libpappsomspp
Library for mass spectrometry
pappso::XtandemPresetReader Class Reference

#include <xtandempresetreader.h>

Inheritance diagram for pappso::XtandemPresetReader:
pappso::XmlStreamReaderInterface

Public Member Functions

 XtandemPresetReader ()
 
virtual ~XtandemPresetReader ()
 
int getNumberOfThreads () const
 
const QString getMs2FiltersOptions () const
 
int getCountNote () 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 Member Functions

void read_note ()
 

Private Attributes

int m_countNote = -1
 
int m_threads = -1
 
PrecisionUnit m_ms2precisionUnit = PrecisionUnit::dalton
 
double m_ms2precisionValue = 0
 

Additional Inherited Members

- Protected Attributes inherited from pappso::XmlStreamReaderInterface
QXmlStreamReader m_qxmlStreamReader
 

Detailed Description

Definition at line 39 of file xtandempresetreader.h.

Constructor & Destructor Documentation

◆ XtandemPresetReader()

pappso::XtandemPresetReader::XtandemPresetReader ( )

Default constructor

Definition at line 35 of file xtandempresetreader.cpp.

36 {
37 }

◆ ~XtandemPresetReader()

pappso::XtandemPresetReader::~XtandemPresetReader ( )
virtual

Destructor

Definition at line 39 of file xtandempresetreader.cpp.

40 {
41 }

Member Function Documentation

◆ getCountNote()

int pappso::XtandemPresetReader::getCountNote ( ) const

Definition at line 162 of file xtandempresetreader.cpp.

163 {
164  return m_countNote;
165 }

References m_countNote.

◆ getMs2FiltersOptions()

const QString pappso::XtandemPresetReader::getMs2FiltersOptions ( ) const

Definition at line 110 of file xtandempresetreader.cpp.

111 {
112  QString filter_suite;
115  QString charge_decon_filter = QString("chargeDeconvolution|%1")
116  .arg(precision->toString().replace(" ", ""));
117 
120  QString mz_exclusion_filter =
121  QString("mzExclusion|%1").arg(precision_exclu->toString().replace(" ", ""));
122  filter_suite = charge_decon_filter + " " + mz_exclusion_filter;
123  return filter_suite;
124 }
static PrecisionPtr getPrecisionPtrInstance(PrecisionUnit unit, double value)
get a precision pointer instance
Definition: precision.cpp:214
const PrecisionBase * PrecisionPtr
Definition: precision.h:122

References pappso::PrecisionFactory::getPrecisionPtrInstance(), m_ms2precisionUnit, m_ms2precisionValue, and pappso::PrecisionBase::toString().

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

◆ getNumberOfThreads()

int pappso::XtandemPresetReader::getNumberOfThreads ( ) const

Definition at line 103 of file xtandempresetreader.cpp.

104 {
105  return m_threads;
106 }

References m_threads.

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

◆ read_note()

void pappso::XtandemPresetReader::read_note ( )
private

Definition at line 45 of file xtandempresetreader.cpp.

46 {
47  // <note type="input"
48  // 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>
49  if(m_qxmlStreamReader.name().toString() != "note")
50  {
51  m_qxmlStreamReader.skipCurrentElement();
52  return;
53  }
54  Q_ASSERT(m_qxmlStreamReader.name().toString() == "note");
55  QString label;
56 
57 
58  m_countNote++;
59  if((m_qxmlStreamReader.attributes().hasAttribute("type")) &&
60  (m_qxmlStreamReader.attributes().value("type").toString() == "input"))
61  {
62  if(m_qxmlStreamReader.attributes().hasAttribute("label"))
63  {
64  label = m_qxmlStreamReader.attributes().value("label").toString();
65  }
66  }
67  if(label.isEmpty())
68  {
69  }
70  else
71  {
72  if(label == "spectrum, timstof MS2 filters")
73  {
74  }
75  else if(label == "spectrum, threads")
76  {
77  m_threads = m_qxmlStreamReader.readElementText().toInt();
78  return;
79  }
80  else if(label == "spectrum, fragment monoisotopic mass error units")
81  {
82 
84  if(m_qxmlStreamReader.readElementText().trimmed().toLower() == "ppm")
85  {
87  }
88  return;
89  }
90  else if(label == "spectrum, fragment monoisotopic mass error")
91  {
92  m_ms2precisionValue = m_qxmlStreamReader.readElementText().toDouble();
93  return;
94  }
95  }
96  m_qxmlStreamReader.skipCurrentElement();
97  // qDebug() << "end ";
98  //
99 }

References pappso::dalton, m_countNote, m_ms2precisionUnit, m_ms2precisionValue, pappso::XmlStreamReaderInterface::m_qxmlStreamReader, m_threads, and pappso::ppm.

Referenced by readStream().

◆ readStream()

void pappso::XtandemPresetReader::readStream ( )
overrideprotectedvirtual

Implements pappso::XmlStreamReaderInterface.

Definition at line 128 of file xtandempresetreader.cpp.

129 {
130  qDebug();
131  m_countNote = 0;
132  m_threads = -1;
134  m_ms2precisionValue = -1;
135  if(m_qxmlStreamReader.readNextStartElement())
136  {
137  if(m_qxmlStreamReader.name().toString() == "bioml")
138  {
139  qDebug();
140  while(m_qxmlStreamReader.readNextStartElement())
141  {
142  // qDebug() << m_qxmlStreamReader.name();
143  read_note();
144  }
145  }
146  else
147  {
148  m_qxmlStreamReader.raiseError(
149  QObject::tr("Not an X!Tandem preset file"));
150  m_qxmlStreamReader.skipCurrentElement();
151  }
152  }
153  if(m_threads == -1)
154  {
155  qDebug();
156  m_qxmlStreamReader.raiseError(QObject::tr("Not an X!Tandem preset file"));
157  }
158  qDebug();
159 }

References pappso::dalton, m_countNote, m_ms2precisionUnit, m_ms2precisionValue, pappso::XmlStreamReaderInterface::m_qxmlStreamReader, m_threads, and read_note().

Member Data Documentation

◆ m_countNote

int pappso::XtandemPresetReader::m_countNote = -1
private

Definition at line 63 of file xtandempresetreader.h.

Referenced by getCountNote(), read_note(), and readStream().

◆ m_ms2precisionUnit

PrecisionUnit pappso::XtandemPresetReader::m_ms2precisionUnit = PrecisionUnit::dalton
private

Definition at line 66 of file xtandempresetreader.h.

Referenced by getMs2FiltersOptions(), read_note(), and readStream().

◆ m_ms2precisionValue

double pappso::XtandemPresetReader::m_ms2precisionValue = 0
private

Definition at line 67 of file xtandempresetreader.h.

Referenced by getMs2FiltersOptions(), read_note(), and readStream().

◆ m_threads

int pappso::XtandemPresetReader::m_threads = -1
private

Definition at line 64 of file xtandempresetreader.h.

Referenced by getNumberOfThreads(), read_note(), and readStream().


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