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;
47 readerName = defaultReaderList.identify(
m_fileName.toStdString());
49 catch(std::runtime_error &error)
51 qDebug() << error.what() <<
" " <<
typeid(error).name();
55 "libpwiz ERROR reading MS data file %1 "
56 "(std::runtime_error):\n%2\nsource file:%3 - source line:%4")
62 catch(std::exception &error)
64 qDebug() << error.what() <<
" " <<
typeid(error).name();
68 "libpwiz ERROR reading MS data file %1 "
69 "(std::runtime_error):\n%2\nsource file:%3 - source line:%4")
76 if(readerName.empty())
78 qDebug() <<
"Failed to identify the file.";
84 if(readerName ==
"mzML")
86 else if(readerName ==
"mzXML")
88 else if(readerName ==
"Mascot Generic")
90 else if(readerName ==
"MZ5")
92 else if(readerName ==
"MSn")
94 else if(readerName ==
"ABSciex WIFF")
96 else if(readerName ==
"ABSciex T2D")
98 else if(readerName ==
"Agilent MassHunter")
100 else if(readerName ==
"Thermo RAW")
102 else if(readerName ==
"Water RAW")
104 else if(readerName ==
"Bruker FID")
106 else if(readerName ==
"Bruker YEP")
108 else if(readerName ==
"Bruker BAF")
127 catch(std::runtime_error &error)
129 qDebug() << error.what() <<
" " <<
typeid(error).name();
133 "libpwiz ERROR reading MS data file %1 "
134 "(std::runtime_error):\n%2\nsource file:%3 - source line:%4")
140 catch(std::exception &error)
142 qDebug() << error.what() <<
" " <<
typeid(error).name();
146 "libpwiz ERROR reading MS data file %1 "
147 "(std::runtime_error):\n%2\nsource file:%3 - source line:%4")
174std::vector<MsRunIdCstSPtr>
177 std::vector<MsRunIdCstSPtr> ms_run_ids;
182 std::size_t iter = 0;
197 ms_run_id.
setSampleName(QString::fromStdString(ms_data_ptr->run.id));
201 if(ms_data_ptr->run.samplePtr !=
nullptr)
204 QString::fromStdString(ms_data_ptr->run.samplePtr->name));
211 ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
MsDataFormat m_fileFormat
MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informa...
void setXmlId(const QString &xml_id)
set an XML unique identifier for this MsRunId
void setMsDataFormat(MsDataFormat format)
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 MsDataFormat 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...