Merge remote-tracking branch 'origin/master' into renne

CMakeLists.txt

@@ -125,7 +125,7 @@ endif( CMAKE_BUILD_TYPE MATCHES "RelWithDebInfo" )
 message(STATUS "${BoldYellow}CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}.${ColourReset}")
 
 #depending on libpappsomspp version :
-set(LIBPAPPSOMSPP_VERSION "0.7.7-2")
+set(LIBPAPPSOMSPP_VERSION "0.7.10")
 configure_file (${CMAKE_SOURCE_DIR}/debian/control.cmake ${CMAKE_SOURCE_DIR}/debian/control  @ONLY)
 
 
@@ -135,9 +135,9 @@ set(BUILD_SYSTEM_NAME "${CMAKE_SYSTEM}")
 
 set(XTPCPP_VERSION_MAJOR "0")
 set(XTPCPP_VERSION_MINOR "4")
-set(XTPCPP_VERSION_PATCH "0")
+set(XTPCPP_VERSION_PATCH "1")
 set(XTPCPP_VERSION "${XTPCPP_VERSION_MAJOR}.${XTPCPP_VERSION_MINOR}.${XTPCPP_VERSION_PATCH}")
-set(VERSION 0.4.0)
+set(VERSION 0.4.1)
 
 # Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
 # standard install location

debian/changelog

+xtpcpp (0.4.1-1) buster; urgency=medium
+
+  * better PTM support
+  * no tims preset required
+  * boost not needed
+  * loss of mzIdentML support
+  * export chemical formula in masschroqML output
+
+ -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 22 Jul 2020 16:53:04 +0200
+
 xtpcpp (0.4.0-2) buster; urgency=medium
 
   * display all digits of XIC areas

src/gui/export/export_spreadsheet_dialog/export_spreadsheet_dialog.ui

@@ -7,11 +7,11 @@
     <x>0</x>
     <y>0</y>
     <width>676</width>
-    <height>588</height>
+    <height>603</height>
    </rect>
   </property>
   <property name="windowTitle">
-   <string>Form</string>
+   <string>Spreadsheet parameters</string>
   </property>
   <layout class="QVBoxLayout" name="verticalLayout_2">
    <item>
@@ -175,7 +175,7 @@
          <item>
           <widget class="QRadioButton" name="ods_radiobutton">
            <property name="text">
-            <string>ODS spreadsheet (Excel or Li&amp;breOffice)</string>
+            <string>ODS spreads&amp;heet (Excel or LibreOffice)</string>
            </property>
            <property name="checked">
             <bool>true</bool>

src/gui/xic_view/xic_box/xicbox.cpp

@@ -438,17 +438,17 @@ XicBox::drawObservedAreaBars(
       qDebug() << " new QCPBars";
       m_observedAreaBars =
         new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis2);
-      m_observedRatioBars =
-        new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis);
+      //       m_observedRatioBars = new QCPBars(ui->histo_widget->xAxis,
+      //       ui->histo_widget->yAxis);
     }
   else
     {
       qDebug() << "plot clearData";
       m_observedAreaBars->data().clear();
-      m_observedRatioBars->data().clear();
+      //       m_observedRatioBars->data().clear();
     }
   m_observedAreaBars->setName("peak area");
-  m_observedRatioBars->setName("obs. ratio");
+  //   m_observedRatioBars->setName("obs. ratio");
   // ui->histo_widget->yAxis2->setLabel("intensity");
 
 
@@ -506,7 +506,7 @@ XicBox::drawObservedAreaBars(
       i++;
     }
 
-  m_observedRatioBars->setPen(QPen(QColor("red")));
+  //   m_observedRatioBars->setPen(QPen(QColor("red")));
   m_observedAreaBars->setPen(QPen(QColor("yellow")));
   //_graph_peak_surface_list.back()->setScatterStyle(QCPScatterStyle::ssDot);
   // observed_intensity->setBrush(QBrush(QColor(170, 255, 0, 0)));
@@ -531,7 +531,7 @@ XicBox::drawObservedAreaBars(
   if(ticks.size() > 0)
     {
       m_observedAreaBars->setData(ticks, observed_intensity_data);
-      m_observedRatioBars->setData(ticks, observed_ratio_data);
+      //       m_observedRatioBars->setData(ticks, observed_ratio_data);
 
       ui->histo_widget->yAxis2->setVisible(true);
       ui->histo_widget->yAxis2->setRange(0, sum);

src/gui/xic_view/xic_box/xicbox.h

@@ -112,7 +112,7 @@ class XicBox : public QWidget
   const PeptideEvidence *_p_peptide_evidence;
   MsRunSp _msrun_sp;
   QCPBars *m_theoreticalRatioBars = nullptr;
-  QCPBars *m_observedRatioBars    = nullptr;
+  // QCPBars *m_observedRatioBars    = nullptr;
   std::vector<const PeptideEvidence *> _peptide_evidence_list;
   std::vector<XicBoxNaturalIsotope> _natural_isotope_list;
   std::vector<pappso::XicWidget *> _xic_widget_list;

src/output/masschroqml.cpp

@@ -523,7 +523,10 @@ MassChroQml::writePeptideListInGroup(const GroupingGroup *p_group)
       mcq_peptide.id =
         peptide_evidence->getGrpPeptideSp().get()->getGroupingId();
       mcq_peptide.mods
-        << peptide_evidence->getPeptideXtpSp().get()->getModifString(true);
+        << QString("[%1]%2")
+             .arg(peptide_evidence->getPeptideXtpSp().get()->getFormula(1))
+             .arg(
+               peptide_evidence->getPeptideXtpSp().get()->getModifString(true));
       mcq_peptide.prot_ids << p_group->getProteinGroupingIdOfSubgroup(
         sg_number);
       mcq_peptide.seq =