From 81b7860f878124d042f7e2174792efc984701347 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 7 Apr 2017 22:57:02 +0200
Subject: [PATCH] compute mass precision
---
src/core/identificationgroup.cpp | 8 ++-
src/core/identificationgroup.h | 2 +
src/core/proteinmatch.cpp | 18 +++++-
src/core/proteinmatch.h | 2 +
src/gui/project_view/project_view.ui | 90 +++++++++++++++++++++++++-
src/gui/project_view/projectwindow.cpp | 46 ++++++++++---
src/gui/project_view/projectwindow.h | 1 +
7 files changed, 155 insertions(+), 12 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 40646661d..2bb1162f6 100644
--- a/src/core/identificationgroup.cpp
+++ b/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) {
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 9726a01be..74ba6ab90 100644
--- a/src/core/identificationgroup.h
+++ b/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;
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index af186f98c..5bb90d79b 100644
--- a/src/core/proteinmatch.cpp
+++ b/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);
+ }
+ }
+}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index a2039e62b..fb125d15d 100644
--- a/src/core/proteinmatch.h
+++ b/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);
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index eaad0707a..cfcc8ba01 100644
--- a/src/gui/project_view/project_view.ui
+++ b/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>
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 5311738fe..d2541b7fc 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/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);
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 2cdbc36b9..8c9c03c73 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/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();
--
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