#include <wraptandeminput.h>

Inheritance diagram for pappso::WrapTandemInput:

Public Member Functions
	WrapTandemInput (const QString &destinationMzXmlFile, const QString &destinationTandemInputFile, const QString &destinationTandemOutputFile)
virtual	~WrapTandemInput ()
const QString &	getOriginalMsDataFileName () const
const QString &	getOriginalTandemOutputFileName () const
const QString &	getOriginalTandemPresetFileName () const
Public Member Functions inherited from pappso::XmlStreamReaderInterface
	XmlStreamReaderInterface ()
virtual	~XmlStreamReaderInterface ()
virtual bool	readFile (const QString &fileName)
bool	read (QIODevice *device)
bool	read (const QString &xml_content)
QString	errorString () const

Protected Member Functions
virtual void	readStream () override
Protected Member Functions inherited from pappso::XmlStreamReaderInterface
void	cloneStartElement (QXmlStreamWriter &output) const
void	cloneElement (QXmlStreamWriter &output)
void	cloneNode (QXmlStreamWriter &output)

Private Attributes
QString	m_destinationMzXmlFileName
QString	m_originMzDataFileName
QString	m_destinationTandemInputFileName
QString	m_originTandemPresetFileName
QString	m_originTandemOutpuFileName
QString	m_destinationTandemOutputFileName
QFile	m_destinationTandemInputFile
QXmlStreamWriter	m_writerXmlTandemInput

Additional Inherited Members
Protected Attributes inherited from pappso::XmlStreamReaderInterface
QXmlStreamReader	m_qxmlStreamReader

Detailed Description

Todo: write docs

Definition at line 42 of file wraptandeminput.h.

Constructor & Destructor Documentation

◆ WrapTandemInput()

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

Default constructor

Definition at line 36 of file wraptandeminput.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));
    }
 
  m_writerXmlTandemInput.setDevice(&m_destinationTandemInputFile);
  m_writerXmlTandemInput.setAutoFormatting(true);
  m_writerXmlTandemInput.writeStartDocument("1.0");
}

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

◆ ~WrapTandemInput()

pappso::WrapTandemInput::~WrapTandemInput ( )

virtual

Destructor

Definition at line 62 of file wraptandeminput.cpp.

{
  m_destinationTandemInputFile.close();
}

References m_destinationTandemInputFile.

Member Function Documentation

◆ getOriginalMsDataFileName()

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

Definition at line 131 of file wraptandeminput.cpp.

{
  return m_originMzDataFileName;
}

References m_originMzDataFileName.

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

◆ getOriginalTandemOutputFileName()

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

Definition at line 137 of file wraptandeminput.cpp.

{
  return m_originTandemOutpuFileName;
}

References m_originTandemOutpuFileName.

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

◆ getOriginalTandemPresetFileName()

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

Definition at line 143 of file wraptandeminput.cpp.

{
  return m_originTandemPresetFileName;
}

References m_originTandemPresetFileName.

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

◆ readStream()

void pappso::WrapTandemInput::readStream ( )

overrideprotectedvirtual

Implements pappso::XmlStreamReaderInterface.

Definition at line 69 of file wraptandeminput.cpp.

{
  qDebug();
  if(m_qxmlStreamReader.readNextStartElement())
    {
      if(m_qxmlStreamReader.name().toString() == "bioml")
        {
          cloneStartElement(m_writerXmlTandemInput);
          qDebug();
          while(m_qxmlStreamReader.readNextStartElement())
            {
              // qDebug() << m_qxmlStreamReader.name();
              // read_note();
              cloneStartElement(m_writerXmlTandemInput);
 
              QString type  = m_qxmlStreamReader.attributes().value("type").toString();
              QString label = m_qxmlStreamReader.attributes().value("label").toString();
 
              if((type == "input") && (label == "spectrum, path"))
                {
                  //<note type="input" label="spectrum, path">
 
