#include <xtandemoutputsaxhandler.h>

Inheritance diagram for pappso::XtandemOutputSaxHandler:

Public Member Functions
	XtandemOutputSaxHandler (const QString &final_tandem_output, const QString &original_msdata_file_name)

	~XtandemOutputSaxHandler ()

bool	startElement (const QString &namespaceURI, const QString &localName, const QString &qName, const QXmlAttributes &attributes) override

bool	endElement (const QString &namespaceURI, const QString &localName, const QString &qName) override

bool	startDocument () override

bool	endDocument () override

bool	characters (const QString &str) override

bool	fatalError (const QXmlParseException &exception) override

bool	error (const QXmlParseException &exception) override

QString	errorString () const

void	setInputParameters (const QString &label_name_attribute, const QString &input_value)

Private Member Functions
bool	startElement_note (QXmlAttributes attributes)

bool	endElement_note ()

void	writeOpenTag (const QString &qName, const QXmlAttributes &attributes)

Private Attributes
std::map< QString, QString >	m_mapTandemInputParameters

std::vector< QString >	m_tagStack

QFile	m_destinationTandemOutputFile

QXmlStreamWriter *	p_writeXmlTandemOutput

QString	m_errorString

QString	m_currentText

bool	m_isTandemParameter = false

QString	m_currentLabel

QString	m_originalMsDataFileName

Detailed Description

Definition at line 54 of file xtandemoutputsaxhandler.h.

Constructor & Destructor Documentation

◆ XtandemOutputSaxHandler()

pappso::XtandemOutputSaxHandler::XtandemOutputSaxHandler	(	const QString &	final_tandem_output,
		const QString &	original_msdata_file_name
	)

Default constructor

Definition at line 51 of file xtandemoutputsaxhandler.cpp.

 {
   if(p_writeXmlTandemOutput != nullptr)
     {
       m_destinationTandemOutputFile.close();
       delete p_writeXmlTandemOutput;
     }
 }
  
 void
 XtandemOutputSaxHandler::writeOpenTag(const QString &qName,
                                       const QXmlAttributes &attributes)
 {
   p_writeXmlTandemOutput->writeStartElement(qName);
   for(std::size_t i = 0; i < attributes.length(); i++)

◆ ~XtandemOutputSaxHandler()

pappso::XtandemOutputSaxHandler::~XtandemOutputSaxHandler ( )

Destructor

Definition at line 69 of file xtandemoutputsaxhandler.cpp.

79 {

Member Function Documentation

◆ characters()

bool pappso::XtandemOutputSaxHandler::characters ( const QString & str )

override

Definition at line 229 of file xtandemoutputsaxhandler.cpp.

◆ endDocument()

bool pappso::XtandemOutputSaxHandler::endDocument ( )

override

Definition at line 218 of file xtandemoutputsaxhandler.cpp.

226 {

◆ endElement()

bool pappso::XtandemOutputSaxHandler::endElement	(	const QString &	namespaceURI,
		const QString &	localName,
		const QString &	qName
	)

override

Definition at line 164 of file xtandemoutputsaxhandler.cpp.

     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemOutputSaxHandler::endElement tag "
                         "%1, PAPPSO exception:\n%2")
                         .arg(qName)
                         .arg(exception_pappso.qwhat());
       return false;
     }
   catch(std::exception exception_std)
     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemOutputSaxHandler::endElement tag "
                         "%1, std exception:\n%2")
                         .arg(qName)
                         .arg(exception_std.what());
       return false;
     }
  
   m_currentText.clear();
   m_tagStack.pop_back();
  
   return is_ok;
 }
  
 bool
 XtandemOutputSaxHandler::startDocument()
 {
  
   p_writeXmlTandemOutput->setAutoFormatting(true);
   p_writeXmlTandemOutput->writeStartDocument("1.0");
   return true;
 }
  
 bool
 XtandemOutputSaxHandler::endDocument()
 {
   p_writeXmlTandemOutput->writeEndDocument();
  
   m_destinationTandemOutputFile.close();

◆ endElement_note()

bool pappso::XtandemOutputSaxHandler::endElement_note ( )

private

Definition at line 295 of file xtandemoutputsaxhandler.cpp.

                           : m_mapTandemInputParameters)
         {
           p_writeXmlTandemOutput->writeStartElement("note");
           p_writeXmlTandemOutput->writeAttribute("type", "input");
           p_writeXmlTandemOutput->writeAttribute("label", pair_input.first);
           p_writeXmlTandemOutput->writeCharacters(pair_input.second);
           p_writeXmlTandemOutput->writeEndElement();
         }
     }
   else if(m_currentLabel == "output, path")
     {
       //<note type="input" label="output,
       // path">/tmp/tandemwrapper-sSGxtE/output_tandem.xml</note>
       p_writeXmlTandemOutput->writeCharacters(
         QFileInfo(m_destinationTandemOutputFile).absoluteFilePath());
       p_writeXmlTandemOutput->writeEndElement();
     }
   else
     {
       p_writeXmlTandemOutput->writeCharacters(m_currentText);
       p_writeXmlTandemOutput->writeEndElement();
     }
   return true;
 }
  
 void
 XtandemOutputSaxHandler::setInputParameters(const QString &label_name_attribute,
                                             const QString &input_value)
 {
   m_mapTandemInputParameters.insert(
     std::pair<QString, QString>(label_name_attribute, input_value));
 }
 } // namespace pappso

References p_writeXmlTandemOutput.

◆ error()

bool pappso::XtandemOutputSaxHandler::error ( const QXmlParseException & exception )

override

Definition at line 241 of file xtandemoutputsaxhandler.cpp.

                                                        :\n"
                     "%3")
                     .arg(exception.lineNumber())
                     .arg(exception.columnNumber())
                     .arg(exception.message());
   qDebug() << m_errorString;
   return false;
 }
  
 QString

◆ errorString()

QString pappso::XtandemOutputSaxHandler::errorString ( ) const

Definition at line 268 of file xtandemoutputsaxhandler.cpp.

     {
       m_currentLabel = attributes.value("label");
     }

References m_currentLabel.

◆ fatalError()

bool pappso::XtandemOutputSaxHandler::fatalError ( const QXmlParseException & exception )

override

Definition at line 255 of file xtandemoutputsaxhandler.cpp.

 {
   // qDebug() << "XtandemParamSaxHandler::startElement_note begin " <<
   // <note type="input"
   // label="output,path">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/test_run/20191222_18_EF1_third_step_test_condor_22janv.xml</note>
  
   writeOpenTag("note", attributes);

◆ setInputParameters()

void pappso::XtandemOutputSaxHandler::setInputParameters	(	const QString &	label_name_attribute,
		const QString &	input_value
	)

Definition at line 337 of file xtandemoutputsaxhandler.cpp.

Referenced by pappso::TandemWrapperRun::readyReadStandardOutput().

◆ startDocument()

bool pappso::XtandemOutputSaxHandler::startDocument ( )

override

Definition at line 209 of file xtandemoutputsaxhandler.cpp.

214 {

215 m_currentText += str;

◆ startElement()

bool pappso::XtandemOutputSaxHandler::startElement	(	const QString &	namespaceURI,
		const QString &	localName,
		const QString &	qName,
		const QXmlAttributes &	attributes
	)

override

Definition at line 91 of file xtandemoutputsaxhandler.cpp.

             {
  
               m_isTandemParameter = true;
  
               // <bioml xmlns:GAML="http://www.bioml.com/gaml/" label="models
               // from '/tmp/msdata.mzxml'">
               p_writeXmlTandemOutput->writeStartElement("bioml");
               p_writeXmlTandemOutput->writeAttribute("xmlns:GAML",
                                                      attributes.value("xmlns:GAML"));
               p_writeXmlTandemOutput->writeAttribute(
                 "label",
                 QString("models from '%1'").arg(m_originalMsDataFileName));
               return true;
             }
         }
       // startElement_group
  
       if(qName == "note")
         {
           is_ok = startElement_note(attributes);
         }
       else
         {
           writeOpenTag(qName, attributes);
         }
     }
   catch(pappso::PappsoException exception_pappso)
     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemOutputSaxHandler::startElement "
                         "tag %1, PAPPSO exception:\n%2")
                         .arg(qName)
                         .arg(exception_pappso.qwhat());
       return false;
     }
   catch(std::exception exception_std)
     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemOutputSaxHandler::startElement "
                         "tag %1, std exception:\n%2")
                         .arg(qName)
                         .arg(exception_std.what());
       return false;
     }
   return is_ok;
 }
  
 bool
 XtandemOutputSaxHandler::endElement(const QString &namespaceURI,
                                     const QString &localName,
                                     const QString &qName)
 {
  
   bool is_ok = true;
   // endElement_peptide_list
   try
     {
  
       if(qName == "note")
         {
           is_ok = endElement_note();
         }

◆ startElement_note()

bool pappso::XtandemOutputSaxHandler::startElement_note ( QXmlAttributes attributes )

private

Definition at line 275 of file xtandemoutputsaxhandler.cpp.

 {
   //    qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
   //   <note type="input" label="spectrum,
   //   path">/tmp/tandemwrapper-IehrEL/msdata.mzxml</note>
  
   if(m_currentLabel == "spectrum, path")
     {
       //<note type="input"
       // label="spectrum,path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
       // m_originMzDataFileName = m_currentText;
       // p_writeXmlTandemOutput->writeCharacters(m_destinationMzXmlFileName);
       p_writeXmlTandemOutput->writeCharacters(m_originalMsDataFileName);
       p_writeXmlTandemOutput->writeEndElement();

◆ writeOpenTag()

void pappso::XtandemOutputSaxHandler::writeOpenTag	(	const QString &	qName,
		const QXmlAttributes &	attributes
	)

private

Definition at line 79 of file xtandemoutputsaxhandler.cpp.

 {
   m_tagStack.push_back(qName);
   bool is_ok = true;
  
   try
     {
       m_currentText.clear();
       //<bioml label="example api document">
       if(m_tagStack.size() == 1)
         {

References m_currentText, and m_tagStack.

Member Data Documentation

◆ m_currentLabel

QString pappso::XtandemOutputSaxHandler::m_currentLabel

private

Definition at line 122 of file xtandemoutputsaxhandler.h.

Referenced by errorString().

◆ m_currentText

QString pappso::XtandemOutputSaxHandler::m_currentText

private

Definition at line 120 of file xtandemoutputsaxhandler.h.

Referenced by writeOpenTag().

◆ m_destinationTandemOutputFile

QFile pappso::XtandemOutputSaxHandler::m_destinationTandemOutputFile

private

Definition at line 117 of file xtandemoutputsaxhandler.h.

◆ m_errorString

QString pappso::XtandemOutputSaxHandler::m_errorString

private

Definition at line 119 of file xtandemoutputsaxhandler.h.

◆ m_isTandemParameter

bool pappso::XtandemOutputSaxHandler::m_isTandemParameter = false

private

Definition at line 121 of file xtandemoutputsaxhandler.h.

◆ m_mapTandemInputParameters

std::map<QString, QString> pappso::XtandemOutputSaxHandler::m_mapTandemInputParameters

private

Definition at line 115 of file xtandemoutputsaxhandler.h.

◆ m_originalMsDataFileName

QString pappso::XtandemOutputSaxHandler::m_originalMsDataFileName

private

Definition at line 123 of file xtandemoutputsaxhandler.h.

◆ m_tagStack

std::vector<QString> pappso::XtandemOutputSaxHandler::m_tagStack

private

Definition at line 116 of file xtandemoutputsaxhandler.h.

Referenced by writeOpenTag().

◆ p_writeXmlTandemOutput

QXmlStreamWriter* pappso::XtandemOutputSaxHandler::p_writeXmlTandemOutput

private

Definition at line 118 of file xtandemoutputsaxhandler.h.

Referenced by endElement_note().

The documentation for this class was generated from the following files:

pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.h
pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ XtandemOutputSaxHandler()

◆ ~XtandemOutputSaxHandler()

Member Function Documentation

◆ characters()

◆ endDocument()

◆ endElement()

◆ endElement_note()

◆ error()

◆ errorString()

◆ fatalError()

◆ setInputParameters()

◆ startDocument()

◆ startElement()

◆ startElement_note()

◆ writeOpenTag()

Member Data Documentation

◆ m_currentLabel

◆ m_currentText

◆ m_destinationTandemOutputFile

◆ m_errorString

◆ m_isTandemParameter

◆ m_mapTandemInputParameters

◆ m_originalMsDataFileName

◆ m_tagStack

◆ p_writeXmlTandemOutput