From a443169effd0b30914ef78bdb35fa203f92e8157 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 19 May 2017 11:44:44 +0200
Subject: [PATCH] WIP: writing proticdbml
---
src/CMakeLists.txt | 1 +
src/core/peptidematch.cpp | 3 +++
src/core/peptidematch.h | 4 ++++
src/core/proteinmatch.cpp | 2 +-
src/gui/main.ui | 25 ++++++++++++++++++++-
src/gui/mainwindow.cpp | 30 ++++++++++++++++++++++++-
src/gui/mainwindow.h | 2 ++
src/gui/workerthread.cpp | 17 +++++++++++++++
src/gui/workerthread.h | 1 +
src/output/proticdbml.cpp | 46 +++++++++++++++++++--------------------
src/output/proticdbml.h | 2 +-
src/utils/utils.h | 7 +++---
12 files changed, 110 insertions(+), 30 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 87fc13db8..b406d160a 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -70,6 +70,7 @@ SET(CPP_FILES
input/xpipsaxhandler.cpp
input/xtandemsaxhandler.cpp
output/masschroqml.cpp
+ output/proticdbml.cpp
output/ods/comparbasesheet.cpp
output/ods/comparspecificspectrasheet.cpp
output/ods/comparspectrasheet.cpp
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 77c4a5df5..95aa807dc 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -93,6 +93,9 @@ pappso::mz PeptideMatch::getDeltaMass() const {
unsigned int PeptideMatch::getStart() const {
return _start;
}
+unsigned int PeptideMatch::getStop() const {
+ return _start+_peptide_sp.get()->size();
+}
void PeptideMatch::setCharge(unsigned int charge) {
_charge =charge;
}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index ed9680c5a..69bbe3efb 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -75,6 +75,10 @@ public :
* @return start position in the protein amino acid sequence (starts at 0)
* */
unsigned int getStart() const;
+ /** @brief get stop position of this peptide inside the protein sequence
+ * @return stop position in the protein amino acid sequence (starts at 0)
+ * */
+ unsigned int getStop() const;
void setCharge(unsigned int charge);
void setPeptideXtpSp (PeptideXtpSp peptide);
void setIdentificationDataSource(IdentificationDataSource* identification_source);
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 5da4dfbf4..ca7b1f7e7 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -189,7 +189,7 @@ std::vector<PeptideMatch *> ProteinMatch::getPeptideMatchList(ValidationState st
std::vector<PeptideMatch *> peptide_match_list;
for (auto & p_peptide_match : _peptide_match_list) {
if (p_peptide_match->getValidationState() >= state) {
- ProteinMatch.push_back(p_peptide_match);
+ peptide_match_list.push_back(p_peptide_match);
}
}
return peptide_match_list;
diff --git a/src/gui/main.ui b/src/gui/main.ui
index 8a765a4af..088de3618 100644
--- a/src/gui/main.ui
+++ b/src/gui/main.ui
@@ -26,7 +26,7 @@
<x>0</x>
<y>0</y>
<width>463</width>
- <height>25</height>
+ <height>23</height>
</rect>
</property>
<widget class="QMenu" name="menuFile">
@@ -40,6 +40,7 @@
<addaction name="actionFasta"/>
<addaction name="actionMassChroQ"/>
<addaction name="actionSpreadsheet"/>
+ <addaction name="actionProticDb"/>
</widget>
<addaction name="actionLoad_results"/>
<addaction name="actionLoad"/>
@@ -102,6 +103,11 @@
<string>&Labeling methods</string>
</property>
</action>
+ <action name="actionProticDb">
+ <property name="text">
+ <string>PROTICdb</string>
+ </property>
+ </action>
</widget>
<resources>
<include location="../xtpcpp.qrc"/>
@@ -235,11 +241,28 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>actionProticDb</sender>
+ <signal>triggered()</signal>
+ <receiver>Main</receiver>
+ <slot>doActionProticDb()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>-1</x>
+ <y>-1</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>231</x>
+ <y>191</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>selectXpipFile()</slot>
<slot>loadResults()</slot>
<slot>doActionMassChroQ()</slot>
+ <slot>doActionProticDb()</slot>
<slot>doActionSpreadsheet()</slot>
<slot>doActionQuit()</slot>
<slot>doActionModifications()</slot>
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index a4c74bee8..c2568e558 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -325,7 +325,7 @@ void MainWindow::doActionMassChroQ() {
settings.setValue("path/mcqfile", QFileInfo(filename).absolutePath());
- showWaitingMessage(tr("Loading %1 XPIP file").arg(QFileInfo(filename).fileName()));
+ showWaitingMessage(tr("Writing %1 XPIP file").arg(QFileInfo(filename).fileName()));
emit operateWritingMassChroqFile(filename, _project_sp);
//emit operateXpipFile(filename);
}
@@ -334,3 +334,31 @@ void MainWindow::doActionMassChroQ() {
}
qDebug() << "MainWindow::doActionMassChroQ end";
}
+
+void MainWindow::doActionProticDb() {
+ qDebug() << "MainWindow::doActionProticDb begin";
+ try {
+ _project_sp.get()->checkPsimodCompliance();
+
+ QSettings settings;
+ QString default_location = settings.value("path/proticfile", "").toString();
+
+ QString filename = QFileDialog::getSaveFileName(this, tr("Save PROTICdbML file"),
+ QString("%1/untitled.proticdbml").arg(default_location),
+ tr("PROTICdbML (*.proticdbml)"));
+
+ if (filename.isEmpty()) {
+ return;
+ }
+
+ settings.setValue("path/proticfile", QFileInfo(filename).absolutePath());
+
+ showWaitingMessage(tr("Writing %1 PROTICdbML file").arg(QFileInfo(filename).fileName()));
+ emit operateWritingProticFile(filename, _project_sp);
+ //emit operateXpipFile(filename);
+ }
+ catch (pappso::PappsoException & error) {
+ viewError(tr("Error while writing PROTICdbML file :\n%1").arg(error.qwhat()));
+ }
+ qDebug() << "MainWindow::doActionProticDb end";
+}
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index 3f72f27b4..956d8cf37 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -59,6 +59,7 @@ public slots:
void doActionQuit();
void doActionFasta();
void doActionMassChroQ();
+ void doActionProticDb();
void doActionLabelingMethods();
void doActionSpreadsheet();
void doActionModifications();
@@ -79,6 +80,7 @@ signals:
void operateLoadingResults(bool is_individual, AutomaticFilterParameters param, QStringList file_list);
void operateWritingOdsFile(QString filename, ProjectSp project_sp);
void operateWritingMassChroqFile(QString filename, ProjectSp project_sp);
+ void operateWritingProticFile(QString filename, ProjectSp project_sp);
void operateGrouping(ProjectSp project_sp);
protected:
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 6e97c8c9c..083e52e0d 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -32,6 +32,7 @@
#include <pappsomspp/pappsoexception.h>
#include <QDebug>
#include "../output/masschroqml.h"
+#include "../output/proticdbml.h"
#include "../output/ods/odsexport.h"
#include "files/xpipfile.h"
#include "mainwindow.h"
@@ -62,6 +63,8 @@ WorkerThread::WorkerThread(MainWindow * p_main_window)
connect(this, SIGNAL(groupingFinished()), p_main_window,SLOT(doGroupingFinished()));
//masschroq write
connect(p_main_window, SIGNAL(operateWritingMassChroqFile(QString, ProjectSp)), this,SLOT(doWritingMassChroqFile(QString, ProjectSp)));
+ //protic write
+ connect(p_main_window, SIGNAL(operateWritingProticFile(QString,ProjectSp)), this,SLOT(doWritingProticFile(QString,ProjectSp)));
//writing ODS file :
connect(p_main_window, SIGNAL(operateWritingOdsFile(QString, ProjectSp)), this,SLOT(doWritingOdsFile(QString, ProjectSp)));
connect(this, SIGNAL(operationFailed(QString)), p_main_window,SLOT(doOperationFailed(QString)));
@@ -200,6 +203,20 @@ void WorkerThread::doWritingMassChroqFile(QString filename, ProjectSp project_sp
}
}
+void WorkerThread::doWritingProticFile(QString filename, ProjectSp project_sp) {
+
+ try {
+ emit loadingMessage(tr("writing PROTICdbML file, please wait"));
+ ProticdbMl output(filename);
+ output.write(project_sp);
+ output.close();
+ emit operationFinished();
+ }
+ catch (pappso::PappsoException & error) {
+ emit operationFailed(tr("Error while writing PROTICdbML file :\n%1").arg(error.qwhat()));
+ }
+}
+
void WorkerThread::doLoadingResults(bool is_individual, AutomaticFilterParameters param, QStringList file_list) {
qDebug() << "WorkerThread::doLoadingResults begin ";
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index 76af2b83a..6cf0c3c9e 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -58,6 +58,7 @@ public slots:
void doLoadingResults(bool is_individual, AutomaticFilterParameters param, QStringList file_list);
void doWritingOdsFile(QString filename, ProjectSp project_sp);
void doWritingMassChroqFile(QString filename, ProjectSp project_sp);
+ void doWritingProticFile(QString filename, ProjectSp project_sp);
void doGrouping(ProjectSp project_sp);
void doGroupingOnIdentification(IdentificationGroup * p_identification_group, GroupingType grouping_type);
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index 0e41c92d5..30ce13725 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -127,10 +127,8 @@ void ProticdbMl::writeSequence(ProteinMatch * p_protein_match) {
// dbname="AGI_LocusCode"></dbxref>
//if (prot.get_dbxref_type().equals("no") == false) {
for (const std::pair<ExternalDatabase, QString> & dbxref :p_protein_match->getProteinXtpSp().get()->getDbxrefList()) {
- //if (false) {
_output_stream->writeStartElement("dbxref");
- _output_stream->writeAttribute("dbname",
- Utils::getDatabaseName (dbxref.first));
+ _output_stream->writeAttribute("dbname", Utils::getDatabaseName(dbxref.first));
_output_stream->writeAttribute("key",
dbxref.second);
_output_stream->writeEndElement();// dbxref
@@ -180,7 +178,7 @@ void ProticdbMl::writeProject() {
_output_stream->writeEndDocument();
- qDebug() << "ProticdbMl::writeProject end duration = " << duracel << "ms";
+ qDebug() << "ProticdbMl::writeProject end duration = " << _duracel << "ms";
}
void ProticdbMl::writeIdentMethod() {
@@ -201,9 +199,9 @@ void ProticdbMl::writeIdentMethod() {
void ProticdbMl::writeSamples() {
_output_stream->writeStartElement("samples");
- for (std::vector<MsRunSp> msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
+ for (MsRunSp msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
_output_stream->writeStartElement("sample");
- QString id_samp = "samp" + pappso::Utils::getLexicalOrderedString(sample_to_id.size());
+ QString id_samp = "samp" + pappso::Utils::getLexicalOrderedString(_sample_to_id.size());
QString id_msrun = msrun_sp.get()->getXmlId();
QString name = msrun_sp.get()->getSampleName();
// balise sample
@@ -225,7 +223,7 @@ void ProticdbMl::writeSamples() {
void ProticdbMl::writeMsRuns() {
_output_stream->writeStartElement("msRuns");
- for (std::vector<MsRunSp> msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
+ for (MsRunSp msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
QString name = msrun_sp.get()->getSampleName();
@@ -415,12 +413,12 @@ void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification)
void ProticdbMl::writepeptideHits(IdentificationGroup * p_identification) {
_output_stream->writeStartElement("peptideHits");
for (std::pair <unsigned int, GroupingGroupSp > group_pair : p_identification->getGroupStore().getGroupMap()) {
- writepeptideHitsbyGroup(group_pair.second);
+ writepeptideHitsbyGroup(group_pair.second.get());
}
_output_stream->writeEndElement();// "peptideHits");
}
-QString getProticPeptideHitKey(PeptideMatch * p_peptide_match) {
+QString getProticPeptideHitKey(const PeptideMatch * p_peptide_match) {
return (QString ("%1 %2 %3").arg(p_peptide_match->getHashSampleScan()).arg(p_peptide_match->getPeptideXtpSp().get()->toAbsoluteString()).arg(p_peptide_match->getIdentificationDataSource()->getResourceName()));
}
@@ -431,15 +429,16 @@ struct ProticPeptideHit {
/** key = getProticPeptideHitKey
* */
QString key;
- PeptideMatch * peptide_match;
+ const PeptideMatch * peptide_match;
};
void ProticdbMl::writepeptideHitsbyGroup(GroupingGroup * p_group) {
std::vector <ProticPeptideHit> protic_peptide_hit_list;
- for (PeptideMatch* p_peptide_match : p_group->getPeptideMatchList()) {
- protic_peptide_hit_list.push_back(ProticPeptideHit(getProticPeptideHitKey(p_peptide_match), p_peptide_match));
+ for (const PeptideMatch* p_peptide_match : p_group->getPeptideMatchList()) {
+ ProticPeptideHit protic_peptide_hit = {getProticPeptideHitKey(p_peptide_match), p_peptide_match};
+ protic_peptide_hit_list.push_back(protic_peptide_hit);
}
std::sort(protic_peptide_hit_list.begin(),protic_peptide_hit_list.end(),[](const ProticPeptideHit & first, const ProticPeptideHit & second) {
return (first.key < second.key) ;
@@ -460,7 +459,7 @@ void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_pepti
// param par default
_output_stream->writeStartElement("peptideHit");
- _output_stream->writeAttribute("calc_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->setPeptideXtpSp().get()->getMass()));
+ _output_stream->writeAttribute("calc_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getPeptideXtpSp().get()->getMass()));
_output_stream->writeAttribute("exp_mz", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getExperimentalMz()));
_output_stream->writeAttribute("delta", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getDeltaMass()));
_output_stream->writeAttribute("exp_mr", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getExperimentalMz()- pappso::MHPLUS));
@@ -469,7 +468,7 @@ void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_pepti
_output_stream->writeAttribute("id", xml_id);
_output_stream->writeAttribute("exp_z", QString ("%1").arg(protic_peptide_hit.peptide_match->getCharge()));
- writeCvParam("PROTICdbO:0000339",protic_peptide_hit.peptide_match->setGrpPeptideSp().get()->getGroupingId(),
+ writeCvParam("PROTICdbO:0000339",protic_peptide_hit.peptide_match->getGrpPeptideSp().get()->getGroupingId(),
"peptide mass id");
/*
if (xtpExperimentType.equals("phospho")) {
@@ -486,7 +485,7 @@ void ProticdbMl::writePeptideHit(QString xml_id, ProticPeptideHit & protic_pepti
writeCvParam("PROTICdbO:0000287", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getEvalue()),
"xtandem peptide evalue");
- writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getParam(PeptideMatchParam::tandem_hyperscore)),
+ writeCvParam("PROTICdbO:0000288", Utils::getXmlDouble(protic_peptide_hit.peptide_match->getParam(PeptideMatchParam::tandem_hyperscore).toDouble()),
"xtandem peptide hyperscore");
}
@@ -520,7 +519,7 @@ void ProticdbMl::writePtms(PeptideXtp * p_peptide) {
_output_stream->writeStartElement("ptm");
_output_stream->writeAttribute("diff_mono", Utils::getXmlDouble(aa_modif->getMass()));
_output_stream->writeAttribute("position", QString ("%1").arg(i));
- _output_stream->writeAttribute("aa", amino_acid.getLetter());
+ _output_stream->writeAttribute("aa", QString(amino_acid.getLetter()));
_output_stream->writeEndElement();// ptm
}
}
@@ -600,19 +599,19 @@ void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg
, "Xtandem log evalue");
// coverage
- this.writeCvParam(
+ writeCvParam(
"PROTICdbO:0000285", Utils::getXmlDouble(p_protein_match->getCoverage()),
"protein coverage");
// [Term]
// id: PROTICdbO:0000335
// name: X!TandemPipeline PAI
- this.writeCvParam("PROTICdbO:0000335",Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
+ writeCvParam("PROTICdbO:0000335",Utils::getXmlDouble(p_protein_match->getPAI()), "PAI");
// [Term]
// id: PROTICdbO:0000337
// name: protein group number
- this.writeCvParam("PROTICdbO:0000337",QString("%1").arg(p_protein_match->getGroupingGroupSp().get()->getGroupNumber()), "grouping number");
+ writeCvParam("PROTICdbO:0000337",QString("%1").arg(p_protein_match->getGroupingGroupSp().get()->getGroupNumber()), "grouping number");
_output_stream->writeEndElement();// "proteinHit");
}
@@ -634,14 +633,14 @@ void ProticdbMl::writeMatch(std::vector<const ProteinMatch *> & protein_match_sg
_output_stream->writeAttribute("stop", QString("%1").arg(p_peptide_match->getStop()+1));
QString residue_before_nter = "-";
if (p_peptide_match->getStart() > 0) {
- residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(QString("%1").arg(p_peptide_match->getStart()-1,1);
+ residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStart()-1,1);
}
- _output_stream->writeAttribute("residue_before_nter", residue_before_nter);
+ _output_stream->writeAttribute("residue_before_nter", residue_before_nter);
QString residue_after_cter = "-";
if (p_peptide_match->getStop() < (p_protein_match->getProteinXtpSp().get()->getSequence().size()-1)) {
- residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(QString("%1").arg(p_peptide_match->getStop()-1,1);
+ residue_before_nter = p_protein_match->getProteinXtpSp().get()->getSequence().mid(p_peptide_match->getStop(),1);
}
- _output_stream->writeAttribute("residue_after_cter", residue_after_cter);
+ _output_stream->writeAttribute("residue_after_cter", residue_after_cter);
_output_stream->writeEndElement();// fromSeq
_output_stream->writeEndElement();// peptideHitRef
@@ -672,3 +671,4 @@ void ProticdbMl::writeCvParam(QString acc, QString value, QString description) {
_output_stream->writeEndElement();// cvParam
}
+
diff --git a/src/output/proticdbml.h b/src/output/proticdbml.h
index 36475e612..65f6bbb06 100644
--- a/src/output/proticdbml.h
+++ b/src/output/proticdbml.h
@@ -64,7 +64,7 @@ private :
void writePeptideHit(QString xml_id, ProticPeptideHit & protic_peptide_hit);
void writePtms(PeptideXtp * p_peptide);
void writeMatchs(IdentificationGroup * p_identification);
- void writeMatch(GroupingGroup * p_group,std::vector<const ProteinMatch *> & protein_match_sg_list);
+ void writeMatch(std::vector<const ProteinMatch *> & protein_match_sg_list);
private :
QFile * _output_file;
diff --git a/src/utils/utils.h b/src/utils/utils.h
index 6dc65bd07..5b5581f0f 100644
--- a/src/utils/utils.h
+++ b/src/utils/utils.h
@@ -23,9 +23,10 @@
#include<QUrl>
#include <QString>
#include "types.h"
+#include <pappsomspp/types.h>
-#ifndef UTILS_H
-#define UTILS_H
+#ifndef XTPUTILS_H
+#define XTPUTILS_H
class Utils
{
public:
@@ -34,4 +35,4 @@ public:
static const QString getXmlDouble(pappso::pappso_double number);
};
-#endif // UTILS_H
+#endif // XTPUTILS_H
--
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