From 0f0e4d5e89a012f70134d1a12170c6cb7f6f08cc Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 27 Jul 2017 09:23:19 +0200
Subject: [PATCH] ptm position list for each ptm peptide
---
src/grouping/ptm/ptmgroupingexperiment.cpp | 26 +++++++++++++++----
src/grouping/ptm/ptmgroupingexperiment.h | 3 +++
src/grouping/ptm/ptmsamplescan.cpp | 7 ++++-
src/grouping/ptm/ptmsamplescan.h | 5 +++-
.../ptmislandlistwindow.cpp | 4 +++
.../ptmislandlistwindow.h | 1 +
.../ptmpeptidelistwindow.cpp | 2 +-
.../ptmpeptidetablemodel.cpp | 16 +++++++++---
.../ptmpeptidetablemodel.h | 3 ++-
9 files changed, 55 insertions(+), 12 deletions(-)
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index 5b157218f..8cbf7bb02 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -28,6 +28,7 @@
******************************************************************************/
#include "ptmgroupingexperiment.h"
+#include "../../grouping/ptm/ptmgroupingexperiment.h"
PtmGroupingExperiment::PtmGroupingExperiment()
{
@@ -162,23 +163,38 @@ unsigned int PtmGroupingExperiment::countPeptideMatchPtm(const PeptideMatch* p_p
}
return number;
}
-std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const ProteinMatch * protein_match) const {
+
+std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const PeptideMatch * p_peptide_match) const {
std::vector<unsigned int> position_list;
- for (PeptideMatch * p_peptide_match: protein_match->getPeptideMatchList(_peptide_validation_state)) {
- unsigned int start = p_peptide_match->getStart();
for (const ModificationAndAa & modification: _modification_list) {
if (modification.aa_list.size() == 0) {
for (unsigned int position : p_peptide_match->getPeptideXtpSp().get()->getModificationPositionList(modification.modification)) {
- position_list.push_back(start+position);
+ position_list.push_back(position);
}
}
else {
for (unsigned int position : p_peptide_match->getPeptideXtpSp().get()->getModificationPositionList(modification.modification, modification.aa_list)) {
- position_list.push_back(start+position);
+ position_list.push_back(position);
}
}
}
+
+ std::sort(position_list.begin(), position_list.end());
+ auto last = std::unique(position_list.begin(), position_list.end());
+ position_list.erase(last, position_list.end());
+ return position_list;
+}
+
+std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const ProteinMatch * protein_match) const {
+ std::vector<unsigned int> position_list;
+
+ for (const PeptideMatch * p_peptide_match: protein_match->getPeptideMatchList(_peptide_validation_state)) {
+ unsigned int start = p_peptide_match->getStart();
+ std::vector<unsigned int> positionb_list = this->getPtmPositions(p_peptide_match);
+ for (unsigned int position: positionb_list) {
+ position_list.push_back(start+position);
+ }
}
std::sort(position_list.begin(), position_list.end());
auto last = std::unique(position_list.begin(), position_list.end());
diff --git a/src/grouping/ptm/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index 852ec8f31..a96a52587 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/src/grouping/ptm/ptmgroupingexperiment.h
@@ -35,6 +35,7 @@
#include "ptmisland.h"
#include "ptmislandsubgroup.h"
#include "ptmislandgroup.h"
+class PtmSampleScan;
struct ModificationAndAa {
pappso::AaModificationP modification;
@@ -43,6 +44,7 @@ struct ModificationAndAa {
class PtmGroupingExperiment
{
+ friend PtmSampleScan;
public:
PtmGroupingExperiment();
~PtmGroupingExperiment();
@@ -60,6 +62,7 @@ public:
private:
std::vector<unsigned int> getPtmPositions(const ProteinMatch * protein_match) const;
+ std::vector<unsigned int> getPtmPositions(const PeptideMatch * p_peptide_match) const;
std::vector< PtmIslandSp > mergePeptideMatchPtmIslandList(vector< PtmIslandSp > ptm_island_list);
void addPtmIsland(PtmIslandSp ptm_island);
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
index 195649f2e..6e2d347b6 100644
--- a/src/grouping/ptm/ptmsamplescan.cpp
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -28,6 +28,7 @@
******************************************************************************/
#include "ptmsamplescan.h"
+#include "../../grouping/ptm/ptmgroupingexperiment.h"
PtmSampleScan::PtmSampleScan(const PeptideMatch * p_peptide_match) {
_peptide_match_list.push_back(p_peptide_match);
@@ -61,7 +62,11 @@ bool PtmSampleScan::add(const PeptideMatch * p_peptide_match) {
return true;
}
- std::vector<unsigned int> PtmSampleScan::getBestPtmPositionList() const {
+ std::vector<unsigned int> PtmSampleScan::getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
+ return p_ptm_grouping_experiment->getPtmPositions(getRepresentativePeptideMatch());
+ }
+
+ std::vector<unsigned int> PtmSampleScan::getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
std::vector<unsigned int> list;
return list;
diff --git a/src/grouping/ptm/ptmsamplescan.h b/src/grouping/ptm/ptmsamplescan.h
index b03cd0177..9036a2768 100644
--- a/src/grouping/ptm/ptmsamplescan.h
+++ b/src/grouping/ptm/ptmsamplescan.h
@@ -33,6 +33,7 @@
#include <memory>
#include "../../core/peptidematch.h"
