Used to load MascotXML files. More...
#include <OpenMS/FORMAT/MascotXMLFile.h>
Public Types | |
| typedef Internal::MascotXMLHandler::RTMapping | RTMapping |
Public Member Functions | |
| MascotXMLFile () | |
| Constructor. More... | |
| void | load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, const RTMapping &rt_mapping=RTMapping(), const String &scan_regex="") |
| loads data from a Mascot XML file More... | |
| void | load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, std::map< String, std::vector< AASequence > > &peptides, const RTMapping &rt_mapping=RTMapping(), const String &scan_regex="") |
| loads data from a Mascot XML file More... | |
Public Member Functions inherited from XMLFile | |
| XMLFile () | |
| Default constructor. More... | |
| XMLFile (const String &schema_location, const String &version) | |
| Constructor that sets the schema location. More... | |
| virtual | ~XMLFile () |
| Destructor. More... | |
| bool | isValid (const String &filename, std::ostream &os=std::cerr) |
| Checks if a file validates against the XML schema. More... | |
| const String & | getVersion () const |
| return the version of the schema More... | |
Static Public Member Functions | |
| static void | generateRTMapping (const MSExperiment<>::ConstIterator begin, const MSExperiment<>::ConstIterator end, RTMapping &rt_mapping) |
| Generates a mapping between scan numbers and retention times in raw data. More... | |
Additional Inherited Members | |
Protected Member Functions inherited from XMLFile | |
| void | parse_ (const String &filename, XMLHandler *handler) |
Parses the XML file given by filename using the handler given by handler. More... | |
| void | save_ (const String &filename, XMLHandler *handler) const |
Stores the contents of the XML handler given by handler in the file given by filename. More... | |
| void | enforceEncoding_ (const String &encoding) |
Protected Attributes inherited from XMLFile | |
| String | schema_location_ |
| XML schema file location. More... | |
| String | schema_version_ |
| Version string. More... | |
| String | enforced_encoding_ |
| Encoding string that replaces the encoding (system dependend or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More... | |
Used to load MascotXML files.
This class is used to load documents that implement the schema of MascotXML files.
| MascotXMLFile | ( | ) |
Constructor.
|
static |
Generates a mapping between scan numbers and retention times in raw data.
| begin | Iterator to the first spectrum |
| end | Iterator past the last spectrum |
| rt_mapping | Output mapping |
The mapping can be used to infer retention times of identifications when a Mascot XML file is loaded.
| void load | ( | const String & | filename, |
| ProteinIdentification & | protein_identification, | ||
| std::vector< PeptideIdentification > & | id_data, | ||
| const RTMapping & | rt_mapping = RTMapping(), |
||
| const String & | scan_regex = "" |
||
| ) |
loads data from a Mascot XML file
| filename | the file to be loaded |
| protein_identification | protein identifications belonging to the whole experiment |
| id_data | the identifications with m/z and RT |
| rt_mapping | An optional mapping of scan indices to RT, in case the file only contains scan numbers |
| scan_regex | An optional regular expression used to extract the scan numbers |
| Exception::FileNotFound | is thrown if the file does not exists. |
| Exception::ParseError | is thrown if the file does not suit to the standard. |
This method serves to read in a Mascot XML file. The information can be retrieved via the load function.
| void load | ( | const String & | filename, |
| ProteinIdentification & | protein_identification, | ||
| std::vector< PeptideIdentification > & | id_data, | ||
| std::map< String, std::vector< AASequence > > & | peptides, | ||
| const RTMapping & | rt_mapping = RTMapping(), |
||
| const String & | scan_regex = "" |
||
| ) |
loads data from a Mascot XML file
| filename | the file to be loaded |
| protein_identification | protein identifications belonging to the whole experiment |
| id_data | the identifications with m/z and RT |
| peptides | a map of modified peptides identified by the String title |
| rt_mapping | An optional mapping of scan indices to RT, in case the file only contains scan numbers |
| scan_regex | An optional regular expression used to extract the scan numbers |
| Exception::FileNotFound | is thrown if the file does not exists. |
| Exception::ParseError | is thrown if the file does not suit to the standard. |
This method serves to read in a Mascot XML file. The information can be retrieved via the load function.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |