diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 904e2c5e65a80714f39b69448362611df61a1321..5a6fc5fa916704ab930ec921f3bdd4b1b5c93e86 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -57,103 +57,177 @@ WorkerThread::WorkerThread(MainWindow *p_main_window)
#if QT_VERSION >= 0x050000
// Qt5 code
// worker message
- connect(_p_work_monitor, &WorkMonitor::workerMessage, p_main_window,
+ connect(_p_work_monitor,
+ &WorkMonitor::workerMessage,
+ p_main_window,
&MainWindow::doDisplayLoadingMessage);
- connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_main_window,
+ connect(_p_work_monitor,
+ &WorkMonitor::workerMessagePercent,
+ p_main_window,
&MainWindow::doDisplayLoadingMessagePercent);
- connect(_p_work_monitor, &WorkMonitor::workerAppendText, p_main_window,
+ connect(_p_work_monitor,
+ &WorkMonitor::workerAppendText,
+ p_main_window,
&MainWindow::doWorkerAppendText);
- connect(_p_work_monitor, &WorkMonitor::workerSetText, p_main_window,
+ connect(_p_work_monitor,
+ &WorkMonitor::workerSetText,
+ p_main_window,
&MainWindow::doWorkerSetText);
- connect(_p_work_monitor, &WorkMonitor::workerJobFinished, p_main_window,
+ connect(_p_work_monitor,
+ &WorkMonitor::workerJobFinished,
+ p_main_window,
&MainWindow::doDisplayJobFinished);
- connect(p_main_window, &MainWindow::operateXpipFile, this,
+ connect(p_main_window,
+ &MainWindow::operateXpipFile,
+ this,
&WorkerThread::doXpipFileLoad);
- connect(p_main_window, &MainWindow::operateWritingXpipFile, this,
+ connect(p_main_window,
+ &MainWindow::operateWritingXpipFile,
+ this,
&WorkerThread::doWritingXpipFile);
- connect(this, &WorkerThread::projectReady, p_main_window,
+ connect(this,
+ &WorkerThread::projectReady,
+ p_main_window,
&MainWindow::doProjectReady);
- connect(this, &WorkerThread::loadingResultsFinished, p_main_window,
+ connect(this,
+ &WorkerThread::loadingResultsFinished,
+ p_main_window,
&MainWindow::doLoadingResultsReady);
- connect(p_main_window, &MainWindow::operateLoadingResults, this,
+ connect(p_main_window,
+ &MainWindow::operateLoadingResults,
+ this,
&WorkerThread::doLoadingResults);
- connect(p_main_window, &MainWindow::operateRunningXtandem, this,
+ connect(p_main_window,
+ &MainWindow::operateRunningXtandem,
+ this,
&WorkerThread::doRunningXtandem);
- connect(this, &WorkerThread::loadingMessage, p_main_window,
+ connect(this,
+ &WorkerThread::loadingMessage,
+ p_main_window,
&MainWindow::doDisplayLoadingMessage);
- connect(this, &WorkerThread::projectNotReady, p_main_window,
+ connect(this,
+ &WorkerThread::projectNotReady,
+ p_main_window,
&MainWindow::doProjectNotReady);
// grouping
- connect(p_main_window, &MainWindow::operateGrouping, this,
+ connect(p_main_window,
+ &MainWindow::operateGrouping,
+ this,
&WorkerThread::doGrouping);
- connect(this, &WorkerThread::groupingFinished, p_main_window,
+ connect(this,
+ &WorkerThread::groupingFinished,
+ p_main_window,
&MainWindow::doGroupingFinished);
// masschroq write
- connect(p_main_window, &MainWindow::operateWritingMassChroqFile, this,
+ connect(p_main_window,
+ &MainWindow::operateWritingMassChroqFile,
+ this,
&WorkerThread::doWritingMassChroqFile);
- connect(p_main_window, &MainWindow::operateWritingMassChroqPrmFile, this,
+ connect(p_main_window,
+ &MainWindow::operateWritingMassChroqPrmFile,
+ this,
&WorkerThread::doWritingMassChroqPrmFile);
- connect(p_main_window, &MainWindow::operateWritingMcqrSpectralCountFile, this,
+ connect(p_main_window,
