From cfb06eabcbaf118368711718973b8480dab925f8 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sun, 13 Aug 2017 08:46:17 +0200
Subject: [PATCH] ptm island ods report OK
---
src/grouping/ptm/ptmgroupingexperiment.cpp | 2 +
src/output/ods/odsexport.cpp | 8 ++++
src/output/ods/proteinsheet.cpp | 9 +++-
src/output/ods/ptmislandsheet.cpp | 50 ++++++++++++++--------
4 files changed, 49 insertions(+), 20 deletions(-)
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index 8cbf7bb02..2e0dbe225 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -29,6 +29,7 @@
#include "ptmgroupingexperiment.h"
#include "../../grouping/ptm/ptmgroupingexperiment.h"
+#include "QDebug"
PtmGroupingExperiment::PtmGroupingExperiment()
{
@@ -74,6 +75,7 @@ PtmGroupingExperiment::~PtmGroupingExperiment()
}
const std::vector<PtmIslandSp> & PtmGroupingExperiment::getPtmIslandList() const {
+ qDebug() << "PtmGroupingExperiment::getPtmIslandList begin" << _ptm_island_list.size();
return _ptm_island_list;
}
diff --git a/src/output/ods/odsexport.cpp b/src/output/ods/odsexport.cpp
index 8cfdd5f68..6ebc5e4ef 100644
--- a/src/output/ods/odsexport.cpp
+++ b/src/output/ods/odsexport.cpp
@@ -38,6 +38,7 @@
#include "infosheet.h"
#include "samplesheet.h"
#include "groupingsheet.h"
+#include "ptmislandsheet.h"
#include <QSettings>
OdsExport::OdsExport(const Project * project):_p_project(project) {
@@ -114,4 +115,11 @@ void OdsExport::write(CalcWriterInterface * p_writer, WorkMonitorInterface * p_m
p_monitor->message(QObject::tr("writing samples"));
SampleSheet(this, p_writer, _p_project);
}
+
+ if (_p_project->hasPtmExperiment()) {
+ if (settings.value("export_ods/ptmislands", "true").toBool()) {
+ p_monitor->message(QObject::tr("writing PTM islands"));
+ PtmIslandSheet(this, p_writer, _p_project);
+ }
+ }
}
diff --git a/src/output/ods/proteinsheet.cpp b/src/output/ods/proteinsheet.cpp
index 8737faf6d..4be82371a 100644
--- a/src/output/ods/proteinsheet.cpp
+++ b/src/output/ods/proteinsheet.cpp
@@ -145,7 +145,14 @@ void ProteinSheet::writeOneProtein(const GroupingGroup * p_group, const ProteinM
_p_writer->writeCell(QString("%1.%2").arg(pappso::Utils::getLexicalOrderedString(group_number)).arg(pappso::Utils::getLexicalOrderedString(subgroup_number)));
_p_writer->clearTableCellStyleRef();
_p_writer->writeCell(p_grp_protein->getGroupingId());
- _p_writer->writeCell(p_protein->getAccession());
+
+ const std::list<DbXref> & dbxref_list = p_protein->getDbxrefList();
+ if (dbxref_list.size() == 0) {
+ _p_writer->writeCell(p_protein->getAccession());
+ }
+ else {
+ _p_writer->writeCell(dbxref_list.front().getUrl(), p_protein->getAccession());
+ }
_p_writer->writeCell(p_protein->getDescription());
_p_writer->writeCell(p_protein_match->getLogEvalue());
// _p_writer->writeCell("Coverage");
diff --git a/src/output/ods/ptmislandsheet.cpp b/src/output/ods/ptmislandsheet.cpp
index 4715a23ed..e5cc53c77 100644
--- a/src/output/ods/ptmislandsheet.cpp
+++ b/src/output/ods/ptmislandsheet.cpp
@@ -34,6 +34,7 @@
#include <pappsomspp/pappsoexception.h>
PtmIslandSheet::PtmIslandSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
+ qDebug() << "PtmIslandSheet::PtmIslandSheet begin" ;
_p_writer = p_writer;
_p_ods_export = p_ods_export;
p_writer->writeSheet("PTM islands");
@@ -43,6 +44,7 @@ PtmIslandSheet::PtmIslandSheet (OdsExport * p_ods_export, CalcWriterInterface *
//writeHeaders(p_ident);
writeIdentificationGroup(p_ident);
}
+ qDebug() << "PtmIslandSheet::PtmIslandSheet end" ;
}
void PtmIslandSheet::writeCellHeader(PtmIslandListColumn column) {
qDebug() << "PtmIslandSheet::writeCellHeader begin " << (std::int8_t) column;
@@ -54,7 +56,7 @@ void PtmIslandSheet::writeCellHeader(PtmIslandListColumn column) {
void PtmIslandSheet::writeHeaders(IdentificationGroup * p_ident) {
//Group ID Sub-group ID PhosphoIsland ID Description MW Phosphosites positions Spectra Uniques number of proteins sharing these phosphosites
//a1 a1.a1 a1.a1.a1 AT1G01100.1 | Symbols: | 60S acidic ribosomal protein family | chr1:50284-50954 REVERSE LENGTH=112 11,1000003814697 102 435 3 6
-
+ qDebug() << "PtmIslandSheet::writeHeaders begin" ;
const std::vector<MsRunSp> msrun_list = p_ident->getMsRunSpList();
if (msrun_list.size() == 1) {
_p_writer->writeCell("sample");
@@ -86,31 +88,40 @@ void PtmIslandSheet::writeHeaders(IdentificationGroup * p_ident) {
_p_writer->setCellAnnotation("Number of proteins sharing this PTM island");
_p_writer->writeCell("Number of proteins");
+ qDebug() << "PtmIslandSheet::writeHeaders end" ;
}
void PtmIslandSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup begin" ;
_p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
- if (_p_ptm_grouping_experiment = nullptr) {
+ if (_p_ptm_grouping_experiment == nullptr) {
throw pappso::PappsoException(QObject::tr("Error writing PTM island :\n_p_ptm_grouping_experiment = nullptr"));
}
writeHeaders(p_ident);
- std::vector<PtmIslandSp> ptm_island_list = _p_ptm_grouping_experiment->getPtmIslandList();
-
- std::sort(ptm_island_list.begin(), ptm_island_list.end(),
- [](PtmIslandSp & a, PtmIslandSp & b)
- {
- return a.get()->getGroupingId() < b.get()->getGroupingId();
- });
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList" ;
+ std::vector<PtmIslandSp> ptm_island_list;
+ for (auto ptm_island_sp : _p_ptm_grouping_experiment->getPtmIslandList() ) {
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup getPtmIslandList copy" ;
+ ptm_island_list.push_back(ptm_island_sp);
+ }
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup sort" ;
+ std::sort(ptm_island_list.begin(), ptm_island_list.end(),
+ [](PtmIslandSp & a, PtmIslandSp & b)
+ {
+ return a.get()->getGroupingId() < b.get()->getGroupingId();
+ });
+
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup 2" ;
+ for (auto & ptm_island:ptm_island_list) {
+ writeOnePtmIsland(ptm_island);
+ }
- for (auto & ptm_island:ptm_island_list) {
- writeOnePtmIsland(ptm_island);
- }
-
_p_writer->writeLine();
+ qDebug() << "PtmIslandSheet::writeIdentificationGroup end" ;
}
@@ -129,7 +140,7 @@ void PtmIslandSheet::writeOnePtmIsland(PtmIslandSp & sp_ptm_island) {
const PtmIslandGroup * p_ptm_island_group = p_ptm_island_subgroup->getPtmIslandGroup();
unsigned int group_number = p_ptm_island_group->getGroupNumber();
unsigned int subgroup_number = p_ptm_island_subgroup->getSubgroupNumber();
-
+
_p_ods_export->setEvenOrOddStyle(group_number, _p_writer);
_p_writer->writeCell(pappso::Utils::getLexicalOrderedString(group_number));
_p_ods_export->setEvenOrOddStyle(subgroup_number, _p_writer);
@@ -139,16 +150,17 @@ void PtmIslandSheet::writeOnePtmIsland(PtmIslandSp & sp_ptm_island) {
_p_writer->writeCell(p_protein->getAccession());
_p_writer->writeCell(p_protein->getDescription());
_p_writer->writeCell(p_protein->getMass());
-
+
QStringList position_list;
- for (unsigned int position : sp_ptm_island.get()->getPositionList()) {
- position_list << QString("%1").arg(position+1);
- }
- _p_writer->writeCell(position_list.join(" "));
+ for (unsigned int position : sp_ptm_island.get()->getPositionList()) {
+ position_list << QString("%1").arg(position+1);
+ }
+ _p_writer->writeCell(position_list.join(" "));
// _p_writer->writeCell("Spectra");
_p_writer->writeCell((unsigned int) sp_ptm_island.get()->getPtmIslandSubroup()->countSampleScan());
// _p_writer->writeCell("Uniques");
_p_writer->writeCell((unsigned int) sp_ptm_island.get()->countSequence());
+ _p_writer->writeCell((unsigned int) sp_ptm_island.get()->getPtmIslandSubroup()->getPtmIslandList().size());
qDebug() << "ProteinSheet::writeOneProtein end" ;
--
GitLab