compute mass precision

src/core/identificationgroup.cpp

@@ -142,7 +142,13 @@ std::size_t IdentificationGroup::countSubGroup()const {
     return _group_store.countSubGroup();
 }
 
-
+void IdentificationGroup::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
+    for (auto & p_protein_match : _protein_match_list) {
+        if (p_protein_match->getValidationState() >= state) {
+            p_protein_match->collectMhDelta(delta_list, unit, state);
+        }
+    }
+}
 void IdentificationGroup::startGrouping (const GroupingType & grouping_type) {
     qDebug() << "IdentificationGroup::startGrouping begin ";
     if (_p_grp_experiment != nullptr) {

src/core/identificationgroup.h

@@ -84,6 +84,8 @@ public:
     const QString getTabName() const;
     
     bool contains (const MsRun * p_msrun) const;
+    
+    void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
 private :
     GroupingExperiment * _p_grp_experiment= nullptr;
 

src/core/proteinmatch.cpp

@@ -50,7 +50,7 @@ ValidationState ProteinMatch::getValidationState() const {
         return ValidationState::validAndChecked;
     } else if (isValid()) {
         return ValidationState::valid;
-    } 
+    }
     return ValidationState::notValid;
 }
 bool ProteinMatch::contains(PeptideMatch * peptide_match) const {
@@ -390,3 +390,19 @@ void ProteinMatch::setGroupInstance(GroupStore & group_store) {
         }
     }
 }
+
+
+void ProteinMatch::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
+    for (auto & p_peptide_match : _peptide_match_list) {
+        if (p_peptide_match->getValidationState() >= state) {
+            pappso::pappso_double diff = p_peptide_match->getDeltaMass();
+            if (unit == pappso::PrecisionUnit::ppm) {
+                while (diff < -0.5) {
+                    diff = diff + pappso::DIFFC12C13;
+                }
+                diff = (diff / p_peptide_match->getPeptideXtpSp().get()->getMz(1)) * pappso::ONEMILLION;
+            }
+            delta_list.push_back(diff);
+        }
+    }
+}

src/core/proteinmatch.h

@@ -93,6 +93,8 @@ public:
     /** @brief tells if this protein match contains this peptides
      */
     bool contains(PeptideMatch * peptide_match) const;
+
+    void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
 protected :
 
     void setGroupingExperiment(GroupingExperiment * p_grp_experiment);

src/gui/project_view/project_view.ui

@@ -177,7 +177,95 @@
        </attribute>
        <layout class="QGridLayout" name="gridLayout_2">
         <item row="0" column="0">
-         <layout class="QFormLayout" name="formLayout_3"/>
+         <layout class="QVBoxLayout" name="verticalLayout_5">
+          <item>
+           <layout class="QFormLayout" name="formLayout_2">
+            <item row="0" column="0">
+             <layout class="QFormLayout" name="formLayout_3"/>
+            </item>
+            <item row="1" column="0">
+             <widget class="QLabel" name="label_2">
+              <property name="text">
+               <string>mean</string>
+              </property>
+             </widget>
+            </item>
+            <item row="2" column="0">
+             <widget class="QLabel" name="label_4">
+              <property name="text">
+               <string>median</string>
+              </property>
+             </widget>
+            </item>
+            <item row="3" column="0">
+             <widget class="QLabel" name="label_5">
+              <property name="text">
+               <string>standard deviation</string>
+              </property>
+             </widget>
+            </item>
+            <item row="0" column="1">
+             <widget class="QComboBox" name="precision_unit_combobox">
+              <item>
+               <property name="text">
+                <string>ppm</string>
+               </property>
+              </item>
+              <item>
+               <property name="text">
+                <string>dalton</string>
+               </property>
+              </item>
+             </widget>
+            </item>
+            <item row="1" column="1">
+             <widget class="QLabel" name="mass_precision_mean_label">
+              <property name="text">
+               <string>0</string>
+              </property>
+             </widget>
+            </item>
+            <item row="2" column="1">
+             <widget class="QLabel" name="mass_precision_median_label">
+              <property name="text">
+               <string>0</string>
+              </property>
+             </widget>
+            </item>
+            <item row="3" column="1">
+             <widget class="QLabel" name="mass_precision_sd_label">
+              <property name="text">
+               <string>0</string>
+              </property>
+             </widget>
+            </item>
+           </layout>
+          </item>
+         </layout>
+        </item>
+        <item row="1" column="0">
+         <layout class="QHBoxLayout" name="horizontalLayout_3">
+          <item>
+           <spacer name="horizontalSpacer_3">
+            <property name="orientation">
+             <enum>Qt::Horizontal</enum>
+            </property>
+            <property name="sizeHint" stdset="0">
+             <size>
+              <width>40</width>
+              <height>20</height>
+             </size>
+            </property>
+           </spacer>
+          </item>
+          <item>
+           <widget class="QPushButton" name="pushButton_3">
+            <property name="text">
+             <string>compute</string>
+            </property>
+           </widget>
+          </item>
+         </layout>
         </item>
        </layout>
       </widget>

src/gui/project_view/projectwindow.cpp

@@ -32,6 +32,7 @@
 #include <QGridLayout>
 #include <QMessageBox>
 #include <pappsomspp/pappsoexception.h>
+#include <numeric>
 
 
 
@@ -141,24 +142,49 @@ void ProjectWindow::refreshGroup(IdentificationGroup * p_ident_group) {
 void ProjectWindow::computeFdr(ValidationState state) {
     pappso::pappso_double total_prot=0;
     pappso::pappso_double false_prot=0;
-    for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
-        total_prot += identification_group->countProteinMatch(state);
-        false_prot += identification_group->countDecoyProteinMatch(state);
-    }
-    ui->protein_fdr_label->setText(QString("%1 %").arg(false_prot/total_prot));
-    
-    
     pappso::pappso_double total_peptide=0;
     pappso::pappso_double false_peptide=0;
     for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
+        total_prot += identification_group->countProteinMatch(state);
+        false_prot += identification_group->countDecoyProteinMatch(state);
         total_peptide += identification_group->countPeptideMatch(state);
         false_peptide += identification_group->countDecoyPeptideMatch(state);
     }
-    qDebug() << "ProjectWindow::computeFdr false_peptide=" <<false_peptide;
-    qDebug() << "ProjectWindow::computeFdr total_peptide=" <<total_peptide;
+    ui->protein_fdr_label->setText(QString("%1 %").arg(false_prot/total_prot));
     ui->peptide_fdr_label->setText(QString("%1 %").arg(false_peptide/total_peptide));
 }
 
+void ProjectWindow::computeMassPrecision(ValidationState state) {
+    std::vector< pappso::pappso_double> delta_list;
+    pappso::PrecisionUnit unit = pappso::PrecisionUnit::dalton;
+    if (ui->precision_unit_combobox->currentText() == "ppm") {
+        unit = pappso::PrecisionUnit::ppm;
+    }
+
+    for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
+        identification_group->collectMhDelta(delta_list, unit, state);
+    }
+
+
+    pappso::pappso_double sum = std::accumulate(delta_list.begin(), delta_list.end(), 0);
+
+    pappso::pappso_double mean = sum / ((pappso::pappso_double) delta_list.size());
+
+    std::sort(delta_list.begin(), delta_list.end());
+    pappso::pappso_double median = delta_list[(delta_list.size()/2)];
+
+    pappso::pappso_double sd = 0;
+    for (pappso::pappso_double val : delta_list) {
+        sd = sd + ((val - mean) * (val - mean));
+    }
+    sd = sd / delta_list.size();
+    sd = std::sqrt(sd);
+
+    ui->mass_precision_mean_label->setText(QString::number(mean,'f',10));
+    ui->mass_precision_median_label->setText(QString::number(median,'f',10));
+    ui->mass_precision_sd_label->setText(QString::number(sd,'f',10));
+}
+
 void ProjectWindow::doFdrChanged() {
     qDebug() << "ProjectWindow::doFdrChanged begin ";
     _project_sp.get()->getProteinStore().setRegexpDecoyPattern(ui->decoy_protein_regexp_line_edit->text());
@@ -348,5 +374,7 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
 
     ui->decoy_protein_regexp_line_edit->setText(_project_sp.get()->getProteinStore().getRegexpDecoy().pattern());
     computeFdr(ValidationState::grouped);
+
+    computeMassPrecision(ValidationState::validAndChecked);
     this->setEnabled(true);
 }

src/gui/project_view/projectwindow.h

@@ -69,6 +69,7 @@ protected :
     void doViewProteinDetail(ProteinMatch * protein_match);
     void doIdentificationGroupEdited(IdentificationGroup * p_identification_group);
     void computeFdr(ValidationState state);
+    void computeMassPrecision(ValidationState state);
 
 private :
     void connectNewProteinListWindow();