+ &MainWindow::operateWritingMcqrSpectralCountFile,
+ this,
&WorkerThread::doWritingMcqrSpectralCountFile);
// protic write
- connect(p_main_window, &MainWindow::operateWritingProticFile, this,
+ connect(p_main_window,
+ &MainWindow::operateWritingProticFile,
+ this,
&WorkerThread::doWritingProticFile);
// writing ODS file :
- connect(p_main_window, &MainWindow::operateWritingOdsFile, this,
+ connect(p_main_window,
+ &MainWindow::operateWritingOdsFile,
+ this,
&WorkerThread::doWritingOdsFile);
- connect(this, &WorkerThread::operationFailed, p_main_window,
+ connect(this,
+ &WorkerThread::operationFailed,
+ p_main_window,
&MainWindow::doOperationFailed);
- connect(this, &WorkerThread::operationFinished, p_main_window,
+ connect(this,
+ &WorkerThread::operationFinished,
+ p_main_window,
&MainWindow::doOperationFinished);
#else
// Qt4 code
// worker message
- connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_main_window,
+ connect(_p_work_monitor,
+ SIGNAL(workerMessage(QString)),
+ p_main_window,
SLOT(doDisplayLoadingMessage(QString)));
- connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)), p_main_window,
+ connect(_p_work_monitor,
+ SIGNAL(workerMessage(QString, int)),
+ p_main_window,
SLOT(doDisplayLoadingMessage(QString, int)));
- connect(_p_work_monitor, SIGNAL(workerAppendText(char *)), p_main_window,
+ connect(_p_work_monitor,
+ SIGNAL(workerAppendText(char *)),
+ p_main_window,
SLOT(doWorkerAppendText(char *)));
- connect(p_main_window, SIGNAL(operateXpipFile(QString)), this,
+ connect(p_main_window,
+ SIGNAL(operateXpipFile(QString)),
+ this,
SLOT(doXpipFileLoad(QString)));
- connect(this, SIGNAL(projectReady(ProjectSp)), p_main_window,
+ connect(this,
+ SIGNAL(projectReady(ProjectSp)),
+ p_main_window,
SLOT(doProjectReady(ProjectSp)));
connect(
p_main_window,
SIGNAL(operateLoadingResults(bool, AutomaticFilterParameters, QStringList)),
- this, SLOT(doLoadingResults(bool, AutomaticFilterParameters, QStringList)));
+ this,
+ SLOT(doLoadingResults(bool, AutomaticFilterParameters, QStringList)));
- connect(p_main_window, SIGNAL(operateRunningXtandem(TandemRunBatch)), this,
+ connect(p_main_window,
+ SIGNAL(operateRunningXtandem(TandemRunBatch)),
+ this,
SLOT(doRunningXtandem(TandemRunBatch)));
- connect(this, SIGNAL(loadingMessage(QString)), p_main_window,
+ connect(this,
+ SIGNAL(loadingMessage(QString)),
+ p_main_window,
SLOT(doDisplayLoadingMessage(QString)));
- connect(this, SIGNAL(projectNotReady(QString)), p_main_window,
+ connect(this,
+ SIGNAL(projectNotReady(QString)),
+ p_main_window,
SLOT(doProjectNotReady(QString)));
// grouping
- connect(p_main_window, SIGNAL(operateGrouping(ProjectSp)), this,
+ connect(p_main_window,
+ SIGNAL(operateGrouping(ProjectSp)),
+ this,
SLOT(doGrouping(ProjectSp)));
- connect(this, SIGNAL(groupingFinished()), p_main_window,
+ connect(this,
+ SIGNAL(groupingFinished()),
+ p_main_window,
SLOT(doGroupingFinished()));
// masschroq write
connect(p_main_window,
- SIGNAL(operateWritingMassChroqFile(QString, ProjectSp)), this,
+ SIGNAL(operateWritingMassChroqFile(QString, ProjectSp)),
+ this,
SLOT(doWritingMassChroqFile(QString, ProjectSp)));
// protic write
- connect(p_main_window, SIGNAL(operateWritingProticFile(QString, ProjectSp)),
- this, SLOT(doWritingProticFile(QString, ProjectSp)));
+ 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,
+ connect(p_main_window,
+ SIGNAL(operateWritingOdsFile(QString, ProjectSp)),
+ this,
+ SLOT(doWritingOdsFile(QString, ProjectSp)));
+ connect(this,
+ SIGNAL(operationFailed(QString)),
+ p_main_window,
SLOT(doOperationFailed(QString)));
- connect(this, SIGNAL(operationFinished()), p_main_window,
+ connect(this,
+ SIGNAL(operationFinished()),
+ p_main_window,
SLOT(doOperationFinished()));
#endif
@@ -162,7 +236,7 @@ WorkerThread::WorkerThread(MainWindow *p_main_window)
WorkerThread::WorkerThread(ProjectWindow *p_project_window)
{
- qDebug() << "WorkerThread::WorkerThread begin ProjectWindow";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_p_work_monitor = new WorkMonitor();
@@ -170,62 +244,96 @@ WorkerThread::WorkerThread(ProjectWindow *p_project_window)
// Qt5 code
// worker message
- connect(_p_work_monitor, &WorkMonitor::workerMessage, p_project_window,
+ connect(_p_work_monitor,
+ &WorkMonitor::workerMessage,
+ p_project_window,
&ProjectWindow::doDisplayLoadingMessage);
- connect(_p_work_monitor, &WorkMonitor::workerMessagePercent, p_project_window,
+ connect(_p_work_monitor,
+ &WorkMonitor::workerMessagePercent,
+ p_project_window,
&ProjectWindow::doDisplayLoadingMessagePercent);
- connect(this, &WorkerThread::loadingMessage, p_project_window,
+ connect(this,
+ &WorkerThread::loadingMessage,
+ p_project_window,
&ProjectWindow::doDisplayLoadingMessage);
// grouping
- connect(p_project_window, &ProjectWindow::operateGrouping, this,
+ connect(p_project_window,
+ &ProjectWindow::operateGrouping,
+ this,
&WorkerThread::doGrouping);
- connect(this, &WorkerThread::groupingFinished, p_project_window,
+ connect(this,
+ &WorkerThread::groupingFinished,
+ p_project_window,
&ProjectWindow::doGroupingFinished);
// PTM grouping on IdentificationGroup
- connect(p_project_window, &ProjectWindow::operatePtmGroupingOnIdentification,
- this, &WorkerThread::doPtmGroupingOnIdentification);
- connect(this, &WorkerThread::ptmGroupingOnIdentificationFinished,
- p_project_window, &ProjectWindow::refreshPtmGroup);
+ connect(p_project_window,
+ &ProjectWindow::operatePtmGroupingOnIdentification,
+ this,
+ &WorkerThread::doPtmGroupingOnIdentification);
+ connect(this,
+ &WorkerThread::ptmGroupingOnIdentificationFinished,
+ p_project_window,
+ &ProjectWindow::refreshPtmGroup);
// grouping on IdentificationGroup
- connect(p_project_window, &ProjectWindow::operateGroupingOnIdentification,
- this, &WorkerThread::doGroupingOnIdentification);
- connect(this, &WorkerThread::groupingOnIdentificationFinished,
- p_project_window, &ProjectWindow::refreshGroup);
+ connect(p_project_window,
+ &ProjectWindow::operateGroupingOnIdentification,
+ this,
+ &WorkerThread::doGroupingOnIdentification);
+ connect(this,
+ &WorkerThread::groupingOnIdentificationFinished,
+ p_project_window,
+ &ProjectWindow::refreshGroup);
- connect(this, &WorkerThread::operationFailed, p_project_window,
+ connect(this,
+ &WorkerThread::operationFailed,
+ p_project_window,
&ProjectWindow::doOperationFailed);
- connect(this, &WorkerThread::operationFinished, p_project_window,
+ connect(this,
+ &WorkerThread::operationFinished,
+ p_project_window,
&ProjectWindow::doOperationFinished);
#else
// Qt4 code
- qDebug() << "WorkerThread::WorkerThread Qt4 code";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
// worker message
- connect(_p_work_monitor, SIGNAL(workerMessage(QString)), p_project_window,
+ connect(_p_work_monitor,
+ SIGNAL(workerMessage(QString)),
+ p_project_window,
SLOT(doDisplayLoadingMessage(QString)));
- connect(_p_work_monitor, SIGNAL(workerMessage(QString, int)),
