Skip to content
Snippets Groups Projects
Commit 9ddf22fb authored by Langella Olivier's avatar Langella Olivier
Browse files

indentation

parent 34694195
No related branches found
No related tags found
No related merge requests found
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
......@@ -34,14 +34,13 @@
XtandemParamSaxHandler::XtandemParamSaxHandler(
TandemParameters *p_tandem_parameters)
TandemParameters *p_tandem_parameters)
{
_p_tandem_parameters = p_tandem_parameters;
//<note type="input" label="output, xsl path">tandem-style.xsl</note>
_p_tandem_parameters->setParamLabelValue("output, xsl path",
"tandem-style.xsl");
_p_tandem_parameters = p_tandem_parameters;
//<note type="input" label="output, xsl path">tandem-style.xsl</note>
_p_tandem_parameters->setParamLabelValue("output, xsl path",
"tandem-style.xsl");
}
XtandemParamSaxHandler::~XtandemParamSaxHandler()
{
......@@ -50,7 +49,7 @@ XtandemParamSaxHandler::~XtandemParamSaxHandler()
bool
XtandemParamSaxHandler::isTandemParameter() const
{
return m_isTandemParameter;
return m_isTandemParameter;
}
bool
XtandemParamSaxHandler::startElement(const QString &namespaceURI,
......@@ -58,58 +57,58 @@ XtandemParamSaxHandler::startElement(const QString &namespaceURI,
const QString &qName,
const QXmlAttributes &attributes)
{
// qDebug()<< "XtandemParamSaxHandler::startElement begin" << namespaceURI <<
// " " << localName << " " << qName ;
_tag_stack.push_back(qName);
bool is_ok = true;
// qDebug()<< "XtandemParamSaxHandler::startElement begin" << namespaceURI <<
// " " << localName << " " << qName ;
_tag_stack.push_back(qName);
bool is_ok = true;
try
try
{
//<bioml label="example api document">
if(_tag_stack.size() == 1)
//<bioml label="example api document">
if(_tag_stack.size() == 1)
{
if(qName != "bioml")
if(qName != "bioml")
{
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::startElement "
"root tag %1 is not <bioml>")
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::startElement "
"root tag %1 is not <bioml>")
.arg(qName);
m_isTandemParameter = false;
return false;
m_isTandemParameter = false;
return false;
}
else
else
{
m_isTandemParameter = true;
m_isTandemParameter = true;
}
}
// startElement_group
// startElement_group
if(qName == "note")
if(qName == "note")
{
is_ok = startElement_note(attributes);
is_ok = startElement_note(attributes);
}
_current_text.clear();
_current_text.clear();
}
catch(pappso::PappsoException exception_pappso)
catch(pappso::PappsoException exception_pappso)
{
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::startElement "
"tag %1, PAPPSO exception:\n%2")
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::startElement "
"tag %1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
return false;
}
catch(std::exception exception_std)
catch(std::exception exception_std)
{
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::startElement "
"tag %1, std exception:\n%2")
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::startElement "
"tag %1, std exception:\n%2")
.arg(qName)
.arg(exception_std.what());
return false;
return false;
}
return is_ok;
return is_ok;
}
bool
......@@ -118,75 +117,75 @@ XtandemParamSaxHandler::endElement(const QString &namespaceURI,
const QString &qName)
{
bool is_ok = true;
// endElement_peptide_list
try
bool is_ok = true;
// endElement_peptide_list
try
{
if(qName == "note")
if(qName == "note")
{
is_ok = endElement_note();
is_ok = endElement_note();
}
}
catch(pappso::PappsoException exception_pappso)
catch(pappso::PappsoException exception_pappso)
{
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::endElement tag "
"%1, PAPPSO exception:\n%2")
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::endElement tag "
"%1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
return false;
}
catch(std::exception exception_std)
catch(std::exception exception_std)
{
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::endElement tag "
"%1, std exception:\n%2")
_errorStr = QObject::tr(
"ERROR in XtandemParamSaxHandler::endElement tag "
"%1, std exception:\n%2")
.arg(qName)
.arg(exception_std.what());
return false;
return false;
}
_current_text.clear();
_tag_stack.pop_back();
_current_text.clear();
_tag_stack.pop_back();
return is_ok;
return is_ok;
}
bool
XtandemParamSaxHandler::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());
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _errorStr;
return false;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _errorStr;
return false;
}
bool
XtandemParamSaxHandler::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());
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _errorStr;
return false;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _errorStr;
return false;
}
QString
XtandemParamSaxHandler::errorString() const
{
return _errorStr;
return _errorStr;
}
......@@ -194,67 +193,67 @@ bool
XtandemParamSaxHandler::endDocument()
{
return true;
return true;
}
bool
XtandemParamSaxHandler::startDocument()
{
/*<?xml version="1.0" encoding="UTF-8"?>
<bioml label="example api document">
<note type="input" label="spectrum, parent monoisotopic mass error
units">ppm</note> <note type="input" label="spectrum, parent monoisotopic mass
error minus">10</note>
*/
return true;
/*<?xml version="1.0" encoding="UTF-8"?>
<bioml label="example api document">
<note type="input" label="spectrum, parent monoisotopic mass error
units">ppm</note> <note type="input" label="spectrum, parent monoisotopic mass
