libpappsomspp
Library for mass spectrometry
pappso::WrapTandemResults Class Reference

#include <wraptandemresults.h>

Inheritance diagram for pappso::WrapTandemResults:
pappso::XmlStreamReaderInterface

Public Member Functions

 WrapTandemResults (const QString &final_tandem_output, const QString &original_msdata_file_name)
 
virtual ~WrapTandemResults ()
 
void setInputParameters (const QString &label_name_attribute, const QString &input_value)
 
- 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 Member Functions

void process_group_note ()
 

Private Attributes

QFile m_destinationTandemOutputFile
 
QXmlStreamWriter m_writerXmlTandemOutput
 
QString m_originalMsDataFileName
 
std::map< QString, QString > m_mapTandemInputParameters
 

Additional Inherited Members

- Protected Attributes inherited from pappso::XmlStreamReaderInterface
QXmlStreamReader m_qxmlStreamReader
 

Detailed Description

Todo:
write docs

Definition at line 42 of file wraptandemresults.h.

Constructor & Destructor Documentation

◆ WrapTandemResults()

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

Default constructor

Definition at line 36 of file wraptandemresults.cpp.

38  : m_destinationTandemOutputFile(final_tandem_output)
39 {
40  qDebug() << final_tandem_output;
42  QFileInfo(original_msdata_file_name).absoluteFilePath();
43  if(!m_destinationTandemOutputFile.open(QIODevice::WriteOnly))
44  {
46  QObject::tr("ERROR: unable to open %1 to write XML output")
47  .arg(final_tandem_output));
48  }
50  m_writerXmlTandemOutput.writeStartDocument("1.0");
51  m_writerXmlTandemOutput.setAutoFormatting(true);
52 }
QXmlStreamWriter m_writerXmlTandemOutput

References m_destinationTandemOutputFile, m_originalMsDataFileName, and m_writerXmlTandemOutput.

◆ ~WrapTandemResults()

pappso::WrapTandemResults::~WrapTandemResults ( )
virtual

Destructor

Definition at line 54 of file wraptandemresults.cpp.

55 {
56 }

Member Function Documentation

◆ process_group_note()

void pappso::WrapTandemResults::process_group_note ( )
private

Definition at line 67 of file wraptandemresults.cpp.

68 {
70  while(m_qxmlStreamReader.readNext() && !m_qxmlStreamReader.isEndElement())
71  {
72  if(m_qxmlStreamReader.isStartElement())
73  {
74  QString type =
75  m_qxmlStreamReader.attributes().value("type").toString();
76  QString label =
77  m_qxmlStreamReader.attributes().value("label").toString();
78  qDebug() << "type=" << type << " label=" << label;
79  // qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
80  // <note type="input" label="spectrum,
81  // path">/tmp/tandemwrapper-IehrEL/msdata.mzxml</note>
82 
83  if(label == "spectrum, path")
84  {
85  //<note type="input"
86  // label="spectrum,path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
87  // m_originMzDataFileName = m_currentText;
88  // p_writeXmlTandemOutput->writeCharacters(m_destinationMzXmlFileName);
89 
90  m_writerXmlTandemOutput.writeStartElement("note");
91  m_writerXmlTandemOutput.writeAttributes(
92  m_qxmlStreamReader.attributes());
94  m_writerXmlTandemOutput.writeEndElement();
95 
96 
97  for(auto pair_input : m_mapTandemInputParameters)
98  {
99  m_writerXmlTandemOutput.writeStartElement("note");
100  m_writerXmlTandemOutput.writeAttribute("type", "input");
101  m_writerXmlTandemOutput.writeAttribute("label",
102  pair_input.first);
103  m_writerXmlTandemOutput.writeCharacters(pair_input.second);
104 
105  m_writerXmlTandemOutput.writeEndElement();
106  }
107  m_qxmlStreamReader.skipCurrentElement();
108  }
109  else if(label == "output, path")
110  {
111 
112  //<note type="input" label="output,
113  // path">/tmp/tandemwrapper-sSGxtE/output_tandem.xml</note>
114 
115  m_writerXmlTandemOutput.writeStartElement("note");
116  m_writerXmlTandemOutput.writeAttributes(
117  m_qxmlStreamReader.attributes());
118  m_writerXmlTandemOutput.writeCharacters(
119  QFileInfo(m_destinationTandemOutputFile).absoluteFilePath());
120  m_writerXmlTandemOutput.writeEndElement();
121  m_qxmlStreamReader.skipCurrentElement();
122  }
123  else
124  {
126  }
127  }
128  }
129  m_writerXmlTandemOutput.writeEndElement();
130 }
std::map< QString, QString > m_mapTandemInputParameters
void cloneStartElement(QXmlStreamWriter &output) const
void cloneElement(QXmlStreamWriter &output)

