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 40 of file timsmsfilereader.h.

Constructor & Destructor Documentation

◆ TimsMsFileReader()

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

Definition at line 38 of file timsmsfilereader.cpp.

39  : MsFileReader(file_name)
40 {
41  qDebug() << " " << m_fileName;
42  initialize();
43 }
MsFileReader(const QString &file_name)
virtual std::size_t initialize()

References initialize(), and pappso::MsFileReader::m_fileName.

◆ ~TimsMsFileReader()

pappso::TimsMsFileReader::~TimsMsFileReader ( )
virtual

Definition at line 46 of file timsmsfilereader.cpp.

47 {
48 }

Member Function Documentation

◆ getFileFormat()

MzFormat pappso::TimsMsFileReader::getFileFormat ( )
overridevirtual

◆ getMsRunIds()

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

Implements pappso::MsFileReader.

Definition at line 78 of file timsmsfilereader.cpp.

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.
86  MsRunId ms_run_id(m_fileName);
87  ms_run_id.setMzFormat(m_fileFormat);
88 
89  // We need to set the unambiguous xmlId string.
90  ms_run_id.setXmlId(QString("%1a1").arg(run_prefix));
91 
92  ms_run_id.setRunId("a1");
93 
94  // Now set the sample name to the run id:
95 
96  ms_run_id.setSampleName(QFileInfo(m_fileName).baseName());
97 
98  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
99  << "Current ms_run_id:" << 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 }

References initialize(), pappso::MsFileReader::m_fileFormat, pappso::MsFileReader::m_fileName, pappso::MsRunId::setMzFormat(), pappso::MsRunId::setRunId(), pappso::MsRunId::setSampleName(), pappso::MsRunId::setXmlId(), and pappso::MsRunId::toString().

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

◆ initialize()

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

Definition at line 52 of file timsmsfilereader.cpp.

53 {
54 
56  try
57  {
58  TimsData tims_data(m_fileName);
60  }
61  catch(PappsoException &error)
62  {
63  return 0;
64  }
65 
66  return 1;
67 }
@ unknown
unknown format

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

Referenced by TimsMsFileReader(), and getMsRunIds().

◆ selectMsRunReader()

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

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