xic box infrastructure

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")
@@ -158,7 +158,9 @@ 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/xic_box/xicbox.cpp
   ./gui/xic_view/xicwindow.cpp
+  ./gui/xic_view/xicworkerthread.cpp
   ./gui/workerthread.cpp
   ./utils/workmonitor.cpp
 )
@@ -183,6 +185,7 @@ 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_box/xic_box.ui
   ./gui/xic_view/xic_window.ui
 )
 
@@ -215,7 +218,9 @@ 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/xic_box/xicbox.h
   ./gui/xic_view/xicwindow.h
+  ./gui/xic_view/xicworkerthread.h
   ./gui/workerthread.h
   ./utils/workmonitor.h
 )

src/gui/peptide_detail_view/peptidewindow.cpp

@@ -239,16 +239,6 @@ void PeptideWindow::doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString er
         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

src/gui/project_view/projectwindow.cpp

@@ -770,5 +770,7 @@ void ProjectWindow::openInXicViewer(const PeptideEvidence * p_peptide_evidence)
     }
     
     _p_xic_window->show();
+    
+    _p_xic_window->addXic(p_peptide_evidence);
     qDebug() << "ProjectWindow::openInXicViewer end";
 }

src/gui/xic_view/xic_box/xic_box.ui

+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>XicBox</class>
+ <widget class="QWidget" name="XicBox">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>400</width>
+    <height>300</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Form</string>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout_2">
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout">
+     <item>
+      <widget class="QLabel" name="peptide_label">
+       <property name="text">
+        <string>TextLabel</string>
+       </property>
+      </widget>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <layout class="QVBoxLayout" name="verticalLayout">
+     <item>
+      <widget class="pappso::XicWidget" name="xic_widget" native="true"/>
+     </item>
+    </layout>
+   </item>
+  </layout>
+ </widget>
+ <customwidgets>
+  <customwidget>
+   <class>pappso::XicWidget</class>
+   <extends>QWidget</extends>
+   <header>pappsomspp/widget/xicwidget/xicwidget.h</header>
+   <container>1</container>
+  </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>

src/gui/xic_view/xic_box/xicbox.cpp

+/**
+ * \file src/gui/xic_view/xic_box/xicbox.cpp
+ * \date 12/1/2018
+ * \author Olivier Langella
+ * \brief XIC box widget
+ */
+/*******************************************************************************
+* 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 "xicbox.h"
+#include "ui_xic_box.h"
+#include <QMessageBox>
+#include <pappsomspp/pappsoexception.h>
+#include "../xicworkerthread.h"
+
+XicBox::XicBox(XicWindow *parent):
+    QWidget(parent),
+    ui(new Ui::XicBox)
+{
+    _p_xic_window = parent;
+    ui->setupUi(this);
+
+    XicWorkerThread * p_worker = new XicWorkerThread();
+    p_worker->moveToThread(&_xic_thread);
+    _xic_thread.start();
+
+#if QT_VERSION >= 0x050000
+    // Qt5 code
+    connect(this, &XicBox::loadXic, p_worker, &XicWorkerThread::doXicLoad);
+    connect(p_worker, &XicWorkerThread::xicLoaded,this, &XicBox::setXic);
+    connect(p_worker, &XicWorkerThread::operationFailed, this, &XicBox::error);
+
+#else
+// Qt4 code
+#endif
+
+
+}
+
+XicBox::~XicBox()
+{
+    qDebug() << "XicBox::~XicBox";
+    _xic_thread.quit();
+    _xic_thread.wait();
+}
+
+void XicBox::error(QString error_message) {
+    QMessageBox::warning(this,
+                         tr("Error trying to save spectrum to SVG file :"), error_message);
+
+}
+void XicBox::setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
+
+    _p_peptide_evidence = p_peptide_evidence;
+    ui->peptide_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->toString());
+
+    emit loadXic(_p_peptide_evidence->getMsRunP(), _p_peptide_evidence->getPeptideXtpSp().get()->getMz(_p_peptide_evidence->getCharge()), _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
+
+}
+
+
+void XicBox::setXic(pappso::XicSp xic_sp) {
+    qDebug() << "XicBox::setXic begin";
+    qDebug() << "XicBox::setXic end";
+    
+}

src/gui/xic_view/xic_box/xicbox.h

+/**
+ * \file src/gui/xic_view/xic_box/xicbox.h
+ * \date 12/1/2018
+ * \author Olivier Langella
+ * \brief XIC box widget
+ */
+/*******************************************************************************
+* 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 XICBOX_H
+#define XICBOX_H
+
+#include <QWidget>
+#include <QThread>
+#include "../../../utils/types.h"
+#include "../../../core/peptideevidence.h"
+#include "../xicwindow.h"
+#include <pappsomspp/xic/xic.h>
+
+namespace Ui {
+class XicBox;
+}
+
+class XicBox: public QWidget 
+{
+    Q_OBJECT
+public:
+
+    explicit XicBox(XicWindow * parent = 0);
+    ~XicBox();
+    void setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) ;
+    
+signals :
+    void loadXic(const MsRun * p_msrun, pappso::mz mz, pappso::PrecisionP precision, XicExtractMethod method);
+private slots:
+    void setXic(pappso::XicSp xic_sp);
+    void error(QString error_message);
+private:
+    Ui::XicBox *ui;
+    QThread _xic_thread;
+    XicWindow * _p_xic_window;
+    const PeptideEvidence * _p_peptide_evidence;
+};
+
+
+#endif // XICBOX_H

src/gui/xic_view/xicwindow.cpp

@@ -30,7 +30,7 @@
 #include "xicwindow.h"
 #include "ui_xic_window.h"
 #include "../project_view/projectwindow.h"
-
+#include "xic_box/xicbox.h"
 
 XicWindow::XicWindow(ProjectWindow *parent):
     QMainWindow(parent),
@@ -39,9 +39,6 @@ XicWindow::XicWindow(ProjectWindow *parent):
     _project_window = parent;
 
     ui->setupUi(this);
-    XicWorkerThread * p_worker = new XicWorkerThread();
-    p_worker->moveToThread(&_xic_thread);
-    _xic_thread.start();
 
 
 #if QT_VERSION >= 0x050000
@@ -58,3 +55,13 @@ XicWindow::~XicWindow()
 {
     qDebug() << "XicWindow::~XicWindow";
 }
+
+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);
+}
+
+pappso::PrecisionP XicWindow::getXicExtractPrecision() const {
+    return (pappso::Precision::getPpmInstance(10));
+}

src/gui/xic_view/xicwindow.h

@@ -29,41 +29,38 @@
 #ifndef XICWINDOW_H
 #define XICWINDOW_H
 
-#include <QThread>
 #include <QMainWindow>
 
-class ProjectWindow;
-
-
-class XicWorkerThread : public QObject
-{
-    Q_OBJECT
-public:
-
-
-protected:
+#include "../../core/peptideevidence.h"
 
-    void closeEvent(QCloseEvent *event);
+class ProjectWindow;
 
-};
 
 
 namespace Ui {
 class XicWindow;
 }
 
+class XicBox;
+
 class XicWindow: public QMainWindow {
     Q_OBJECT
-
+friend XicBox;
 public:
 
     explicit XicWindow(ProjectWindow * parent = 0);
     ~XicWindow();
 
-
+    void addXic(const PeptideEvidence * p_peptide_evidence);
+    
+    pappso::PrecisionP getXicExtractPrecision() const;
+    
+protected:
+    
 private:
     ProjectWindow * _project_window;
-    QThread _xic_thread;
     Ui::XicWindow *ui;
+    pappso::PrecisionP _xic_extract_precision;
 };
+
 #endif // XICWINDOW_H

src/gui/xic_view/xicworkerthread.cpp

+/**
+ * \file src/gui/xic_view/xicworkerthread.cpp
+ * \date 12/1/2018
+ * \author Olivier Langella
+ * \brief XIC worker
+ */
+/*******************************************************************************
+* 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 "xicworkerthread.h"
+#include "../../utils/readspectrum.h"
+#include <pappsomspp/pappsoexception.h>
+
+void XicWorkerThread::doXicLoad(const MsRun * p_msrun, pappso::mz mz, pappso::PrecisionP precision, XicExtractMethod method) {
+
+    try {
+        pappso::MassRange mass_range(mz, precision);
+        pappso::XicSp xic_sp = SpectrumStore::getXicSpFromMsRunSp(p_msrun, mass_range, method);
+
+        emit xicLoaded(xic_sp);
+
+    }
+    catch (pappso::PappsoException & error) {
+        emit operationFailed(tr("Error extracting XIC :\n%1").arg(error.qwhat()));
+    }
+}

src/gui/xic_view/xicworkerthread.h

+/**
+ * \file src/gui/xic_view/xicworkerthread.h
+ * \date 12/1/2018
+ * \author Olivier Langella
+ * \brief XIC worker
+ */
+/*******************************************************************************
+* 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 XICWORKERTHREAD_H
+#define XICWORKERTHREAD_H
+
+#include <pappsomspp/xic/xic.h>
+#include<QObject>
+#include "../../core/msrun.h"
+
+class XicWorkerThread : public QObject
+{
+    Q_OBJECT
+public:
+
+public slots:
+    void doXicLoad(const MsRun * p_msrun, pappso::mz mz, pappso::PrecisionP precision, XicExtractMethod method);
+
+signals:
+    void xicLoaded(pappso::XicSp xic_sp);
+    void operationFailed(QString error);
+
+};
+#endif // XICWORKERTHREAD_H

src/main.cpp

@@ -27,6 +27,7 @@
 #include <pappsomspp/pappsoexception.h>
 #include "config.h"
 #include "gui/mainwindow.h"
+#include "utils/types.h"
 
 using namespace std;
 
@@ -36,6 +37,11 @@ int main(int argc, char *argv[])
     QApplication app(argc, argv);
 
     qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
+    qRegisterMetaType<pappso::mz>("pappso::mz");
+    qRegisterMetaType<pappso::PrecisionP>("pappso::PrecisionP");
+    qRegisterMetaType<pappso::XicSp>("pappso::XicSp");
+    qRegisterMetaType<XicExtractMethod>("XicExtractMethod");
+    
 
     try {
         QCoreApplication::setOrganizationName("PAPPSO");

src/utils/readspectrum.cpp

@@ -47,7 +47,7 @@ pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename);
 
 pappso::QualifiedSpectrum getQualifiedSpectrumFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num);
 
-void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_mzdata, pappso::Xic * p_xic, const pappso::MassRange & mass_range,  XixExtactMethod method);
+void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_mzdata, pappso::Xic * p_xic, const pappso::MassRange & mass_range,  XicExtractMethod method);
 
 
 pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename) {
@@ -78,7 +78,7 @@ pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename) {
     return dataFile;
 }
 
-void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso::Xic * p_xic, const pappso::MassRange & mass_range,  XixExtactMethod method) {
+void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso::Xic * p_xic, const pappso::MassRange & mass_range,  XicExtractMethod method) {
 
     std::string env;
     env=setlocale(LC_ALL,"");
@@ -110,7 +110,7 @@ void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso:
             {
                 //qDebug() << "it->mz " << it->mz << " it->intensity" << it->intensity;
                 if (mass_range.contains(it->mz)) {
-                    if (method == XixExtactMethod::max) {
+                    if (method == XicExtractMethod::max) {
                         if (peak.intensity < it->intensity) {
                             peak.intensity = it->intensity;
                         }
@@ -380,7 +380,7 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRun * msrun, unsign
 
 }
 
-pappso::XicSp SpectrumStore::getXicSpFromMsRunSp(const MsRun * p_msrun, const pappso::MassRange & mass_range, XixExtactMethod method) {
+pappso::XicSp SpectrumStore::getXicSpFromMsRunSp(const MsRun * p_msrun, const pappso::MassRange & mass_range, XicExtractMethod method) {
     qDebug() << "SpectrumStore::getXicSpFromMsRunSp begin" ;
     pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(p_msrun);
 

src/utils/readspectrum.h

@@ -43,7 +43,7 @@ class MSDataFile;
 class SpectrumStore {
 public:
     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);
+    static pappso::XicSp getXicSpFromMsRunSp(const MsRun * p_msrun, const pappso::MassRange & mass_range, XicExtractMethod method);
     /** @brief try to find MS run statistics
      */
     static void checkMsRunStatistics(MsRun *);

src/utils/types.h

@@ -91,9 +91,9 @@ enum class MsRunStatistics: std::int8_t {
 /** \def XixExtactMethod method to extract Xic
  *
  */
-enum class XixExtactMethod {
-    sum, ///< sum of intensities
-    max ///< maximum of intensities
+enum class XicExtractMethod: std::int8_t {
+    sum=1, ///< sum of intensities
+    max=2 ///< maximum of intensities
 };