElement "
- "tag %1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::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 XtandemParamSaxHandler::startElement "
- "tag %1, std exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::startElement "
+ "tag %1, std exception:\n%2")
.arg(qName)
.arg(exception_std.what());
return false;
@@ -119,16 +121,18 @@ XtandemParamSaxHandler::endElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtandemParamSaxHandler::endElement tag "
- "%1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::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 XtandemParamSaxHandler::endElement tag "
- "%1, std exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemParamSaxHandler::endElement tag "
+ "%1, std exception:\n%2")
.arg(qName)
.arg(exception_std.what());
return false;
@@ -144,8 +148,9 @@ XtandemParamSaxHandler::endElement(const QString &namespaceURI,
bool
XtandemParamSaxHandler::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());
@@ -157,8 +162,9 @@ XtandemParamSaxHandler::error(const QXmlParseException &exception)
bool
XtandemParamSaxHandler::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/xtandemparamsaxhandler.h b/src/input/xtandemparamsaxhandler.h
index 398f516ca..f475174c9 100644
--- a/src/input/xtandemparamsaxhandler.h
+++ b/src/input/xtandemparamsaxhandler.h
@@ -41,10 +41,13 @@ class XtandemParamSaxHandler : public QXmlDefaultHandler
XtandemParamSaxHandler(TandemParameters *p_tandem_parameters);
~XtandemParamSaxHandler();
- 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/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 57b17071e..30df3c4a8 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -40,7 +40,8 @@
XtandemSaxHandler::XtandemSaxHandler(
- Project *p_project, IdentificationGroup *p_identification_group,
+ Project *p_project,
+ IdentificationGroup *p_identification_group,
IdentificationDataSource *p_identification_data_source)
: _p_project(p_project)
{
@@ -57,7 +58,8 @@ XtandemSaxHandler::~XtandemSaxHandler()
bool
XtandemSaxHandler::startElement(const QString &namespaceURI,
- const QString &localName, const QString &qName,
+ const QString &localName,
+ const QString &qName,
const QXmlAttributes &attributes)
{
// qDebug() << namespaceURI << " " << localName << " " << qName ;
@@ -96,8 +98,9 @@ XtandemSaxHandler::startElement(const QString &namespaceURI,
}
catch(pappso::PappsoException &exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtandemSaxHandler::startElement tag "
- "%1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemSaxHandler::startElement tag "
+ "%1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -116,7 +119,8 @@ XtandemSaxHandler::startElement(const QString &namespaceURI,
bool
XtandemSaxHandler::endElement(const QString &namespaceURI,
- const QString &localName, const QString &qName)
+ const QString &localName,
+ const QString &qName)
{
bool is_ok = true;
@@ -138,8 +142,9 @@ XtandemSaxHandler::endElement(const QString &namespaceURI,
}
catch(pappso::PappsoException &exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtandemSaxHandler::endElement tag %1, "
- "PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemSaxHandler::endElement tag %1, "
+ "PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -219,9 +224,10 @@ XtandemSaxHandler::startElement_file(QXmlAttributes attributes)
// attrs.getValue("URL")));
if(_p_protein_match == nullptr)
{
- throw pappso::PappsoException("ERROR in "
- "XtandemSaxHandler::startElement_file "
- ": _p_protein_match == nullptr");
+ throw pappso::PappsoException(
+ "ERROR in "
+ "XtandemSaxHandler::startElement_file "
+ ": _p_protein_match == nullptr");
}
_p_protein_match->getProteinXtpSp().get()->setFastaFileP(
_p_project->getFastaFileStore()
@@ -251,9 +257,10 @@ XtandemSaxHandler::startElement_domain(QXmlAttributes attributes)
//""));
if(_p_protein_match == nullptr)
{
- throw pappso::PappsoException("ERROR in "
- "XtandemSaxHandler::startElement_"
- "domain : _p_protein_match == nullptr");
+ throw pappso::PappsoException(
