libpappsomspp
Library for mass spectrometry
pappso::MsFileAccessor Class Reference

#include <msfileaccessor.h>

Public Member Functions

 MsFileAccessor (const QString &file_name, const QString &xml_prefix)
 
 MsFileAccessor (const MsFileAccessor &other)
 
virtual ~MsFileAccessor ()
 
const QString & getFileName () const
 
MzFormat getFileFormat () const
 get the raw format of mz data More...
 
void setPreferedFileReaderType (MzFormat format, FileReaderType reader_type)
 given an mz format, explicitly set the prefered reader More...
 
std::vector< MsRunIdCstSPtrgetMsRunIds ()
 
MsRunReaderSPtr msRunReaderSp (MsRunIdCstSPtr ms_run_id)
 
MsRunReaderSPtr getMsRunReaderSPtrByRunId (const QString &run_id, const QString &xml_id)
 get an msrun reader by finding the run_id in file More...
 
TimsMsRunReaderMs2SPtr buildTimsMsRunReaderMs2SPtr ()
 if possible, builds directly a dedicated Tims TOF tdf file reader More...
 

Static Public Member Functions

static MsRunReaderSPtr buildMsRunReaderSPtr (MsRunIdCstSPtr ms_run_id)
 get an MsRunReader directly from a valid MsRun ID More...
 

Private Attributes

QString m_fileName
 
const QString m_xmlPrefix
 
MzFormat m_fileFormat = MzFormat::unknown
 
FileReaderType m_fileReaderType
 
std::map< MzFormat, FileReaderTypem_preferedFileReaderTypeMap
 

Detailed Description

Definition at line 34 of file msfileaccessor.h.

Constructor & Destructor Documentation

◆ MsFileAccessor() [1/2]

pappso::MsFileAccessor::MsFileAccessor ( const QString &  file_name,
const QString &  xml_prefix 
)

Definition at line 28 of file msfileaccessor.cpp.

30  : m_fileName(file_name), m_xmlPrefix(xml_prefix)
31 {
32  QFile file(file_name);
33  if(!file.exists())
34  throw(ExceptionNotFound(QObject::tr("File %1 not found.")
35  .arg(QFileInfo(file_name).absoluteFilePath())));
36 }

◆ MsFileAccessor() [2/2]

pappso::MsFileAccessor::MsFileAccessor ( const MsFileAccessor other)

Definition at line 39 of file msfileaccessor.cpp.

40  : m_fileName(other.m_fileName),
41  m_xmlPrefix(other.m_xmlPrefix),
42  m_fileFormat(other.m_fileFormat),
43  m_fileReaderType(other.m_fileReaderType)
44 {
45 }

◆ ~MsFileAccessor()

pappso::MsFileAccessor::~MsFileAccessor ( )
virtual

Definition at line 47 of file msfileaccessor.cpp.

48 {
49 }

Member Function Documentation

◆ buildMsRunReaderSPtr()

MsRunReaderSPtr pappso::MsFileAccessor::buildMsRunReaderSPtr ( MsRunIdCstSPtr  ms_run_id)
static

get an MsRunReader directly from a valid MsRun ID

no need to check the file format or filename : all is already part of the msrunid

Definition at line 224 of file msfileaccessor.cpp.

225 {
226 
227  QFile file(ms_run_id.get()->getFileName());
228  if(!file.exists())
229  throw(ExceptionNotFound(
230  QObject::tr("unable to build a reader : file %1 not found.")
231  .arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
232 
233  MzFormat file_format = ms_run_id.get()->getMzFormat();
234 
235  if(file_format == MzFormat::xy)
236  {
237  qDebug() << "Returning a XyMsRunReader.";
238 
239  return std::make_shared<XyMsRunReader>(ms_run_id);
240  }
241  else if(file_format == MzFormat::unknown)
242  {
243  throw(PappsoException(
244  QObject::tr("unable to build a reader for %1 : unknown file format")
245  .arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
246  }
247  else if(file_format == MzFormat::brukerTims)
248  {
249  qDebug() << "by default, build a TimsMsRunReader.";
250  return std::make_shared<TimsMsRunReader>(ms_run_id);
251  }
252  else
253  {
254  qDebug() << "Returning a PwizMsRunReader .";
255 
256  return std::make_shared<PwizMsRunReader>(ms_run_id);
257  }
258 }

◆ buildTimsMsRunReaderMs2SPtr()

TimsMsRunReaderMs2SPtr pappso::MsFileAccessor::buildTimsMsRunReaderMs2SPtr ( )

if possible, builds directly a dedicated Tims TOF tdf file reader

Definition at line 143 of file msfileaccessor.cpp.

144 {
145 
146  // try TimsData reader
147  QString tims_dir = m_fileName;
148  if(!QFileInfo(tims_dir).isDir())
149  {
150  tims_dir = QFileInfo(m_fileName).absolutePath();
151  }
152  TimsMsFileReader tims_file_reader(tims_dir);
153 
154  std::vector<MsRunIdCstSPtr> ms_run_ids =
155  tims_file_reader.getMsRunIds(m_xmlPrefix);
156 
157  if(ms_run_ids.size())
158  {
159  // qDebug() << "Might well be handled using the Bruker code";
161  m_fileFormat = tims_file_reader.getFileFormat();
162  m_fileName = tims_dir;
163 
164  return std::make_shared<TimsMsRunReaderMs2>(ms_run_ids.front());
165  }
166  else
167  {
168  throw(ExceptionNotPossible(
169  QObject::tr("Unable to read mz data directory %1 with TimsTOF reader.")
170  .arg(tims_dir)));
171  }
172 }

References pappso::TimsMsFileReader::getFileFormat(), pappso::TimsMsFileReader::getMsRunIds(), m_fileFormat, m_fileName, m_fileReaderType, m_xmlPrefix, and pappso::pwiz.

◆ getFileFormat()

MzFormat pappso::MsFileAccessor::getFileFormat ( ) const

get the raw format of mz data

Definition at line 60 of file msfileaccessor.cpp.

61 {
62  return m_fileFormat;
63 }

References m_fileFormat.

◆ getFileName()

const QString & pappso::MsFileAccessor::getFileName ( ) const

Definition at line 53 of file msfileaccessor.cpp.

54 {
55  return m_fileName;
56 }

References m_fileName.

◆ getMsRunIds()

std::vector< MsRunIdCstSPtr > pappso::MsFileAccessor::getMsRunIds ( )

Definition at line 67 of file msfileaccessor.cpp.

68 {
69  //qDebug();
70 
71  // Try the PwizMsFileReader
72 
73  PwizMsFileReader pwiz_ms_file_reader(m_fileName);
74 
75  std::vector<MsRunIdCstSPtr> ms_run_ids =
76  pwiz_ms_file_reader.getMsRunIds(m_xmlPrefix);
77 
78  if(ms_run_ids.size())
79  {
80  // qDebug() << "Might well be handled using the Pwiz code.";
81  m_fileReaderType = FileReaderType::pwiz;
82 
83  m_fileFormat = pwiz_ms_file_reader.getFileFormat();
84 
85  return ms_run_ids;
86  }
87 
88  //qDebug() << "The Pwiz reader did not work.";
89 
90  // Try the TimsData reader
91 
92  QString tims_dir = m_fileName;
93  if(!QFileInfo(tims_dir).isDir())
94  {
95  tims_dir = QFileInfo(m_fileName).absolutePath();
96  }
97  TimsMsFileReader tims_file_reader(tims_dir);
98 
99  ms_run_ids = tims_file_reader.getMsRunIds(m_xmlPrefix);
100 
101  if(ms_run_ids.size())
102  {
103  // qDebug() << "Might well be handled using the Bruker code";
104  m_fileReaderType = FileReaderType::tims;
105  m_fileFormat = tims_file_reader.getFileFormat();
106  m_fileName = tims_dir;
107 
108 
109  auto pref = m_preferedFileReaderTypeMap.find(m_fileFormat);
110  if(pref != m_preferedFileReaderTypeMap.end())
111  {
112  m_fileReaderType = pref->second;
113  }
114 
115  return ms_run_ids;
116  }
117 
118  //qDebug() << "The Tims reader did not work.";
119 
120  // At this point try the XyMsFileReader
121 
122  XyMsFileReader xy_ms_file_reader(m_fileName);
123 
124  ms_run_ids = xy_ms_file_reader.getMsRunIds(m_xmlPrefix);
125 
126  if(ms_run_ids.size())
127  {
128  // qDebug() << "Might well be handled using the XY code";
129  m_fileReaderType = FileReaderType::xy;
130 
131  m_fileFormat = xy_ms_file_reader.getFileFormat();
132 
133  return ms_run_ids;
134  }
135 
136  //qDebug() << "The XY reader did not work.";
137 
138  return ms_run_ids;
139 }

