From d4397f216a5e58f17d3977b472b0af28e79d203b Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 11 Jan 2018 23:06:04 +0100
Subject: [PATCH] new window to display XIC
---
src/CMakeLists.txt | 13 ++--
.../identificationdatasource.cpp | 2 +-
.../peptide_detail_view.ui | 51 ++++++++++---
src/gui/peptide_detail_view/peptidewindow.cpp | 22 +++++-
src/gui/peptide_detail_view/peptidewindow.h | 1 +
src/gui/project_view/projectwindow.cpp | 10 +++
src/gui/project_view/projectwindow.h | 3 +
src/gui/xic_view/xic_window.ui | 37 ++++++++++
src/gui/xic_view/xicwindow.cpp | 60 ++++++++++++++++
src/gui/xic_view/xicwindow.h | 69 ++++++++++++++++++
src/output/ods/samplesheet.cpp | 2 +-
src/utils/readspectrum.cpp | 71 +++++++++++--------
src/utils/readspectrum.h | 11 +--
13 files changed, 301 insertions(+), 51 deletions(-)
create mode 100644 src/gui/xic_view/xic_window.ui
create mode 100644 src/gui/xic_view/xicwindow.cpp
create mode 100644 src/gui/xic_view/xicwindow.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 2548c7a41..eab1a55a0 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -27,12 +27,12 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
-FIND_PACKAGE( Pappsomspp REQUIRED )
-# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+#FIND_PACKAGE( Pappsomspp REQUIRED )
+ SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
-# SET (PAPPSOMSPP_INCLUDE_DIR "${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")
+ SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
+ SET (PAPPSOMSPP_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt5.so")
+ SET (PAPPSOMSPP_WIDGET_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")
# SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
IF (PAPPSOMSPP_QT5_FOUND)
ELSE (PAPPSOMSPP_QT5_FOUND)
@@ -158,6 +158,7 @@ SET(XTPCPP_SRCS
./gui/ptm_peptide_list_view/ptmsequencedelegate.cpp
./gui/tandem_run_dialog/tandemrundialog.cpp
./gui/waiting_message_dialog/waitingmessagedialog.cpp
+ ./gui/xic_view/xicwindow.cpp
./gui/workerthread.cpp
./utils/workmonitor.cpp
)
@@ -182,6 +183,7 @@ SET (GUI_UIS
./gui/ptm_peptide_list_view/ptm_peptide_list_view.ui
./gui/tandem_run_dialog/tandem_run_dialog.ui
./gui/waiting_message_dialog/waiting_message_dialog.ui
+ ./gui/xic_view/xic_window.ui
)
SET(XTPCPP_MOC_HDRS
@@ -213,6 +215,7 @@ SET(XTPCPP_MOC_HDRS
./gui/ptm_peptide_list_view/ptmsequencedelegate.h
./gui/tandem_run_dialog/tandemrundialog.h
./gui/waiting_message_dialog/waitingmessagedialog.h
+ ./gui/xic_view/xicwindow.h
./gui/workerthread.h
./utils/workmonitor.h
)
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index 0cf8bcc2c..d368fd091 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -144,7 +144,7 @@ pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_num
if (_ms_run_sp.get()->getMzFormat() == MzFormat::MGF) {
scan_number = scan_number-1;
}
- pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunSp(_ms_run_sp, scan_number);
+ pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunSp(_ms_run_sp.get(), scan_number);
return spectrum_sp;
}
diff --git a/src/gui/peptide_detail_view/peptide_detail_view.ui b/src/gui/peptide_detail_view/peptide_detail_view.ui
index dfa3b2df1..73c43a1b9 100644
--- a/src/gui/peptide_detail_view/peptide_detail_view.ui
+++ b/src/gui/peptide_detail_view/peptide_detail_view.ui
@@ -7,7 +7,7 @@
<x>0</x>
<y>0</y>
<width>826</width>
- <height>430</height>
+ <height>443</height>
</rect>
</property>
<property name="windowTitle">
@@ -114,11 +114,25 @@
</layout>
</item>
<item>
- <widget class="QPushButton" name="pushButton">
- <property name="text">
- <string>Open in peptide viewer</string>
- </property>
- </widget>
+ <layout class="QVBoxLayout" name="verticalLayout_3">
+ <item>
+ <widget class="QPushButton" name="pushButton">
+ <property name="text">
+ <string>Open in peptide viewer</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QPushButton" name="xic_button">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="text">
+ <string>XIC</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
</item>
</layout>
</item>
@@ -397,8 +411,8 @@
<slot>chooseDefaultMzDataDir()</slot>
<hints>
<hint type="sourcelabel">
- <x>373</x>
- <y>117</y>
+ <x>462</x>
+ <y>145</y>
</hint>
<hint type="destinationlabel">
<x>977</x>
@@ -413,8 +427,8 @@
<slot>doMsmsPrecisionChanged(pappso::PrecisionP)</slot>
<hints>
<hint type="sourcelabel">
- <x>373</x>
- <y>117</y>
+ <x>801</x>
+ <y>346</y>
</hint>
<hint type="destinationlabel">
<x>977</x>
@@ -422,11 +436,28 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>xic_button</sender>
+ <signal>clicked()</signal>
+ <receiver>PeptideDetailView</receiver>
+ <slot>openInXicViewer()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>685</x>
+ <y>86</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>924</x>
+ <y>119</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>chooseDefaultMzDataDir()</slot>
<slot>openInPeptideViewer()</slot>
<slot>doSaveSvg()</slot>
<slot>doMsmsPrecisionChanged(pappso::PrecisionP)</slot>
+ <slot>openInXicViewer()</slot>
</slots>
</ui>
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 07b41feee..01bd32985 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -23,6 +23,7 @@
#include "peptidewindow.h"
#include "../project_view/projectwindow.h"
+#include "../../utils/readspectrum.h"
#include "../../config.h"
#include "ui_peptide_detail_view.h"
#include <pappsomspp/exception/exceptionnotfound.h>
@@ -77,7 +78,7 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent):
QSettings settings;
QString precision_str = settings.value("peptideview/precision", "0.2 dalton").toString();
-
+
_p_precision = pappso::Precision::fromString(precision_str);
ui->file_not_found->setVisible(false);
@@ -199,6 +200,7 @@ void PeptideWindow::chooseDefaultMzDataDir() {
qDebug() << "PeptideWindow::chooseDefaultMzDataDir begin";
ui->file_not_found->setVisible(false);
+ ui->xic_button->setEnabled(true);
ui->spectrum_widget->setVisible(true);
emit loadSpectrumSp(_p_peptide_evidence);
ui->statusbar->showMessage(tr("loading spectrum"));
@@ -216,12 +218,18 @@ void PeptideWindow::openInPeptideViewer() {
myProcess->start(program, arguments);
}
+
+void PeptideWindow::openInXicViewer() {
+ _p_project_window->openInXicViewer(_p_peptide_evidence);
+}
+
void PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error, QString fatal_error) {
qDebug() << "PeptideWindow::doSpectrumSpReady begin error=" << error << " fatal_error=" << fatal_error;
if ((error.isEmpty()) && (fatal_error.isEmpty())) {
ui->statusbar->showMessage(tr(""));
ui->file_not_found->setVisible(false);
ui->spectrum_widget->setVisible(true);
+ ui->xic_button->setEnabled(true);
ui->spectrum_widget->setMsLevel(2);
ui->spectrum_widget->setSpectrumSp(spectrum_sp);
@@ -230,6 +238,17 @@ void PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString er
qDebug() << "PeptideWindow::doSpectrumSpReady rescale";
ui->spectrum_widget->rescale();
_spectrum_is_ready = true;
+
+
+ try {
+ pappso::MassRange mass_range(_p_peptide_evidence->getPeptideXtpSp().get()->getMz(_p_peptide_evidence->getCharge()), pappso::Precision::getPpmInstance(10));
+
+ pappso::XicSp xic_sp = SpectrumStore::getXicSpFromMsRunSp(_p_peptide_evidence->getMsRunP(), mass_range, XixExtactMethod::max);
+ }
+ catch (pappso::PappsoException & error) {
+ QMessageBox::warning(this,
+ tr("Error trying to save spectrum to SVG file :"), error.qwhat());
+ }
}
if (!error.isEmpty()) {
//not found
@@ -242,6 +261,7 @@ void PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString er
ui->file_not_found->setVisible(true);
ui->spectrum_widget->setVisible(false);
+ ui->xic_button->setEnabled(false);
_spectrum_is_ready = false;
}
if (!fatal_error.isEmpty()) {
diff --git a/src/gui/peptide_detail_view/peptidewindow.h b/src/gui/peptide_detail_view/peptidewindow.h
index 6c1709138..c165f1649 100644
--- a/src/gui/peptide_detail_view/peptidewindow.h
+++ b/src/gui/peptide_detail_view/peptidewindow.h
@@ -83,6 +83,7 @@ protected slots:
void doSaveSvg();
void chooseDefaultMzDataDir();
void openInPeptideViewer();
+ void openInXicViewer();
protected :
void updateDisplay();
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 5a9189483..134f16d82 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -762,3 +762,13 @@ void ProjectWindow::doAcceptedLabelingMethod() {
}
+
+void ProjectWindow::openInXicViewer(const PeptideEvidence * p_peptide_evidence) {
+ qDebug() << "ProjectWindow::openInXicViewer begin";
+ if (_p_xic_window == nullptr) {
+ _p_xic_window = new XicWindow(this);
+ }
+
+ _p_xic_window->show();
+ qDebug() << "ProjectWindow::openInXicViewer end";
+}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 727708b8b..a9439ef4f 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -37,6 +37,7 @@
#include "../peptide_detail_view/peptidewindow.h"
#include "gui/project_view/automatic_filter_widget/automaticfilterwidget.h"
#include "../waiting_message_dialog/waitingmessagedialog.h"
+#include "../xic_view/xicwindow.h"
#include <qcustomplot.h>
class MainWindow;
@@ -58,6 +59,7 @@ public:
void setProjectSp(ProjectSp project_sp);
void editModifications();
void editLabelingMethods();
+ void openInXicViewer(const PeptideEvidence * p_peptide_evidence);
~ProjectWindow();
public slots:
@@ -127,6 +129,7 @@ private:
EditModifications * _p_edit_modifications = nullptr;
EditLabelMethods * _p_edit_label_methods = nullptr;
+ XicWindow * _p_xic_window = nullptr;
ProjectSp _project_sp;
diff --git a/src/gui/xic_view/xic_window.ui b/src/gui/xic_view/xic_window.ui
new file mode 100644
index 000000000..fa9b6cb85
--- /dev/null
+++ b/src/gui/xic_view/xic_window.ui
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>XicWindow</class>
+ <widget class="QMainWindow" name="XicWindow">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>800</width>
+ <height>600</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>XIC viewer</string>
+ </property>
+ <widget class="QWidget" name="centralwidget">
+ <layout class="QVBoxLayout" name="verticalLayout_2">
+ <item>
+ <layout class="QVBoxLayout" name="xic_vertical_layout"/>
+ </item>
+ </layout>
+ </widget>
+ <widget class="QMenuBar" name="menubar">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>800</width>
+ <height>25</height>
+ </rect>
+ </property>
+ </widget>
+ <widget class="QStatusBar" name="statusbar"/>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/src/gui/xic_view/xicwindow.cpp b/src/gui/xic_view/xicwindow.cpp
new file mode 100644
index 000000000..4c5f13f2e
--- /dev/null
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -0,0 +1,60 @@
+/**
+ * \file src/gui/xic_view/xicwindow.cpp
+ * \date 11/1/2018
+ * \author Olivier Langella
+ * \brief XIC window
+ */
+
+/*******************************************************************************
+* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "xicwindow.h"
+#include "ui_xic_window.h"
+#include "../project_view/projectwindow.h"
+
+
+XicWindow::XicWindow(ProjectWindow *parent):
+ QMainWindow(parent),
+ ui(new Ui::XicWindow)
+{
+ _project_window = parent;
+
+ ui->setupUi(this);
+ XicWorkerThread * p_worker = new XicWorkerThread();
+ p_worker->moveToThread(&_xic_thread);
+ _xic_thread.start();
+
+
+#if QT_VERSION >= 0x050000
+ // Qt5 code
+
+#else
+// Qt4 code
+#endif
+
+
+}
+
+XicWindow::~XicWindow()
+{
+ qDebug() << "XicWindow::~XicWindow";
+}
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
new file mode 100644
index 000000000..6cfe806be
--- /dev/null
+++ b/src/gui/xic_view/xicwindow.h
@@ -0,0 +1,69 @@
+/**
+ * \file src/gui/xic_view/xicwindow.h
+ * \date 11/1/2018
+ * \author Olivier Langella
+ * \brief XIC window
+ */
+/*******************************************************************************
+* Copyright (c) 2018 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef XICWINDOW_H
+#define XICWINDOW_H
+
+#include <QThread>
+#include <QMainWindow>
+
+class ProjectWindow;
+
+
+class XicWorkerThread : public QObject
+{
+ Q_OBJECT
+public:
+
+
+protected:
+
+ void closeEvent(QCloseEvent *event);
+
+};
+
+
+namespace Ui {
+class XicWindow;
+}
+
+class XicWindow: public QMainWindow {
+ Q_OBJECT
+
+public:
+
+ explicit XicWindow(ProjectWindow * parent = 0);
+ ~XicWindow();
+
+
+private:
+ ProjectWindow * _project_window;
+ QThread _xic_thread;
+ Ui::XicWindow *ui;
+};
+#endif // XICWINDOW_H
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index a435cd359..e7b647de2 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -105,7 +105,7 @@ void SampleSheet::writeIdentificationDataSource(IdentificationDataSource * p_ide
_p_writer->writeLine();
MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
if (_msrun_statistics) {
- SpectrumStore::checkMsRunStatistics(msrun_sp);
+ SpectrumStore::checkMsRunStatistics(msrun_sp.get());
}
_p_writer->writeCell(msrun_sp.get()->getXmlId());
diff --git a/src/utils/readspectrum.cpp b/src/utils/readspectrum.cpp
index d889642a1..bb9d4082f 100644
--- a/src/utils/readspectrum.cpp
+++ b/src/utils/readspectrum.cpp
@@ -90,9 +90,9 @@ void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso:
const pwiz::msdata::SpectrumList * p_spectrum_list = p_ms_data_file->run.spectrumListPtr.get();
std::size_t spectrum_list_size = p_spectrum_list->size();
pwiz::msdata::SpectrumPtr spectrum;
-
+
XicElement peak;
-
+
for (std::size_t i=0; i < spectrum_list_size; i++) {
spectrum = p_spectrum_list->spectrum(i, false);
unsigned int ms_level(QString(spectrum->cvParam(pwiz::msdata::MS_ms_level).value.c_str()).toUInt());
@@ -101,7 +101,7 @@ void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso:
spectrum = p_spectrum_list->spectrum(i, true);
peak.rt = QString(spectrum->scanList.scans[0].cvParam(pwiz::msdata::MS_scan_start_time).value.c_str()).toDouble();
peak.intensity = 0;
-
+
vector<pwiz::msdata::MZIntensityPair> pairs;
spectrum->getMZIntensityPairs(pairs);
@@ -109,7 +109,7 @@ void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso:
for (vector<pwiz::msdata::MZIntensityPair>::const_iterator it=pairs.begin(), end=pairs.end(); it!=end; ++it)
{
//qDebug() << "it->mz " << it->mz << " it->intensity" << it->intensity;
- if (mass_range.contains(it->mz)){
+ if (mass_range.contains(it->mz)) {
if (method == XixExtactMethod::max) {
if (peak.intensity < it->intensity) {
peak.intensity = it->intensity;
@@ -120,7 +120,7 @@ void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso:
}
}
}
-
+
p_xic->push_back(peak);
}
@@ -259,13 +259,13 @@ pappso::QualifiedSpectrum getQualifiedSpectrumFromPwizMSDataFile(pwiz::msdata::M
return qspectrum;
}
-std::map<MsRunSp, pwiz::msdata::MSDataFile *> create_map()
+std::map<const MsRun *, pwiz::msdata::MSDataFile *> create_map()
{
- std::map<MsRunSp, pwiz::msdata::MSDataFile *> m;
+ std::map<const MsRun *, pwiz::msdata::MSDataFile *> m;
return m;
}
-std::map<MsRunSp, pwiz::msdata::MSDataFile *> SpectrumStore::_map_msrun_msdatafile = create_map();
+std::map<const MsRun *, pwiz::msdata::MSDataFile *> SpectrumStore::_map_msrun_msdatafile = create_map();
const QString SpectrumStore::findMzFile(const QString &filename) {
@@ -300,14 +300,14 @@ const QString SpectrumStore::findMzFile(const QString &filename) {
return QString();
}
-void SpectrumStore::checkMsRunStatistics(MsRunSp msrun) {
- QVariant msrun_var = msrun.get()->getMsRunStatistics(MsRunStatistics::total_spectra);
+void SpectrumStore::checkMsRunStatistics(MsRun * msrun) {
+ QVariant msrun_var = msrun->getMsRunStatistics(MsRunStatistics::total_spectra);
if (msrun_var.isNull()) {
try {
pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(msrun);
const pwiz::msdata::SpectrumList * p_spectrum_list = p_msdatafile->run.spectrumListPtr.get();
std::size_t spectrum_list_size = p_spectrum_list->size();
- msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) spectrum_list_size);
+ msrun->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) spectrum_list_size);
unsigned int count_mslevel[50] = {0};
for (std::size_t i=0; i < spectrum_list_size; i++) {
@@ -316,10 +316,10 @@ void SpectrumStore::checkMsRunStatistics(MsRunSp msrun) {
count_mslevel[msLevel]++;
}
- msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) spectrum_list_size);
- msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra_ms1, (unsigned int) count_mslevel[1]);
- msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra_ms2, (unsigned int) count_mslevel[2]);
- msrun.get()->setMsRunStatistics(MsRunStatistics::total_spectra_ms3, (unsigned int) count_mslevel[3]);
+ msrun->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) spectrum_list_size);
+ msrun->setMsRunStatistics(MsRunStatistics::total_spectra_ms1, (unsigned int) count_mslevel[1]);
+ msrun->setMsRunStatistics(MsRunStatistics::total_spectra_ms2, (unsigned int) count_mslevel[2]);
+ msrun->setMsRunStatistics(MsRunStatistics::total_spectra_ms3, (unsigned int) count_mslevel[3]);
}
catch (pappso::ExceptionNotFound& error) {
//no file found, no statistics
@@ -327,22 +327,35 @@ void SpectrumStore::checkMsRunStatistics(MsRunSp msrun) {
}
}
-pwiz::msdata::MSDataFile * SpectrumStore::findPwizMSDataFile(MsRunSp msrun) {
+pwiz::msdata::MSDataFile * SpectrumStore::findPwizMSDataFile(const MsRun * p_msrun) {
+ pwiz::msdata::MSDataFile * p_msdatafile = nullptr;
+ std::map<const MsRun *, pwiz::msdata::MSDataFile *>::iterator it_msdata = _map_msrun_msdatafile.find(p_msrun);
+ if (it_msdata == _map_msrun_msdatafile.end()) {
+ //not found
+ throw pappso::ExceptionNotFound(QObject::tr("mz data \"%1\" file not found").arg(p_msrun->getFilename()));
+ }
+ else {
+ p_msdatafile =it_msdata->second;
+ }
+ return p_msdatafile;
+}
+
+pwiz::msdata::MSDataFile * SpectrumStore::findPwizMSDataFile(MsRun * p_msrun) {
pwiz::msdata::MSDataFile * p_msdatafile = nullptr;
- std::map<MsRunSp, pwiz::msdata::MSDataFile *>::iterator it_msdata = _map_msrun_msdatafile.find(msrun);
+ std::map<const MsRun *, pwiz::msdata::MSDataFile *>::iterator it_msdata = _map_msrun_msdatafile.find(p_msrun);
if (it_msdata == _map_msrun_msdatafile.end()) {
//not found
- QString mz_file = findMzFile(msrun.get()->getFilename());
+ QString mz_file = findMzFile(p_msrun->getFilename());
if (mz_file.isEmpty()) {
- qDebug() << "SpectrumStore::getSpectrumSpFromMsRunIdSp ERROR file not found " << msrun.get()->getFilename();
- throw pappso::ExceptionNotFound(QObject::tr("mz data \"%1\" file not found").arg(msrun.get()->getFilename()));
+ qDebug() << "SpectrumStore::getSpectrumSpFromMsRunIdSp ERROR file not found " << p_msrun->getFilename();
+ throw pappso::ExceptionNotFound(QObject::tr("mz data \"%1\" file not found").arg(p_msrun->getFilename()));
//return spectrum;
}
- msrun.get()->setFilename(mz_file);
+ p_msrun->setFilename(mz_file);
p_msdatafile = getPwizMSDataFile(mz_file);
//msrun.get()->setMzFormat(getPwizMSDataFileFormat(p_msdatafile));
- _map_msrun_msdatafile.insert(std::pair<MsRunSp, pwiz::msdata::MSDataFile *>(msrun, p_msdatafile));
+ _map_msrun_msdatafile.insert(std::pair<const MsRun *, pwiz::msdata::MSDataFile *>(p_msrun, p_msdatafile));
}
else {
p_msdatafile =it_msdata->second;
@@ -350,7 +363,7 @@ pwiz::msdata::MSDataFile * SpectrumStore::findPwizMSDataFile(MsRunSp msrun) {
return p_msdatafile;
}
-pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsigned int scan_num) {
+pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRun * msrun, unsigned int scan_num) {
pappso::QualifiedSpectrum spectrum;
pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(msrun);
@@ -358,7 +371,7 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsign
return spectrum.getOriginalSpectrumSp();
}
spectrum = getQualifiedSpectrumFromPwizMSDataFile(p_msdatafile, scan_num);
- if (msrun.get()->getMzFormat() == MzFormat::MGF) {
+ if (msrun->getMzFormat() == MzFormat::MGF) {
if (spectrum.getRtInSeconds() == 0) {
spectrum = getQualifiedSpectrumFromPwizMSDataFile(p_msdatafile, scan_num-1);
}
@@ -367,14 +380,16 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsign
}
-pappso::XicSp SpectrumStore::getXicSpFromMsRunSp(MsRunSp msrun, const pappso::MassRange & mass_range, XixExtactMethod method) {
- pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(msrun);
+pappso::XicSp SpectrumStore::getXicSpFromMsRunSp(const MsRun * p_msrun, const pappso::MassRange & mass_range, XixExtactMethod method) {
+ qDebug() << "SpectrumStore::getXicSpFromMsRunSp begin" ;
+ pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(p_msrun);
XicSp xic_sp;
- if (p_msdatafile == nullptr) {
- Xix xic;
+ if (p_msdatafile != nullptr) {
+ Xic xic;
getXicFromPwizMSDataFile(p_msdatafile, &xic, mass_range, method);
xic_sp = xic.makeXicSp();
+ qDebug() << "SpectrumStore::getXicSpFromMsRunSp end" << xic_sp.get()->size();
}
return (xic_sp);
}
diff --git a/src/utils/readspectrum.h b/src/utils/readspectrum.h
index 507bb2fd5..c8eef8cc1 100644
--- a/src/utils/readspectrum.h
+++ b/src/utils/readspectrum.h
@@ -42,15 +42,16 @@ class MSDataFile;
class SpectrumStore {
public:
- static pappso::SpectrumSp getSpectrumSpFromMsRunSp(MsRunSp msrun, unsigned int scan_num);
- static pappso::XicSp getXicSpFromMsRunSp(MsRunSp msrun, const pappso::MassRange & mass_range, XixExtactMethod method);
+ static pappso::SpectrumSp getSpectrumSpFromMsRunSp(MsRun * p_msrun, unsigned int scan_num);
+ static pappso::XicSp getXicSpFromMsRunSp(const MsRun * p_msrun, const pappso::MassRange & mass_range, XixExtactMethod method);
/** @brief try to find MS run statistics
*/
- static void checkMsRunStatistics(MsRunSp msrun);
+ static void checkMsRunStatistics(MsRun *);
private:
static const QString findMzFile(const QString &filename);
- static pwiz::msdata::MSDataFile * findPwizMSDataFile(MsRunSp msrun) ;
+ static pwiz::msdata::MSDataFile * findPwizMSDataFile(MsRun * p_msrun) ;
+ static pwiz::msdata::MSDataFile * findPwizMSDataFile(const MsRun * p_msrun) ;
private:
- static std::map<MsRunSp, pwiz::msdata::MSDataFile *> _map_msrun_msdatafile;
+ static std::map<const MsRun *, pwiz::msdata::MSDataFile *> _map_msrun_msdatafile;
};
#endif // READSPECTRUM_H
--
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