- p_project_window, SLOT(doDisplayLoadingMessage(QString, int)));
+ connect(_p_work_monitor,
+ SIGNAL(workerMessage(QString, int)),
+ p_project_window,
+ SLOT(doDisplayLoadingMessage(QString, int)));
- connect(this, SIGNAL(loadingMessage(QString)), p_project_window,
+ connect(this,
+ SIGNAL(loadingMessage(QString)),
+ p_project_window,
SLOT(doDisplayLoadingMessage(QString)));
// grouping
- connect(p_project_window, SIGNAL(operateGrouping(ProjectSp)), this,
+ connect(p_project_window,
+ SIGNAL(operateGrouping(ProjectSp)),
+ this,
SLOT(doGrouping(ProjectSp)));
- connect(this, SIGNAL(groupingFinished()), p_project_window,
+ connect(this,
+ SIGNAL(groupingFinished()),
+ p_project_window,
SLOT(doGroupingFinished()));
// PTM grouping on IdentificationGroup
connect(p_project_window,
SIGNAL(operatePtmGroupingOnIdentification(IdentificationGroup *)),
- this, SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
+ this,
+ SLOT(doPtmGroupingOnIdentification(IdentificationGroup *)));
connect(this,
SIGNAL(ptmGroupingOnIdentificationFinished(IdentificationGroup *)),
- p_project_window, SLOT(refreshPtmGroup(IdentificationGroup *)));
+ p_project_window,
+ SLOT(refreshPtmGroup(IdentificationGroup *)));
// grouping on IdentificationGroup
connect(
@@ -234,21 +342,27 @@ WorkerThread::WorkerThread(ProjectWindow *p_project_window)
operateGroupingOnIdentification(IdentificationGroup *, GroupingType)),
this,
SLOT(doGroupingOnIdentification(IdentificationGroup *, GroupingType)));
- connect(this, SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)),
- p_project_window, SLOT(refreshGroup(IdentificationGroup *)));
+ connect(this,
+ SIGNAL(groupingOnIdentificationFinished(IdentificationGroup *)),
+ p_project_window,
+ SLOT(refreshGroup(IdentificationGroup *)));
- connect(this, SIGNAL(operationFailed(QString)), p_project_window,
+ connect(this,
+ SIGNAL(operationFailed(QString)),
+ p_project_window,
SLOT(doOperationFailed(QString)));
- connect(this, SIGNAL(operationFinished()), p_project_window,
+ connect(this,
+ SIGNAL(operationFinished()),
+ p_project_window,
SLOT(doOperationFinished()));
#endif
- qDebug() << "WorkerThread::WorkerThread end ProjectWindow";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
WorkerThread::~WorkerThread()
{
- qDebug() << "WorkerThread::WorkerThread destructor";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
@@ -279,7 +393,7 @@ void
WorkerThread::doPtmGroupingOnIdentification(
IdentificationGroup *p_identification_group)
{
- qDebug() << "WorkerThread::doPtmGroupingOnIdentification begin ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
try
{
emit loadingMessage(tr("computing PTM islands"));
@@ -305,14 +419,14 @@ WorkerThread::doPtmGroupingOnIdentification(
emit operationFailed(
tr("Error while computing PTM islands :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doPtmGroupingOnIdentification end ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
WorkerThread::doGroupingOnIdentification(
IdentificationGroup *p_identification_group, GroupingType grouping_type)
{
- qDebug() << "WorkerThread::doGroupingOnIdentification begin ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
try
{
emit loadingMessage(tr("grouping proteins"));
@@ -337,12 +451,12 @@ WorkerThread::doGroupingOnIdentification(
{
emit operationFailed(tr("Error while grouping :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doGroupingOnIdentification end ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
WorkerThread::doGrouping(ProjectSp project_sp)
{
- qDebug() << "WorkerThread::doGrouping begin ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
try
{
emit loadingMessage(tr("grouping proteins"));
@@ -367,7 +481,7 @@ WorkerThread::doGrouping(ProjectSp project_sp)
{
emit operationFailed(tr("Error while grouping :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doGrouping end ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
@@ -519,7 +633,7 @@ WorkerThread::doLoadingResults(bool is_individual,
QStringList file_list)
{
- qDebug() << "WorkerThread::doLoadingResults begin ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
try
{
if(file_list.size() == 0)
@@ -551,22 +665,22 @@ WorkerThread::doLoadingResults(bool is_individual,
emit loadingMessage(tr("filtering proteins"));
project_sp.get()->updateAutomaticFilters(param);
- qDebug() << "WorkerThread::doLoadingResults emit "
- "loadingResultsFinished(project_sp) ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
emit loadingResultsFinished(project_sp);
}
catch(pappso::PappsoException &error)
{
- qDebug() << "WorkerThread::doLoadingResults error ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << error.qwhat();
emit projectNotReady(
tr("Error while reading result files :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doLoadingResults end ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch)
{
- qDebug() << "WorkerThread::doRunningXtandem begin ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
try
{
emit loadingMessage(tr("Running X!Tandem, please wait"));
@@ -579,14 +693,14 @@ WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch)
if(use_htcondor)
{
- TandemCondorProcess xt_process(_p_main_window, _p_work_monitor,
- tandem_run_batch);
+ TandemCondorProcess xt_process(
+ _p_main_window, _p_work_monitor, tandem_run_batch);
xt_process.run();
}
else
{
- TandemBatchProcess xt_process(_p_main_window, _p_work_monitor,
- tandem_run_batch);
+ TandemBatchProcess xt_process(
+ _p_main_window, _p_work_monitor, tandem_run_batch);
xt_process.run();
}
@@ -594,8 +708,10 @@ WorkerThread::doRunningXtandem(TandemRunBatch tandem_run_batch)
}
catch(pappso::PappsoException &error)
{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << error.qwhat();
emit operationFailed(
tr("Error while running X!Tandem job :\n%1").arg(error.qwhat()));
}
- qDebug() << "WorkerThread::doRunningXtandem end ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index 1fde28eaf9217af05778419f962f0147087358e5..681ce94486b1b0e4621bb73aba4b45f2d6f1b61b 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;
@@ -415,8 +416,9 @@ MascotDatParser::parsePeptidesLine(const QString &peptide_line)
catch(pappso::PappsoException exception_pappso)
{
- _error_str = QObject::tr("ERROR in MascotDatParser::parsePeptidesLine "
- "%1, PAPPSO exception:\n%2")
+ _error_str = QObject::tr(
+ "ERROR in MascotDatParser::parsePeptidesLine "
+ "%1, PAPPSO exception:\n%2")
.arg(peptide_line)
.arg(exception_pappso.qwhat());
qDebug() << _error_str;
@@ -633,9 +635,10 @@ MascotDatParser::savePeptideList(std::vector<PeptideLine> &peptide_list,
if(is_decoy)
{
- peptide_evidence.setEvalue(getEvalue(
- ion_score, _decoy_summary_list.at(_current_query.query_index - 1),
- 0.05));
+ peptide_evidence.setEvalue(
+ getEvalue(ion_score,
+ _decoy_summary_list.at(_current_query.query_index - 1),
+ 0.05));
}
else
{
@@ -767,7 +770,8 @@ 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).
