From 1b4de1825504c1e8cc9b9ba1c7e2538fe1f5a2a4 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 12 Jan 2018 22:45:51 +0100
Subject: [PATCH] draw xic with all MSMS events
---
src/CMakeLists.txt | 4 ++--
src/core/identificationgroup.cpp | 9 +++++++++
src/core/identificationgroup.h | 8 ++++++++
src/core/project.cpp | 6 ++++++
src/core/project.h | 18 ++++++++++++------
src/gui/xic_view/xic_box/xic_box.ui | 15 ++++++++++++++-
src/gui/xic_view/xic_box/xicbox.cpp | 12 +++++++++++-
src/gui/xic_view/xic_box/xicbox.h | 1 +
src/gui/xic_view/xic_window.ui | 17 ++++++++++++++++-
src/gui/xic_view/xicwindow.cpp | 6 ++++--
src/gui/xic_view/xicwindow.h | 2 +-
src/utils/peptideevidencestore.cpp | 10 ++++++++++
src/utils/peptideevidencestore.h | 9 +++++++++
src/utils/readspectrum.cpp | 1 +
14 files changed, 104 insertions(+), 14 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 159b03b3f..71bd578d3 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -28,8 +28,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
#FIND_PACKAGE( Pappsomspp REQUIRED )
-# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
- SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
SET (PAPPSOMSPP_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt5.so")
SET (PAPPSOMSPP_WIDGET_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index dd7ec45b7..267c9e895 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -320,3 +320,12 @@ pappso::pappso_double IdentificationGroup::getProteinFdr(ValidationState state)
return (false_prot/total_prot);
}
+
+void IdentificationGroup::getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const {
+ if (!contains(p_peptide_evidence->getMsRunP())) return;
+ for (const IdentificationDataSource * p_identification_source:_id_source_list) {
+ if (p_peptide_evidence->getMsRunP() == p_identification_source->getMsRunSp().get()) {
+ p_identification_source->getPeptideEvidenceStore().getSameXicPeptideEvidenceList(p_peptide_evidence, peptide_evidence_list);
+ }
+ }
+}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 0469f961e..ea4ade657 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -132,6 +132,14 @@ public:
* each peptide evidence is only counted once
*/
void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
+
+
+ /** @brief look for a peptide in the same XIC
+ * @param p_peptide_evidence the peptide to look for
+ * @param peptide_evidence_list the peptide evidence list to build
+ */
+ void getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const;
+
private :
void addMsRunSp(MsRunSp ms_run_sp);
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 937fec4e5..1bd84997c 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -200,3 +200,9 @@ bool Project::hasPtmExperiment() const {
if (getIdentificationGroupList().at(0)->getPtmGroupingExperiment() != nullptr) return true;
return false;
}
+
+void Project::getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const {
+ for (const IdentificationGroup * p_ident_group: _identification_goup_list) {
+ p_ident_group->getSameXicPeptideEvidenceList(p_peptide_evidence, peptide_evidence_list);
+ }
+}
diff --git a/src/core/project.h b/src/core/project.h
index c4e762931..b21d48385 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -72,21 +72,27 @@ public:
std::vector<IdentificationGroup *> getIdentificationGroupList();
const std::vector<IdentificationGroup *> getIdentificationGroupList() const;
void readResultFile(QString filename);
-
+
/** @brief check that modifications are coded with PSI MOD accessions
*/
bool checkPsimodCompliance() const;
-
+
/** @brief apply labeling method to all peptide match
* */
void setLabelingMethodSp(LabelingMethodSp labeling_method_sp);
-
+
/** @brief get labeling method shared pointer
* */
LabelingMethodSp getLabelingMethodSp() const;
-
+
bool hasPtmExperiment() const;
-
+
+ /** @brief look for a peptide in the same XIC
+ * @param p_peptide_evidence the peptide to look for
+ * @param peptide_evidence_list the peptide evidence list to build
+ */
+ void getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const;
+
private :
LabelingMethodSp _labeling_method_sp;
ProjectMode _project_mode = ProjectMode::combined;
@@ -102,7 +108,7 @@ private :
IdentificationDataSourceStore _identification_data_source_store;
MsRunStore _msrun_store;
FastaFileStore _fasta_file_store;
-
+
};
#endif // PROJECT_H
diff --git a/src/gui/xic_view/xic_box/xic_box.ui b/src/gui/xic_view/xic_box/xic_box.ui
index f6a62be40..b7e5d597b 100644
--- a/src/gui/xic_view/xic_box/xic_box.ui
+++ b/src/gui/xic_view/xic_box/xic_box.ui
@@ -18,6 +18,12 @@
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
<widget class="QLabel" name="peptide_label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
<property name="text">
<string>TextLabel</string>
</property>
@@ -28,7 +34,14 @@
<item>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
- <widget class="pappso::XicWidget" name="xic_widget" native="true"/>
+ <widget class="pappso::XicWidget" name="xic_widget" native="true">
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>150</height>
+ </size>
+ </property>
+ </widget>
</item>
</layout>
</item>
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index 169eef1e8..92bae7c23 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -31,6 +31,7 @@
#include <QMessageBox>
#include <pappsomspp/pappsoexception.h>
#include "../xicworkerthread.h"
+#include "../../project_view/projectwindow.h"
XicBox::XicBox(XicWindow *parent):
QWidget(parent),
@@ -73,6 +74,11 @@ void XicBox::setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
_p_peptide_evidence = p_peptide_evidence;
ui->peptide_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->toString());
+ //get same xic peptide evidence (msrun, peptide, charge)
+ //p_projet
+ _peptide_evidence_list.clear();
+ _p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(p_peptide_evidence, _peptide_evidence_list);
+
emit loadXic(_p_peptide_evidence->getMsRunP(), _p_peptide_evidence->getPeptideXtpSp().get()->getMz(_p_peptide_evidence->getCharge()), _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
}
@@ -81,7 +87,11 @@ void XicBox::setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
void XicBox::setXic(pappso::XicSp xic_sp) {
qDebug() << "XicBox::setXic begin";
ui->xic_widget->setXicSp(xic_sp);
+ for (const PeptideEvidence * peptide_evidence:_peptide_evidence_list) {
+ ui->xic_widget->addMsMsEvent(peptide_evidence->getRetentionTime());
+ }
+ ui->xic_widget->rescale();
ui->xic_widget->plot();
qDebug() << "XicBox::setXic end";
-
+
}
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index 4ad6e9162..b28336fc2 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/src/gui/xic_view/xic_box/xicbox.h
@@ -59,6 +59,7 @@ private:
QThread _xic_thread;
XicWindow * _p_xic_window;
const PeptideEvidence * _p_peptide_evidence;
+ std::vector<const PeptideEvidence *> _peptide_evidence_list;
};
diff --git a/src/gui/xic_view/xic_window.ui b/src/gui/xic_view/xic_window.ui
index fa9b6cb85..87a851d17 100644
--- a/src/gui/xic_view/xic_window.ui
+++ b/src/gui/xic_view/xic_window.ui
@@ -16,7 +16,22 @@
<widget class="QWidget" name="centralwidget">
<layout class="QVBoxLayout" name="verticalLayout_2">
<item>
- <layout class="QVBoxLayout" name="xic_vertical_layout"/>
+ <widget class="QScrollArea" name="scrollArea">
+ <property name="widgetResizable">
+ <bool>true</bool>
+ </property>
+ <widget class="QWidget" name="xic_vertical_layout">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>780</width>
+ <height>530</height>
+ </rect>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout"/>
+ </widget>
+ </widget>
</item>
</layout>
</widget>
diff --git a/src/gui/xic_view/xicwindow.cpp b/src/gui/xic_view/xicwindow.cpp
index 56118dbd4..c7af95449 100644
--- a/src/gui/xic_view/xicwindow.cpp
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -55,11 +55,13 @@ XicWindow::~XicWindow()
{
qDebug() << "XicWindow::~XicWindow";
}
-
+ProjectWindow * XicWindow::getProjectWindow() {
+ return _project_window;
+}
void XicWindow::addXic(const PeptideEvidence * p_peptide_evidence) {
XicBox * p_box = new XicBox(this);
p_box->setPeptideEvidence(p_peptide_evidence);
- ui->xic_vertical_layout->addWidget(p_box);
+ ui->xic_vertical_layout->layout()->addWidget(p_box);
}
pappso::PrecisionP XicWindow::getXicExtractPrecision() const {
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
index b6462314a..d48531dc2 100644
--- a/src/gui/xic_view/xicwindow.h
+++ b/src/gui/xic_view/xicwindow.h
@@ -56,7 +56,7 @@ public:
pappso::PrecisionP getXicExtractPrecision() const;
protected:
-
+ ProjectWindow * getProjectWindow();
private:
ProjectWindow * _project_window;
Ui::XicWindow *ui;
diff --git a/src/utils/peptideevidencestore.cpp b/src/utils/peptideevidencestore.cpp
index e002f542a..28b2928f6 100644
--- a/src/utils/peptideevidencestore.cpp
+++ b/src/utils/peptideevidencestore.cpp
@@ -93,3 +93,13 @@ void PeptideEvidenceStore::updateAutomaticFilters(const AutomaticFilterParameter
const std::vector<std::shared_ptr<PeptideEvidence>> & PeptideEvidenceStore::getPeptideEvidenceList() const {
return _peptide_evidence_list;
}
+
+
+void PeptideEvidenceStore::getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const {
+ for (const PeptideEvidenceSp & peptide_evidence_sp:_peptide_evidence_list) {
+ if (p_peptide_evidence->getMsRunP() != peptide_evidence_sp.get()->getMsRunP()) continue;
+ if (p_peptide_evidence->getPeptideXtpSp().get() != peptide_evidence_sp.get()->getPeptideXtpSp().get()) continue;
+ if (p_peptide_evidence->getCharge() != peptide_evidence_sp.get()->getCharge()) continue;
+ peptide_evidence_list.push_back(peptide_evidence_sp.get());
+ }
+}
diff --git a/src/utils/peptideevidencestore.h b/src/utils/peptideevidencestore.h
index 755ec66ea..c1d4ff894 100644
--- a/src/utils/peptideevidencestore.h
+++ b/src/utils/peptideevidencestore.h
@@ -52,6 +52,15 @@ public:
const std::vector<std::shared_ptr<PeptideEvidence>> & getPeptideEvidenceList() const;
std::size_t size() const;
void clearMap();
+
+
+
+ /** @brief look for a peptide in the same XIC
+ * @param p_peptide_evidence the peptide to look for
+ * @param peptide_evidence_list the peptide evidence list to build
+ */
+ void getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const;
+
private:
std::vector<std::shared_ptr<PeptideEvidence>> _peptide_evidence_list;
diff --git a/src/utils/readspectrum.cpp b/src/utils/readspectrum.cpp
index 50f208feb..051cf3c39 100644
--- a/src/utils/readspectrum.cpp
+++ b/src/utils/readspectrum.cpp
@@ -127,6 +127,7 @@ void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso:
}
+ p_xic->sortByRetentionTime();
--
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