libpappsomspp
Library for mass spectrometry
pappso::TimsMsFileReader Class Reference

#include <timsmsfilereader.h>

Inheritance diagram for pappso::TimsMsFileReader:
pappso::MsFileReader

Public Member Functions

 TimsMsFileReader (const QString &file_name)
 
virtual ~TimsMsFileReader ()
 
virtual MzFormat getFileFormat () override
 
virtual std::vector< MsRunIdCstSPtrgetMsRunIds (const QString &run_prefix) override
 
MsRunReaderselectMsRunReader (const QString &file_name) const
 

Private Member Functions

virtual std::size_t initialize ()
 
- Private Member Functions inherited from pappso::MsFileReader
 MsFileReader (const QString &file_name)
 
virtual ~MsFileReader ()
 

Additional Inherited Members

- Private Attributes inherited from pappso::MsFileReader
QString m_fileName
 
MzFormat m_fileFormat = MzFormat::unknown
 

Detailed Description

Todo:
write docs

Definition at line 58 of file timsmsfilereader.h.

Constructor & Destructor Documentation

◆ TimsMsFileReader()

pappso::TimsMsFileReader::TimsMsFileReader ( const QString &  file_name)

Definition at line 56 of file timsmsfilereader.cpp.

57  {
58  TimsData tims_data(m_fileName);
60  }
61  catch(PappsoException &error)

References pappso::brukerTims, pappso::MsFileReader::m_fileFormat, and pappso::MsFileReader::m_fileName.

◆ ~TimsMsFileReader()

pappso::TimsMsFileReader::~TimsMsFileReader ( )
virtual

Definition at line 64 of file timsmsfilereader.cpp.

Member Function Documentation

◆ getFileFormat()

MzFormat pappso::TimsMsFileReader::getFileFormat ( )
overridevirtual

Implements pappso::MsFileReader.

Definition at line 89 of file timsmsfilereader.cpp.

99  :" << ms_run_id.toString();

Referenced by pappso::MsFileAccessor::buildTimsMsRunReaderMs2SPtr(), and pappso::MsFileAccessor::getMsRunIds().

◆ getMsRunIds()

std::vector< MsRunIdCstSPtr > pappso::TimsMsFileReader::getMsRunIds ( const QString &  run_prefix)
overridevirtual

Implements pappso::MsFileReader.

Definition at line 96 of file timsmsfilereader.cpp.

99  :" << ms_run_id.toString();
100 
101  // Finally make a shared pointer out of it and append it to the vector.
102  ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
103 
104  return ms_run_ids;
105 }
106 
107 
108 } // namespace pappso

Referenced by pappso::MsFileAccessor::buildTimsMsRunReaderMs2SPtr(), and pappso::MsFileAccessor::getMsRunIds().

◆ initialize()

std::size_t pappso::TimsMsFileReader::initialize ( )
privatevirtual

Definition at line 70 of file timsmsfilereader.cpp.

72 {
73  return m_fileFormat;
74 }
75 
76 
77 std::vector<MsRunIdCstSPtr>
78 TimsMsFileReader::getMsRunIds(const QString &run_prefix)
79 {
80  std::vector<MsRunIdCstSPtr> ms_run_ids;
81 
82  if(!initialize())
83  return ms_run_ids;
84 
85  // Finally create the MsRunId with the file name.

References pappso::MsFileReader::m_fileFormat.

◆ selectMsRunReader()

MsRunReader* pappso::TimsMsFileReader::selectMsRunReader ( const QString &  file_name) const

The documentation for this class was generated from the following files:
pappso::MzFormat::brukerTims
@ brukerTims
pappso::TimsMsFileReader::getMsRunIds
virtual std::vector< MsRunIdCstSPtr > getMsRunIds(const QString &run_prefix) override
Definition: timsmsfilereader.cpp:96
pappso::TimsMsFileReader::initialize
virtual std::size_t initialize()
Definition: timsmsfilereader.cpp:70
pappso::MsFileReader::m_fileFormat
MzFormat m_fileFormat
Definition: msfilereader.h:18
pappso::MsFileReader::m_fileName
QString m_fileName
Definition: msfilereader.h:17