14 #include "../exception/exceptionnotfound.h"
15 #include "../exception/exceptionnotpossible.h"
17 #include "../msrun/msrunid.h"
18 #include "../msrun/private/pwizmsrunreader.h"
19 #include "../msrun/private/timsmsrunreader.h"
20 #include "../msrun/private/timsmsrunreaderms2.h"
21 #include "../msrun/xymsrunreader.h"
29 const QString &xml_prefix)
30 : m_fileName(file_name), m_xmlPrefix(xml_prefix)
32 QFile file(file_name);
35 .arg(QFileInfo(file_name).absoluteFilePath())));
40 : m_fileName(other.m_fileName),
41 m_xmlPrefix(other.m_xmlPrefix),
42 m_fileFormat(other.m_fileFormat),
43 m_fileReaderType(other.m_fileReaderType)
66 std::vector<MsRunIdCstSPtr>
75 std::vector<MsRunIdCstSPtr> ms_run_ids =
93 if(!QFileInfo(tims_dir).isDir())
95 tims_dir = QFileInfo(
m_fileName).absolutePath();
101 if(ms_run_ids.size())
126 if(ms_run_ids.size())
148 if(!QFileInfo(tims_dir).isDir())
150 tims_dir = QFileInfo(
m_fileName).absolutePath();
154 std::vector<MsRunIdCstSPtr> ms_run_ids =
157 if(ms_run_ids.size())
164 return std::make_shared<TimsMsRunReaderMs2>(ms_run_ids.front());
169 QObject::tr(
"Unable to read mz data directory %1 with TimsTOF reader.")
179 QObject::tr(
"The MsRunId instance must have the name file name as the "
180 "MsFileAccessor.")));
184 qDebug() <<
"Returning a PwizMsRunReader.";
186 return std::make_shared<PwizMsRunReader>(ms_run_id);
190 qDebug() <<
"Returning a XyMsRunReader.";
192 return std::make_shared<XyMsRunReader>(ms_run_id);
197 qDebug() <<
"Returning a TimsMsRunReader.";
199 return std::make_shared<TimsMsRunReader>(ms_run_id);
203 qDebug() <<
"Returning a TimsMsRunReaderMs2.";
205 return std::make_shared<TimsMsRunReaderMs2>(ms_run_id);
212 return std::make_shared<XyMsRunReader>(ms_run_id);
216 return std::make_shared<PwizMsRunReader>(ms_run_id);
227 QFile file(ms_run_id.get()->getFileName());
230 QObject::tr(
"unable to build a reader : file %1 not found.")
231 .arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
233 MzFormat file_format = ms_run_id.get()->getMzFormat();
237 qDebug() <<
"Returning a XyMsRunReader.";
239 return std::make_shared<XyMsRunReader>(ms_run_id);
244 QObject::tr(
"unable to build a reader for %1 : unknown file format")
245 .arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
249 qDebug() <<
"by default, build a TimsMsRunReader.";
250 return std::make_shared<TimsMsRunReader>(ms_run_id);
254 qDebug() <<
"Returning a PwizMsRunReader .";
256 return std::make_shared<PwizMsRunReader>(ms_run_id);
262 const QString &xml_id)
264 std::vector<MsRunIdCstSPtr> run_list =
getMsRunIds();
269 if(original_run_id.get()->getRunId() == run_id)
271 MsRunId new_run_id(*original_run_id.get());
278 if((run_id.isEmpty()) && (run_list.size() == 1))
280 MsRunId new_run_id(*run_list[0].get());
287 if(reader_sp ==
nullptr)
292 .arg(QFileInfo(
m_fileName).absoluteFilePath())));
302 std::pair<MzFormat, FileReaderType>(format, reader_type));
306 ret.first->second = reader_type;