Used to load OMSSAXML files.
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#include <OpenMS/FORMAT/OMSSAXMLFile.h>
List of all members.
Public Member Functions |
| | OMSSAXMLFile () |
| | Default constructor.
|
| virtual | ~OMSSAXMLFile () |
| | Destructor.
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| void | load (const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true) |
| | loads data from a OMSSAXML file
|
| void | setModificationDefinitionsSet (const ModificationDefinitionsSet &rhs) |
| | sets the valid modifications
|
Protected Member Functions |
| void | endElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname) |
| void | startElement (const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes) |
| void | characters (const XMLCh *const chars, const XMLSize_t) |
Private Member Functions |
| | OMSSAXMLFile (const OMSSAXMLFile &rhs) |
| OMSSAXMLFile & | operator= (const OMSSAXMLFile &rhs) |
| void | readMappingFile_ () |
| | reads the mapping file needed for modifications
|
Private Attributes |
std::vector
< PeptideIdentification > * | peptide_identifications_ |
| | the identifications (storing the peptide hits)
|
| ProteinHit | actual_protein_hit_ |
| PeptideHit | actual_peptide_hit_ |
| PeptideIdentification | actual_peptide_id_ |
| ProteinIdentification | actual_protein_id_ |
| String | tag_ |
| UInt | actual_mod_site_ |
| | site of the actual modification (simple position in the peptide)
|
| String | actual_mod_type_ |
| | type of the modification
|
std::vector< std::pair< UInt,
String > > | modifications_ |
| | modifications of the peptide defined by site and type
|
| bool | load_proteins_ |
| | should protein hits be read from the file?
|
Map< UInt, std::vector
< ResidueModification > > | mods_map_ |
| | modifications mapping file from OMSSA mod num to UniMod accession
|
| Map< String, UInt > | mods_to_num_ |
| | modification mapping reverse, from the modification to the mod_num
|
| ModificationDefinitionsSet | mod_def_set_ |
| | modification definitions set of the search, needed to annotate fixed modifications
|
Detailed Description
Used to load OMSSAXML files.
This class is used to load documents that implement the schema of OMSSAXML files.
Constructor & Destructor Documentation
Member Function Documentation
| void characters |
( |
const XMLCh *const |
chars, |
|
|
const |
XMLSize_t | |
|
) |
| | [protected] |
| void endElement |
( |
const XMLCh * |
const, |
|
|
const XMLCh * |
const, |
|
|
const XMLCh *const |
qname | |
|
) |
| | [protected] |
| void readMappingFile_ |
( |
|
) |
[private] |
reads the mapping file needed for modifications
sets the valid modifications
| void startElement |
( |
const XMLCh * |
const, |
|
|
const XMLCh * |
const, |
|
|
const XMLCh *const |
qname, |
|
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const xercesc::Attributes & |
attributes | |
|
) |
| | [protected] |
Member Data Documentation
site of the actual modification (simple position in the peptide)
should protein hits be read from the file?
modification definitions set of the search, needed to annotate fixed modifications
modifications of the peptide defined by site and type
modifications mapping file from OMSSA mod num to UniMod accession
modification mapping reverse, from the modification to the mod_num
the identifications (storing the peptide hits)
| OpenMS / TOPP release 1.10.0 |
Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1 |
