From 6d2a9bb6d48a7d6d062dd884b8bbae707f0f5952 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 13 Jun 2019 13:44:48 +0200
Subject: [PATCH] first msrun reference finder
---
src/core/msrun.cpp | 6 ++-
src/core/project.cpp | 15 ++++---
.../export_masschroq_dialog.ui | 34 +++++++++++++---
.../exportmasschroqdialog.cpp | 40 +++++++++++++++++++
4 files changed, 83 insertions(+), 12 deletions(-)
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 1585259c3..b4cec6b36 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -340,8 +340,10 @@ MsRun::buildMsRunRetentionTime(
void
MsRun::computeMsRunRetentionTime()
{
- if(mpa_msrunRetentionTime == nullptr)
+ if(mpa_msrunRetentionTime != nullptr)
{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << " msrun id=" << getXmlId();
mpa_msrunRetentionTime->computePeptideRetentionTimes();
}
}
@@ -349,7 +351,7 @@ MsRun::computeMsRunRetentionTime()
void
MsRun::clearMsRunRetentionTime()
{
- if(mpa_msrunRetentionTime == nullptr)
+ if(mpa_msrunRetentionTime != nullptr)
{
delete mpa_msrunRetentionTime;
mpa_msrunRetentionTime = nullptr;
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 3f6a073ba..661aa6b9c 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -300,6 +300,7 @@ Project::prepareMsrunRetentionTimesForAlignment() const
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
bool is_ok = true;
+ PeptideEvidenceStore empty_store;
for(IdentificationDataSourceSp p_ident_data_source :
this->getIdentificationDataSourceStore()
.getIdentificationDataSourceList())
@@ -313,11 +314,15 @@ Project::prepareMsrunRetentionTimesForAlignment() const
MsRun *p_msrun = peptide_evidence.get()->getMsRunPtr();
if(p_msrun->getMsRunRetentionTimePtr() == nullptr)
{
- throw pappso::PappsoException(
- QObject::tr(
- "Error preparing msrun retention time for %1 :\n "
- "p_msrun->getMsRunRetentionTimePtr() == nullptr")
- .arg(p_msrun->getXmlId()));
+
+ p_msrun->buildMsRunRetentionTime(empty_store);
+ /*
+ throw pappso::PappsoException(
+ QObject::tr(
+ "Error preparing msrun retention time
+ for %1 :\n " "p_msrun->getMsRunRetentionTimePtr() ==
+ nullptr") .arg(p_msrun->getXmlId()));
+ */
}
p_msrun->getMsRunRetentionTimePtr()->addPeptideAsSeamark(
peptide_evidence.get()
diff --git a/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui b/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
index b128ffc4c..7d61d638e 100644
--- a/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
+++ b/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
@@ -17,7 +17,7 @@
<item>
<widget class="QTabWidget" name="tabWidget">
<property name="currentIndex">
- <number>0</number>
+ <number>1</number>
</property>
<widget class="QWidget" name="resultTab">
<attribute name="title">
@@ -175,6 +175,13 @@
</layout>
</widget>
</item>
+ <item>
+ <widget class="QPushButton" name="pushButton">
+ <property name="text">
+ <string>Find best MS run reference for alignment</string>
+ </property>
+ </widget>
+ </item>
<item>
<spacer name="verticalSpacer_2">
<property name="orientation">
@@ -439,8 +446,8 @@
<slot>doCheckMsrunFilepath()</slot>
<hints>
<hint type="sourcelabel">
- <x>530</x>
- <y>58</y>
+ <x>101</x>
+ <y>49</y>
</hint>
<hint type="destinationlabel">
<x>779</x>
@@ -455,8 +462,8 @@
<slot>doBrowseMsrunDirectory()</slot>
<hints>
<hint type="sourcelabel">
- <x>557</x>
- <y>137</y>
+ <x>119</x>
+ <y>84</y>
</hint>
<hint type="destinationlabel">
<x>787</x>
@@ -464,11 +471,28 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>pushButton</sender>
+ <signal>clicked()</signal>
+ <receiver>ExportMasschroqDialog</receiver>
+ <slot>doFindBestMsrunForAlignment()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>399</x>
+ <y>296</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>887</x>
+ <y>309</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>reject()</slot>
<slot>accept()</slot>
<slot>doCheckMsrunFilepath()</slot>
<slot>doBrowseMsrunDirectory()</slot>
+ <slot>doFindBestMsrunForAlignment()</slot>
</slots>
</ui>
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index dd20c7972..beab656e4 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -289,6 +289,46 @@ ExportMasschroqDialog::doFindBestMsrunForAlignment()
try
{
mp_project->prepareMsrunRetentionTimesForAlignment();
+
+ MsRunSp ms_run_best_reference;
+ std::size_t best_number = 0;
+ for(auto &msrun_ref_sp : mp_project->getMsRunStore().getMsRunList())
+ {
+ if(ms_run_best_reference == nullptr)
+ {
+ ms_run_best_reference = msrun_ref_sp;
+ }
+
+ std::size_t min_number = std::numeric_limits<std::size_t>::max();
+ for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
+ {
+ if(msrun_sp.get() != msrun_ref_sp.get())
+ {
+ pappso::Trace trace;
+ trace = msrun_sp.get()
+ ->getMsRunRetentionTimePtr()
+ ->getCommonDeltaRt(msrun_ref_sp.get()
+ ->getMsRunRetentionTimePtr()
+ ->getSeamarks());
+ if(trace.size() < min_number)
+ {
+ min_number = trace.size();
+ }
+ }
+ }
+
+ if(min_number > best_number)
+ {
+ best_number = min_number;
+
+ ms_run_best_reference = msrun_ref_sp;
+ }
+ }
+ if(ms_run_best_reference != nullptr)
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << ms_run_best_reference.get()->getXmlId()<< " best_number=" << best_number;
+ }
}
catch(pappso::PappsoException &error)
{
--
GitLab