@@ -780,16 +784,41 @@ void
MascotDatParser::setVariableModifications(PeptideXtpSp &peptide_sp,
QString variable_modifications_string)
{
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << variable_modifications_string;
//
for(unsigned int i = 0; i < variable_modifications_string.size(); i++)
{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << variable_modifications_string.mid(i, 1).toUInt();
if(variable_modifications_string.mid(i, 1).toUInt() > 0)
{
MascotModification mascot_modification = _delta_modification_list
[variable_modifications_string.mid(i, 1).toUInt() - 1];
- peptide_sp.get()->addAaModification(mascot_modification.modification,
- i - 1);
+ try
+ {
+ if(i == 0)
+ {
+ peptide_sp.get()->addAaModification(
+ mascot_modification.modification, 0);
+ }
+ else
+ {
+ peptide_sp.get()->addAaModification(
+ mascot_modification.modification, i - 1);
+ }
+ }
+ catch(pappso::PappsoException &error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("ERROR adding modification %1 to peptide %2 at "
+ "position %3 :\n %4")
+ .arg(mascot_modification.modification->getAccession())
+ .arg(peptide_sp.get()->toAbsoluteString())
+ .arg(i - 1)
+ .arg(error.qwhat()));
+ }
}
}
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
index bd170cc00018859dab0e19e6621ec318c195ecd3..8003831506bb5fde72cebc9240d3e72a97c3c744 100644
--- a/src/input/mascot/mascotdatparser.h
+++ b/src/input/mascot/mascotdatparser.h
@@ -80,13 +80,14 @@ class MascotDatParser
};
struct SummaryLine
{
- pappso::pappso_double match = 0; // qmatch, identity threshold
- pappso::pappso_double exp_mass = 0;
+ pappso::pappso_double match = 0; // qmatch, identity threshold
+ pappso::pappso_double exp_mass = 0;
pappso::pappso_double plug_hole = 0; // qplughole, homology threshold
};
void savePeptideList(std::vector<PeptideLine> &peptide_list, bool is_decoy);
pappso::pappso_double
- getEvalue(pappso::pappso_double ion_score, SummaryLine &summary_line,
+ getEvalue(pappso::pappso_double ion_score,
+ SummaryLine &summary_line,
pappso::pappso_double confidence_interval = 0.05) const;
pappso::pappso_double
getEvalueExperimental(pappso::pappso_double ion_score,
diff --git a/src/input/mascot/mimeparser.cpp b/src/input/mascot/mimeparser.cpp
index 9afe6a3e3f869e02d905c83efdf20bb67e76abc3..74ac11f03f7f610ec9b8b9d4309c658a249ece86 100644
--- a/src/input/mascot/mimeparser.cpp
+++ b/src/input/mascot/mimeparser.cpp
@@ -40,12 +40,14 @@ MimeParser::MimeParser(QIODevice *p_inputstream)
MimeParser::~MimeParser()
{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
close();
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
bool
MimeParser::open()
{
- qDebug() << "MimeParser::open begin";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(_p_inputstream->open(QIODevice::ReadOnly))
{
_real_in = new QTextStream(_p_inputstream);
@@ -55,12 +57,12 @@ MimeParser::open()
throw pappso::PappsoException(
QObject::tr("Error opening mime QIODevice"));
}
- qDebug() << "MimeParser::open end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
bool
MimeParser::close()
{
- qDebug() << "MimeParser::close begin";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_priv_file_string = "";
if(_p_current_file_content != nullptr)
@@ -68,21 +70,21 @@ MimeParser::close()
delete _p_current_file_content;
_p_current_file_content = nullptr;
}
- qDebug() << "MimeParser::close delete _real_in";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(_real_in != nullptr)
{
delete _real_in;
_real_in = nullptr;
}
- qDebug() << "MimeParser::close delete _p_inputstream";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(_p_inputstream != nullptr)
{
_p_inputstream->close();
// delete _p_inputstream;
_p_inputstream = nullptr;
}
- qDebug() << "MimeParser::close end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
bool
MimeParser::goToFirstFile()