References pappso::PwizMsFileReader::getFileFormat(), pappso::TimsMsFileReader::getFileFormat(), pappso::XyMsFileReader::getFileFormat(), pappso::PwizMsFileReader::getMsRunIds(), pappso::TimsMsFileReader::getMsRunIds(), pappso::XyMsFileReader::getMsRunIds(), m_fileFormat, m_fileName, m_fileReaderType, m_preferedFileReaderTypeMap, and m_xmlPrefix.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), and getMsRunReaderSPtrByRunId().

◆ getMsRunReaderSPtrByRunId()

MsRunReaderSPtr pappso::MsFileAccessor::getMsRunReaderSPtrByRunId ( const QString &  run_id,
const QString &  xml_id 
)

get an msrun reader by finding the run_id in file

Parameters
run_ididentifier within file of the MSrun
xml_idXML identifier given by the user to identify this MSrun in our experiment (not in the file)

Definition at line 261 of file msfileaccessor.cpp.

263 {
264  std::vector<MsRunIdCstSPtr> run_list = getMsRunIds();
265  MsRunReaderSPtr reader_sp;
266 
267  for(MsRunIdCstSPtr &original_run_id : run_list)
268  {
269  if(original_run_id.get()->getRunId() == run_id)
270  {
271  MsRunId new_run_id(*original_run_id.get());
272  new_run_id.setXmlId(xml_id);
273 
274  return msRunReaderSp(std::make_shared<MsRunId>(new_run_id));
275  }
276  }
277 
278  if((run_id.isEmpty()) && (run_list.size() == 1))
279  {
280  MsRunId new_run_id(*run_list[0].get());
281  new_run_id.setXmlId(xml_id);
282 
283  return msRunReaderSp(std::make_shared<MsRunId>(new_run_id));
284  }
285 
286 
287  if(reader_sp == nullptr)
288  {
289  throw(
290  ExceptionNotFound(QObject::tr("run id %1 not found in file %2")
291  .arg(run_id)
292  .arg(QFileInfo(m_fileName).absoluteFilePath())));
293  }
294  return reader_sp;
295 }

References getMsRunIds(), m_fileName, msRunReaderSp(), and pappso::MsRunId::setXmlId().

◆ msRunReaderSp()

MsRunReaderSPtr pappso::MsFileAccessor::msRunReaderSp ( MsRunIdCstSPtr  ms_run_id)

Definition at line 175 of file msfileaccessor.cpp.

176 {
177  if(m_fileName != ms_run_id->getFileName())
178  throw(ExceptionNotPossible(
179  QObject::tr("The MsRunId instance must have the name file name as the "
180  "MsFileAccessor.")));
181 
182  if(m_fileReaderType == FileReaderType::pwiz)
183  {
184  qDebug() << "Returning a PwizMsRunReader.";
185 
186  return std::make_shared<PwizMsRunReader>(ms_run_id);
187  }
188  else if(m_fileReaderType == FileReaderType::xy)
189  {
190  qDebug() << "Returning a XyMsRunReader.";
191 
192  return std::make_shared<XyMsRunReader>(ms_run_id);
193  }
194 
195  else if(m_fileReaderType == FileReaderType::tims)
196  {
197  qDebug() << "Returning a TimsMsRunReader.";
198 
199  return std::make_shared<TimsMsRunReader>(ms_run_id);
200  }
202  {
203  qDebug() << "Returning a TimsMsRunReaderMs2.";
204 
205  return std::make_shared<TimsMsRunReaderMs2>(ms_run_id);
206  }
207 
208  if(m_fileFormat == MzFormat::unknown)
209  {
210  if(ms_run_id.get()->getMzFormat() == MzFormat::xy)
211  {
212  return std::make_shared<XyMsRunReader>(ms_run_id);
213  }
214  else
215  {
216  return std::make_shared<PwizMsRunReader>(ms_run_id);
217  }
218  }
219 
220  return nullptr;
221 }

References m_fileFormat, m_fileName, m_fileReaderType, and pappso::pwiz.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), and getMsRunReaderSPtrByRunId().

◆ setPreferedFileReaderType()

void pappso::MsFileAccessor::setPreferedFileReaderType ( MzFormat  format,
FileReaderType  reader_type 
)

given an mz format, explicitly set the prefered reader

Definition at line 298 of file msfileaccessor.cpp.

300 {
301  auto ret = m_preferedFileReaderTypeMap.insert(
302  std::pair<MzFormat, FileReaderType>(format, reader_type));
303  if(!ret.second)
304  {
305  // replace
306  ret.first->second = reader_type;
307  }
308 }

References m_preferedFileReaderTypeMap.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

Member Data Documentation

◆ m_fileFormat

MzFormat pappso::MsFileAccessor::m_fileFormat = MzFormat::unknown
private

◆ m_fileName

QString pappso::MsFileAccessor::m_fileName
private

◆ m_fileReaderType

FileReaderType pappso::MsFileAccessor::m_fileReaderType
private

Definition at line 85 of file msfileaccessor.h.

Referenced by buildTimsMsRunReaderMs2SPtr(), getMsRunIds(), and msRunReaderSp().

◆ m_preferedFileReaderTypeMap

std::map<MzFormat, FileReaderType> pappso::MsFileAccessor::m_preferedFileReaderTypeMap
private

Definition at line 87 of file msfileaccessor.h.

Referenced by getMsRunIds(), and setPreferedFileReaderType().

◆ m_xmlPrefix

const QString pappso::MsFileAccessor::m_xmlPrefix
private

Definition at line 80 of file msfileaccessor.h.

Referenced by buildTimsMsRunReaderMs2SPtr(), and getMsRunIds().


The documentation for this class was generated from the following files:
pappso::MsFileAccessor::m_preferedFileReaderTypeMap
std::map< MzFormat, FileReaderType > m_preferedFileReaderTypeMap
Definition: msfileaccessor.h:87
pappso::MsFileAccessor::m_fileFormat
MzFormat m_fileFormat
Definition: msfileaccessor.h:82
pappso::MsFileAccessor::m_fileReaderType
FileReaderType m_fileReaderType
Definition: msfileaccessor.h:85
pappso::MsRunReaderSPtr
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition: msrunreader.h:151
pappso::FileReaderType::pwiz
@ pwiz
pappso::MsRunIdCstSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition: msrunid.h:44
pappso::MsFileAccessor::m_xmlPrefix
const QString m_xmlPrefix
Definition: msfileaccessor.h:80
pappso::MsFileAccessor::getMsRunIds
std::vector< MsRunIdCstSPtr > getMsRunIds()
Definition: msfileaccessor.cpp:67
pappso::MsFileAccessor::msRunReaderSp
MsRunReaderSPtr msRunReaderSp(MsRunIdCstSPtr ms_run_id)
Definition: msfileaccessor.cpp:175
pappso::MsFileAccessor::m_fileName
QString m_fileName
Definition: msfileaccessor.h:76
pappso::MzFormat
MzFormat
Definition: types.h:107