error minus">10</note>
*/
return true;
}
bool
XtandemParamSaxHandler::characters(const QString &str)
{
_current_text += str;
return true;
_current_text += str;
return true;
}
bool
XtandemParamSaxHandler::startElement_note(QXmlAttributes attributes)
{
// qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
// attributes.value("type");
_current_label = "";
// qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
// attributes.value("type");
_current_label = "";
if(attributes.value("type") == "input")
if(attributes.value("type") == "input")
{
_current_label = attributes.value("label");
_current_label = attributes.value("label");
}
// qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
// _current_label;
return true;
// qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
// _current_label;
return true;
}
bool
XtandemParamSaxHandler::endElement_note()
{
// qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
// _current_label << " " << _current_text.simplified();
if(!_current_label.isEmpty())
// qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
// _current_label << " " << _current_text.simplified();
if(!_current_label.isEmpty())
{
try
try
{
_p_tandem_parameters->setParamLabelValue(_current_label,
_current_text.simplified());
_p_tandem_parameters->setParamLabelValue(_current_label,
_current_text.simplified());
}
catch(pappso::PappsoException &exception)
catch(pappso::PappsoException &exception)
{
_errorStr =
QObject::tr("Error reading tandem input parameter \"%1\" :\n%2")
.arg(_current_label)
.arg(exception.qwhat());
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _errorStr;
return false;
_errorStr =
QObject::tr("Error reading tandem input parameter \"%1\" :\n%2")
.arg(_current_label)
.arg(exception.qwhat());
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _errorStr;
return false;
}
}
return true;
return true;
}
......@@ -35,53 +35,53 @@ using namespace std;
int
main(int argc, char *argv[])
{
QTextStream errorStream(stderr, QIODevice::WriteOnly);
QApplication app(argc, argv);
QTextStream errorStream(stderr, QIODevice::WriteOnly);
QApplication app(argc, argv);
qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
qRegisterMetaType<std::vector<pappso::pappso_double>>(
"std::vector<pappso::pappso_double>");
qRegisterMetaType<pappso::PrecisionPtr>("pappso::PrecisionPtr");
qRegisterMetaType<std::vector<pappso::XicCstSPtr>>(
"std::vector<pappso::XicCstSPtr>");
qRegisterMetaType<pappso::PeptideSp>("pappso::PeptideSp");
qRegisterMetaType<pappso::XicExtractMethod>("pappso::XicExtractMethod");
qRegisterMetaType<pappso::MassSpectrumCstSPtr>("pappso::MassSpectrumCstSPtr");
qRegisterMetaType<MsRunSp>("MsRunSp");
qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>(
"std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
qRegisterMetaType<ExportFastaType>("ExportFastaType");
qRegisterMetaType<MasschroqFileParameters>("MasschroqFileParameters");
qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
qRegisterMetaType<std::vector<pappso::pappso_double>>(
"std::vector<pappso::pappso_double>");
qRegisterMetaType<pappso::PrecisionPtr>("pappso::PrecisionPtr");
qRegisterMetaType<std::vector<pappso::XicCstSPtr>>(
"std::vector<pappso::XicCstSPtr>");
qRegisterMetaType<pappso::PeptideSp>("pappso::PeptideSp");
qRegisterMetaType<pappso::XicExtractMethod>("pappso::XicExtractMethod");
qRegisterMetaType<pappso::MassSpectrumCstSPtr>("pappso::MassSpectrumCstSPtr");
qRegisterMetaType<MsRunSp>("MsRunSp");
qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>(
"std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
qRegisterMetaType<ExportFastaType>("ExportFastaType");
qRegisterMetaType<MasschroqFileParameters>("MasschroqFileParameters");
qRegisterMetaType<ContaminantRemovalMode>("ContaminantRemovalMode");
qRegisterMetaType<ContaminantRemovalMode>("ContaminantRemovalMode");
// qRegisterMetaType<pappso::PeakIonIsotopeMatch>("pappso::PeakIonIsotopeMatch");
// qRegisterMetaType<pappso::PeakIonIsotopeMatch>("pappso::PeakIonIsotopeMatch");
try
try
{
QCoreApplication::setOrganizationName("PAPPSO");
QCoreApplication::setOrganizationDomain("pappso.inra.fr");
QCoreApplication::setApplicationName("xtpcpp");
MainWindow window;
window.show();
QCoreApplication::setOrganizationName("PAPPSO");
QCoreApplication::setOrganizationDomain("pappso.inra.fr");
QCoreApplication::setApplicationName("xtpcpp");
MainWindow window;
window.show();
// This code will start the messaging engine in QT and in
// 10ms it will start the execution in the MainClass.run routine;
QTimer::singleShot(10, &window, SLOT(run()));
// This code will start the messaging engine in QT and in
// 10ms it will start the execution in the MainClass.run routine;
QTimer::singleShot(10, &window, SLOT(run()));
return app.exec();
return app.exec();
}
catch(pappso::PappsoException &error)
catch(pappso::PappsoException &error)
{
errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
errorStream << error.qwhat() << endl;
app.exit(1);
errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
errorStream << error.qwhat() << endl;
app.exit(1);
}
catch(std::exception &error)
catch(std::exception &error)
{
errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
errorStream << error.what() << endl;
app.exit(1);
errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
errorStream << error.what() << endl;
app.exit(1);
}
}
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment