This class is a helper class to read and convert a mz5 file to a MSData object.
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#include <ReferenceRead_mz5.hpp>
List of all members.
Public Member Functions |
| ReferenceRead_mz5 (pwiz::msdata::MSData &msd) |
| Default constructor.
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pwiz::cv::CVID | getCVID (const unsigned long) const |
| Getter.
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pwiz::data::ParamGroupPtr | getParamGroupPtr (const unsigned long) const |
| Getter.
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void | fill (std::vector< pwiz::msdata::CVParam > &cv, std::vector< pwiz::msdata::UserParam > &user, std::vector< pwiz::msdata::ParamGroupPtr > ¶m, const unsigned long &cvstart, const unsigned long &cvend, const unsigned long &usrstart, const unsigned long &usrend, const unsigned long &refstart, const unsigned long &refend) const |
pwiz::msdata::SourceFilePtr | getSourcefilePtr (const unsigned long) const |
| Getter.
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pwiz::msdata::SamplePtr | getSamplePtr (const unsigned long) const |
| Getter.
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pwiz::msdata::SoftwarePtr | getSoftwarePtr (const unsigned long) const |
| Getter.
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pwiz::msdata::ScanSettingsPtr | getScanSettingPtr (const unsigned long) const |
| Getter.
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pwiz::msdata::InstrumentConfigurationPtr | getInstrumentPtr (const unsigned long) const |
| Getter.
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pwiz::msdata::DataProcessingPtr | getDataProcessingPtr (const unsigned long) const |
| Getter.
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std::string | getSpectrumId (const unsigned long) const |
| Getter.
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void | addSpectrumIndexPair (const std::string &name, const unsigned long index) const |
| Adds a spectrum index pair to an internal map.
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void | setCVRefMZ5 (CVRefMZ5 *, size_t) |
| Sets internal controlled vocabulary map.
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void | fill (boost::shared_ptr< Connection_mz5 > &connection) |
| Fills the internal MSData reference with the data from an mz5 file.
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pwiz::msdata::DataProcessingPtr | getDefaultChromatogramDP (const size_t index) |
pwiz::msdata::DataProcessingPtr | getDefaultSpectrumDP (const size_t index) |
Detailed Description
This class is a helper class to read and convert a mz5 file to a MSData object.
Definition at line 44 of file ReferenceRead_mz5.hpp.
Constructor & Destructor Documentation
Default constructor.
- Parameters:
-
msd | this MSData object will be filled |
Member Function Documentation
pwiz::cv::CVID pwiz::msdata::mz5::ReferenceRead_mz5::getCVID |
( |
const unsigned |
long | ) |
const |
Getter.
- Parameters:
-
- Returns:
- object with this index. Can throw out_of_range.
Getter.
- Parameters:
-
- Returns:
- object with this index. Can throw out_of_range.
void pwiz::msdata::mz5::ReferenceRead_mz5::fill |
( |
std::vector< pwiz::msdata::CVParam > & |
cv, |
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std::vector< pwiz::msdata::UserParam > & |
user, |
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std::vector< pwiz::msdata::ParamGroupPtr > & |
param, |
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const unsigned long & |
cvstart, |
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const unsigned long & |
cvend, |
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const unsigned long & |
usrstart, |
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const unsigned long & |
usrend, |
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const unsigned long & |
refstart, |
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const unsigned long & |
refend |
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) |
| const |
Getter.
- Parameters:
-
- Returns:
- object with this index. Can throw out_of_range.
Getter.
- Parameters:
-
- Returns:
- object with this index. Can throw out_of_range.
Getter.
- Parameters:
-
- Returns:
- object with this index. Can throw out_of_range.
Getter.
- Parameters:
-
- Returns:
- object with this index. Can throw out_of_range.
Getter.
- Parameters:
-
- Returns:
- object with this index. Can throw out_of_range.
Getter.
- Parameters:
-
- Returns:
- object with this index. Can throw out_of_range.
std::string pwiz::msdata::mz5::ReferenceRead_mz5::getSpectrumId |
( |
const unsigned |
long | ) |
const |
Getter.
- Parameters:
-
- Returns:
- object with this index. Can throw out_of_range.
void pwiz::msdata::mz5::ReferenceRead_mz5::addSpectrumIndexPair |
( |
const std::string & |
name, |
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const unsigned long |
index |
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) |
| const |
Adds a spectrum index pair to an internal map.
- Parameters:
-
void pwiz::msdata::mz5::ReferenceRead_mz5::setCVRefMZ5 |
( |
CVRefMZ5 * |
, |
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size_t |
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) |
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Sets internal controlled vocabulary map.
void pwiz::msdata::mz5::ReferenceRead_mz5::fill |
( |
boost::shared_ptr< Connection_mz5 > & |
connection | ) |
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Fills the internal MSData reference with the data from an mz5 file.
- Parameters:
-
connection | open mz5 connection to a mz5 file |
Member Data Documentation
std::vector<CVRefMZ5> pwiz::msdata::mz5::ReferenceRead_mz5::cvrefs_ |
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mutableprivate |
std::map<unsigned long, pwiz::cv::CVID> pwiz::msdata::mz5::ReferenceRead_mz5::bbmapping_ |
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mutableprivate |
std::vector<CVParamMZ5> pwiz::msdata::mz5::ReferenceRead_mz5::cvParams_ |
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mutableprivate |
std::vector<UserParamMZ5> pwiz::msdata::mz5::ReferenceRead_mz5::usrParams_ |
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mutableprivate |
std::vector<RefMZ5> pwiz::msdata::mz5::ReferenceRead_mz5::refParms_ |
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mutableprivate |
std::map<unsigned long, std::string> pwiz::msdata::mz5::ReferenceRead_mz5::spectrumIndex_ |
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mutableprivate |
unsigned long pwiz::msdata::mz5::ReferenceRead_mz5::defaultChromatogramDataProcessingRefID_ |
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mutableprivate |
unsigned long pwiz::msdata::mz5::ReferenceRead_mz5::defaultSpectrumDataProcessingRefID_ |
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mutableprivate |
The documentation for this class was generated from the following file: