pappso::XtandemOutputSaxHandler Class Reference

#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 38 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 35 of file xtandemoutputsaxhandler.cpp.

  : m_destinationTandemOutputFile(final_tandem_output)
{
  qDebug() << final_tandem_output;
  m_originalMsDataFileName =
    QFileInfo(original_msdata_file_name).absoluteFilePath();
  if(!m_destinationTandemOutputFile.open(QIODevice::WriteOnly))
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: unable to open %1 to write XML output")
          .arg(final_tandem_output));
    }
  p_writeXmlTandemOutput = new QXmlStreamWriter();
  p_writeXmlTandemOutput->setAutoFormatting(true);
  p_writeXmlTandemOutput->setDevice(&m_destinationTandemOutputFile);
}

References m_destinationTandemOutputFile, m_originalMsDataFileName, and p_writeXmlTandemOutput.

~XtandemOutputSaxHandler()

pappso::XtandemOutputSaxHandler::~XtandemOutputSaxHandler

(

)

Destructor

Definition at line 53 of file xtandemoutputsaxhandler.cpp.

{
  if(p_writeXmlTandemOutput != nullptr)
    {
      m_destinationTandemOutputFile.close();
      delete p_writeXmlTandemOutput;
    }
}

References m_destinationTandemOutputFile, and p_writeXmlTandemOutput.

Member Function Documentation

characters()

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

override

Definition at line 215 of file xtandemoutputsaxhandler.cpp.

{
  m_currentText += str;
  if(m_tagStack.back() != "note")
    {
      p_writeXmlTandemOutput->writeCharacters(str);
    }
  return true;
}

References m_currentText, m_tagStack, and p_writeXmlTandemOutput.

endDocument()

bool pappso::XtandemOutputSaxHandler::endDocument ( )

override

Definition at line 204 of file xtandemoutputsaxhandler.cpp.

{
  p_writeXmlTandemOutput->writeEndDocument();
 
  m_destinationTandemOutputFile.close();
  delete p_writeXmlTandemOutput;
  p_writeXmlTandemOutput = nullptr;
  return true;
}

References m_destinationTandemOutputFile, and p_writeXmlTandemOutput.

endElement()

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

override

Definition at line 149 of file xtandemoutputsaxhandler.cpp.

{
 
  bool is_ok = true;
  // endElement_peptide_list
  try
    {
 
      if(qName == "note")
        {
          is_ok = endElement_note();
        }
      else
        {
          p_writeXmlTandemOutput->writeEndElement();
        }
    }
  catch(const pappso::PappsoException &exception_pappso)
    {
      m_errorString = QObject::tr(
                        "ERROR in XtandemOutputSaxHandler::endElement tag "
                        "%1, PAPPSO exception:\n%2")
                        .arg(qName)
                        .arg(exception_pappso.qwhat());
      return false;
    }
  catch(const 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;
}

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

endElement_note()

bool pappso::XtandemOutputSaxHandler::endElement_note ( )

private

Definition at line 281 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();
 
 
      for(auto pair_input : 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;
}

References m_currentLabel, m_currentText, m_destinationTandemOutputFile, m_mapTandemInputParameters, m_originalMsDataFileName, and p_writeXmlTandemOutput.

Referenced by endElement().

error()

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

override

Definition at line 227 of file xtandemoutputsaxhandler.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::XtandemOutputSaxHandler::errorString

(

)

const

Definition at line 254 of file xtandemoutputsaxhandler.cpp.

{
  return m_errorString;
}

References m_errorString.

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

fatalError()

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

override

Definition at line 241 of file xtandemoutputsaxhandler.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.

setInputParameters()

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

Definition at line 323 of file xtandemoutputsaxhandler.cpp.

{
  m_mapTandemInputParameters.insert(
    std::pair<QString, QString>(label_name_attribute, input_value));
}

References m_mapTandemInputParameters.

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

startDocument()

bool pappso::XtandemOutputSaxHandler::startDocument ( )

override

Definition at line 195 of file xtandemoutputsaxhandler.cpp.

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

References p_writeXmlTandemOutput.

startElement()

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

override

Definition at line 75 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)
        {
          if(qName != "bioml")
            {
              m_errorString =
                QObject::tr(
                  "ERROR in XtandemOutputSaxHandler::startElement "
                  "root tag %1 is not <bioml>")
                  .arg(qName);
              m_isTandemParameter = false;
              return false;
            }
          else
            {
 
              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(const 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(const 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;
}

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

startElement_note()

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

private

Definition at line 261 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);
  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::XtandemOutputSaxHandler::writeOpenTag ( const QString &  qName, const QXmlAttributes &  attributes  )

private

Definition at line 63 of file xtandemoutputsaxhandler.cpp.

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

References p_writeXmlTandemOutput.

Referenced by startElement(), and startElement_note().

Member Data Documentation

m_currentLabel

QString pappso::XtandemOutputSaxHandler::m_currentLabel

private

Definition at line 89 of file xtandemoutputsaxhandler.h.

Referenced by endElement_note(), and startElement_note().

m_currentText

QString pappso::XtandemOutputSaxHandler::m_currentText

private

Definition at line 87 of file xtandemoutputsaxhandler.h.

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

m_destinationTandemOutputFile

QFile pappso::XtandemOutputSaxHandler::m_destinationTandemOutputFile

private

Definition at line 84 of file xtandemoutputsaxhandler.h.

Referenced by XtandemOutputSaxHandler(), ~XtandemOutputSaxHandler(), endDocument(), and endElement_note().

m_errorString

QString pappso::XtandemOutputSaxHandler::m_errorString

private

Definition at line 86 of file xtandemoutputsaxhandler.h.

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

m_isTandemParameter

bool pappso::XtandemOutputSaxHandler::m_isTandemParameter = false

private

Definition at line 88 of file xtandemoutputsaxhandler.h.

Referenced by startElement().

m_mapTandemInputParameters

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

private

Definition at line 82 of file xtandemoutputsaxhandler.h.

Referenced by endElement_note(), and setInputParameters().

m_originalMsDataFileName

QString pappso::XtandemOutputSaxHandler::m_originalMsDataFileName

private

Definition at line 90 of file xtandemoutputsaxhandler.h.

Referenced by XtandemOutputSaxHandler(), endElement_note(), and startElement().

m_tagStack

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

private

Definition at line 83 of file xtandemoutputsaxhandler.h.

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

p_writeXmlTandemOutput

QXmlStreamWriter* pappso::XtandemOutputSaxHandler::p_writeXmlTandemOutput

private

Definition at line 85 of file xtandemoutputsaxhandler.h.

Referenced by XtandemOutputSaxHandler(), ~XtandemOutputSaxHandler(), characters(), endDocument(), endElement(), endElement_note(), startDocument(), startElement(), and writeOpenTag().

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

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