From 3674e012f27748aca8d8713eebc359e7ff0f1925 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 30 May 2017 23:21:04 +0200
Subject: [PATCH] new columns and titles
---
src/grouping/ptm/ptmgroupingexperiment.cpp | 7 +++
src/grouping/ptm/ptmgroupingexperiment.h | 3 +
src/grouping/ptm/ptmisland.cpp | 27 ++++++++-
src/grouping/ptm/ptmisland.h | 4 ++
.../protein_list_view/proteintablemodel.cpp | 2 +-
.../ptmislandtablemodel.cpp | 58 +++++++++++++++++--
.../ptmislandtablemodel.h | 4 ++
src/utils/types.h | 14 +++--
8 files changed, 106 insertions(+), 13 deletions(-)
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index cf62c0ed6..b92db88d5 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -150,6 +150,13 @@ std::vector< PtmIslandSp > PtmGroupingExperiment::mergePeptideMatchPtmIslandList
}
+ unsigned int PtmGroupingExperiment::countPeptideMatchPtm(const PeptideMatch* p_peptide_match)const {
+ unsigned int number=0;
+ for (pappso::AaModificationP modification: _modification_list) {
+ number += p_peptide_match->getPeptideXtpSp().get()->getNumberOfModification(modification);
+ }
+ return number;
+ }
std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const ProteinMatch * protein_match) const {
std::vector<unsigned int> position_list;
diff --git a/src/grouping/ptm/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index e51e27cba..a8002b377 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/src/grouping/ptm/ptmgroupingexperiment.h
@@ -47,6 +47,9 @@ public:
void startGrouping();
const std::vector<PtmIslandSp> & getPtmIslandList() const;
+ /** @brief count number of modifications in a PeptideMatch
+ * */
+ unsigned int countPeptideMatchPtm(const PeptideMatch* p_peptide_match)const;
private:
std::vector<unsigned int> getPtmPositions(const ProteinMatch * protein_match) const;
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 6d588704e..732c69e26 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -31,7 +31,9 @@
#include <pappsomspp/pappsoexception.h>
#include "ptmislandsubgroup.h"
#include "ptmislandgroup.h"
+#include "ptmgroupingexperiment.h"
#include <pappsomspp/utils.h>
+#include <set>
PtmIsland::PtmIsland(const ProteinMatch* p_protein_match, unsigned int position):_protein_match_p(p_protein_match)
{
@@ -47,9 +49,30 @@ PtmIsland::~PtmIsland()
}
- const std::vector<unsigned int> & PtmIsland::getPositionList() const {
- return _position_list;
+unsigned int PtmIsland::countSampleScanMultiPtm(const PtmGroupingExperiment * p_ptm_grouping_experiment) const {
+ std::set<std::size_t> sample_scan_list;
+ for (auto & p_peptide_match : _peptide_match_list) {
+ if (p_ptm_grouping_experiment->countPeptideMatchPtm(p_peptide_match) > 1) {
+ sample_scan_list.insert(p_peptide_match->getHashSampleScan());
+ }
+ }
+ return sample_scan_list.size();
+}
+
+unsigned int PtmIsland::countSequence() const {
+ std::set<QString> sequence_list;
+ for (auto & p_peptide_match : _peptide_match_list) {
+ sequence_list.insert(p_peptide_match->getPeptideXtpSp().get()->getSequence());
}
+ //qDebug() <<"ProteinMatch::countValidAndCheckedPeptide end " << sequence_list.size();
+ return sequence_list.size();
+}
+const PtmIslandSubgroup * PtmIsland::getPtmIslandSubroup() const {
+ return _ptm_island_subgroup_p;
+}
+const std::vector<unsigned int> & PtmIsland::getPositionList() const {
+ return _position_list;
+}
const QString PtmIsland::getGroupingId() const {
if(_prot_number==0) {
return "";
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index a06a6f17c..f811f016e 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -34,6 +34,7 @@
#include "../../core/peptidematch.h"
#include <memory>
+class PtmGroupingExperiment;
class PtmIslandSubgroup;
class PtmIsland;
@@ -64,6 +65,9 @@ public:
const QString getGroupingId() const;
const std::vector<unsigned int> & getPositionList() const;
+ const PtmIslandSubgroup * getPtmIslandSubroup() const;
+ unsigned int countSequence() const;
+ unsigned int countSampleScanMultiPtm(const PtmGroupingExperiment * p_ptm_grouping_experiment) const;
private:
const ProteinMatch * _protein_match_p;
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 8a7d41767..680c54020 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -170,7 +170,7 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getLogEvalue());
}
if (_column_assignment[col] == (std::int8_t) ProteinListColumn::spectrum ) {
- return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countPeptideMatch(ValidationState::validAndChecked));
+ return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countSampleScan(ValidationState::validAndChecked));
}
if (_column_assignment[col] == (std::int8_t) ProteinListColumn::specific_spectrum ) {
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index 43ed0b6de..97102a3a9 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -30,13 +30,16 @@
#include "ptmislandtablemodel.h"
#include "ptmislandlistwindow.h"
-#include "../../utils/types.h"
PtmIslandTableModel::columnMap PtmIslandTableModel::_column_assignment = {
(std::int8_t)PtmIslandListColumn::ptm_island_id,
(std::int8_t)PtmIslandListColumn::accession,
- (std::int8_t)PtmIslandListColumn::ptm_position_list
+ (std::int8_t)PtmIslandListColumn::description,
+ (std::int8_t)PtmIslandListColumn::spectrum,
+ (std::int8_t)PtmIslandListColumn::sequence,
+ (std::int8_t)PtmIslandListColumn::ptm_position_list,
+ (std::int8_t)PtmIslandListColumn::multiptm
};
@@ -48,6 +51,34 @@ PtmIslandTableModel::PtmIslandTableModel(PtmIslandListWindow * p_ptm_island_list
PtmIslandTableModel::~PtmIslandTableModel()
{
+}
+const QString PtmIslandTableModel::getTitle(std::int8_t column) const {
+ switch (column) {
+
+ case (std::int8_t) PtmIslandListColumn::spectrum:
+ return "spectrum";
+ break;
+
+ case (std::int8_t) PtmIslandListColumn::description:
+ return "description";
+ break;
+ case (std::int8_t) PtmIslandListColumn::multiptm:
+ return "multi PTM";
+ break;
+ case (std::int8_t) PtmIslandListColumn::sequence:
+ return "sequence";
+ break;
+ case (std::int8_t) PtmIslandListColumn::ptm_island_id:
+ return "PTM island ID";
+ break;
+ case (std::int8_t) PtmIslandListColumn::accession:
+ return "accession";
+ break;
+ case (std::int8_t) PtmIslandListColumn::ptm_position_list:
+ return "ptm positions";
+
+ }
+ return "";
}
void PtmIslandTableModel::setIdentificationGroup(IdentificationGroup * p_identification_group) {
qDebug() << "PtmIslandTableModel::setIdentificationGroup begin ";
@@ -75,7 +106,7 @@ int PtmIslandTableModel::rowCount(const QModelIndex &parent ) const {
int PtmIslandTableModel::columnCount(const QModelIndex &parent ) const {
//qDebug() << "ProteinTableModel::columnCount begin ";
if (getPtmGroupingExperiment() != nullptr) {
- return 3;
+ return 7;
}
return 0;
}
@@ -84,6 +115,10 @@ QVariant PtmIslandTableModel::headerData(int section, Qt::Orientation orientatio
if (getPtmGroupingExperiment() == nullptr) return QVariant();
if (orientation == Qt::Horizontal)
{
+ if (role == Qt::DisplayRole)
+ {
+ return QVariant(getTitle(_column_assignment [section]));
+ }
}
return QVariant();
}
@@ -98,6 +133,20 @@ QVariant PtmIslandTableModel::data(const QModelIndex &index, int role ) const {
return QVariant();
}
switch (_column_assignment [col]) {
+
+ case (std::int8_t) PtmIslandListColumn::spectrum:
+ return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getPtmIslandSubroup()->countSampleScan());
+ break;
+
+ case (std::int8_t) PtmIslandListColumn::description:
+ return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getProteinMatch()->getProteinXtpSp().get()->getDescription());
+ break;
+ case (std::int8_t) PtmIslandListColumn::multiptm:
+ return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->countSampleScanMultiPtm(getPtmGroupingExperiment()));
+ break;
+ case (std::int8_t) PtmIslandListColumn::sequence:
+ return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->countSequence());
+ break;
case (std::int8_t) PtmIslandListColumn::ptm_island_id:
return QVariant(getPtmGroupingExperiment()->getPtmIslandList().at(row).get()->getGroupingId());
break;
@@ -110,7 +159,6 @@ QVariant PtmIslandTableModel::data(const QModelIndex &index, int role ) const {
position_list << QString("%1").arg(position+1);
}
return QVariant(position_list.join(" "));
- break;
}
}
return QVariant();
@@ -121,4 +169,4 @@ void PtmIslandTableModel::onPtmIslandDataChanged() {
qDebug() << "PtmIslandTableModel::onPtmIslandDataChanged begin " << rowCount();
emit layoutAboutToBeChanged();
emit layoutChanged();
-}
\ No newline at end of file
+}
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index 7cb1ca930..808cca8d5 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -33,6 +33,7 @@
#include <QAbstractTableModel>
#include "../../core/identificationgroup.h"
#include "../../grouping/ptm/ptmgroupingexperiment.h"
+#include "../../utils/types.h"
class PtmIslandListWindow;
class PtmIslandTableModel: public QAbstractTableModel
@@ -50,6 +51,9 @@ public:
virtual QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
+ const QString getTitle(std::int8_t column) const;
+
+
using columnMap = std::int8_t[20];
public slots:
diff --git a/src/utils/types.h b/src/utils/types.h
index a3934d2f6..38491498f 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -118,11 +118,15 @@ enum class ProteinListColumn {
*
*/
-enum class PtmIslandListColumn: std::int8_t {
- ptm_island_id=0, ///< ptm_island_id
- accession=1, ///< protein accession
- description=2, ///< protein description
- ptm_position_list=3, ///< protein description
+enum class PtmIslandListColumn {
+ ptm_island_id, ///< ptm_island_id
+ accession, ///< protein accession
+ description, ///< protein description
+ ptm_position_list, ///< ptm position list
+ spectrum, ///< count sample scans
+ sequence, ///< unique sequence count
+ multiptm, ///< count multi ptm peptide match
+
};
#endif /* _TYPES_H_ */
--
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