launch peptide viewer

src/CMakeLists.txt

@@ -27,11 +27,11 @@ 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 "${PAPPSOMSPP_DIR}/src")
-# SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
+ SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
+ SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
 
 
 set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake_modules)

src/gui/peptide_detail_view/peptide_detail_view.ui

@@ -33,6 +33,9 @@
             <property name="text">
              <string>sequence</string>
             </property>
+            <property name="textInteractionFlags">
+             <set>Qt::LinksAccessibleByMouse|Qt::TextSelectableByKeyboard|Qt::TextSelectableByMouse</set>
+            </property>
            </widget>
           </item>
          </layout>
@@ -82,6 +85,9 @@
             <property name="text">
              <string>TextLabel</string>
             </property>
+            <property name="textInteractionFlags">
+             <set>Qt::LinksAccessibleByMouse|Qt::TextSelectableByKeyboard|Qt::TextSelectableByMouse</set>
+            </property>
            </widget>
           </item>
          </layout>
@@ -100,6 +106,9 @@
             <property name="text">
              <string>TextLabel</string>
             </property>
+            <property name="textInteractionFlags">
+             <set>Qt::LinksAccessibleByMouse|Qt::TextSelectableByKeyboard|Qt::TextSelectableByMouse</set>
+            </property>
            </widget>
           </item>
          </layout>
@@ -122,10 +131,17 @@
           </item>
          </layout>
         </item>
+        <item>
+         <widget class="QPushButton" name="pushButton">
+          <property name="text">
+           <string>Open in peptide viewer</string>
+          </property>
+         </widget>
+        </item>
        </layout>
       </item>
       <item>
-	<widget class="QWidget" name="file_not_found">
+          <widget class="QWidget" name="file_not_found">
        <layout class="QFormLayout" name="file_not_found_layout">
         <item row="0" column="0">
          <widget class="QLabel" name="mz_data_dir_label">
@@ -142,7 +158,7 @@
          </widget>
         </item>
        </layout>
-     </widget>
+       </widget>
       </item>
       <item>
        <layout class="QHBoxLayout" name="horizontalLayout_2">
@@ -175,7 +191,7 @@
      <x>0</x>
      <y>0</y>
      <width>826</width>
-     <height>23</height>
+     <height>25</height>
     </rect>
    </property>
   </widget>
@@ -206,8 +222,25 @@
     </hint>
    </hints>
   </connection>
+  <connection>
+   <sender>pushButton</sender>
+   <signal>clicked()</signal>
+   <receiver>PeptideDetailView</receiver>
+   <slot>openInPeptideViewer()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>754</x>
+     <y>62</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>850</x>
+     <y>222</y>
+    </hint>
+   </hints>
+  </connection>
  </connections>
  <slots>
   <slot>chooseDefaultMzDataDir()</slot>
+  <slot>openInPeptideViewer()</slot>
  </slots>
 </ui>

src/gui/peptide_detail_view/peptidewindow.cpp

@@ -30,6 +30,7 @@
 #include <QFileDialog>
 #include <QSettings>
 #include <QDebug>
+#include <QProcess>
 
 
 void SpectrumSpLoaderThread::doLoadSpectrumSp (PeptideMatch * p_peptide_match) {
@@ -156,6 +157,15 @@ void PeptideWindow::chooseDefaultMzDataDir() {
 
 }
 
+void PeptideWindow::openInPeptideViewer() {
+    QString program = "/home/olivier/eclipse/git/pappsoms-tools/cbuild/src/gui/pt-peptideviewer";
+    QStringList arguments;
+    arguments << _p_peptide_match->getPeptideXtpSp().get()->toString() << QString("%1").arg(_p_peptide_match->getCharge()) << _p_peptide_match->getMsRunP()->getFilename() << QString("%1").arg(_p_peptide_match->getScan());
+
+    qDebug() << "PeptideWindow::openInPeptideViewer " << program << " " << arguments.join(" ");
+    QProcess *myProcess = new QProcess(this);
+    myProcess->start(program, arguments);
+}
 
 void PeptideWindow::doSpectrumSpReady(SpectrumSp spectrum_sp, QString error) {
     qDebug() << "PeptideWindow::doSpectrumSpReady begin";

src/gui/peptide_detail_view/peptidewindow.h

@@ -77,6 +77,7 @@ signals:
 protected slots:
     void doSpectrumSpReady(pappso::SpectrumSp spectrum_sp, QString error);
     void chooseDefaultMzDataDir();
+    void openInPeptideViewer();
 protected :
     void updateDisplay();
 

src/utils/readspectrum.cpp

@@ -272,11 +272,11 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRunSp msrun, unsign
         QString mz_file = findMzFile(msrun.get()->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()));
+            throw pappso::ExceptionNotFound(QObject::tr("mz data \"%1\" file not found").arg(msrun.get()->getFilename()));
             //return spectrum;
         }
-        p_msdatafile = getPwizMSDataFile(mz_file);
         msrun.get()->setFilename(mz_file);
+        p_msdatafile = getPwizMSDataFile(mz_file);
         _map_msrun_msdatafile.insert(std::pair<MsRunSp, pwiz::msdata::MSDataFile *>(msrun, p_msdatafile));
     }
     else {