From 6bc6d58cbf98af080732af1ce73526b8730a167c Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 26 Jan 2018 23:02:17 +0100
Subject: [PATCH] extract XIC in other MsRun
---
src/gui/xic_view/xic_box/xic_box.ui | 21 +++++++++++--
src/gui/xic_view/xic_box/xicbox.cpp | 47 +++++++++++++++++++++++++++--
src/gui/xic_view/xic_box/xicbox.h | 2 ++
src/gui/xic_view/xicwindow.cpp | 5 +++
src/gui/xic_view/xicwindow.h | 1 +
5 files changed, 72 insertions(+), 4 deletions(-)
diff --git a/src/gui/xic_view/xic_box/xic_box.ui b/src/gui/xic_view/xic_box/xic_box.ui
index e438ff7c1..f35f69a28 100644
--- a/src/gui/xic_view/xic_box/xic_box.ui
+++ b/src/gui/xic_view/xic_box/xic_box.ui
@@ -180,8 +180,8 @@
<slot>remove()</slot>
<hints>
<hint type="sourcelabel">
- <x>378</x>
- <y>25</y>
+ <x>592</x>
+ <y>39</y>
</hint>
<hint type="destinationlabel">
<x>585</x>
@@ -189,8 +189,25 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>pushButton_2</sender>
+ <signal>clicked()</signal>
+ <receiver>XicBox</receiver>
+ <slot>extractXicInOtherMsRun()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>414</x>
+ <y>38</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>891</x>
+ <y>69</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>remove()</slot>
+ <slot>extractXicInOtherMsRun()</slot>
</slots>
</ui>
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index 41ff464e3..6abf1eaae 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -29,7 +29,7 @@
#include "xicbox.h"
#include "ui_xic_box.h"
#include <QMessageBox>
-#include <pappsomspp/pappsoexception.h>
+#include <pappsomspp/exception/exceptionnotfound.h>
#include "../xicworkerthread.h"
#include "../../project_view/projectwindow.h"
#include <pappsomspp/xic/detection/xicdetectionzivy.h>
@@ -110,6 +110,19 @@ XicBox::XicBox(XicWindow *parent):
#endif
+ QStringList msrun_list;
+ for (MsRunSp msrun_sp : _p_xic_window->getProjectWindow()->getProjectP()->getMsRunStore().getMsRunList()) {
+ msrun_list << msrun_sp.get()->getFilename();
+ qDebug() << "ProteinListWindow::setIdentificationGroup " << msrun_sp.get()->getFilename();
+ }
+ QCompleter *completer = new QCompleter(msrun_list, this);
+ completer->setCaseSensitivity(Qt::CaseInsensitive);
+
+ completer->setCompletionMode(QCompleter::PopupCompletion);
+ completer->setModelSorting(QCompleter::CaseSensitivelySortedModel);
+ completer->setFilterMode(Qt::MatchContains);
+ ui->msrun_autocompletion->setCompleter(completer);
+
}
XicBox::~XicBox()
@@ -128,10 +141,23 @@ void XicBox::error(QString error_message) {
tr("Error trying to save spectrum to SVG file :"), error_message);
}
+
+void XicBox::extractXicInOtherMsRun() {
+ qDebug() << "XicBox::extractXicInOtherMsRun begin";
+ try {
+ MsRunSp msrun_sp = _p_xic_window->getProjectWindow()->getProjectP()->getMsRunStore().getInstance(ui->msrun_autocompletion->text());
+ _p_xic_window->addXicInMsRun(_p_peptide_evidence, msrun_sp);
+ }
+ catch (pappso::ExceptionNotFound & error) {
+ qDebug() << "XicBox::extractXicInOtherMsRun not found " << ui->msrun_autocompletion->text();
+ }
+}
+
void XicBox::setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
+
_p_peptide_evidence = p_peptide_evidence;
- _msrun_sp = _p_xic_window->getProjectWindow()->getProjectP()->getMsRunStore().getInstance(_p_peptide_evidence->getMsRunP());
+ _msrun_sp = p_peptide_evidence->getIdentificationDataSource()->getMsRunSp();
ui->peptide_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->toString());
ui->msrun_label->setText(_p_peptide_evidence->getMsRunP()->getFilename());
@@ -147,6 +173,23 @@ void XicBox::setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
}
+void XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp) {
+ _p_peptide_evidence = p_peptide_evidence;
+ _msrun_sp = msrun_sp;
+
+ ui->peptide_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->toString());
+ ui->msrun_label->setText(msrun_sp->getFilename());
+ ui->charge_label->setText(QString("%1").arg(_p_peptide_evidence->getCharge()));
+ ui->mz_label->setText(QString::number(_p_peptide_evidence->getTheoreticalMz(), 'f', 4));
+
+ //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 computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(), _p_peptide_evidence->getCharge(), _p_xic_window->getXicExtractPrecision(), 0.8);
+
+}
void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
qDebug() << "XicBox::setXic begin " << xic_sp_list.size();
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index 33ae45e20..c06e56d53 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/src/gui/xic_view/xic_box/xicbox.h
@@ -51,6 +51,7 @@ public:
explicit XicBox(XicWindow * parent = 0);
~XicBox();
void setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) ;
+ void setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp);
signals :
void loadXic(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, XicExtractMethod method);
@@ -61,6 +62,7 @@ private slots:
void setXic(std::vector< pappso::XicSp> xic_sp_list);
void setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
void error(QString error_message);
+ void extractXicInOtherMsRun();
private:
Ui::XicBox *ui;
QThread _xic_thread;
diff --git a/src/gui/xic_view/xicwindow.cpp b/src/gui/xic_view/xicwindow.cpp
index 703195a7e..f4fbaf6a5 100644
--- a/src/gui/xic_view/xicwindow.cpp
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -78,6 +78,11 @@ void XicWindow::addXic(const PeptideEvidence * p_peptide_evidence) {
ui->xic_vertical_layout->layout()->addWidget(p_box);
}
+void XicWindow::addXicInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp) {
+ XicBox * p_box = new XicBox(this);
+ p_box->setPeptideEvidenceInMsRun(p_peptide_evidence, msrun_sp);
+ ui->xic_vertical_layout->layout()->addWidget(p_box);
+}
void XicWindow::removeXicBox(XicBox * xic_box) {
xic_box->setVisible(false);
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
index e04745b6b..30bef1125 100644
--- a/src/gui/xic_view/xicwindow.h
+++ b/src/gui/xic_view/xicwindow.h
@@ -52,6 +52,7 @@ public:
~XicWindow();
void addXic(const PeptideEvidence * p_peptide_evidence);
+ void addXicInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp);
pappso::PrecisionP getXicExtractPrecision() const;
--
GitLab