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
virtual void readStream ()=0
 
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:216
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
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;
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: