From 9225e6b9d29cbe6081e75b06de685738ab56bb4d Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sun, 9 Jun 2019 20:25:17 +0200
Subject: [PATCH] WIP: using msrunretention object
---
src/core/msrun.cpp | 44 +++++++++++++++----
src/core/msrun.h | 6 ++-
.../exportmasschroqdialog.cpp | 21 +++++++--
3 files changed, 58 insertions(+), 13 deletions(-)
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 124e89dcc..6c3cb0fe0 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -309,18 +309,46 @@ MsRun::getMsRunXicExtractorInterfaceSp()
}
void
-MsRun::initializeMsRunRetentionTime(
+MsRun::buildMsRunRetentionTime(
const PeptideEvidenceStore &peptide_evidence_store)
{
pappso::MsRunReaderSPtr reader = getMsRunReaderSPtr();
- mpa_msrunRetentionTime =
- new pappso::MsRunRetentionTime<const pappso::Peptide *>(reader);
-
+ if(mpa_msrunRetentionTime == nullptr)
+ {
+ mpa_msrunRetentionTime =
+ new pappso::MsRunRetentionTime<const pappso::Peptide *>(reader);
+ }
for(auto &peptide_evidence : peptide_evidence_store.getPeptideEvidenceList())
{
- mpa_msrunRetentionTime->addPeptideAsSeamark(
- peptide_evidence.get()->getPeptideXtpSp().get()->getNativePeptideP(),
- reader.get()->scanNumber2SpectrumIndex(
- peptide_evidence.get()->getScanNumber()));
+ if(peptide_evidence.get()->getMsRunP() == this)
+ {
+ mpa_msrunRetentionTime->addPeptideAsSeamark(
+ peptide_evidence.get()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNativePeptideP(),
+ reader.get()->scanNumber2SpectrumIndex(
+ peptide_evidence.get()->getScanNumber()));
+ }
+ }
+ // mpa_msrunRetentionTime->computePeptideRetentionTimes();
+}
+
+void
+MsRun::computeMsRunRetentionTime()
+{
+ if(mpa_msrunRetentionTime == nullptr)
+ {
+ mpa_msrunRetentionTime->computePeptideRetentionTimes();
+ }
+}
+
+void
+MsRun::clearMsRunRetentionTime()
+{
+ if(mpa_msrunRetentionTime == nullptr)
+ {
+ delete mpa_msrunRetentionTime;
+ mpa_msrunRetentionTime = nullptr;
}
}
diff --git a/src/core/msrun.h b/src/core/msrun.h
index 4038311ee..2d1e1ed26 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -81,8 +81,10 @@ class MsRun : public pappso::MsRunId
pappso::MsRunXicExtractorInterfaceSp getMsRunXicExtractorInterfaceSp();
- void initializeMsRunRetentionTime(
- const PeptideEvidenceStore &peptide_evidence_store);
+ void
+ buildMsRunRetentionTime(const PeptideEvidenceStore &peptide_evidence_store);
+ void computeMsRunRetentionTime();
+ void clearMsRunRetentionTime();
private:
std::map<MsRunStatistics, QVariant> _param_stats;
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index 4e2643b0f..6d615df0b 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -277,22 +277,22 @@ ExportMasschroqDialog::doFindBestMsrunForAlignment()
// p_identification_group =
// mp_project->getIdentificationGroupList()[0]->get
}
- std::vector<MsRunSp> msrun_list;
+ bool is_ok = true;
for(IdentificationDataSourceSp p_ident_data_source :
mp_project->getIdentificationDataSourceStore()
.getIdentificationDataSourceList())
{
MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
- msrun_list.push_back(msrun_sp);
if(msrun_sp->findMsRunFile())
{
// msrun_sp->checkMsRunStatistics();
- msrun_sp->initializeMsRunRetentionTime(
+ msrun_sp->buildMsRunRetentionTime(
p_ident_data_source->getPeptideEvidenceStore());
}
else
{
+ is_ok = false;
ui->warningDirectoryLabel->setText(
tr("%1 not found : Please choose the directory to look for this MS "
"run file.")
@@ -301,4 +301,19 @@ ExportMasschroqDialog::doFindBestMsrunForAlignment()
break;
}
}
+ if(is_ok)
+ {
+ for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
+ {
+ msrun_sp->computeMsRunRetentionTime();
+ }
+ //find the best reference
+ }
+ else
+ {
+ for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
+ {
+ msrun_sp->clearMsRunRetentionTime();
+ }
+ }
}
--
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