+ "ERROR in "
+ "XtandemSaxHandler::startElement_"
+ "domain : _p_protein_match == nullptr");
}
_p_protein_match->getProteinXtpSp().get()->setSequence(_current_text);
@@ -415,9 +422,10 @@ XtandemSaxHandler::endElement_domain()
.getInstance(_p_peptide_evidence));
if(_p_protein_match == nullptr)
{
- throw pappso::PappsoException("ERROR in "
- "XtandemSaxHandler::endElement_domain : "
- "_p_protein_match == nullptr");
+ throw pappso::PappsoException(
+ "ERROR in "
+ "XtandemSaxHandler::endElement_domain : "
+ "_p_protein_match == nullptr");
}
_p_protein_match->addPeptideMatch(_current_peptide_match);
@@ -713,8 +721,9 @@ XtandemSaxHandler::endElement_note()
bool
XtandemSaxHandler::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());
@@ -726,8 +735,9 @@ XtandemSaxHandler::error(const QXmlParseException &exception)
bool
XtandemSaxHandler::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/xtandemsaxhandler.h b/src/input/xtandemsaxhandler.h
index aa5bef914..75502f33f 100644
--- a/src/input/xtandemsaxhandler.h
+++ b/src/input/xtandemsaxhandler.h
@@ -49,10 +49,13 @@ class XtandemSaxHandler : public QXmlDefaultHandler
IdentificationDataSource *p_identification_data_source);
~XtandemSaxHandler();
- 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 d577fd393..7c006d9f1 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -58,7 +58,8 @@ XtpXpipSaxHandler::isXtpXpip() const
}
bool
XtpXpipSaxHandler::startElement(const QString &namespaceURI,
- const QString &localName, const QString &qName,
+ const QString &localName,
+ const QString &qName,
const QXmlAttributes &attributes)
{
qDebug() << "XtpXpipSaxHandler::startElement begin" << namespaceURI << " "
@@ -195,8 +196,9 @@ XtpXpipSaxHandler::startElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtpXpipSaxHandler::startElement tag "
- "%1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtpXpipSaxHandler::startElement tag "
+ "%1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -215,7 +217,8 @@ XtpXpipSaxHandler::startElement(const QString &namespaceURI,
bool
XtpXpipSaxHandler::endElement(const QString &namespaceURI,
- const QString &localName, const QString &qName)
+ const QString &localName,
+ const QString &qName)
{
qDebug() << "XtpXpipSaxHandler::endElement begin" << namespaceURI << " "
@@ -267,8 +270,9 @@ XtpXpipSaxHandler::endElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtpXpipSaxHandler::endElement tag %1, "
- "PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtpXpipSaxHandler::endElement tag %1, "
+ "PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -864,8 +868,9 @@ XtpXpipSaxHandler::endElement_protein_match()
bool
XtpXpipSaxHandler::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());
@@ -877,8 +882,9 @@ XtpXpipSaxHandler::error(const QXmlParseException &exception)
bool
XtpXpipSaxHandler::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/xtpxpipsaxhandler.h b/src/input/xtpxpipsaxhandler.h
index 29f876795..1c595984d 100644
--- a/src/input/xtpxpipsaxhandler.h
+++ b/src/input/xtpxpipsaxhandler.h
@@ -47,10 +47,13 @@ class XtpXpipSaxHandler : public QXmlDefaultHandler
XtpXpipSaxHandler(WorkMonitorInterface *p_monitor, Project *p_project);
~XtpXpipSaxHandler();
- 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/main.cpp b/src/main.cpp
index d3ad894d1..67b076de8 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -39,22 +39,21 @@ main(int argc, char *argv[])
QApplication app(argc, argv);
qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
- qRegisterMetaType<std::vector<pappso::mz>>("std::vector<pappso::mz>");
- qRegisterMetaType<pappso::PrecisionP>("pappso::PrecisionP");
- qRegisterMetaType<std::vector<pappso::XicSp>>("std::vector<pappso::XicSp>");
+ qRegisterMetaType<std::vector<pappso::pappso_double>>(
+ "std::vector<pappso::pappso_double>");
+ qRegisterMetaType<pappso::PrecisionPtr>("pappso::PrecisionPtr");
+ qRegisterMetaType<std::vector<pappso::XicCstSPtr>>(
+ "std::vector<pappso::XicCstSPtr>");
qRegisterMetaType<pappso::PeptideSp>("pappso::PeptideSp");
qRegisterMetaType<pappso::XicExtractMethod>("pappso::XicExtractMethod");
- qRegisterMetaType<pappso::SpectrumSp>("pappso::SpectrumSp");
+ qRegisterMetaType<pappso::MassSpectrumCstSPtr>("pappso::MassSpectrumCstSPtr");
qRegisterMetaType<MsRunSp>("MsRunSp");
qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>(
"std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
qRegisterMetaType<ExportFastaType>("ExportFastaType");
qRegisterMetaType<MasschroqFileParameters>("MasschroqFileParameters");
- qRegisterMetaType<std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>>>(
- "std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>>");
- qRegisterMetaType<pappso::Peak>("pappso::Peak");
- //qRegisterMetaType<pappso::PeakIonIsotopeMatch>("pappso::PeakIonIsotopeMatch");
+ // qRegisterMetaType<pappso::PeakIonIsotopeMatch>("pappso::PeakIonIsotopeMatch");
try
{
diff --git a/src/output/exportfastafile.h b/src/output/exportfastafile.h
index ef99fe55e..e6c2b4303 100644
--- a/src/output/exportfastafile.h
+++ b/src/output/exportfastafile.h
@@ -39,7 +39,8 @@ class ExportFastaFile
ExportFastaType m_exportType;
private:
- void writeIdentificationGroup(pappso::FastaOutputStream & fasta_output,IdentificationGroup *p_ident);
+ void writeIdentificationGroup(pappso::FastaOutputStream &fasta_output,
+ IdentificationGroup *p_ident);
public:
ExportFastaFile(QString filename, ExportFastaType type);
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index 809cbbf80..c23754a28 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -32,7 +32,7 @@
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/utils.h>
#include <pappsomspp/grouping/grpprotein.h>
-#include <pappsomspp/amino_acid/Aa.h>
+#include <pappsomspp/amino_acid/aa.h>
#include <QStringList>
#include <QSettings>
@@ -305,11 +305,11 @@ MassChroQml::writeQuantificationMethods()
_output_stream->writeComment("For XIC extraction on Da use: mz_range");
- if(m_params.xic_extraction_range->getUnit() == pappso::PrecisionUnit::ppm)
+ if(m_params.xic_extraction_range->unit() == pappso::PrecisionUnit::ppm)
{
_output_stream->writeStartElement("ppm_range");
}
- if(m_params.xic_extraction_range->getUnit() == pappso::PrecisionUnit::dalton)
+ if(m_params.xic_extraction_range->unit() == pappso::PrecisionUnit::dalton)
{
_output_stream->writeStartElement("mz_range");
}
@@ -322,9 +322,9 @@ MassChroQml::writeQuantificationMethods()
.arg(m_params.xic_extraction_range->toString()));
}
_output_stream->writeAttribute(
- "min", QString("%1").arg(m_params.xic_extraction_range->getValue()));
+ "min", QString("%1").arg(m_params.xic_extraction_range->getNominal()));
_output_stream->writeAttribute(
- "max", QString("%1").arg(m_params.xic_extraction_range->getValue()));
+ "max", QString("%1").arg(m_params.xic_extraction_range->getNominal()));
_output_stream->writeEndElement();
//</xic_extraction>
_output_stream->writeEndElement();
diff --git a/src/output/mcqr/mcqrscpeptide.cpp b/src/output/mcqr/mcqrscpeptide.cpp
index 6bbcf76c1..8d9bca9bd 100644
--- a/src/output/mcqr/mcqrscpeptide.cpp
+++ b/src/output/mcqr/mcqrscpeptide.cpp
@@ -35,8 +35,8 @@
bool
ScPeptideLabel::operator<(const ScPeptideLabel &other) const
{
- return tie(_p_grp_peptide, _p_label) <
- tie(other._p_grp_peptide, other._p_label);
+ return std::tie(_p_grp_peptide, _p_label) <
+ std::tie(other._p_grp_peptide, other._p_label);
}
McqRscPeptide::McqRscPeptide(CalcWriterInterface *p_writer,
diff --git a/src/output/mcqr/mcqrscprotein.cpp b/src/output/mcqr/mcqrscprotein.cpp
index b77b4830c..c6c34ce3c 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.h b/src/output/mcqrspectralcount.h
index 9401ade80..d6a401335 100644
--- a/src/output/mcqrspectralcount.h
+++ b/src/output/mcqrspectralcount.h
@@ -46,7 +46,11 @@ class McqrSpectralCount
void writeHeaders(IdentificationGroup *p_ident);
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 ProteinXtp *p_protein, const ProteinMatch *p_protein_match);
+ void writeOneProteinLabel(const pappso::GrpProtein *p_grp_protein,
+ const MsRun *p_msrun,
+ const Label *p_label,
+ const ProteinXtp *p_protein,
+ const ProteinMatch *p_protein_match);
private:
const Project *_p_project;
diff --git a/src/output/ods/comparspecificspectrasheet.h b/src/output/ods/comparspecificspectrasheet.h
index e09db019a..e677f28f9 100644
--- a/src/output/ods/comparspecificspectrasheet.h
+++ b/src/output/ods/comparspecificspectrasheet.h
@@ -61,4 +61,3 @@ class ComparSpecificSequenceSheet : public ComparBaseSheet
};
#endif // COMPARSPECIFICSPECTRASHEET_H
-
diff --git a/src/output/ods/groupingsheet.cpp b/src/output/ods/groupingsheet.cpp
index 372c521ed..524e37dc6 100644
--- a/src/output/ods/groupingsheet.cpp
+++ b/src/output/ods/groupingsheet.cpp
@@ -73,8 +73,10 @@ GroupingSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
//_p_writer->writeCell(p_ident->countSequence(ValidationState::grouped));
_p_writer->writeCell(
p_ident->countPeptideMassSample(ValidationState::grouped));
- _p_writer->writeCellPercentage(p_ident->getProteinFdr(ValidationState::valid));
- _p_writer->writeCellPercentage(p_ident->getPeptideMassFdr(ValidationState::valid));
+ _p_writer->writeCellPercentage(
+ p_ident->getProteinFdr(ValidationState::valid));
+ _p_writer->writeCellPercentage(
+ p_ident->getPeptideMassFdr(ValidationState::valid));
_p_writer->writeCellPercentage(p_ident->getPsmFdr(ValidationState::valid));
}
@@ -103,8 +105,9 @@ GroupingSheet::writeHeaders()
"identification engine");
_p_writer->writeCell("psm");
//_p_writer->writeCell("sequences");
- _p_writer->setCellAnnotation("number of unique combinations : grouped "
- "peptide sequence+modifications+sample name");
+ _p_writer->setCellAnnotation(
+ "number of unique combinations : grouped "
+ "peptide sequence+modifications+sample name");
_p_writer->writeCell("peptide/mass/sample");
_p_writer->setCellAnnotation(
"FDR at the protein level (number of decoy valid proteins / total number "
@@ -115,7 +118,9 @@ GroupingSheet::writeHeaders()
"of valid peptides)");
_p_writer->writeCell("pep FDR");
_p_writer->setCellAnnotation(
- "FDR at the peptide spectrum match (peptide evidences for each association of a spectrum to a peptide, overall identification engines) level (number of decoy valid psm / total number "
+ "FDR at the peptide spectrum match (peptide evidences for each association "
+ "of a spectrum to a peptide, overall identification engines) level (number "
+ "of decoy valid psm / total number "
"of valid psm)");
_p_writer->writeCell("psm FDR");
}
diff --git a/src/output/ods/groupingsheet.h b/src/output/ods/groupingsheet.h
index 9202bc4fd..ec253be64 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 364bacfba..4b6699e6f 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/infosheet.h b/src/output/ods/infosheet.h
index e3ec4d420..c85a4f673 100644
--- a/src/output/ods/infosheet.h
+++ b/src/output/ods/infosheet.h
@@ -39,7 +39,8 @@
class InfoSheet
{
public:
- InfoSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ InfoSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
private:
diff --git a/src/output/ods/peptidepossheet.cpp b/src/output/ods/peptidepossheet.cpp
index 9918513ab..e3e859627 100644
--- a/src/output/ods/peptidepossheet.cpp
+++ b/src/output/ods/peptidepossheet.cpp
@@ -149,7 +149,8 @@ PeptidePosSheet::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();
@@ -174,7 +175,8 @@ PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
continue;
peptide_match_list.push_back(peptide_match);
}
- 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) {
unsigned int arank =
a.getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
diff --git a/src/output/ods/peptidepossheet.h b/src/output/ods/peptidepossheet.h
index a7b32bf8c..d65740fd4 100644
--- a/src/output/ods/peptidepossheet.h
+++ b/src/output/ods/peptidepossheet.h
@@ -41,7 +41,8 @@
class PeptidePosSheet
{
public:
- PeptidePosSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ PeptidePosSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
private:
diff --git a/src/output/ods/peptidesheet.cpp b/src/output/ods/peptidesheet.cpp