                  m_originMzDataFileName = m_qxmlStreamReader.readElementText();
                  m_writerXmlTandemInput.writeCharacters(m_destinationMzXmlFileName);
                  // m_qxmlStreamReader.skipCurrentElement();
                }
              else if((type == "input") && (label == "output, path"))
                {
                  //<note type="input" label="output, path">
                  m_originTandemOutpuFileName = m_qxmlStreamReader.readElementText();
                  m_writerXmlTandemInput.writeCharacters(m_destinationTandemOutputFileName);
                  // m_qxmlStreamReader.skipCurrentElement();
                }
              // list path, default parameters
              else if((type == "input") && (label == "list path, default parameters"))
                {
                  //<note type="input" label="list path, default
                  // parameters">/gorgone/pappso/tmp/xtpcpp.AjyZGg/Lumos_trypsin_rev_camC_oxM_10ppm_HCDOT_12102017CH.xml</note>
 
                  m_originTandemPresetFileName = m_qxmlStreamReader.readElementText();
                  m_writerXmlTandemInput.writeCharacters(m_originTandemPresetFileName);
                }
              else
                {
                  m_writerXmlTandemInput.writeCharacters(m_qxmlStreamReader.readElementText());
                }
              m_writerXmlTandemInput.writeEndElement();
            }
        }
      else
        {
          m_qxmlStreamReader.raiseError(QObject::tr("Not an X!Tandem input file"));
          m_qxmlStreamReader.skipCurrentElement();
        }
    }
  m_writerXmlTandemInput.writeEndDocument();
  m_destinationTandemInputFile.close();
  qDebug();
}

References pappso::XmlStreamReaderInterface::cloneStartElement(), m_destinationMzXmlFileName, m_destinationTandemInputFile, m_destinationTandemOutputFileName, m_originMzDataFileName, m_originTandemOutpuFileName, m_originTandemPresetFileName, pappso::XmlStreamReaderInterface::m_qxmlStreamReader, and m_writerXmlTandemInput.

Member Data Documentation

◆ m_destinationMzXmlFileName

QString pappso::WrapTandemInput::m_destinationMzXmlFileName

private

Definition at line 68 of file wraptandeminput.h.

Referenced by WrapTandemInput(), and readStream().

◆ m_destinationTandemInputFile

QFile pappso::WrapTandemInput::m_destinationTandemInputFile

private

Definition at line 74 of file wraptandeminput.h.

Referenced by WrapTandemInput(), ~WrapTandemInput(), and readStream().

◆ m_destinationTandemInputFileName

QString pappso::WrapTandemInput::m_destinationTandemInputFileName

private

Definition at line 70 of file wraptandeminput.h.

Referenced by WrapTandemInput().

◆ m_destinationTandemOutputFileName

QString pappso::WrapTandemInput::m_destinationTandemOutputFileName

private

Definition at line 73 of file wraptandeminput.h.

Referenced by WrapTandemInput(), and readStream().

◆ m_originMzDataFileName

QString pappso::WrapTandemInput::m_originMzDataFileName

private

Definition at line 69 of file wraptandeminput.h.

Referenced by getOriginalMsDataFileName(), and readStream().

◆ m_originTandemOutpuFileName

QString pappso::WrapTandemInput::m_originTandemOutpuFileName

private

Definition at line 72 of file wraptandeminput.h.

Referenced by getOriginalTandemOutputFileName(), and readStream().

◆ m_originTandemPresetFileName

QString pappso::WrapTandemInput::m_originTandemPresetFileName

private

Definition at line 71 of file wraptandeminput.h.

Referenced by getOriginalTandemPresetFileName(), and readStream().

◆ m_writerXmlTandemInput

QXmlStreamWriter pappso::WrapTandemInput::m_writerXmlTandemInput

private

Definition at line 75 of file wraptandeminput.h.

Referenced by WrapTandemInput(), and readStream().

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

pappsomspp/core/processing/tandemwrapper/wraptandeminput.h
pappsomspp/core/processing/tandemwrapper/wraptandeminput.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ WrapTandemInput()

◆ ~WrapTandemInput()

Member Function Documentation

◆ getOriginalMsDataFileName()

◆ getOriginalTandemOutputFileName()

◆ getOriginalTandemPresetFileName()

◆ readStream()

Member Data Documentation

◆ m_destinationMzXmlFileName

◆ m_destinationTandemInputFile

◆ m_destinationTandemInputFileName

◆ m_destinationTandemOutputFileName

◆ m_originMzDataFileName

◆ m_originTandemOutpuFileName

◆ m_originTandemPresetFileName

◆ m_writerXmlTandemInput