References pappso::XmlStreamReaderInterface::cloneElement(), pappso::XmlStreamReaderInterface::cloneStartElement(), m_destinationTandemOutputFile, m_mapTandemInputParameters, m_originalMsDataFileName, pappso::XmlStreamReaderInterface::m_qxmlStreamReader, and m_writerXmlTandemOutput.

Referenced by readStream().

◆ readStream()

void pappso::WrapTandemResults::readStream ( )
overrideprotectedvirtual

Implements pappso::XmlStreamReaderInterface.

Definition at line 133 of file wraptandemresults.cpp.

134 {
135  qDebug();
136  if(m_qxmlStreamReader.readNextStartElement())
137  {
138  if(m_qxmlStreamReader.name().toString() == "bioml")
139  {
141  qDebug();
142  while(m_qxmlStreamReader.readNextStartElement())
143  {
144  if(m_qxmlStreamReader.name().toString() == "group")
145  {
146  QString type =
147  m_qxmlStreamReader.attributes().value("type").toString();
148  if(type == "model")
149  {
151  }
152  else if(type == "parameters")
153  {
154  QString label = m_qxmlStreamReader.attributes()
155  .value("label")
156  .toString();
157  if(label == "performance parameters")
158  {
160  }
161  else if(label == "input parameters")
162  {
164  // cloneElement(m_writerXmlTandemOutput);
165  }
166  else if(label == "unused input parameters")
167  {
169  }
170  else
171  {
172  m_qxmlStreamReader.skipCurrentElement();
173  }
174  }
175  }
176  else
177  {
178  qDebug() << m_qxmlStreamReader.name();
179  // read_note();
181 
182 
183  m_writerXmlTandemOutput.writeCharacters(
184  m_qxmlStreamReader.readElementText());
185 
186  m_writerXmlTandemOutput.writeEndElement();
187  }
188  }
189  }
190  else
191  {
192  m_qxmlStreamReader.raiseError(
193  QObject::tr("Not an X!Tandem result file"));
194  m_qxmlStreamReader.skipCurrentElement();
195  }
196  }
197  m_writerXmlTandemOutput.writeEndDocument();
199  qDebug();
200 }

References pappso::XmlStreamReaderInterface::cloneElement(), pappso::XmlStreamReaderInterface::cloneStartElement(), m_destinationTandemOutputFile, pappso::XmlStreamReaderInterface::m_qxmlStreamReader, m_writerXmlTandemOutput, and process_group_note().

◆ setInputParameters()

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

Definition at line 59 of file wraptandemresults.cpp.

61 {
63  std::pair<QString, QString>(label_name_attribute, input_value));
64 }

References m_mapTandemInputParameters.

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

Member Data Documentation

◆ m_destinationTandemOutputFile

QFile pappso::WrapTandemResults::m_destinationTandemOutputFile
private

Definition at line 67 of file wraptandemresults.h.

Referenced by WrapTandemResults(), process_group_note(), and readStream().

◆ m_mapTandemInputParameters

std::map<QString, QString> pappso::WrapTandemResults::m_mapTandemInputParameters
private

Definition at line 71 of file wraptandemresults.h.

Referenced by process_group_note(), and setInputParameters().

◆ m_originalMsDataFileName

QString pappso::WrapTandemResults::m_originalMsDataFileName
private

Definition at line 69 of file wraptandemresults.h.

Referenced by WrapTandemResults(), and process_group_note().

◆ m_writerXmlTandemOutput

QXmlStreamWriter pappso::WrapTandemResults::m_writerXmlTandemOutput
private

Definition at line 68 of file wraptandemresults.h.

Referenced by WrapTandemResults(), process_group_note(), and readStream().


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