From c798286525afeb6b75e991aef16cadfb5d89d2b1 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 22 Mar 2018 17:13:01 +0100
Subject: [PATCH] WIP: writing PTM spectra ODS sheet
---
src/CMakeLists.txt | 1 +
src/grouping/ptm/ptmisland.cpp | 3 +
src/grouping/ptm/ptmisland.h | 2 +
.../export_spreadsheet_dialog.ui | 74 ++++++---
.../exportspreadsheetdialog.cpp | 8 +
.../exportspreadsheetdialog.h | 1 +
.../peptide_list_view/peptidetablemodel.cpp | 22 ++-
src/gui/peptide_list_view/peptidetablemodel.h | 8 +-
src/output/ods/odsexport.cpp | 6 +
src/output/ods/ptm/ptmspectrasheet.cpp | 156 ++++++++++++------
src/output/ods/ptm/ptmspectrasheet.h | 3 +-
11 files changed, 201 insertions(+), 83 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 69230341c..62d206981 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -102,6 +102,7 @@ SET(CPP_FILES
input/xtandemsaxhandler.cpp
input/xtpxpipsaxhandler.cpp
output/ods/ptm/ptmislandsheet.cpp
+ output/ods/ptm/ptmspectrasheet.cpp
output/ods/comparbasesheet.cpp
output/ods/comparspecificspectrasheet.cpp
output/ods/comparspectrasheet.cpp
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index bae1d3bf0..388780249 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -172,6 +172,9 @@ bool PtmIsland::merge(PtmIslandSp ptm_island_sp) {
return true;
}
}
+const std::vector<PeptideMatch> & PtmIsland::getPeptideMatchList() const {
+ return _peptide_match_list;
+}
std::vector<PtmSampleScanSp> PtmIsland::getPtmSampleScanSpList() const {
qDebug() << "PtmIsland::getPtmSampleScanSpList begin" ;
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index b1fe701b5..7d66eaa3d 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -74,6 +74,8 @@ public:
unsigned int size() const;
std::vector<PtmSampleScanSp> getPtmSampleScanSpList() const;
+
+ const std::vector<PeptideMatch> & getPeptideMatchList() const;
private:
const ProteinMatch * _protein_match_p;
diff --git a/src/gui/export_spreadsheet_dialog/export_spreadsheet_dialog.ui b/src/gui/export_spreadsheet_dialog/export_spreadsheet_dialog.ui
index 72cf2b741..c2d5c0c1d 100644
--- a/src/gui/export_spreadsheet_dialog/export_spreadsheet_dialog.ui
+++ b/src/gui/export_spreadsheet_dialog/export_spreadsheet_dialog.ui
@@ -121,14 +121,21 @@
<property name="title">
<string>PTM</string>
</property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
+ <layout class="QGridLayout" name="gridLayout_2">
+ <item row="0" column="0">
<widget class="QCheckBox" name="ptmislands_checkbox">
<property name="text">
<string>PTM islands</string>
</property>
</widget>
</item>
+ <item row="0" column="1">
+ <widget class="QCheckBox" name="ptmspectra_checkbox">
+ <property name="text">
+ <string>PTM spectra</string>
+ </property>
+ </widget>
+ </item>
</layout>
</widget>
</item>
@@ -178,7 +185,7 @@
<hints>
<hint type="sourcelabel">
<x>665</x>
- <y>523</y>
+ <y>507</y>
</hint>
<hint type="destinationlabel">
<x>286</x>
@@ -194,7 +201,7 @@
<hints>
<hint type="sourcelabel">
<x>579</x>
- <y>523</y>
+ <y>507</y>
</hint>
<hint type="destinationlabel">
<x>286</x>
@@ -209,8 +216,8 @@
<slot>doGroups(bool)</slot>
<hints>
<hint type="sourcelabel">
- <x>210</x>
- <y>101</y>
+ <x>231</x>
+ <y>69</y>
</hint>
<hint type="destinationlabel">
<x>839</x>
@@ -225,8 +232,8 @@
<slot>doProteins(bool)</slot>
<hints>
<hint type="sourcelabel">
- <x>108</x>
- <y>133</y>
+ <x>129</x>
+ <y>101</y>
</hint>
<hint type="destinationlabel">
<x>814</x>
@@ -241,8 +248,8 @@
<slot>doPeptides(bool)</slot>
<hints>
<hint type="sourcelabel">
- <x>382</x>
- <y>165</y>
+ <x>403</x>
+ <y>133</y>
</hint>
<hint type="destinationlabel">
<x>857</x>
@@ -257,8 +264,8 @@
<slot>doSpectra(bool)</slot>
<hints>
<hint type="sourcelabel">
- <x>99</x>
- <y>197</y>
+ <x>120</x>
+ <y>165</y>
</hint>
<hint type="destinationlabel">
<x>760</x>
@@ -273,8 +280,8 @@
<slot>doPeptidePos(bool)</slot>
<hints>
<hint type="sourcelabel">
- <x>317</x>
- <y>229</y>
+ <x>338</x>
+ <y>197</y>
</hint>
<hint type="destinationlabel">
<x>764</x>
@@ -289,8 +296,8 @@
<slot>doSamples(bool)</slot>
<hints>
<hint type="sourcelabel">
- <x>244</x>
- <y>261</y>
+ <x>265</x>
+ <y>229</y>
</hint>
<hint type="destinationlabel">
<x>835</x>
@@ -305,8 +312,8 @@
<slot>doComparSpectra(bool)</slot>
<hints>
<hint type="sourcelabel">
- <x>124</x>
- <y>328</y>
+ <x>157</x>
+ <y>296</y>
</hint>
<hint type="destinationlabel">
<x>785</x>
@@ -322,7 +329,7 @@
<hints>
<hint type="sourcelabel">
<x>437</x>
- <y>328</y>
+ <y>296</y>
</hint>
<hint type="destinationlabel">
<x>836</x>
@@ -338,7 +345,7 @@
<hints>
<hint type="sourcelabel">
<x>231</x>
- <y>360</y>
+ <y>328</y>
</hint>
<hint type="destinationlabel">
<x>736</x>
@@ -354,7 +361,7 @@
<hints>
<hint type="sourcelabel">
<x>437</x>
- <y>360</y>
+ <y>328</y>
</hint>
<hint type="destinationlabel">
<x>753</x>
@@ -370,7 +377,7 @@
<hints>
<hint type="sourcelabel">
<x>642</x>
- <y>328</y>
+ <y>296</y>
</hint>
<hint type="destinationlabel">
<x>790</x>
@@ -386,7 +393,7 @@
<hints>
<hint type="sourcelabel">
<x>642</x>
- <y>360</y>
+ <y>328</y>
</hint>
<hint type="destinationlabel">
<x>793</x>
@@ -401,8 +408,8 @@
<slot>doPtmIslands(bool)</slot>
<hints>
<hint type="sourcelabel">
- <x>79</x>
- <y>427</y>
+ <x>112</x>
+ <y>407</y>
</hint>
<hint type="destinationlabel">
<x>765</x>
@@ -410,6 +417,22 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>ptmspectra_checkbox</sender>
+ <signal>clicked(bool)</signal>
+ <receiver>ExportSpreadsheetDialog</receiver>
+ <slot>doPtmSpectra(bool)</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>389</x>
+ <y>392</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>976</x>
+ <y>366</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>reject()</slot>
@@ -428,5 +451,6 @@
<slot>doComparPai(bool)</slot>
<slot>doComparEmpai(bool)</slot>
<slot>doPtmIslands(bool)</slot>
+ <slot>doPtmSpectra(bool)</slot>
</slots>
</ui>
diff --git a/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp b/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
index 7a28da0d2..45a1a878f 100644
--- a/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
+++ b/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.cpp
@@ -96,6 +96,10 @@ ExportSpreadsheetDialog::ExportSpreadsheetDialog(QWidget * parent):
if (settings.value("export_ods/ptmislands", "true").toBool()) {
ui->ptmislands_checkbox->setCheckState(Qt::Checked);
}
+ ui->ptmspectra_checkbox->setCheckState(Qt::Unchecked);
+ if (settings.value("export_ods/ptmspectra", "true").toBool()) {
+ ui->ptmspectra_checkbox->setCheckState(Qt::Checked);
+ }
//param.setFilterCrossSamplePeptideNumber(settings.value("automatic_filter/cross_sample", "true").toBool());
#if QT_VERSION >= 0x050000
@@ -192,6 +196,10 @@ void ExportSpreadsheetDialog::doPtmIslands(bool simple) {
QSettings settings;
settings.setValue("export_ods/ptmislands", QString("%1").arg(simple));
}
+void ExportSpreadsheetDialog::doPtmSpectra(bool simple) {
+ QSettings settings;
+ settings.setValue("export_ods/ptmspectra", QString("%1").arg(simple));
+}
void ExportSpreadsheetDialog::setProject(const Project * p_project) {
diff --git a/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.h b/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.h
index 15113e8da..33892c523 100644
--- a/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.h
+++ b/src/gui/export_spreadsheet_dialog/exportspreadsheetdialog.h
@@ -60,6 +60,7 @@ public slots:
void doPeptides(bool simple);
void doProteins(bool simple);
void doPtmIslands(bool simple);
+ void doPtmSpectra(bool simple);
signals:
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index 866894021..396aac97e 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -68,7 +68,7 @@ int PeptideTableModel::rowCount(const QModelIndex &parent ) const {
return 0;
}
int PeptideTableModel::columnCount(const QModelIndex &parent ) const {
- return 20;
+ return 22;
}
QVariant PeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
{
@@ -185,12 +185,18 @@ QVariant PeptideTableModel::data(const QModelIndex &index, int role ) const {
case (std::int8_t)PeptideListColumn::Evalue:
return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getEvalue());
break;
+ case (std::int8_t)PeptideListColumn::experimental_mhplus:
+ return QVariant((qreal) (_p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getExperimentalMass()+pappso::MHPLUS));
+ break;
case (std::int8_t)PeptideListColumn::theoretical_mhplus:
return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPeptideXtpSp().get()->getMz(1));
break;
case (std::int8_t)PeptideListColumn::delta_mhplus:
return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getDeltaMass());
break;
+ case (std::int8_t)PeptideListColumn::delta_ppm:
+ return QVariant((qreal) _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getPpmDeltaMass());
+ break;
case (std::int8_t)PeptideListColumn::hyperscore:
return _p_protein_match->getPeptideMatchList().at(row).getPeptideEvidence()->getParam(PeptideEvidenceParam::tandem_hyperscore);
break;
@@ -281,12 +287,18 @@ const QString PeptideTableModel::getTitle(std::int8_t column) {
case (std::int8_t) PeptideListColumn::Evalue:
return "Evalue";
break;
+ case (std::int8_t) PeptideListColumn::experimental_mhplus:
+ return "observed MH+";
+ break;
case (std::int8_t) PeptideListColumn::theoretical_mhplus:
return "theoretical MH+";
break;
case (std::int8_t) PeptideListColumn::delta_mhplus:
return "delta MH+";
break;
+ case (std::int8_t) PeptideListColumn::delta_ppm:
+ return "delta ppm";
+ break;
case (std::int8_t) PeptideListColumn::hyperscore:
return "hyperscore";
break;
@@ -350,11 +362,17 @@ const QString PeptideTableModel::getDescription(std::int8_t column) {
case (std::int8_t) PeptideListColumn::Evalue:
return "peptide Evalue";
break;
+ case (std::int8_t) PeptideListColumn::experimental_mhplus:
+ return "observed peptide mass + H+";
+ break;
case (std::int8_t) PeptideListColumn::theoretical_mhplus:
return "peptide theoretical MH+";
break;
case (std::int8_t) PeptideListColumn::delta_mhplus:
- return "peptide mass difference between observed mass and theoretical mass";
+ return "peptide mass difference in dalton between theoretical mass and observed mass (theoretical - observed)";
+ break;
+ case (std::int8_t) PeptideListColumn::delta_ppm:
+ return "peptide mass difference in ppm between theoretical mass and observed mass";
break;
case (std::int8_t) PeptideListColumn::hyperscore:
return "X!Tandem hyperscore";
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index 2281ede65..5aa61a294 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -49,9 +49,11 @@ enum class PeptideListColumn: std::int8_t {
subgroups=14,
Evalue=15,
theoretical_mhplus=16,
- delta_mhplus=17,
- hyperscore=18,
- mascot_score=19
+ experimental_mhplus=17,
+ delta_mhplus=18,
+ delta_ppm=19,
+ hyperscore=20,
+ mascot_score=21
};
class PeptideListWindow;
diff --git a/src/output/ods/odsexport.cpp b/src/output/ods/odsexport.cpp
index 86699dee8..ad1b661c6 100644
--- a/src/output/ods/odsexport.cpp
+++ b/src/output/ods/odsexport.cpp
@@ -39,6 +39,7 @@
#include "samplesheet.h"
#include "groupingsheet.h"
#include "ptm/ptmislandsheet.h"
+#include "ptm/ptmspectrasheet.h"
#include <QSettings>
OdsExport::OdsExport(const Project * project):_p_project(project) {
@@ -124,5 +125,10 @@ void OdsExport::write(CalcWriterInterface * p_writer, WorkMonitorInterface * p_m
p_monitor->message(QObject::tr("writing PTM islands"));
PtmIslandSheet(this, p_writer, _p_project);
}
+
+ if (settings.value("export_ods/ptmspectra", "true").toBool()) {
+ p_monitor->message(QObject::tr("writing PTM spectra"));
+ PtmSpectraSheet(this, p_writer, _p_project);
+ }
}
}
diff --git a/src/output/ods/ptm/ptmspectrasheet.cpp b/src/output/ods/ptm/ptmspectrasheet.cpp
index 49bc3ff82..b8010e170 100644
--- a/src/output/ods/ptm/ptmspectrasheet.cpp
+++ b/src/output/ods/ptm/ptmspectrasheet.cpp
@@ -70,33 +70,82 @@ void PtmSpectraSheet::writeHeaders(IdentificationGroup * p_ident) {
_p_writer->writeLine();
+
+ // Group ID
_p_writer->writeCell("Group ID");
+
+ // Sub-group ID
+
+ // Phosphopeptide ID
_p_writer->writeCell("Peptide ID");
- _p_writer->setCellAnnotation("MS sample name (MS run)");
- _p_writer->writeCell("Sample");
+
+ // Modifs (top) Best position in peptide All observed positions in phosphopeptide Number of phosphoislands Phosphoislands Ids Best e-value Charge MH+ Obs MH+ theo DeltaMH+ Delta-ppm
+
+ // Sample
+ writeCellHeader(PeptideListColumn::sample);
+
+ // Scan
writeCellHeader(PeptideListColumn::scan);
- _p_writer->setCellAnnotation("retention time in seconds");
- _p_writer->writeCell("Rt (seconds)");
- _p_writer->setCellAnnotation("experimental precursor m/z");
- _p_writer->writeCell("Precursor m/z");
+
+ // Rt
+ writeCellHeader(PeptideListColumn::rt);
+
+ // Sequence (top)
_p_writer->setCellAnnotation("peptide sequence (best match)");
- _p_writer->writeCell("Sequence (top)");
- _p_writer->setCellAnnotation("peptide charge (best match)");
- _p_writer->writeCell("Charge (top)");
- _p_writer->setCellAnnotation("peptide modifications (best match)");
- _p_writer->writeCell("Modifs (top)");
+ _p_writer->writeCell("sequence (top)");
+
+
+ // Modifs (top)
+ _p_writer->setCellAnnotation("peptide modification list (best match)");
+ _p_writer->writeCell("modifs (top)");
+
if (_p_project->getLabelingMethodSp().get() != nullptr) {
_p_writer->setCellAnnotation("peptide label (best match)");
_p_writer->writeCell("Label (top)");
}
- _p_writer->writeCell("Best E-value");
- _p_writer->writeCell("Best hyperscore");
+
+ // Best position in peptide
+ _p_writer->setCellAnnotation("best PTM positions for this sample/scan");
+ _p_writer->writeCell("best positions in peptide");
+
+ // All observed positions in phosphopeptide
+ _p_writer->setCellAnnotation("All observed positions for this sample/scan");
+ _p_writer->writeCell("all positions in peptide");
+
+ // Number of phosphoislands
+ _p_writer->setCellAnnotation("Number of phosphoislands share this sample/scan");
+ _p_writer->writeCell("number of phosphoislands");
+
+ // Phosphoislands Ids
+ _p_writer->setCellAnnotation("Phosphoislands id list");
+ _p_writer->writeCell("phosphoislands");
+
+ // Best e-value
+ _p_writer->writeCell("best E-value");
+
+
+ _p_writer->writeCell("best hyperscore");
+
+
+ // Charge
+ writeCellHeader(PeptideListColumn::charge);
+
+ // MH+ Obs
+ writeCellHeader(PeptideListColumn::experimental_mhplus);
+
+ // MH+ theo
+ writeCellHeader(PeptideListColumn::theoretical_mhplus);
+
+ // DeltaMH+
writeCellHeader(PeptideListColumn::delta_mhplus);
+ // Delta-ppm
+ writeCellHeader(PeptideListColumn::delta_ppm);
+
}
-void PtmSpectraSheet::writeBestPeptideEvidence(const GroupingGroup * p_group,const PeptideEvidence * p_peptide_evidence) {
+void PtmSpectraSheet::writeBestPeptideEvidence(const PeptideEvidence * p_peptide_evidence, std::set<const PtmIsland *> & ptmisland_occurence_list) {
_p_writer->writeLine();
@@ -136,50 +185,53 @@ void PtmSpectraSheet::writeIdentificationGroup(IdentificationGroup * p_ident) {
_p_ptm_grouping_experiment = p_ident->getPtmGroupingExperiment();
writeHeaders(p_ident);
- _p_ptm_grouping_experiment->get
- for (const std::pair<unsigned int, GroupingGroupSp> & group_pair : p_ident->getGroupStore().getGroupMap()) {
-
- std::vector<const PeptideEvidence *> peptide_evidence_list = group_pair.second.get()->getPeptideEvidenceList();
-
- std::sort(peptide_evidence_list.begin(), peptide_evidence_list.end(),
- [](const PeptideEvidence * a, const PeptideEvidence * b)
- {
- unsigned int arank = a->getGrpPeptideSp().get()->getRank();
- unsigned int ascan = a->getScan();
- unsigned int brank = b->getGrpPeptideSp().get()->getRank();
- unsigned int bscan = b->getScan();
- return std::tie(arank, a->getMsRunP()->getSampleName(), ascan) < std::tie(brank, b->getMsRunP()->getSampleName(), bscan);
- });
-
- const PeptideEvidence * p_best_peptide_evidence = nullptr;
-
- for (auto & peptide_evidence:peptide_evidence_list) {
- if (p_best_peptide_evidence == nullptr) {
- p_best_peptide_evidence = peptide_evidence;
+ for (const PtmIslandSubgroupSp & ptm_island_subgroup_sp : _p_ptm_grouping_experiment->getPtmIslandSubgroupList() ) {
+ writePtmIslandSubgroupSp(ptm_island_subgroup_sp);
+ }
+
+ _p_writer->writeLine();
+ _p_writer->writeLine();
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+}
+
+void PtmSpectraSheet::writePtmIslandSubgroupSp(const PtmIslandSubgroupSp & ptm_island_subgroup_sp) {
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ struct PtmSampleScanOccurence {
+ PtmSampleScan ptm_sample_scan;
+ std::set<const PtmIsland *> ptmisland_occurence_list;
+ };
+ std::vector<PtmSampleScanOccurence> ptm_sample_scan_occurence_list;
+
+ for (PtmIslandSp ptm_island_sp :ptm_island_subgroup_sp.get()->getPtmIslandList()) {
+ for (PeptideMatch peptide_match: ptm_island_sp.get()->getPeptideMatchList()) {
+ std::vector<PtmSampleScanOccurence>::iterator it_ptm = ptm_sample_scan_occurence_list.begin();
+ std::vector<PtmSampleScanOccurence>::iterator it_ptm_end = ptm_sample_scan_occurence_list.end();
+ while ((it_ptm != it_ptm_end) && (it_ptm->ptm_sample_scan.add(peptide_match) == false)) {
+ //peptide added
+ it_ptm++;
}
- //change spectra :
- unsigned int arank = p_best_peptide_evidence->getGrpPeptideSp().get()->getRank();
- unsigned int ascan = p_best_peptide_evidence->getScan();
- unsigned int brank = peptide_evidence->getGrpPeptideSp().get()->getRank();
- unsigned int bscan = peptide_evidence->getScan();
-
- if (std::tie(arank, p_best_peptide_evidence->getMsRunP()->getSampleName(), ascan) != std::tie(brank, peptide_evidence->getMsRunP()->getSampleName(), bscan)) {
- //write p_best_peptide_match
- writeBestPeptideEvidence(group_pair.second.get(), p_best_peptide_evidence);
- p_best_peptide_evidence = peptide_evidence;
+ if (it_ptm == it_ptm_end) {
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ //peptide NOT added
+ PtmSampleScanOccurence new_occurence = {PtmSampleScan(peptide_match),std::set<const PtmIsland *>()};
+ new_occurence.ptmisland_occurence_list.insert(ptm_island_sp.get());
+ ptm_sample_scan_occurence_list.push_back(new_occurence);
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
}
else {
- if (p_best_peptide_evidence->getEvalue()> peptide_evidence->getEvalue()) {
- p_best_peptide_evidence = peptide_evidence;
- }
+ //peptide added
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
+ it_ptm->ptmisland_occurence_list.insert(ptm_island_sp.get());
+
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
}
}
+ }
+
+ qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
- if (p_best_peptide_evidence != nullptr) {
- writeBestPeptideEvidence(group_pair.second.get(), p_best_peptide_evidence);
- }
+ for (PtmSampleScanOccurence & occurence: ptm_sample_scan_occurence_list) {
+ writeBestPeptideEvidence(occurence.ptm_sample_scan.getRepresentativePeptideMatch().getPeptideEvidence(), occurence.ptmisland_occurence_list);
}
- _p_writer->writeLine();
- _p_writer->writeLine();
qDebug() << __FILE__ << " " << __FUNCTION__<< " " << __LINE__;
}
diff --git a/src/output/ods/ptm/ptmspectrasheet.h b/src/output/ods/ptm/ptmspectrasheet.h
index deba3a2c2..3a7f48bfd 100644
--- a/src/output/ods/ptm/ptmspectrasheet.h
+++ b/src/output/ods/ptm/ptmspectrasheet.h
@@ -45,9 +45,10 @@ protected :
PtmSpectraSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project, const QString & sheet_name);
virtual void writeIdentificationGroup(IdentificationGroup * p_ident);
void writeHeaders(IdentificationGroup * p_ident);
- void writeBestPeptideEvidence(const GroupingGroup * p_group, const PeptideEvidence * p_peptide_evidence);
+ void writeBestPeptideEvidence(const PeptideEvidence * p_peptide_evidence, std::set<const PtmIsland *> & ptmisland_occurence_list);
void writeCellHeader(PeptideListColumn column);
+ void writePtmIslandSubgroupSp(const PtmIslandSubgroupSp & ptm_island_subgroup_sp);
protected :
OdsExport * _p_ods_export;
const PtmGroupingExperiment * _p_ptm_grouping_experiment;
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