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 41 of file timsmsfilereader.h.

Constructor & Destructor Documentation

◆ TimsMsFileReader()

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

Definition at line 39 of file timsmsfilereader.cpp.

40  : MsFileReader(file_name)
41 {
42  qDebug() << " " << m_fileName;
43  initialize();
44 }
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 47 of file timsmsfilereader.cpp.

48 {
49 }

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 87 of file timsmsfilereader.cpp.

88 {
89  std::vector<MsRunIdCstSPtr> ms_run_ids;
90 
91  if(!initialize())
92  return ms_run_ids;
93 
94  // Finally create the MsRunId with the file name.
95  MsRunId ms_run_id(m_fileName);
96  ms_run_id.setMzFormat(m_fileFormat);
97 
98  // We need to set the unambiguous xmlId string.
99  ms_run_id.setXmlId(QString("%1a1").arg(run_prefix));
100 
101  ms_run_id.setRunId("a1");
102 
103  // Now set the sample name to the run id:
104 
105  ms_run_id.setSampleName(QFileInfo(m_fileName).baseName());
106 
107  qDebug() << "Current ms_run_id:" << ms_run_id.toString();
108 
109  // Finally make a shared pointer out of it and append it to the vector.
110  ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
111 
112  return ms_run_ids;
113 }

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 53 of file timsmsfilereader.cpp.

54 {
55 
57  try
58  {
59  TimsData tims_data(m_fileName);
61  }
62  catch(ExceptionNotImplemented &error)
63  {
66  QObject::tr("Error reading Bruker tims data in %1 :\n%2")
67  .arg(m_fileName)
68  .arg(error.qwhat()));
69  }
70  catch(PappsoException &error)
71  {
72  return 0;
73  }
74 
75  return 1;
76 }
@ unknown
unknown format

References pappso::brukerTims, pappso::MsFileReader::m_fileFormat, pappso::MsFileReader::m_fileName, pappso::PappsoException::qwhat(), 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: