[Fix] Add prompt to confirm MS/MS type ElucidataInc#1347

When loading a sample having MS1 and MS2 scans El-MAVEN has no way
of being able to tell whether these samples were from a DDA or a
PRM experiment. From now on, an input dialog will ask the user to
confirm the MS/MS data type, whenever they load such samples. For
now, this prevents MS2 events logic from interfering with PRM data
analysis. It could potentially help with other things in the
future.

src/core/libmaven/PeakGroup.cpp

@@ -862,8 +862,10 @@ vector<Scan*> PeakGroup::getFragmentationEvents()
         mzSample* sample = peak.getSample();
         if (sample == nullptr)
             continue;
-        if (sample->ms2ScanCount() == 0)
+        if (sample->ms2ScanCount() == 0
+            || sample->msMsType() != mzSample::MsMsType::DDA) {
             continue;
+        }
 
         mzSlice slice(minMz, maxMz, peak.rtmin, peak.rtmax);
         vector<Scan*> scans = sample->getFragmentationEvents(&slice);

src/core/libmaven/mzSample.cpp

@@ -25,6 +25,7 @@ mzSample::mzSample() : _setName(""), injectionOrder(0)
     _id = -1;
     _numMS1Scans = 0;
     _numMS2Scans = 0;
+    _msMsType = MsMsType::None;
     maxMz = maxRt = 0;
     minMz = minRt = 0;
     isBlank = false;

src/core/libmaven/mzSample.h

@@ -180,8 +180,13 @@ class mzLink
 */
 class mzSample
 {
+public:
+    enum class MsMsType {
+        DDA,
+        PRM,
+        None
+    };
 
-  public:
     /**
     * @brief Constructor for class mzSample
     */
@@ -681,6 +686,9 @@ class mzSample
 
     vector<float> getIntensityDistribution(int mslevel);
 
+    inline void setMsMsType(MsMsType msMsType) { _msMsType = msMsType; }
+    inline MsMsType msMsType() const { return _msMsType; }
+
     deque<Scan *> scans;
     string sampleName;
     string fileName;
@@ -728,6 +736,7 @@ class mzSample
     int _id;
     unsigned int _numMS1Scans;
     unsigned int _numMS2Scans;
+    MsMsType _msMsType;
 
     void sampleNaming(const char *filename);
     void checkSampleBlank(const char *filename);

src/gui/mzroll/eicwidget.cpp

@@ -2120,7 +2120,11 @@ void EicWidget::addMS2Events(float mzmin, float mzmax)
 
     int count = 0;
     for (auto const& sample : samples) {
-        if (sample->ms1ScanCount() == 0) continue;
+        if (sample->ms1ScanCount() == 0
+            || sample->msMsType() != mzSample::MsMsType::DDA) {
+            continue;
+        }
+
         for (auto const& scan : sample->scans) {
             if (scan->mslevel == 2 && scan->precursorMz >= mzmin
                 && scan->precursorMz <= mzmax) {

src/gui/mzroll/mainwindow.cpp

@@ -605,6 +605,10 @@ using namespace mzUtils;
             SIGNAL(sampleLoaded()),
             this,
             SLOT(_warnIfNISTPolarityMismatch()));
+    connect(fileLoader,
+            &mzFileIO::sampleLoaded,
+            this,
+            &MainWindow::_confirmMsMsType);
 
 	connect(fileLoader,SIGNAL(sampleLoaded()), this, SLOT(setInjectionOrderFromTimeStamp()));
     connect(fileLoader,SIGNAL(sampleLoaded()),projectDockWidget, SLOT(updateSampleList()));
@@ -1543,8 +1547,6 @@ void MainWindow::setCompoundFocus(Compound* compound,
     if (fragPanel->isVisible())
         showFragmentationScans(mz);
 
-    QString compoundName(compound->name().c_str());
-
     if (compound)
         setUrl(compound);
 }
@@ -2143,6 +2145,38 @@ void MainWindow::_warnIfNISTPolarityMismatch()
     }
 }
 
+void MainWindow::_confirmMsMsType()
+{
+    QList<mzSample*> msMsSamples;
+    for (auto sample : samples) {
+        if (sample->ms1ScanCount() > 0 && sample->ms2ScanCount() > 0)
+            msMsSamples.append(sample);
+    }
+
+    if (msMsSamples.isEmpty())
+        return;
+
+    // TODO: add DIA when/if SWATH branch is merged
+    QStringList msMsTypes;
+    msMsTypes << tr("DDA") << tr("PRM");
+
+    QString type = QInputDialog::getItem(this,
+                                         tr("Select MS/MS type"),
+                                         tr("One or more samples have MS/MS "
+                                            "data. Please tell El-MAVEN the\n"
+                                            "acquisition type of this data:"),
+                                         msMsTypes,
+                                         0,
+                                         false);
+    for (auto sample : msMsSamples) {
+        if (type == "PRM") {
+            sample->setMsMsType(mzSample::MsMsType::PRM);
+        } else {
+            sample->setMsMsType(mzSample::MsMsType::DDA);
+        }
+    }
+}
+
 void MainWindow::setLastLoadedDatabase(QString filename)
 {
     QFileInfo fileInfo(filename);
@@ -4002,8 +4036,10 @@ void MainWindow::showFragmentationScans(float pmz)
         return;
     fragPanel->clearTree();
     for (auto sample : samples) {
-        if (sample->ms1ScanCount() == 0)
+        if (sample->ms1ScanCount() == 0
+            || sample->msMsType() != mzSample::MsMsType::DDA) {
             continue;
+        }
 
         for (auto scan : sample->scans) {
 	        if (scan->mslevel != 2) continue;

src/gui/mzroll/mainwindow.h

@@ -494,6 +494,7 @@ private Q_SLOTS:
 
     void _postProjectLoadActions();
     void _handleUnrecognizedProjectVersion(QString projectFilename);
+    void _confirmMsMsType();
 
 private:
     Controller* _controller;

src/gui/mzroll/peakdetectiondialog.cpp

@@ -448,8 +448,9 @@ void PeakDetectionDialog::toggleFragmentation()
     auto iter = find_if(begin(samples),
                         end(samples),
                         [](mzSample* s) {
-                           return ((s->ms1ScanCount() > 0)
-                                   && (s->ms2ScanCount() > 0));
+                           return (s->ms1ScanCount() > 0
+                                   && s->ms2ScanCount() > 0
+                                   && s->msMsType() == mzSample::MsMsType::DDA);
                         });
     bool foundDda = iter != end(samples);