index 8e97e737a..c05710d44 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 7db49c459..1f64c4bed 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.cpp b/src/output/ods/proteinsheet.cpp
index 70fc14d52..90a6d82e4 100644
--- a/src/output/ods/proteinsheet.cpp
+++ b/src/output/ods/proteinsheet.cpp
@@ -141,7 +141,8 @@ ProteinSheet::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()->getGroupingId() <
b->getGrpProteinSp().get()->getGroupingId();
diff --git a/src/output/ods/proteinsheet.h b/src/output/ods/proteinsheet.h
index 660256246..a4e7347af 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 87e15abec..e6d9489f0 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 b9e9071fd..dcf46ad29 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 6b589c045..4832ebeeb 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/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index 5fe39259f..a3c78b2a6 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 12677f5f2..ce0181945 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.cpp b/src/output/ods/spectrasheet.cpp
index c260028ca..4fc181276 100644
--- a/src/output/ods/spectrasheet.cpp
+++ b/src/output/ods/spectrasheet.cpp
@@ -34,7 +34,8 @@
SpectraSheet::SpectraSheet(OdsExport *p_ods_export,
CalcWriterInterface *p_writer,
- const Project *p_project, const QString &sheet_name)
+ const Project *p_project,
+ const QString &sheet_name)
: _p_project(p_project)
{
_p_ods_export = p_ods_export;
@@ -175,7 +176,8 @@ SpectraSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
group_pair.second.get()->getPeptideEvidenceList();
std::sort(
- peptide_evidence_list.begin(), peptide_evidence_list.end(),
+ peptide_evidence_list.begin(),
+ peptide_evidence_list.end(),
[](const PeptideEvidence *a, const PeptideEvidence *b) {
unsigned int arank = a->getGrpPeptideSp().get()->getRank();
unsigned int ascan = a->getScan();
@@ -204,8 +206,8 @@ SpectraSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
if(std::tie(arank,
p_best_peptide_evidence->getMsRunP()->getSampleName(),
ascan) !=
- std::tie(brank, peptide_evidence->getMsRunP()->getSampleName(),
- bscan))
+ std::tie(
+ brank, peptide_evidence->getMsRunP()->getSampleName(), bscan))
{
// write p_best_peptide_match
writeBestPeptideEvidence(group_pair.second.get(),
diff --git a/src/output/ods/spectrasheet.h b/src/output/ods/spectrasheet.h
index 5035d45ae..afbecc2c1 100644
--- a/src/output/ods/spectrasheet.h
+++ b/src/output/ods/spectrasheet.h
@@ -40,12 +40,15 @@
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,
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index b6a7faafc..8e08e19f9 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -32,7 +32,7 @@
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/utils.h>
#include <pappsomspp/grouping/grpprotein.h>
-#include <pappsomspp/amino_acid/Aa.h>
+#include <pappsomspp/amino_acid/aa.h>
#include "../core/msrun.h"
#include "../config.h"
#include "../utils/utils.h"
@@ -542,7 +542,8 @@ ProticdbMl::writepeptideHitsbyGroup(GroupingGroup *p_group)
protic_peptide_hit_list.push_back(protic_peptide_hit);
}
}
- std::sort(protic_peptide_hit_list.begin(), protic_peptide_hit_list.end(),
+ std::sort(protic_peptide_hit_list.begin(),
+ protic_peptide_hit_list.end(),
[](const ProticPeptideHit &first, const ProticPeptideHit &second) {
return (first.key < second.key);
});
@@ -615,9 +616,10 @@ ProticdbMl::writePeptideHit(QString xml_id,
protic_peptide_hit.peptide_match.getPeptideEvidence()->getScan()));
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_output_stream->writeAttribute(
- "ms_run_id", protic_peptide_hit.peptide_match.getPeptideEvidence()
- ->getMsRunP()
- ->getXmlId());
+ "ms_run_id",
+ protic_peptide_hit.peptide_match.getPeptideEvidence()
+ ->getMsRunP()
+ ->getXmlId());
_output_stream->writeAttribute("id", xml_id);
_output_stream->writeAttribute(
"exp_z",
@@ -737,7 +739,8 @@ ProticdbMl::writeMatchs(IdentificationGroup *p_identification)
std::vector<const ProteinMatch *> protein_match_list =
group_pair.second.get()->getProteinMatchList();
// sort protein match by subgroup
- 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();
@@ -850,8 +853,9 @@ ProticdbMl::writeMatch(std::vector<const ProteinMatch *> &protein_match_sg_list)
.arg(p_protein_match->getProteinXtpSp().get()->getDescription()));
// proteinHit.setAttribute("score", "");
_output_stream->writeAttribute(
- "rank", QString("%1").arg(
- p_protein_match->getGrpProteinSp().get()->getRank()));
+ "rank",
+ QString("%1").arg(
+ p_protein_match->getGrpProteinSp().get()->getRank()));
// //cvparam
writeCvParam("PROTICdbO:0000284",
@@ -872,7 +876,8 @@ ProticdbMl::writeMatch(std::vector<const ProteinMatch *> &protein_match_sg_list)
// id: PROTICdbO:0000335
// name: X!TandemPipeline PAI
writeCvParam("PROTICdbO:0000335",
- Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
+ Utils::getXmlDouble(p_protein_match->getPAI()),
+ "PAI");
// [Term]
// id: PROTICdbO:0000337
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index ad9205994..2d3290c4b 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -253,8 +253,9 @@ Xpip::writeIdentificationDataSourceList(
ident_source_sp.get()->getResourceName());
_output_stream->writeAttribute(
- "engine", QString("%1").arg(static_cast<std::int8_t>(
- ident_source_sp.get()->getIdentificationEngine())));
+ "engine",
+ QString("%1").arg(static_cast<std::int8_t>(
+ ident_source_sp.get()->getIdentificationEngine())));
_output_stream->writeAttribute(
"version", ident_source_sp.get()->getIdentificationEngineVersion());
@@ -317,9 +318,9 @@ Xpip::writeMsrunList(const MsRunStore &msrun_store)
_output_stream->writeStartElement("msrun");
_output_stream->writeAttribute("id", msrun_sp.get()->getXmlId());
_output_stream->writeAttribute("name", msrun_sp.get()->getSampleName());
- _output_stream->writeAttribute(
- "format", QString("%1").arg(
- static_cast<std::int8_t>(msrun_sp.get()->getMzFormat())));
+ _output_stream->writeAttribute("format",
+ QString("%1").arg(static_cast<std::int8_t>(
+ msrun_sp.get()->getMzFormat())));
QFileInfo mz_info(msrun_sp.get()->getFilename());
if(mz_info.exists())
{
@@ -578,7 +579,7 @@ Xpip::writePeptideEvidence(const PeptideEvidence *p_peptide_evidence)
"peptide_id",
_map_peptides.at(p_peptide_evidence->getPeptideXtpSp().get()));
}
- catch(out_of_range exception_std)
+ catch(std::out_of_range exception_std)
{
throw pappso::PappsoException(
QObject::tr("ERROR in Xpip::writePeptideEvidence peptide %1 not found "
@@ -591,8 +592,9 @@ Xpip::writePeptideEvidence(const PeptideEvidence *p_peptide_evidence)
"scan", QString("%1").arg(p_peptide_evidence->getScan()));
writeDoubleAttribute("rt", p_peptide_evidence->getRetentionTime());
_output_stream->writeAttribute(
- "eng", QString("%1").arg(
- (unsigned int)p_peptide_evidence->getIdentificationEngine()));
+ "eng",
+ QString("%1").arg(
+ (unsigned int)p_peptide_evidence->getIdentificationEngine()));
writeDoubleAttribute("evalue", p_peptide_evidence->getEvalue());
writeDoubleAttribute("exp_mass", p_peptide_evidence->getExperimentalMass());
_output_stream->writeAttribute(
diff --git a/src/utils/httpversion.h b/src/utils/httpversion.h
index d37da9e44..5680dc65d 100644
--- a/src/utils/httpversion.h
+++ b/src/utils/httpversion.h
@@ -40,8 +40,8 @@ class HttpVersion : public QObject
QNetworkAccessManager *mpa_manager;
QNetworkRequest m_request;
QString m_onlineVersion;
-
-public:
+
+ public:
signals:
void httpVersionReady();
diff --git a/src/utils/msrunstatisticshandler.cpp b/src/utils/msrunstatisticshandler.cpp
index cd1c3d0d8..23120773b 100644
--- a/src/utils/msrunstatisticshandler.cpp
+++ b/src/utils/msrunstatisticshandler.cpp
@@ -37,8 +37,8 @@ MsRunStatisticsHandler::needPeakList() const
return true;
}
void
-MsRunStatisticsHandler::setQualifiedSpectrum(
- const pappso::QualifiedSpectrum &qspectrum)
+MsRunStatisticsHandler::setQualifiedMassSpectrum(
+ const pappso::QualifiedMassSpectrum &qspectrum)
{
unsigned int ms_level = qspectrum.getMsLevel();
if(ms_level == 0)
@@ -50,13 +50,13 @@ MsRunStatisticsHandler::setQualifiedSpectrum(
}
