30 #include "../../../pappsomspp/pappsoexception.h"
36 const QString &final_tandem_output,
const QString &original_msdata_file_name)
37 : m_destinationTandemOutputFile(final_tandem_output)
39 qDebug() << final_tandem_output;
41 QFileInfo(original_msdata_file_name).absoluteFilePath();
45 QObject::tr(
"ERROR: unable to open %1 to write XML output")
46 .arg(final_tandem_output));
64 const QXmlAttributes &attributes)
67 for(
int i = 0; i < attributes.length(); i++)
76 [[maybe_unused]]
const QString &namespaceURI,
77 [[maybe_unused]]
const QString &localName,
79 const QXmlAttributes &attributes)
94 "ERROR in XtandemOutputSaxHandler::startElement "
95 "root tag %1 is not <bioml>")
109 "xmlns:GAML", attributes.value(
"xmlns:GAML"));
130 "ERROR in XtandemOutputSaxHandler::startElement "
131 "tag %1, PAPPSO exception:\n%2")
133 .arg(exception_pappso.
qwhat());
136 catch(
const std::exception &exception_std)
139 "ERROR in XtandemOutputSaxHandler::startElement "
140 "tag %1, std exception:\n%2")
142 .arg(exception_std.what());
150 [[maybe_unused]]
const QString &namespaceURI,
151 [[maybe_unused]]
const QString &localName,
152 const QString &qName)
172 "ERROR in XtandemOutputSaxHandler::endElement tag "
173 "%1, PAPPSO exception:\n%2")
175 .arg(exception_pappso.
qwhat());
178 catch(
const std::exception &exception_std)
181 "ERROR in XtandemOutputSaxHandler::endElement tag "
182 "%1, std exception:\n%2")
184 .arg(exception_std.what());
230 "Parse error at line %1, column %2 :\n"
232 .arg(exception.lineNumber())
233 .arg(exception.columnNumber())
234 .arg(exception.message());
244 "Parse error at line %1, column %2 :\n"
246 .arg(exception.lineNumber())
247 .arg(exception.columnNumber())
248 .arg(exception.message());
270 if(attributes.value(
"type") ==
"input")
324 const QString &input_value)
327 std::pair<QString, QString>(label_name_attribute, input_value));
virtual const QString & qwhat() const
XtandemOutputSaxHandler(const QString &final_tandem_output, const QString &original_msdata_file_name)
bool error(const QXmlParseException &exception) override
~XtandemOutputSaxHandler()
void setInputParameters(const QString &label_name_attribute, const QString &input_value)
QXmlStreamWriter * p_writeXmlTandemOutput
QString errorString() const
bool startDocument() override
void writeOpenTag(const QString &qName, const QXmlAttributes &attributes)
bool startElement(const QString &namespaceURI, const QString &localName, const QString &qName, const QXmlAttributes &attributes) override
std::vector< QString > m_tagStack
bool fatalError(const QXmlParseException &exception) override
QFile m_destinationTandemOutputFile
bool startElement_note(QXmlAttributes attributes)
std::map< QString, QString > m_mapTandemInputParameters
QString m_originalMsDataFileName
bool endElement(const QString &namespaceURI, const QString &localName, const QString &qName) override
bool characters(const QString &str) override
bool endDocument() override
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
rewrites tandem xml output file with temporary files