#include <xtandeminputsaxhandler.h>

Inheritance diagram for pappso::XtandemInputSaxHandler:

Public Member Functions
	XtandemInputSaxHandler (const QString &destinationMzXmlFile, const QString &destinationTandemInputFile, const QString &destinationTandemOutputFile)

	~XtandemInputSaxHandler ()

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

const QString &	getOriginalMsDataFileName () const

const QString &	getOriginalTandemOutputFileName () const

const QString &	getOriginalTandemPresetFileName () const

Private Member Functions
bool	startElement_note (QXmlAttributes attributes)

bool	endElement_note ()

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

Private Attributes
QString	m_destinationMzXmlFileName

QString	m_originMzDataFileName

QString	m_destinationTandemInputFileName

QString	m_originTandemPresetFileName

QString	m_originTandemOutpuFileName

QString	m_destinationTandemOutputFileName

QFile	m_destinationTandemInputFile

QXmlStreamWriter *	p_writeXmlTandemInput

std::vector< QString >	m_tagStack

bool	m_isTandemParameter = false

QString	m_errorString

QString	m_currentText

QString	m_currentLabel

QString	m_labelName

Detailed Description

Definition at line 38 of file xtandeminputsaxhandler.h.

Constructor & Destructor Documentation

◆ XtandemInputSaxHandler()

pappso::XtandemInputSaxHandler::XtandemInputSaxHandler	(	const QString &	destinationMzXmlFile,
		const QString &	destinationTandemInputFile,
		const QString &	destinationTandemOutputFile
	)

Default constructor

Definition at line 34 of file xtandeminputsaxhandler.cpp.

   : m_destinationTandemInputFile(destinationTandemInputFile)
 {
   m_destinationMzXmlFileName        = destinationMzXmlFile;
   m_destinationTandemOutputFileName = destinationTandemOutputFile;
   m_destinationTandemInputFileName =
     QFileInfo(destinationTandemInputFile).absoluteFilePath();
  
   if(destinationTandemInputFile.isEmpty())
     {
       throw pappso::PappsoException(
         QObject::tr("ERROR: X!Tandem input file path is empty"));
     }
  
   if(!m_destinationTandemInputFile.open(QIODevice::WriteOnly))
     {
       throw pappso::PappsoException(
         QObject::tr("ERROR: unable to open %1 tandem output file for write")
           .arg(destinationTandemInputFile));
     }
  
   p_writeXmlTandemInput = new QXmlStreamWriter();
   p_writeXmlTandemInput->setDevice(&m_destinationTandemInputFile);
 }

References m_destinationMzXmlFileName, m_destinationTandemInputFile, m_destinationTandemInputFileName, m_destinationTandemOutputFileName, and p_writeXmlTandemInput.

◆ ~XtandemInputSaxHandler()

pappso::XtandemInputSaxHandler::~XtandemInputSaxHandler ( )

Destructor

Definition at line 62 of file xtandeminputsaxhandler.cpp.

 {
   if(p_writeXmlTandemInput != nullptr)
     {
       m_destinationTandemInputFile.close();
       delete p_writeXmlTandemInput;
     }
 }

References m_destinationTandemInputFile, and p_writeXmlTandemInput.

Member Function Documentation

◆ characters()

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

override

Definition at line 230 of file xtandeminputsaxhandler.cpp.

 {
   m_currentText += str;
   return true;
 }

References m_currentText.

◆ endDocument()

bool pappso::XtandemInputSaxHandler::endDocument ( )

override

Definition at line 219 of file xtandeminputsaxhandler.cpp.

 {
   p_writeXmlTandemInput->writeEndDocument();
  
   m_destinationTandemInputFile.close();
   delete p_writeXmlTandemInput;
   p_writeXmlTandemInput = nullptr;
   return true;
 }

References m_destinationTandemInputFile, and p_writeXmlTandemInput.

◆ endElement()

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

override

Definition at line 164 of file xtandeminputsaxhandler.cpp.

 {
  
   bool is_ok = true;
   // endElement_peptide_list
   try
     {
  
       if(qName == "note")
         {
           is_ok = endElement_note();
         }
       else
         {
           p_writeXmlTandemInput->writeCharacters(m_currentText);
           p_writeXmlTandemInput->writeEndElement();
         }
     }
   catch(pappso::PappsoException &exception_pappso)
     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemInputSaxHandler::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 XtandemInputSaxHandler::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;
 }

References endElement_note(), m_currentText, m_errorString, m_tagStack, p_writeXmlTandemInput, and pappso::PappsoException::qwhat().

◆ endElement_note()

bool pappso::XtandemInputSaxHandler::endElement_note ( )

private

Definition at line 292 of file xtandeminputsaxhandler.cpp.

 {
   //    qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
   //    _current_label << " " << _current_text.simplified();
   if(m_currentLabel == "output, path")
     {
       m_originTandemOutpuFileName = m_currentText;
       p_writeXmlTandemInput->writeCharacters(m_destinationTandemOutputFileName);
     }
   else if(m_currentLabel == "list path, default parameters")
     {
       // <note type="input" label="list path, default parameters">
       p_writeXmlTandemInput->writeCharacters(m_currentText);
       m_originTandemPresetFileName =
         QFileInfo(m_currentText).absoluteFilePath();
     }
   else 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_writeXmlTandemInput->writeCharacters(m_destinationMzXmlFileName);
     }
   else
     {
       p_writeXmlTandemInput->writeCharacters(m_currentText);
     }
   p_writeXmlTandemInput->writeEndElement();
   return true;
 }

References m_currentLabel, m_currentText, m_destinationMzXmlFileName, m_destinationTandemOutputFileName, m_originMzDataFileName, m_originTandemOutpuFileName, m_originTandemPresetFileName, and p_writeXmlTandemInput.

Referenced by endElement().

◆ error()

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

override

Definition at line 238 of file xtandeminputsaxhandler.cpp.

 {
   m_errorString = QObject::tr(
                     "Parse error at line %1, column %2 :\n"
                     "%3")
                     .arg(exception.lineNumber())
                     .arg(exception.columnNumber())
                     .arg(exception.message());
   qDebug() << m_errorString;
   return false;
 }

References m_errorString.

◆ errorString()

QString pappso::XtandemInputSaxHandler::errorString ( ) const

Definition at line 265 of file xtandeminputsaxhandler.cpp.

 {
   return m_errorString;
 }

References m_errorString.

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

◆ fatalError()

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

override

Definition at line 252 of file xtandeminputsaxhandler.cpp.

 {
   m_errorString = QObject::tr(
                     "Parse error at line %1, column %2 :\n"
                     "%3")
                     .arg(exception.lineNumber())
                     .arg(exception.columnNumber())
                     .arg(exception.message());
   qDebug() << m_errorString;
   return false;
 }

References m_errorString.

◆ getOriginalMsDataFileName()

const QString & pappso::XtandemInputSaxHandler::getOriginalMsDataFileName ( ) const

Definition at line 325 of file xtandeminputsaxhandler.cpp.

 {
   return m_originMzDataFileName;
 }

References m_originMzDataFileName.

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

◆ getOriginalTandemOutputFileName()

const QString & pappso::XtandemInputSaxHandler::getOriginalTandemOutputFileName ( ) const

Definition at line 331 of file xtandeminputsaxhandler.cpp.

 {
   return m_originTandemOutpuFileName;
 }

References m_originTandemOutpuFileName.

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

◆ getOriginalTandemPresetFileName()

const QString & pappso::XtandemInputSaxHandler::getOriginalTandemPresetFileName ( ) const

Definition at line 337 of file xtandeminputsaxhandler.cpp.

 {
   return m_originTandemPresetFileName;
 }

References m_originTandemPresetFileName.

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

◆ startDocument()

bool pappso::XtandemInputSaxHandler::startDocument ( )

override

Definition at line 210 of file xtandeminputsaxhandler.cpp.

 {
  
   p_writeXmlTandemInput->setAutoFormatting(true);
   p_writeXmlTandemInput->writeStartDocument("1.0");
   return true;
 }

References p_writeXmlTandemInput.

◆ startElement()

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

override

Definition at line 84 of file xtandeminputsaxhandler.cpp.

 {
   /*
 <?xml version="1.0" encoding="UTF-8"?>
 <bioml label="20191222_18_EF1_test_condor_22janv_third_step.xml">
 <note type="heading">Paths</note>
 <note type="input" label="list path, default
 parameters">/gorgone/pappso/jouy/presets/metapappso/Lumos_04112019_PROTEOCARDIS_THIRD_STEP_AB.xml</note>
 <note type="input" label="list path, taxonomy
 information">/gorgone/pappso/jouy/users/Celine/2019_Lumos/20191222_107_Juste_APD/metapappso_condor/params/xtandem_database_third_step_test_condor_22janv.database</note>
 <note type="input" label="spectrum,
 path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
 <note type="heading">Protein general</note>
 <note type="input" label="protein, taxon">usedefined</note>
 <note type="heading">Output</note>
 <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>
 </bioml>
 */
   m_tagStack.push_back(qName);
   bool is_ok = true;
  
   try
     {
       m_currentText.clear();
       //<bioml label="example api document">
       if(m_tagStack.size() == 1)
         {
           if(qName != "bioml")
             {
               m_errorString = QObject::tr(
                                 "ERROR in XtandemInputSaxHandler::startElement "
                                 "root tag %1 is not <bioml>")
                                 .arg(qName);
               m_isTandemParameter = false;
               return false;
             }
           else
             {
  
               m_isTandemParameter = true;
               // label="20191222_18_EF1_test_condor_22janv_third_step.xml"
               m_labelName = attributes.value("label");
  
               writeOpenTag(qName, attributes);
             }
         }
       // startElement_group
  
       if(qName == "note")
         {
           is_ok = startElement_note(attributes);
         }
     }
   catch(pappso::PappsoException &exception_pappso)
     {
       m_errorString = QObject::tr(
                         "ERROR in XtandemInputSaxHandler::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 XtandemInputSaxHandler::startElement "
                         "tag %1, std exception:\n%2")
                         .arg(qName)
                         .arg(exception_std.what());
       return false;
     }
   return is_ok;
 }

References m_currentText, m_errorString, m_isTandemParameter, m_labelName, m_tagStack, pappso::PappsoException::qwhat(), startElement_note(), and writeOpenTag().

◆ startElement_note()

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

private

Definition at line 272 of file xtandeminputsaxhandler.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);
   m_currentLabel = "";
  
   if(attributes.value("type") == "input")
     {
       m_currentLabel = attributes.value("label");
     }
  
   //  qDebug() << "XtandemParamSaxHandler::startElement_note _current_label " <<
   //  _current_label;
   return true;
 }

References m_currentLabel, and writeOpenTag().

Referenced by startElement().

◆ writeOpenTag()

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

private

Definition at line 72 of file xtandeminputsaxhandler.cpp.

 {
   p_writeXmlTandemInput->writeStartElement(qName);
   for(int i = 0; i < attributes.length(); i++)
     {
       p_writeXmlTandemInput->writeAttribute(attributes.qName(i),
                                             attributes.value(i));
     }
 }

References p_writeXmlTandemInput.

Referenced by startElement(), and startElement_note().

Member Data Documentation

◆ m_currentLabel

QString pappso::XtandemInputSaxHandler::m_currentLabel

private

Definition at line 98 of file xtandeminputsaxhandler.h.

Referenced by endElement_note(), and startElement_note().

◆ m_currentText

QString pappso::XtandemInputSaxHandler::m_currentText

private

Definition at line 97 of file xtandeminputsaxhandler.h.

Referenced by characters(), endElement(), endElement_note(), and startElement().

◆ m_destinationMzXmlFileName

QString pappso::XtandemInputSaxHandler::m_destinationMzXmlFileName

private

Definition at line 86 of file xtandeminputsaxhandler.h.

Referenced by XtandemInputSaxHandler(), and endElement_note().

◆ m_destinationTandemInputFile

QFile pappso::XtandemInputSaxHandler::m_destinationTandemInputFile

private

Definition at line 92 of file xtandeminputsaxhandler.h.

Referenced by XtandemInputSaxHandler(), ~XtandemInputSaxHandler(), and endDocument().

◆ m_destinationTandemInputFileName

QString pappso::XtandemInputSaxHandler::m_destinationTandemInputFileName

private

Definition at line 88 of file xtandeminputsaxhandler.h.

Referenced by XtandemInputSaxHandler().

◆ m_destinationTandemOutputFileName

QString pappso::XtandemInputSaxHandler::m_destinationTandemOutputFileName

private

Definition at line 91 of file xtandeminputsaxhandler.h.

Referenced by XtandemInputSaxHandler(), and endElement_note().

◆ m_errorString

QString pappso::XtandemInputSaxHandler::m_errorString

private

Definition at line 96 of file xtandeminputsaxhandler.h.

Referenced by endElement(), error(), errorString(), fatalError(), and startElement().

◆ m_isTandemParameter

bool pappso::XtandemInputSaxHandler::m_isTandemParameter = false

private

Definition at line 95 of file xtandeminputsaxhandler.h.

Referenced by startElement().

◆ m_labelName

QString pappso::XtandemInputSaxHandler::m_labelName

private

Definition at line 99 of file xtandeminputsaxhandler.h.

Referenced by startElement().

◆ m_originMzDataFileName

QString pappso::XtandemInputSaxHandler::m_originMzDataFileName

private

Definition at line 87 of file xtandeminputsaxhandler.h.

Referenced by endElement_note(), and getOriginalMsDataFileName().

◆ m_originTandemOutpuFileName

QString pappso::XtandemInputSaxHandler::m_originTandemOutpuFileName

private

Definition at line 90 of file xtandeminputsaxhandler.h.

Referenced by endElement_note(), and getOriginalTandemOutputFileName().

◆ m_originTandemPresetFileName

QString pappso::XtandemInputSaxHandler::m_originTandemPresetFileName

private

Definition at line 89 of file xtandeminputsaxhandler.h.

Referenced by endElement_note(), and getOriginalTandemPresetFileName().

◆ m_tagStack

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

private

Definition at line 94 of file xtandeminputsaxhandler.h.

Referenced by endElement(), and startElement().

◆ p_writeXmlTandemInput

QXmlStreamWriter* pappso::XtandemInputSaxHandler::p_writeXmlTandemInput

private

Definition at line 93 of file xtandeminputsaxhandler.h.

Referenced by XtandemInputSaxHandler(), ~XtandemInputSaxHandler(), endDocument(), endElement(), endElement_note(), startDocument(), and writeOpenTag().

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

pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.h
pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ XtandemInputSaxHandler()

◆ ~XtandemInputSaxHandler()

Member Function Documentation

◆ characters()

◆ endDocument()

◆ endElement()

◆ endElement_note()

◆ error()

◆ errorString()

◆ fatalError()

◆ getOriginalMsDataFileName()

◆ getOriginalTandemOutputFileName()

◆ getOriginalTandemPresetFileName()

◆ startDocument()

◆ startElement()

◆ startElement_note()

◆ writeOpenTag()

Member Data Documentation

◆ m_currentLabel

◆ m_currentText

◆ m_destinationMzXmlFileName

◆ m_destinationTandemInputFile

◆ m_destinationTandemInputFileName

◆ m_destinationTandemOutputFileName

◆ m_errorString

◆ m_isTandemParameter

◆ m_labelName

◆ m_originMzDataFileName

◆ m_originTandemOutpuFileName

◆ m_originTandemPresetFileName

◆ m_tagStack

◆ p_writeXmlTandemInput