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... | |
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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) |
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 | |
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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) |
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String | schema_location_ |
XML schema file location. More... | |
String | schema_version_ |
Version string. More... | |
String | enforced_encoding_ |
Encoding string that replaces the encoding (system dependent 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.
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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() , |
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const String & | scan_regex = "" |
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) |
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() , |
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const String & | scan_regex = "" |
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) |
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 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |