From 8be1c1d8666b11d7814973a4f7ed5456da505719 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 8 May 2019 09:28:00 +0200
Subject: [PATCH] WIP: replacing scan number by index
---
src/core/peptideevidence.cpp | 20 ++++++++++++--------
src/core/peptideevidence.h | 7 ++++---
src/output/ods/ptm/ptmspectrasheet.cpp | 2 +-
src/output/ods/spectrasheet.cpp | 2 +-
win64/home.cmake | 10 +++++-----
5 files changed, 23 insertions(+), 18 deletions(-)
diff --git a/src/core/peptideevidence.cpp b/src/core/peptideevidence.cpp
index 1c94405a4..e07eacfa2 100644
--- a/src/core/peptideevidence.cpp
+++ b/src/core/peptideevidence.cpp
@@ -35,18 +35,20 @@
std::hash<std::string> PeptideEvidence::_hash_fn;
-PeptideEvidence::PeptideEvidence(MsRun *msrunid_sp, unsigned int scan)
+PeptideEvidence::PeptideEvidence(MsRun *msrunid_sp, std::size_t scan_index)
{
- _msrunid_sp = msrunid_sp;
- _scan = scan;
+ _msrunid_sp = msrunid_sp;
+ m_scan_index = scan_index;
- _hash_sample_scan = PeptideEvidence::_hash_fn(
- QString("%1 %2").arg(msrunid_sp->getXmlId()).arg(_scan).toStdString());
+ _hash_sample_scan = PeptideEvidence::_hash_fn(QString("%1 %2")
+ .arg(msrunid_sp->getXmlId())
+ .arg(m_scan_index)
+ .toStdString());
_identification_engine = IdentificationEngine::unknown;
}
PeptideEvidence::PeptideEvidence(const PeptideEvidence &other)
- : PeptideEvidence(other._msrunid_sp, other._scan)
+ : PeptideEvidence(other._msrunid_sp, other.m_scan_index)
{
_hash_sample_scan = other._hash_sample_scan;
_sp_grp_peptide = other._sp_grp_peptide;
@@ -60,6 +62,8 @@ PeptideEvidence::PeptideEvidence(const PeptideEvidence &other)
_checked = other._checked;
_proxy_valid = other._proxy_valid;
_identification_engine = other._identification_engine;
+ m_scan_index = other.m_scan_index;
+ m_scan_number = other.m_scan_number;
}
pappso::pappso_double
@@ -291,9 +295,9 @@ PeptideEvidence::getIdentificationDataSource() const
return _p_identification_source;
}
unsigned int
-PeptideEvidence::getScan() const
+PeptideEvidence::getScanNumber() const
{
- return _scan;
+ return m_scan_number;
}
pappso::pappso_double
PeptideEvidence::getRetentionTime() const
diff --git a/src/core/peptideevidence.h b/src/core/peptideevidence.h
index 65e9971a2..1964151c2 100644
--- a/src/core/peptideevidence.h
+++ b/src/core/peptideevidence.h
@@ -49,7 +49,7 @@ typedef std::shared_ptr<PeptideEvidence> PeptideEvidenceSp;
class PeptideEvidence
{
public:
- PeptideEvidence(MsRun *msrunid_sp, unsigned int scan);
+ PeptideEvidence(MsRun *msrunid_sp, std::size_t scan_index);
PeptideEvidence(const PeptideEvidence &other);
std::size_t getHashSampleScan() const;
std::size_t getHashPeptideMassSample() const;
@@ -117,7 +117,7 @@ class PeptideEvidence
const MsRun *getMsRunP() const;
IdentificationDataSource *getIdentificationDataSource() const;
- unsigned int getScan() const;
+ unsigned int getScanNumber() const;
pappso::pappso_double getRetentionTime() const;
unsigned int getCharge() const;
const PeptideXtpSp &getPeptideXtpSp() const;
@@ -154,7 +154,8 @@ class PeptideEvidence
private:
static std::hash<std::string> _hash_fn;
MsRun *_msrunid_sp;
- unsigned int _scan = 0;
+ std::size_t m_scan_index = 0;
+ unsigned int m_scan_number = 0;
size_t _hash_sample_scan;
pappso::GrpPeptideSp _sp_grp_peptide;
PeptideXtpSp _peptide_sp;
diff --git a/src/output/ods/ptm/ptmspectrasheet.cpp b/src/output/ods/ptm/ptmspectrasheet.cpp
index 015382f70..ece27a441 100644
--- a/src/output/ods/ptm/ptmspectrasheet.cpp
+++ b/src/output/ods/ptm/ptmspectrasheet.cpp
@@ -194,7 +194,7 @@ PtmSpectraSheet::writeBestPeptideEvidence(
p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
_p_writer->clearTableCellStyleRef();
_p_writer->writeCell(p_peptide_evidence->getMsRunP()->getSampleName());
- _p_writer->writeCell(p_peptide_evidence->getScan());
+ _p_writer->writeCell(p_peptide_evidence->getScanNumber());
_p_writer->writeCell(p_peptide_evidence->getRetentionTime());
_p_writer->writeCell(p_peptide_evidence->getCharge());
_p_writer->writeCell(p_peptide_evidence->getExperimentalMz());
diff --git a/src/output/ods/spectrasheet.cpp b/src/output/ods/spectrasheet.cpp
index e5ef76946..1e27a34d5 100644
--- a/src/output/ods/spectrasheet.cpp
+++ b/src/output/ods/spectrasheet.cpp
@@ -136,7 +136,7 @@ SpectraSheet::writeBestPeptideEvidence(
p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
_p_writer->clearTableCellStyleRef();
_p_writer->writeCell(p_peptide_evidence->getMsRunP()->getSampleName());
- _p_writer->writeCell(p_peptide_evidence->getScan());
+ _p_writer->writeCell(p_peptide_evidence->getScanNumber());
_p_writer->writeCell(p_peptide_evidence->getRetentionTime());
_p_writer->writeCell(p_peptide_evidence->getExperimentalMz());
_p_writer->writeCell(
diff --git a/win64/home.cmake b/win64/home.cmake
index 5cfb37995..728e28f93 100644
--- a/win64/home.cmake
+++ b/win64/home.cmake
@@ -6,9 +6,9 @@ set(ODSSTREAM_QT5_FOUND 1)
set(ODSSTREAM_INCLUDE_DIR "/home/olivier/eclipse/git/libodsstream/src")
set(ODSSTREAM_QT5_LIBRARY "/home/olivier/eclipse/git/libodsstream/build/src/libodsstream-qt5.so")
-#set(PAPPSOMSPP_QT5_FOUND 1)
-#set(PAPPSOMSPP_WIDGET_QT5_FOUND 1)
-#set(PAPPSOMSPP_INCLUDE_DIR "/home/olivier/eclipse/git/pappsomspp/src")
-#set(PAPPSOMSPP_QT5_LIBRARY "/home/olivier/eclipse/git/pappsomspp/cbuild/src/libpappsomspp-qt5.so")
-#set(PAPPSOMSPP_WIDGET_QT5_LIBRARY "/home/olivier/eclipse/git/pappsomspp/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
+set(PAPPSOMSPP_QT5_FOUND 1)
+set(PAPPSOMSPP_WIDGET_QT5_FOUND 1)
+set(PAPPSOMSPP_INCLUDE_DIR "/home/olivier/eclipse/git/pappsomspp/src")
+set(PAPPSOMSPP_QT5_LIBRARY "/home/olivier/eclipse/git/pappsomspp/cbuild/src/libpappsomspp-qt5.so")
+set(PAPPSOMSPP_WIDGET_QT5_LIBRARY "/home/olivier/eclipse/git/pappsomspp/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
--
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