WIP: all isotopes in one plot

src/gui/xic_view/xic_box/xic_box.ui

@@ -93,10 +93,18 @@
     </widget>
    </item>
    <item>
-    <widget class="QWidget" name="xic_list_widget" native="true"/>
+    <widget class="pappso::XicWidget" name="xic_widget" native="true"/>
    </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>
   <connection>

src/gui/xic_view/xic_box/xicbox.cpp

@@ -44,7 +44,7 @@ XicBox::XicBox(XicWindow *parent):
     p_worker->moveToThread(&_xic_thread);
     _xic_thread.start();
 
-    ui->xic_list_widget->setLayout(new QVBoxLayout(ui->xic_list_widget));
+    //ui->xic_list_widget->setLayout(new QVBoxLayout(ui->xic_list_widget));
 
 #if QT_VERSION >= 0x050000
     // Qt5 code
@@ -100,20 +100,20 @@ void XicBox::setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
 void XicBox::setXic(pappso::XicSp xic_sp) {
     qDebug() << "XicBox::setXic begin";
 
-    pappso::XicWidget * xic_widget = new pappso::XicWidget(this);
-    ui->xic_list_widget->layout()->addWidget(xic_widget);
-    xic_widget->setXicSp(xic_sp);
+    //pappso::XicWidget * xic_widget = new pappso::XicWidget(this);
+    //ui->xic_list_widget->layout()->addWidget(xic_widget);
+    ui->xic_widget->addXicSp(xic_sp);
     for (const PeptideEvidence * peptide_evidence:_peptide_evidence_list) {
-        xic_widget->addMsMsEvent(peptide_evidence->getRetentionTime());
+        ui->xic_widget->addMsMsEvent(xic_sp.get(), peptide_evidence->getRetentionTime());
     }
-    xic_widget->rescale();
-    xic_widget->plot();
-    
-    _xic_widget_list.push_back(xic_widget);
-    
+    ui->xic_widget->rescale();
+    ui->xic_widget->plot();
+
+    /*
     if (_isotope_mass_list.size() > _xic_widget_list.size()) {
         emit loadXic(_p_peptide_evidence->getMsRunP(), _isotope_mass_list[_xic_widget_list.size()].get()->getMz(), _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
     }
+    */
 
     qDebug() << "XicBox::setXic end";
 
@@ -123,8 +123,11 @@ void XicBox::setXic(pappso::XicSp xic_sp) {
 void XicBox::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list) {
     _isotope_mass_list = isotope_mass_list;
 
-    if (_isotope_mass_list.size() > 0) {
-        emit loadXic(_p_peptide_evidence->getMsRunP(), _isotope_mass_list[0].get()->getMz(), _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
+    std::vector<pappso::mz> mass_list;
+    for (pappso::PeptideNaturalIsotopeAverageSp & natural_isotope_average: isotope_mass_list) {
+        mass_list.push_back(natural_isotope_average.get()->getMz());
     }
+    emit loadXic(_p_peptide_evidence->getMsRunP(), mass_list, _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
+
 
 }

src/gui/xic_view/xic_box/xicbox.h

@@ -52,7 +52,7 @@ public:
     void setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) ;
     
 signals :
-    void loadXic(const MsRun * p_msrun, pappso::mz mz, pappso::PrecisionP precision, XicExtractMethod method);
+    void loadXic(const MsRun * p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, XicExtractMethod method);
     void computeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge, pappso::PrecisionP precision, double minimum_isotope_pattern_ratio);
 private slots:
     void remove();

src/gui/xic_view/xicworkerthread.cpp

@@ -32,13 +32,16 @@
 #include <pappsomspp/peptide/peptidenaturalisotopelist.h>
 #include <pappsomspp/pappsoexception.h>
 
-void XicWorkerThread::doXicLoad(const MsRun * p_msrun, pappso::mz mz, pappso::PrecisionP precision, XicExtractMethod method) {
+void XicWorkerThread::doXicLoad(const MsRun * p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, XicExtractMethod method) {
 
     try {
-        pappso::MassRange mass_range(mz, precision);
-        pappso::XicSp xic_sp = SpectrumStore::getXicSpFromMsRunSp(p_msrun, mass_range, method);
+        std::vector<pappso::MassRange> mass_list;
+        for (pappso::mz mass:mz_list) {
+            mass_list.push_back(pappso::MassRange(mass, precision));
+        }
+        std::vector<pappso::XicSp> xic_sp_list = SpectrumStore::getXicSpFromMsRunSp(p_msrun, mass_list, method);
 
-        emit xicLoaded(xic_sp);
+        emit xicLoaded(xic_sp_list);
 
     }
     catch (pappso::PappsoException & error) {

src/gui/xic_view/xicworkerthread.h

@@ -40,7 +40,7 @@ class XicWorkerThread : public QObject
 public:
 
 public slots:
-    void doXicLoad(const MsRun * p_msrun, pappso::mz mz, pappso::PrecisionP precision, XicExtractMethod method);
+    void doXicLoad(const MsRun * p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, XicExtractMethod method);
     void doComputeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge, pappso::PrecisionP precision, double minimum_isotope_pattern_ratio);
 
 signals:

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,  XicExtractMethod method);
+void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_mzdata, pappso::Xic * p_xic, const std::vector<pappso::MassRange> & mass_range_list,  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,  XicExtractMethod method) {
+void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso::Xic * p_xic, const std::vector<pappso::MassRange> & mass_range_list,  XicExtractMethod method) {
 
     std::string env;
     env=setlocale(LC_ALL,"");
@@ -91,7 +91,10 @@ void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso:
     std::size_t spectrum_list_size = p_spectrum_list->size();
     pwiz::msdata::SpectrumPtr spectrum;
 
-    XicElement peak;
+    std::vector<XicElement> peak_for_mass;
+    for (const pappso::MassRange & mass_range: mass_range_list) {
+        peak_for_mass.push_back(XicElement());
+    }
 
     for (std::size_t i=0; i < spectrum_list_size; i++) {
         spectrum = p_spectrum_list->spectrum(i, false);
@@ -99,8 +102,10 @@ void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, pappso:
 
         if (ms_level == 1) {
             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;
+            for (XicElement & peak: peak_for_mass) {
+                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);
@@ -109,16 +114,18 @@ 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)) {
+                for (int i=0; i < mass_range_list.size(); i++) {
+                if (mass_range_list[i].contains(it->mz)) {
                     if (method == XicExtractMethod::max) {
-                        if (peak.intensity < it->intensity) {
-                            peak.intensity = it->intensity;
+                        if (peak_for_mass[i].intensity < it->intensity) {
+                            peak_for_mass[i].intensity = it->intensity;
                         }
                     }
                     else {
-                        peak.intensity += it->intensity;
+                        peak_for_mass[i].intensity += it->intensity;
                     }
                 }
+                }
             }
 
             p_xic->push_back(peak);
@@ -381,14 +388,14 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRun * msrun, unsign
 
 }
 
-pappso::XicSp SpectrumStore::getXicSpFromMsRunSp(const MsRun * p_msrun, const pappso::MassRange & mass_range, XicExtractMethod method) {
+std::vector<pappso::XicSp> SpectrumStore::getXicSpFromMsRunSp(const MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, XicExtractMethod method) {
     qDebug() << "SpectrumStore::getXicSpFromMsRunSp begin" ;
     pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(p_msrun);
 
-    XicSp xic_sp;
+    std::vector<pappso::XicSp> xic_sp_list;
     if (p_msdatafile != nullptr) {
-        Xic xic;
-        getXicFromPwizMSDataFile(p_msdatafile, &xic, mass_range, method);
+        std::vector<Xic> xic_list;
+        getXicFromPwizMSDataFile(p_msdatafile, &xic_list, mass_range_list, method);
         xic_sp = xic.makeXicSp();
         qDebug() << "SpectrumStore::getXicSpFromMsRunSp end"  << xic_sp.get()->size();
     }

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, XicExtractMethod method);
+    static std::vector<pappso::XicSp> getXicSpFromMsRunSp(const MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, XicExtractMethod method);
     /** @brief try to find MS run statistics
      */
     static void checkMsRunStatistics(MsRun *);