From 62ead64094b80b2e3b4c3ef2e756daf6e9fdda17 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 30 Apr 2019 08:34:48 +0200
Subject: [PATCH] WIP: adapting xtpcpp to new PAPPSOms++ library
---
src/core/msrun.cpp | 50 ++++++++++++++++++++----
src/input/mascot/mascotdatparser.cpp | 57 ++++++++++++++++------------
src/input/pepxmlsaxhandler.cpp | 42 +++++++++++---------
src/input/xpipsaxhandler.cpp | 2 +-
src/input/xtandemsaxhandler.cpp | 2 +-
src/input/xtpxpipsaxhandler.cpp | 2 +-
src/utils/msrunstore.cpp | 13 ++++---
7 files changed, 110 insertions(+), 58 deletions(-)
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index b4ca0879c..ec29da3d8 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -164,10 +164,27 @@ MsRun::findMsRunFile()
{
if(_msrun_reader_sp == nullptr)
{
- _msrun_reader_sp =
- pappso::MsRunReaderFactory::getInstance()
- .buildPwizMsRunReaderSp(*this);
+ pappso::MsFileAccessor accessor(getFilename(), 0);
+ qDebug()
+ << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";
+ auto msrunid_list = accessor.getMsRunIds();
+ if(msrunid_list.size() == 1)
+ {
+ _msrun_reader_sp =
+ accessor.msRunReaderSp(msrunid_list.front());
+ }
+ else
+ {
+ throw(pappso::ExceptionNotImplemented(
+ QObject::tr("multiple msruns inside mz data file "
+ "not yet implemented")));
+ }
+ /*
+ _msrun_reader_sp =
+ pappso::MsRunReaderFactory::getInstance()
+ .buildPwizMsRunReaderSp(*this);
+ */
return true;
}
}
@@ -182,13 +199,30 @@ MsRun::findMsRunFile()
{
try
{
- this->setFilename(file.absoluteFilePath());
+ this->setFileName(file.absoluteFilePath());
if(_msrun_reader_sp == nullptr)
{
- _msrun_reader_sp =
- pappso::MsRunReaderFactory::getInstance()
- .buildPwizMsRunReaderSp(*this);
+
+ pappso::MsFileAccessor accessor(getFilename(), 0);
+ qDebug()
+ << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";
+ auto msrunid_list = accessor.getMsRunIds();
+ if(msrunid_list.size() == 1)
+ {
+ _msrun_reader_sp =
+ accessor.msRunReaderSp(msrunid_list.front());
+ }
+ else
+ {
+ throw(pappso::ExceptionNotImplemented(
+ QObject::tr("multiple msruns inside mz data file "
+ "not yet implemented")));
+ }
+ /*
+ _msrun_reader_sp =
+ pappso::MsRunReaderFactory::getInstance()
+ .buildPwizMsRunReaderSp(*this);*/
return true;
}
}
@@ -199,7 +233,7 @@ MsRun::findMsRunFile()
}
}
}
- this->setFilename(file_original.absoluteFilePath());
+ this->setFileName(file_original.absoluteFilePath());
_msrun_reader_sp = nullptr;
return false;
}
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index e0ea73b2a..306d71a2e 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -38,7 +38,8 @@
#include "../../core/peptideevidence.h"
MascotDatParser::MascotDatParser(
- Project *p_project, IdentificationGroup *p_identification_group,
+ Project *p_project,
+ IdentificationGroup *p_identification_group,
IdentificationDataSource *p_identification_data_source)
{
_p_project = p_project;
@@ -418,7 +419,7 @@ INTERNALS=0.0,700.0
{
// FILE=F:\MSData\Batch4 Qex+TOUL Injection2\QEKAC160601_02.raw.mgf
- _p_identification_data_source->getMsRunSp().get()->setFilename(
+ _p_identification_data_source->getMsRunSp().get()->setFileName(
header_list[2]);
QFileInfo fileinfo(header_list[2]);
@@ -550,8 +551,9 @@ MascotDatParser::parsePeptidesLine(const QString &peptide_line)
catch(pappso::PappsoException exception_pappso)
{
- _error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine "
- "%1, PAPPSO exception:\n%2 near q%3_p%4")
+ _error_str = QObject::tr(
+ "ERROR in MascotDatParser::parsePeptidesLine "
+ "%1, PAPPSO exception:\n%2 near q%3_p%4")
.arg(peptide_line)
.arg(exception_pappso.qwhat())
.arg(_current_peptide.query_index)
@@ -561,13 +563,13 @@ MascotDatParser::parsePeptidesLine(const QString &peptide_line)
}
catch(std::exception exception_std)
{
- _error_str =
- QObject::tr("ERROR in MascotDatParser::parsePeptidesLine %1, std "
- "exception:\n%2 near q%3_p%4")
- .arg(peptide_line)
- .arg(exception_std.what())
- .arg(_current_peptide.query_index)
- .arg(_current_peptide.peptide_index);
+ _error_str = QObject::tr(
+ "ERROR in MascotDatParser::parsePeptidesLine %1, std "
+ "exception:\n%2 near q%3_p%4")
+ .arg(peptide_line)
+ .arg(exception_std.what())
+ .arg(_current_peptide.query_index)
+ .arg(_current_peptide.peptide_index);
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
}
@@ -637,11 +639,11 @@ MascotDatParser::parseQueryLine(const QString &query_line)
catch(pappso::PappsoException exception_pappso)
{
- _error_str =
- QObject::tr("ERROR in MascotDatParser::parseQueryLine %1, PAPPSO "
- "exception:\n%2")
- .arg(query_line)
- .arg(exception_pappso.qwhat());
+ _error_str = QObject::tr(
+ "ERROR in MascotDatParser::parseQueryLine %1, PAPPSO "
+ "exception:\n%2")
+ .arg(query_line)
+ .arg(exception_pappso.qwhat());
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
}
@@ -846,13 +848,15 @@ MascotDatParser::savePeptideList(std::vector<PeptideLine> &peptide_list,
{
peptide_evidence.setEvalue(getEvalue(
ion_score,
- _decoy_summary_list.at(_current_query.query_index - 1), 0.05));
+ _decoy_summary_list.at(_current_query.query_index - 1),
+ 0.05));
}
else
{
- peptide_evidence.setEvalue(getEvalue(
- ion_score, _summary_list.at(_current_query.query_index - 1),
- 0.05));
+ peptide_evidence.setEvalue(
+ getEvalue(ion_score,
+ _summary_list.at(_current_query.query_index - 1),
+ 0.05));
}
peptide_evidence.setParam(
@@ -984,16 +988,18 @@ MascotDatParser::savePeptideList(std::vector<PeptideLine> &peptide_list,
catch(pappso::PappsoException exception_pappso)
{
- _error_str = QObject::tr("ERROR in MascotDatParser::savePeptideList "
- " PAPPSO exception:\n%2")
+ _error_str = QObject::tr(
+ "ERROR in MascotDatParser::savePeptideList "
+ " PAPPSO exception:\n%2")
.arg(exception_pappso.qwhat());
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
}
catch(std::exception exception_std)
{
- _error_str = QObject::tr("ERROR in MascotDatParser::savePeptideList std "
- "exception:\n%2")
+ _error_str = QObject::tr(
+ "ERROR in MascotDatParser::savePeptideList std "
+ "exception:\n%2")
.arg(exception_std.what());
qDebug() << _error_str;
throw pappso::PappsoException(_error_str);
@@ -1019,7 +1025,8 @@ MascotDatParser::getEvalue(pappso::pappso_double ion_score,
pappso::pappso_double
MascotDatParser::getEvalueExperimental(
- pappso::pappso_double ion_score, SummaryLine &summary_line,
+ pappso::pappso_double ion_score,
+ SummaryLine &summary_line,
pappso::pappso_double confidence_interval) const
{
// Evalue experimental Homology threshold (QPlughole value from .dat file).
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index af6b1be03..bdc252be1 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -38,7 +38,8 @@
PepXmlSaxHandler::PepXmlSaxHandler(
- Project *p_project, IdentificationGroup *p_identification_group,
+ Project *p_project,
+ IdentificationGroup *p_identification_group,
IdentificationDataSource *p_identification_data_source)
: _p_project(p_project)
{
@@ -55,7 +56,8 @@ PepXmlSaxHandler::~PepXmlSaxHandler()
bool
PepXmlSaxHandler::startElement(const QString &namespaceURI,
- const QString &localName, const QString &qName,
+ const QString &localName,
+ const QString &qName,
const QXmlAttributes &attributes)
{
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -128,8 +130,9 @@ PepXmlSaxHandler::startElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::startElement tag "
- "%1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in PepXmlSaxHandler::startElement tag "
+ "%1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -148,7 +151,8 @@ PepXmlSaxHandler::startElement(const QString &namespaceURI,
bool
PepXmlSaxHandler::endElement(const QString &namespaceURI,
- const QString &localName, const QString &qName)
+ const QString &localName,
+ const QString &qName)
{
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -171,8 +175,9 @@ PepXmlSaxHandler::endElement(const QString &namespaceURI,
}
catch(pappso::PappsoException exception_pappso)
{
- _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::endElement tag %1, "
- "PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in PepXmlSaxHandler::endElement tag %1, "
+ "PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -234,7 +239,7 @@ PepXmlSaxHandler::startElement_msms_run_summary(QXmlAttributes attributes)
.arg(old_file)
.arg(_current_complete_msrun_file_path));
}
- _sp_msrun.get()->setFilename(attributes.value("base_name"));
+ _sp_msrun.get()->setFileName(attributes.value("base_name"));
_sp_msrun.get()->setSampleName(
QFileInfo(_current_complete_msrun_file_path).baseName());
return is_ok;
@@ -285,7 +290,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
QString spectrum_ref = attributes.value("spectrum");
if(_current_complete_msrun_file_path.isEmpty())
{
- _sp_msrun.get()->setFilename(QFileInfo(spectrum_ref).baseName());
+ _sp_msrun.get()->setFileName(QFileInfo(spectrum_ref).baseName());
}
unsigned int start_scan = attributes.value("start_scan").toUInt();
unsigned int end_scan = attributes.value("end_scan").toUInt();
@@ -304,9 +309,10 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
if(attributes.value("retention_time_sec").isEmpty())
{
QString message =
- QObject::tr("ERROR reading pepxml file :\n"
- "unable to read search results from '%1' as retention time "
- "is not given in spectrum_query elements")
+ QObject::tr(
+ "ERROR reading pepxml file :\n"
+ "unable to read search results from '%1' as retention time "
+ "is not given in spectrum_query elements")
.arg(_current_search_engine);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< message;
@@ -326,7 +332,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
//<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
// ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-// \
+// \
//S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
// peptide_next_aa="N"/>
bool
@@ -690,8 +696,9 @@ PepXmlSaxHandler::endElement_modification_info()
bool
PepXmlSaxHandler::error(const QXmlParseException &exception)
{
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3")
+ _errorStr = QObject::tr(
+ "Parse error at line %1, column %2 :\n"
+ "%3")
.arg(exception.lineNumber())
.arg(exception.columnNumber())
.arg(exception.message());
@@ -703,8 +710,9 @@ PepXmlSaxHandler::error(const QXmlParseException &exception)
bool
PepXmlSaxHandler::fatalError(const QXmlParseException &exception)
{
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3")
+ _errorStr = QObject::tr(
+ "Parse error at line %1, column %2 :\n"
+ "%3")
.arg(exception.lineNumber())
.arg(exception.columnNumber())
.arg(exception.message());
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 7f869c494..60b5f0238 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -282,7 +282,7 @@ XpipSaxHandler::startElement_sample(QXmlAttributes attributes)
MsRunSp ms_run = _p_project->getMsRunStore().getInstance(
attributes.value("value").simplified());
- ms_run.get()->setFilename(attributes.value("value").simplified());
+ ms_run.get()->setFileName(attributes.value("value").simplified());
//_current_identification_group_p->addMsRunSp(ms_run);
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
return true;
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index dfb409b71..7fbee73cd 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -607,7 +607,7 @@ XtandemSaxHandler::endElement_note()
if(_current_note_label == "spectrum, path")
{
- _sp_msrun.get()->setFilename(_current_text);
+ _sp_msrun.get()->setFileName(_current_text);
}
/*
diff --git a/src/input/xtpxpipsaxhandler.cpp b/src/input/xtpxpipsaxhandler.cpp
index b40d362ab..97d3c303a 100644
--- a/src/input/xtpxpipsaxhandler.cpp
+++ b/src/input/xtpxpipsaxhandler.cpp
@@ -556,7 +556,7 @@ XtpXpipSaxHandler::startElement_msrun(QXmlAttributes attributes)
_sp_msrun = _p_project->getMsRunStore().getInstance(
attributes.value("path").simplified());
- _sp_msrun.get()->setFilename(attributes.value("path").simplified());
+ _sp_msrun.get()->setFileName(attributes.value("path").simplified());
_sp_msrun.get()->setSampleName(attributes.value("name").simplified());
_sp_msrun.get()->setXmlId(attributes.value("id").simplified());
_map_msruns.insert(
diff --git a/src/utils/msrunstore.cpp b/src/utils/msrunstore.cpp
index f867fb0b9..2a3719c49 100644
--- a/src/utils/msrunstore.cpp
+++ b/src/utils/msrunstore.cpp
@@ -46,8 +46,9 @@ MsRunSp
MsRunStore::getInstance(const MsRun *p_msrun)
{
auto it = std::find_if(
- _map_msrun.begin(), _map_msrun.end(),
- [p_msrun](const MsRunSp &msrun_sp) { return msrun_sp.get() == p_msrun; });
+ _map_msrun.begin(), _map_msrun.end(), [p_msrun](const MsRunSp &msrun_sp) {
+ return msrun_sp.get() == p_msrun;
+ });
if(it != _map_msrun.end())
{
return (*it);
@@ -65,7 +66,8 @@ MsRunStore::getInstance(const QString &location)
if(file_ondisk.baseName() == location)
{
// look only for the same sample name
- it = std::find_if(_map_msrun.begin(), _map_msrun.end(),
+ it = std::find_if(_map_msrun.begin(),
+ _map_msrun.end(),
[location](const MsRunSp &msrun_sp) {
return msrun_sp.get()->getSampleName() == location;
});
@@ -73,7 +75,8 @@ MsRunStore::getInstance(const QString &location)
else
{
// look for an absolute file path
- it = std::find_if(_map_msrun.begin(), _map_msrun.end(),
+ it = std::find_if(_map_msrun.begin(),
+ _map_msrun.end(),
[location](const MsRunSp &msrun_sp) {
if(msrun_sp.get()->getSampleName() ==
msrun_sp.get()->getFilename())
@@ -93,7 +96,7 @@ MsRunStore::getInstance(const QString &location)
MsRunSp p_xtfile = std::make_shared<MsRun>(location);
p_xtfile.get()->setXmlId(QString("msrun%1").arg(
pappso::Utils::getLexicalOrderedString(_map_msrun.size() + 1)));
- p_xtfile.get()->setFilename(location);
+ p_xtfile.get()->setFileName(location);
_map_msrun.push_back(p_xtfile);
return p_xtfile;
}
--
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