libpappsomspp
Library for mass spectrometry
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pappso::MsRunXicExtractorFactory Class Reference

factory to build different kinds of XIC extractors More...

#include <msrunxicextractorfactory.h>

Public Member Functions

MsRunXicExtractorInterfaceSp buildMsRunXicExtractorSp (MsRunReaderSPtr &msrun_reader) const
 build a simple XIC extractor that directly uses Proeowizard library to read and extract XICs building the xic extractor is fast, but extracting each XIC is slow
 
void setTmpDir (const QString &dir_name)
 set the temporary working directory
 
void setMsRunXicExtractorFactoryType (pappso::MsRunXicExtractorFactoryType type)
 sets the xic extractor type
 

Static Public Member Functions

static MsRunXicExtractorFactorygetInstance ()
 singleton to get the only instance of the factory
 

Private Member Functions

 MsRunXicExtractorFactory ()
 
virtual ~MsRunXicExtractorFactory ()
 

Private Attributes

QString m_tmpDirName
 
MsRunXicExtractorFactoryType m_type = MsRunXicExtractorFactoryType::nose
 

Static Private Attributes

static MsRunXicExtractorFactory m_instance
 

Detailed Description

factory to build different kinds of XIC extractors

Definition at line 67 of file msrunxicextractorfactory.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractorFactory()

pappso::MsRunXicExtractorFactory::MsRunXicExtractorFactory ( )
private

Definition at line 52 of file msrunxicextractorfactory.cpp.

53{
54}

◆ ~MsRunXicExtractorFactory()

pappso::MsRunXicExtractorFactory::~MsRunXicExtractorFactory ( )
privatevirtual

Definition at line 55 of file msrunxicextractorfactory.cpp.

56{
57}

Member Function Documentation

◆ buildMsRunXicExtractorSp()

MsRunXicExtractorInterfaceSp pappso::MsRunXicExtractorFactory::buildMsRunXicExtractorSp ( MsRunReaderSPtr msrun_reader) const

build a simple XIC extractor that directly uses Proeowizard library to read and extract XICs building the xic extractor is fast, but extracting each XIC is slow

Parameters
msrun_readerthe MsRun reader on which the XIC extractor will run

Definition at line 72 of file msrunxicextractorfactory.cpp.

74{
75
76 pappso::TimsMsRunReaderMs2 *tims2_reader =
77 dynamic_cast<pappso::TimsMsRunReaderMs2 *>(msrun_reader.get());
78 if(tims2_reader == nullptr)
79 {
80 // NO TIMS
83 {
84 std::shared_ptr<MsRunXicExtractor> msrun_xic_extractor_sp =
85 std::make_shared<MsRunXicExtractor>(
86 MsRunXicExtractor(msrun_reader));
87 return (msrun_xic_extractor_sp);
88 }
90 {
91
92 std::shared_ptr<MsRunXicExtractorDisk> msrun_xic_extractor_sp =
93 std::make_shared<MsRunXicExtractorDisk>(
94 MsRunXicExtractorDisk(msrun_reader, QDir(m_tmpDirName)));
95
96 msrun_xic_extractor_sp.get()->prepareExtractor();
97 return (msrun_xic_extractor_sp);
98 }
100 {
101
102 std::shared_ptr<MsRunXicExtractorDiskBuffer> msrun_xic_extractor_sp =
103 std::make_shared<MsRunXicExtractorDiskBuffer>(
104 MsRunXicExtractorDiskBuffer(msrun_reader, QDir(m_tmpDirName)));
105 msrun_xic_extractor_sp.get()->prepareExtractor();
106 return (msrun_xic_extractor_sp);
107 }
108 }
109 else
110 {
111 // TIMS
112 std::shared_ptr<TimsDirectXicExtractor> msrun_xic_extractor_sp =
113 std::make_shared<TimsDirectXicExtractor>(msrun_reader);
114 return (msrun_xic_extractor_sp);
115 }
116 return nullptr;
117}
MsRunXicExtractorFactoryType m_type

References pappso::direct, pappso::disk, pappso::diskbuffer, m_tmpDirName, m_type, and pappso::nose.

◆ getInstance()

MsRunXicExtractorFactory & pappso::MsRunXicExtractorFactory::getInstance ( )
static

singleton to get the only instance of the factory

Definition at line 46 of file msrunxicextractorfactory.cpp.

47{
48 return m_instance;
49}
static MsRunXicExtractorFactory m_instance

References m_instance.

◆ setMsRunXicExtractorFactoryType()

void pappso::MsRunXicExtractorFactory::setMsRunXicExtractorFactoryType ( pappso::MsRunXicExtractorFactoryType  type)

sets the xic extractor type

Parameters
typesee the documentation of enumerations

Definition at line 65 of file msrunxicextractorfactory.cpp.

67{
68 m_type = type;
69}

References m_type.

◆ setTmpDir()

void pappso::MsRunXicExtractorFactory::setTmpDir ( const QString &  dir_name)

set the temporary working directory

Definition at line 60 of file msrunxicextractorfactory.cpp.

61{
62 m_tmpDirName = dir_name;
63}

References m_tmpDirName.

Member Data Documentation

◆ m_instance

MsRunXicExtractorFactory pappso::MsRunXicExtractorFactory::m_instance
staticprivate
Initial value:

Definition at line 97 of file msrunxicextractorfactory.h.

Referenced by getInstance().

◆ m_tmpDirName

QString pappso::MsRunXicExtractorFactory::m_tmpDirName
private

Definition at line 98 of file msrunxicextractorfactory.h.

Referenced by buildMsRunXicExtractorSp(), and setTmpDir().

◆ m_type

MsRunXicExtractorFactoryType pappso::MsRunXicExtractorFactory::m_type = MsRunXicExtractorFactoryType::nose
private

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