13 #include <pwiz/data/msdata/DefaultReaderList.hpp>
18 #include "../exception/exceptionnotfound.h"
21 #include "../msrun/msrunid.h"
42 pwiz::msdata::DefaultReaderList defaultReaderList;
43 std::string readerName;
46 readerName = defaultReaderList.identify(
m_fileName.toStdString());
48 catch(std::runtime_error &error)
50 qDebug() << error.what() <<
" " <<
typeid(error).name();
54 "libpwiz ERROR reading MS data file %1 "
55 "(std::runtime_error):\n%2\nsource file:%3 - source line:%4")
61 catch(std::exception &error)
63 qDebug() << error.what() <<
" " <<
typeid(error).name();
67 "libpwiz ERROR reading MS data file %1 "
68 "(std::runtime_error):\n%2\nsource file:%3 - source line:%4")
75 if(readerName.empty())
77 qDebug() <<
"Failed to identify the file.";
83 if(readerName ==
"mzML")
85 else if(readerName ==
"mzXML")
87 else if(readerName ==
"Mascot Generic")
89 else if(readerName ==
"MZ5")
91 else if(readerName ==
"MSn")
93 else if(readerName ==
"ABSciex WIFF")
95 else if(readerName ==
"ABSciex T2D")
97 else if(readerName ==
"Agilent MassHunter")
99 else if(readerName ==
"Thermo RAW")
101 else if(readerName ==
"Water RAW")
103 else if(readerName ==
"Bruker FID")
105 else if(readerName ==
"Bruker YEP")
107 else if(readerName ==
"Bruker BAF")
126 catch(std::runtime_error &error)
128 qDebug() << error.what() <<
" " <<
typeid(error).name();
132 "libpwiz ERROR reading MS data file %1 "
133 "(std::runtime_error):\n%2\nsource file:%3 - source line:%4")
139 catch(std::exception &error)
141 qDebug() << error.what() <<
" " <<
typeid(error).name();
145 "libpwiz ERROR reading MS data file %1 "
146 "(std::runtime_error):\n%2\nsource file:%3 - source line:%4")
173 std::vector<MsRunIdCstSPtr>
176 std::vector<MsRunIdCstSPtr> ms_run_ids;
181 std::size_t iter = 0;
201 ms_run_id.
setSampleName(QString::fromStdString(ms_data_ptr->run.id));
204 if(ms_data_ptr->run.samplePtr !=
nullptr)
207 QString::fromStdString(ms_data_ptr->run.samplePtr->name));
214 ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informa...
void setMzFormat(MzFormat format)
void setXmlId(const QString &xml_id)
set an XML unique identifier for this MsRunId
void setSampleName(const QString &name)
set a sample name for this MsRunId
virtual std::vector< MsRunIdCstSPtr > getMsRunIds(const QString &run_prefix) override
PwizMsFileReader(const QString &file_name)
std::vector< pwiz::msdata::MSDataPtr > m_msDataPtrVector
virtual std::size_t initialize()
virtual ~PwizMsFileReader()
virtual MzFormat getFileFormat() override
static std::string toUtf8StandardString(const QString &text)
static const QString getLexicalOrderedString(unsigned int num)
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...