From b9a03178331b858d83ed5d27aa9b21bc20e8002a Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 30 May 2017 14:44:42 +0200
Subject: [PATCH] get ptm grouping id
---
src/core/identificationgroup.cpp | 24 ++++-
src/core/identificationgroup.h | 5 ++
src/grouping/ptm/ptmgroupingexperiment.cpp | 23 ++---
src/grouping/ptm/ptmgroupingexperiment.h | 7 +-
src/grouping/ptm/ptmisland.cpp | 15 ++++
src/grouping/ptm/ptmisland.h | 6 ++
src/grouping/ptm/ptmislandgroup.cpp | 3 +
src/grouping/ptm/ptmislandgroup.h | 1 +
src/grouping/ptm/ptmislandsubgroup.cpp | 21 +++++
src/grouping/ptm/ptmislandsubgroup.h | 2 +
.../ptm_island_list_view.ui | 89 +------------------
11 files changed, 93 insertions(+), 103 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 1dbc4b558..287f58151 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -150,13 +150,13 @@ bool IdentificationGroup::contains (const MsRun * p_msrun) const {
return false;
}
- void IdentificationGroup::addIdentificationDataSourceP(IdentificationDataSource * p_identification_source) {
- addMsRunSp(p_identification_source->getMsRunSp());
- auto it = std::find (_id_source_list.begin() ,_id_source_list.end(),p_identification_source);
+void IdentificationGroup::addIdentificationDataSourceP(IdentificationDataSource * p_identification_source) {
+ addMsRunSp(p_identification_source->getMsRunSp());
+ auto it = std::find (_id_source_list.begin() ,_id_source_list.end(),p_identification_source);
if (it == _id_source_list.end()) {
_id_source_list.push_back(p_identification_source);
}
- }
+}
void IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp) {
auto it = std::find (_ms_run_list.begin() ,_ms_run_list.end(),ms_run_sp);
if (it == _ms_run_list.end()) {
@@ -209,6 +209,22 @@ void IdentificationGroup::startGrouping (const GroupingType & grouping_type) {
qDebug() << "IdentificationGroup::startGrouping end ";
}
+void IdentificationGroup::startPtmGrouping () {
+ qDebug() << "IdentificationGroup::startPtmGrouping begin ";
+ if (_p_grp_ptm_experiment != nullptr) {
+ delete _p_grp_ptm_experiment;
+ }
+ _p_grp_ptm_experiment = new PtmGroupingExperiment();
+ _p_grp_ptm_experiment->setValidationState(ValidationState::grouped);
+ for (ProteinMatch * p_protein_match : _protein_match_list) {
+ _p_grp_ptm_experiment->addProteinMatch(p_protein_match);
+ }
+
+ _p_grp_ptm_experiment->startGrouping();
+
+ qDebug() << "IdentificationGroup::startPtmGrouping end ";
+}
+
const QString IdentificationGroup::getTabName() const {
return _ms_run_list[0]->getFilename();
}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 1ed50884c..56ea6baa9 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -26,6 +26,7 @@
#include "msrun.h"
#include "grouping/groupingexperiment.h"
+#include "grouping/ptm/ptmgroupingexperiment.h"
#include "../utils/types.h"
#ifndef IDENTIFICATIONGROUP_H
@@ -91,6 +92,9 @@ public:
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
void startGrouping (const GroupingType & grouping_type);
+ /** @brief creates a new PTM grouping experiment
+ * */
+ void startPtmGrouping ();
const std::vector<MsRunSp> & getMsRunSpList() const;
const std::vector<IdentificationDataSource *> & getIdentificationDataSourceList() const;
@@ -107,6 +111,7 @@ private :
void addMsRunSp(MsRunSp ms_run_sp);
private :
GroupingExperiment * _p_grp_experiment= nullptr;
+ PtmGroupingExperiment * _p_grp_ptm_experiment= nullptr;
Project * _p_project;
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index 193b53b5f..69676cf3e 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -29,7 +29,7 @@
#include "ptmgroupingexperiment.h"
-PtmGroupingExperiment::PtmGroupingExperiment(const PtmGroupingExperiment& other)
+PtmGroupingExperiment::PtmGroupingExperiment()
{
/*
* accession MOD:00696
@@ -73,16 +73,16 @@ PtmGroupingExperiment::~PtmGroupingExperiment()
}
void PtmGroupingExperiment::numbering() {
- std::sort(_ptm_island_group_list.begin(), _ptm_island_group_list.end(),[](const PtmIslandGroupSp a, const PtmIslandGroupSp b)
- {
- return *(a.get()) < *(b.get());
- });
-
- unsigned int number=0;
- for (PtmIslandGroupSp ptm_island_group:_ptm_island_group_list) {
- number ++;
- ptm_island_group.get()->setGroupNumber(number);
- }
+ std::sort(_ptm_island_group_list.begin(), _ptm_island_group_list.end(),[](const PtmIslandGroupSp a, const PtmIslandGroupSp b)
+ {
+ return *(a.get()) < *(b.get());
+ });
+
+ unsigned int number=0;
+ for (PtmIslandGroupSp ptm_island_group:_ptm_island_group_list) {
+ number ++;
+ ptm_island_group.get()->setGroupNumber(number);
+ }
}
void PtmGroupingExperiment::startGrouping() {
//we have a list of ptm island subgroups to group :
@@ -97,6 +97,7 @@ void PtmGroupingExperiment::startGrouping() {
numbering();
}
void PtmGroupingExperiment::addPtmIsland(PtmIslandSp ptm_island_sp) {
+ _ptm_island_list.push_back(ptm_island_sp);
if (std::none_of(_ptm_island_subgroup_list.begin(), _ptm_island_subgroup_list.end(), [ptm_island_sp](PtmIslandSubgroupSp element) {
return element.get()->mergePtmIslandSp(ptm_island_sp);
})) {
diff --git a/src/grouping/ptm/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index e7fabb0bf..ea80af13a 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/src/grouping/ptm/ptmgroupingexperiment.h
@@ -39,22 +39,23 @@
class PtmGroupingExperiment
{
public:
- PtmGroupingExperiment(const PtmGroupingExperiment& other);
+ PtmGroupingExperiment();
~PtmGroupingExperiment();
-
+
void setValidationState(ValidationState validation_state);
void addProteinMatch(const ProteinMatch* p_protein_match);
void startGrouping();
private:
std::vector<unsigned int> getPtmPositions(const ProteinMatch * protein_match) const;
-
+
std::vector< PtmIslandSp > mergePeptideMatchPtmIslandList(vector< PtmIslandSp > ptm_island_list);
void addPtmIsland(PtmIslandSp ptm_island);
void numbering();
private:
std::list<pappso::AaModificationP> _modification_list;
ValidationState _peptide_validation_state = ValidationState::validAndChecked;
+ std::vector<PtmIslandSp> _ptm_island_list;
std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
std::vector<PtmIslandGroupSp> _ptm_island_group_list;
};
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index acd224f40..0603f9fba 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -30,6 +30,8 @@
#include "ptmisland.h"
#include <pappsomspp/pappsoexception.h>
#include "ptmislandsubgroup.h"
+#include "ptmislandgroup.h"
+#include <pappsomspp/utils.h>
PtmIsland::PtmIsland(const ProteinMatch* p_protein_match, unsigned int position):_protein_match_p(p_protein_match)
{
@@ -45,6 +47,19 @@ PtmIsland::~PtmIsland()
}
+const QString PtmIsland::getGroupingId() const {
+ if(_prot_number==0) {
+ return "";
+ }
+ return QString("ptm%1%2%3").arg(pappso::Utils::getLexicalOrderedString(_ptm_island_subgroup_p->getPtmIslandGroup()->getGroupNumber()))
+ .arg(pappso::Utils::getLexicalOrderedString(_ptm_island_subgroup_p->getSubgroupNumber())).arg(pappso::Utils::getLexicalOrderedString(_prot_number));
+}
+void PtmIsland::setPtmIslandSubgroup(PtmIslandSubgroup* p_ptm_island_subgroup) {
+ _ptm_island_subgroup_p = p_ptm_island_subgroup;
+}
+void PtmIsland::setProteinNumber(unsigned int prot_number) {
+ _prot_number = prot_number;
+}
const ProteinMatch * PtmIsland::getProteinMatch() const {
return _protein_match_p;
}
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index cb9be5b13..62f13ac63 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -58,6 +58,11 @@ public:
std::vector<std::size_t> getSampleScanSet() const;
const ProteinMatch * getProteinMatch() const;
unsigned int getProteinStartPosition() const;
+ void setPtmIslandSubgroup(PtmIslandSubgroup* p_ptm_island_subgroup);
+ void setProteinNumber(unsigned int prot_number);
+
+
+ const QString getGroupingId() const;
private:
const ProteinMatch * _protein_match_p;
@@ -66,6 +71,7 @@ private:
std::vector<unsigned int> _position_list;
unsigned int _protein_stop=0;
unsigned int _protein_start=0;
+ unsigned int _prot_number=0;
PtmIslandSubgroup * _ptm_island_subgroup_p = nullptr;
};
diff --git a/src/grouping/ptm/ptmislandgroup.cpp b/src/grouping/ptm/ptmislandgroup.cpp
index b4abe62f9..c7cc921d3 100644
--- a/src/grouping/ptm/ptmislandgroup.cpp
+++ b/src/grouping/ptm/ptmislandgroup.cpp
@@ -57,6 +57,9 @@ QString PtmIslandGroup::getFirstAccession() const {
return accession_list[0];
}
+unsigned int PtmIslandGroup::getGroupNumber() const {
+ return _group_number;
+}
void PtmIslandGroup::setGroupNumber(unsigned int number) {
_group_number = number;
for (PtmIslandSubgroupSp ptm_island_subgroup:_ptm_island_subgroup_list) {
diff --git a/src/grouping/ptm/ptmislandgroup.h b/src/grouping/ptm/ptmislandgroup.h
index 18038220e..bb3702d1f 100644
--- a/src/grouping/ptm/ptmislandgroup.h
+++ b/src/grouping/ptm/ptmislandgroup.h
@@ -54,6 +54,7 @@ public:
unsigned int maxCountSampleScan() const;
QString getFirstAccession() const;
void setGroupNumber(unsigned int number);
+ unsigned int getGroupNumber() const;
private :
std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
diff --git a/src/grouping/ptm/ptmislandsubgroup.cpp b/src/grouping/ptm/ptmislandsubgroup.cpp
index 6a0d99e5f..f1df0c123 100644
--- a/src/grouping/ptm/ptmislandsubgroup.cpp
+++ b/src/grouping/ptm/ptmislandsubgroup.cpp
@@ -50,8 +50,29 @@ const PtmIsland * PtmIslandSubgroup::getFirstPtmIsland() const {
return _ptm_island_list.begin()->get();
}
+const PtmIslandGroup * PtmIslandSubgroup::getPtmIslandGroup() const {
+ return _ptm_island_group_p;
+}
+
+unsigned int PtmIslandSubgroup::getSubgroupNumber() const {
+ return _subgroup_number;
+}
void PtmIslandSubgroup::setSubgroupNumber(unsigned int number) {
_subgroup_number = number;
+
+ for (PtmIslandSp ptm_island:_ptm_island_list) {
+ ptm_island.get()->setPtmIslandSubgroup(this);
+ }
+ std::sort(_ptm_island_list.begin(), _ptm_island_list.end(), [](const PtmIslandSp& a, const PtmIslandSp& b)
+ {
+ return (a.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession() < b.get()->getProteinMatch()->getProteinXtpSp().get()->getAccession());
+ });
+
+ unsigned int prot_number=0;
+ for (PtmIslandSp ptm_island:_ptm_island_list) {
+ prot_number ++;
+ ptm_island.get()->setProteinNumber(prot_number);
+ }
}
void PtmIslandSubgroup::setPtmIslandGroup(PtmIslandGroup * p_ptm_island_group) {
_ptm_island_group_p = p_ptm_island_group;
diff --git a/src/grouping/ptm/ptmislandsubgroup.h b/src/grouping/ptm/ptmislandsubgroup.h
index 4148fa31f..0f83c6df7 100644
--- a/src/grouping/ptm/ptmislandsubgroup.h
+++ b/src/grouping/ptm/ptmislandsubgroup.h
@@ -60,7 +60,9 @@ public:
void setPtmIslandGroup(PtmIslandGroup * p_ptm_island_group);
const PtmIsland * getFirstPtmIsland() const;
+ unsigned int getSubgroupNumber() const;
void setSubgroupNumber(unsigned int number);
+ const PtmIslandGroup * getPtmIslandGroup() const;
private:
std::vector< PtmIslandSp > _ptm_island_list;
diff --git a/src/gui/ptm_island_list_view/ptm_island_list_view.ui b/src/gui/ptm_island_list_view/ptm_island_list_view.ui
index c000cdcdf..f30486e35 100644
--- a/src/gui/ptm_island_list_view/ptm_island_list_view.ui
+++ b/src/gui/ptm_island_list_view/ptm_island_list_view.ui
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
- <class>PtmIslandListView</class>
+ <class>ptm_island_list_window</class>
<widget class="QMainWindow" name="ptm_island_list_window">
<property name="geometry">
<rect>
@@ -54,7 +54,7 @@
</layout>
</item>
<item>
- <widget class="QTableView" name="tableView">
+ <widget class="QTableView" name="ptm_island_tableview">
<property name="contextMenuPolicy">
<enum>Qt::DefaultContextMenu</enum>
</property>
@@ -111,95 +111,14 @@
<x>0</x>
<y>0</y>
<width>826</width>
- <height>25</height>
+ <height>23</height>
</rect>
</property>
</widget>
<widget class="QStatusBar" name="statusbar"/>
</widget>
<resources/>
- <connections>
- <connection>
- <sender>hideNotValidCheckBox</sender>
- <signal>toggled(bool)</signal>
- <receiver>ProteinView</receiver>
- <slot>doNotValidHide(bool)</slot>
- <hints>
- <hint type="sourcelabel">
- <x>245</x>
- <y>53</y>
- </hint>
- <hint type="destinationlabel">
- <x>839</x>
- <y>171</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>hideNotCheckedCheckBox</sender>
- <signal>toggled(bool)</signal>
- <receiver>ProteinView</receiver>
- <slot>doNotCheckedHide(bool)</slot>
- <hints>
- <hint type="sourcelabel">
- <x>482</x>
- <y>47</y>
- </hint>
- <hint type="destinationlabel">
- <x>920</x>
- <y>269</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>hideNotGroupedCheckBox</sender>
- <signal>toggled(bool)</signal>
- <receiver>ProteinView</receiver>
- <slot>doNotGroupedHide(bool)</slot>
- <hints>
- <hint type="sourcelabel">
- <x>688</x>
- <y>57</y>
- </hint>
- <hint type="destinationlabel">
- <x>1079</x>
- <y>360</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>protein_search_edit</sender>
- <signal>textChanged(QString)</signal>
- <receiver>ProteinView</receiver>
- <slot>onProteinSearchEdit(QString)</slot>
- <hints>
- <hint type="sourcelabel">
- <x>352</x>
- <y>363</y>
- </hint>
- <hint type="destinationlabel">
- <x>879</x>
- <y>391</y>
- </hint>
- </hints>
- </connection>
- <connection>
- <sender>search_combobox</sender>
- <signal>activated(QString)</signal>
- <receiver>ProteinView</receiver>
- <slot>doSearchOn(QString)</slot>
- <hints>
- <hint type="sourcelabel">
- <x>121</x>
- <y>354</y>
- </hint>
- <hint type="destinationlabel">
- <x>867</x>
- <y>386</y>
- </hint>
- </hints>
- </connection>
- </connections>
+ <connections/>
<slots>
<slot>doNotValidHide(bool)</slot>
<slot>doNotCheckedHide(bool)</slot>
--
GitLab