+class PtmGroupingExperiment;
class PtmSampleScan;
/** \brief shared pointer on a PtmSampleScan object
@@ -49,7 +50,9 @@ public:
const PeptideMatch * getRepresentativePeptideMatch() const;
bool add(const PeptideMatch * p_peptide_match);
- std::vector<unsigned int> getBestPtmPositionList() const;
+ std::vector<unsigned int> getBestPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
+ std::vector<unsigned int> getObservedPtmPositionList(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
+
private:
std::vector<const PeptideMatch *> _peptide_match_list;
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index e2ad12ad0..23c23804a 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -150,3 +150,7 @@ void PtmIslandListWindow::askViewPtmPeptideList(PtmIsland * ptm_island) {
_p_current_ptm_peptide_list_window->show();
}
+
+ const IdentificationGroup * PtmIslandListWindow::getIdentificationGroup() const {
+ return _p_identification_group;
+ }
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index 868fdb7fb..e454e9834 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -50,6 +50,7 @@ public:
~PtmIslandListWindow();
void setIdentificationGroup(IdentificationGroup * p_identification_group);
void resizeColumnsToContents();
+ const IdentificationGroup * getIdentificationGroup() const;
public slots:
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index 4b1bd7019..15ec5d135 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -72,5 +72,5 @@ PtmPeptideListWindow::~PtmPeptideListWindow() {
}
void PtmPeptideListWindow::setPtmIsland(PtmIsland * p_ptm_island) {
_p_ptm_island = p_ptm_island;
- _ptm_table_model_p->setPtmIsland(_p_ptm_island);
+ _ptm_table_model_p->setPtmIsland(_p_ptm_island_list_window->getIdentificationGroup()->getPtmGroupingExperiment(), _p_ptm_island);
}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
index 225405c54..9a7a17818 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
@@ -29,6 +29,7 @@
#include "ptmpeptidetablemodel.h"
#include "ptmpeptidelistwindow.h"
#include <QDebug>
+#include <QStringList>
PtmPeptideTableModel::PtmPeptideTableModel(PtmPeptideListWindow * p_ptm_peptide_list_window) {
}
@@ -153,7 +154,7 @@ int PtmPeptideTableModel::rowCount(const QModelIndex &parent ) const {
}
int PtmPeptideTableModel::columnCount(const QModelIndex &parent ) const {
//qDebug() << "ProteinTableModel::columnCount begin ";
- return 12;
+ return 15;
}
QVariant PtmPeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
{
@@ -175,6 +176,7 @@ QVariant PtmPeptideTableModel::data(const QModelIndex &index, int role ) const {
// generate a log message when this method gets called
int row = index.row();
int col = index.column();
+ QStringList position_list;
if (row >= _ptm_sample_scan_list.size()) return QVariant();
switch(role) {
@@ -221,10 +223,17 @@ QVariant PtmPeptideTableModel::data(const QModelIndex &index, int role ) const {
return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getParam(PeptideMatchParam::tandem_hyperscore);
break;
case (std::int8_t)PtmPeptideListColumn::bestposition:
- //return _ptm_sample_scan_list.at(row).get()->getBestPtmPositionList();
+ for (unsigned int position :_ptm_sample_scan_list.at(row).get()->getBestPtmPositionList(_p_ptm_grouping_experiment)) {
+ position_list << QString("%1").arg(position+1);
+ }
+ return QVariant(position_list.join(" "));
break;
case (std::int8_t)PtmPeptideListColumn::allobservedposition:
//return _ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList();
+ for (unsigned int position :_ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList(_p_ptm_grouping_experiment)) {
+ position_list << QString("%1").arg(position+1);
+ }
+ return QVariant(position_list.join(" "));
break;
}
@@ -232,10 +241,11 @@ QVariant PtmPeptideTableModel::data(const QModelIndex &index, int role ) const {
return QVariant();
}
-void PtmPeptideTableModel::setPtmIsland(PtmIsland * ptm_island) {
+void PtmPeptideTableModel::setPtmIsland(const PtmGroupingExperiment * p_ptm_grouping_experiment, PtmIsland * ptm_island) {
qDebug() << "tmPeptideTableModel::setPtmIsland begin ";
beginResetModel();
+ _p_ptm_grouping_experiment = p_ptm_grouping_experiment;
_p_ptm_island = ptm_island;
_ptm_sample_scan_list = ptm_island->getPtmSampleScanSpList();
//emit headerDataChanged(Qt::Horizontal, 0,11);
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
index d16270d49..603d5346c 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
@@ -73,7 +73,7 @@ public:
static const QString getDescription(PtmPeptideListColumn column);
~PtmPeptideTableModel();
- void setPtmIsland(PtmIsland * ptm_island);
+ void setPtmIsland(const PtmGroupingExperiment * p_ptm_grouping_experiment, PtmIsland * ptm_island);
private :
static const QString getTitle(std::int8_t column);
@@ -82,6 +82,7 @@ private :
private:
std::vector<PtmSampleScanSp> _ptm_sample_scan_list;
const PtmIsland * _p_ptm_island;
+ const PtmGroupingExperiment * _p_ptm_grouping_experiment;
};
#endif // PTMPEPTIDETABLEMODEL_H
--
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