_count_ms_level_spectrum[ms_level - 1]++;
- pappso::SpectrumSp spectrum_sp = qspectrum.getOriginalSpectrumSp();
+ pappso::MassSpectrumCstSPtr spectrum_sp = qspectrum.getMassSpectrumCstSPtr();
if(spectrum_sp != nullptr)
{
for(auto &&peak : *(spectrum_sp.get()))
{
- _tic_ms_level_spectrum[ms_level - 1] += peak.intensity;
+ _tic_ms_level_spectrum[ms_level - 1] += peak.y;
}
}
}
diff --git a/src/utils/msrunstatisticshandler.h b/src/utils/msrunstatisticshandler.h
index c0a645ef6..974545ecb 100644
--- a/src/utils/msrunstatisticshandler.h
+++ b/src/utils/msrunstatisticshandler.h
@@ -34,8 +34,8 @@
class MsRunStatisticsHandler : public pappso::SpectrumCollectionHandlerInterface
{
public:
- virtual void
- setQualifiedSpectrum(const pappso::QualifiedSpectrum &qspectrum) override;
+ virtual void setQualifiedMassSpectrum(
+ const pappso::QualifiedMassSpectrum &qspectrum) override;
virtual bool needPeakList() const override;
unsigned long getMsLevelCount(unsigned int ms_level) const;
diff --git a/src/utils/msrunstore.cpp b/src/utils/msrunstore.cpp
index f867fb0b9..d5312dc88 100644
--- a/src/utils/msrunstore.cpp
+++ b/src/utils/msrunstore.cpp
@@ -46,8 +46,9 @@ MsRunSp
MsRunStore::getInstance(const MsRun *p_msrun)
{
auto it = std::find_if(
- _map_msrun.begin(), _map_msrun.end(),
- [p_msrun](const MsRunSp &msrun_sp) { return msrun_sp.get() == p_msrun; });
+ _map_msrun.begin(), _map_msrun.end(), [p_msrun](const MsRunSp &msrun_sp) {
+ return msrun_sp.get() == p_msrun;
+ });
if(it != _map_msrun.end())
{
return (*it);
@@ -65,7 +66,8 @@ MsRunStore::getInstance(const QString &location)
if(file_ondisk.baseName() == location)
{
// look only for the same sample name
- it = std::find_if(_map_msrun.begin(), _map_msrun.end(),
+ it = std::find_if(_map_msrun.begin(),
+ _map_msrun.end(),
[location](const MsRunSp &msrun_sp) {
return msrun_sp.get()->getSampleName() == location;
});
@@ -73,7 +75,8 @@ MsRunStore::getInstance(const QString &location)
else
{
// look for an absolute file path
- it = std::find_if(_map_msrun.begin(), _map_msrun.end(),
+ it = std::find_if(_map_msrun.begin(),
+ _map_msrun.end(),
[location](const MsRunSp &msrun_sp) {
if(msrun_sp.get()->getSampleName() ==
msrun_sp.get()->getFilename())
diff --git a/src/utils/peptideevidencestore.cpp b/src/utils/peptideevidencestore.cpp
index a99100907..ea5318fa3 100644
--- a/src/utils/peptideevidencestore.cpp
+++ b/src/utils/peptideevidencestore.cpp
@@ -129,7 +129,9 @@ PeptideEvidenceStore::getPeptideEvidenceList() const
void
PeptideEvidenceStore::getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
+ unsigned int charge) const
{
for(const PeptideEvidenceSp &peptide_evidence_sp : _peptide_evidence_list)
{
diff --git a/src/utils/peptideevidencestore.h b/src/utils/peptideevidencestore.h
index 515cc6605..ed356fc64 100644
--- a/src/utils/peptideevidencestore.h
+++ b/src/utils/peptideevidencestore.h
@@ -70,7 +70,8 @@ class PeptideEvidenceStore
*/
void getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide,
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
unsigned int charge) const;
private:
diff --git a/src/utils/peptidestore.cpp b/src/utils/peptidestore.cpp
index f22a1e6c6..6001f0025 100644
--- a/src/utils/peptidestore.cpp
+++ b/src/utils/peptidestore.cpp
@@ -29,7 +29,7 @@
******************************************************************************/
#include "peptidestore.h"
-#include <pappsomspp/amino_acid/Aa.h>
+#include <pappsomspp/amino_acid/aa.h>
#include <pappsomspp/pappsoexception.h>
PeptideStore::PeptideStore()
diff --git a/src/utils/types.h b/src/utils/types.h
index 6615853b2..7e0417f75 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -185,8 +185,8 @@ enum class ExportFastaType : std::int8_t
*/
enum class TableFileFormat : std::int8_t
{
- ods = 1, ///< Open Document Spreadsheet
- tsv = 2, ///< tabulated separated values
+ ods = 1, ///< Open Document Spreadsheet
+ tsv = 2, ///< tabulated separated values
};
diff --git a/src/utils/utils.cpp b/src/utils/utils.cpp
index 25e82c8b3..db8dfd052 100644
--- a/src/utils/utils.cpp
+++ b/src/utils/utils.cpp
@@ -1,6 +1,6 @@
#include "utils.h"
#include <pappsomspp/exception/exceptionnotfound.h>
-#include <pappsomspp/mass_range.h>
+#include <pappsomspp/mzrange.h>
#include <cmath>
#include <QProcess>
#include <QDebug>
@@ -129,70 +129,70 @@ Utils::getHistogram(std::vector<pappso::pappso_double> data_values,
pappso::AaModificationP
-Utils::guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass)
+Utils::guessAaModificationPbyMonoisotopicMassDelta(pappso::pappso_double mass)
{
- pappso::PrecisionP precision = pappso::Precision::getDaltonInstance(0.01);
+ pappso::PrecisionPtr precision =
+ pappso::PrecisionFactory::getDaltonInstance(0.01);
pappso::AaModificationP oxidation =
pappso::AaModification::getInstance("MOD:00719");
- if(pappso::MassRange(oxidation->getMass(), precision).contains(mass))
+ if(pappso::MzRange(oxidation->getMass(), precision).contains(mass))
{
return oxidation;
}
pappso::AaModificationP iodoacetamide =
pappso::AaModification::getInstance("MOD:00397");
- if(pappso::MassRange(iodoacetamide->getMass(), precision).contains(mass))
+ if(pappso::MzRange(iodoacetamide->getMass(), precision).contains(mass))
{
return iodoacetamide;
}
pappso::AaModificationP acetylated =
pappso::AaModification::getInstance("MOD:00408");
- if(pappso::MassRange(acetylated->getMass(), precision).contains(mass))
+ if(pappso::MzRange(acetylated->getMass(), precision).contains(mass))
{
return acetylated;
}
pappso::AaModificationP phosphorylated =
pappso::AaModification::getInstance("MOD:00696");
- if(pappso::MassRange(phosphorylated->getMass(), precision).contains(mass))
+ if(pappso::MzRange(phosphorylated->getMass(), precision).contains(mass))
{
return phosphorylated;
}
pappso::AaModificationP ammonia =
pappso::AaModification::getInstance("MOD:01160");
- if(pappso::MassRange(ammonia->getMass(), precision).contains(mass))
+ if(pappso::MzRange(ammonia->getMass(), precision).contains(mass))
{
return ammonia;
}
pappso::AaModificationP dehydrated =
pappso::AaModification::getInstance("MOD:00704");
- if(pappso::MassRange(dehydrated->getMass(), precision).contains(mass))
+ if(pappso::MzRange(dehydrated->getMass(), precision).contains(mass))
{
return dehydrated;
}
pappso::AaModificationP dimethylated =
pappso::AaModification::getInstance("MOD:00429");
- if(pappso::MassRange(dimethylated->getMass(), precision).contains(mass))
+ if(pappso::MzRange(dimethylated->getMass(), precision).contains(mass))
{
return dimethylated;
}
pappso::AaModificationP dimethylated_medium =
pappso::AaModification::getInstance("MOD:00552");
- if(pappso::MassRange(dimethylated_medium->getMass(), precision)
- .contains(mass))
+ if(pappso::MzRange(dimethylated_medium->getMass(), precision).contains(mass))
{
return dimethylated_medium;
}
pappso::AaModificationP dimethylated_heavy =
pappso::AaModification::getInstance("MOD:00638");
- if(pappso::MassRange(dimethylated_heavy->getMass(), precision).contains(mass))
+ if(pappso::MzRange(dimethylated_heavy->getMass(), precision).contains(mass))
{
return dimethylated_heavy;
}
pappso::AaModificationP DimethylpyrroleAdduct =
pappso::AaModification::getInstance("MOD:00628");
- if(pappso::MassRange(DimethylpyrroleAdduct->getMass(), precision)
+ if(pappso::MzRange(DimethylpyrroleAdduct->getMass(), precision)
.contains(mass))
{
return DimethylpyrroleAdduct;
diff --git a/src/utils/utils.h b/src/utils/utils.h
index 52ecc77f5..847d54049 100644
--- a/src/utils/utils.h
+++ b/src/utils/utils.h
@@ -38,7 +38,7 @@ class Utils
static const QString getXmlDouble(pappso::pappso_double number);
static const QString checkXtandemVersion(const QString &tandem_bin_path);
static pappso::AaModificationP
- guessAaModificationPbyMonoisotopicMassDelta(pappso::mz mass);
+ guessAaModificationPbyMonoisotopicMassDelta(pappso::pappso_double mass);
static pappso::AaModificationP
translateAaModificationFromUnimod(const QString &unimod_accession);
static std::vector<std::pair<pappso::pappso_double, size_t>>
--
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