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OpenMS
2.5.0
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58 static std::map<String, UInt>
months;
62 std::vector< PeptideIdentification > & pep_ids,
63 std::vector< ProteinIdentification > & prot_ids
68 const std::vector<PeptideIdentification>& pep_id,
76 void endElement(
const XMLCh *
const uri,
const XMLCh *
const local_name,
const XMLCh *
const qname)
override;
79 void startElement(
const XMLCh *
const uri,
const XMLCh *
const local_name,
const XMLCh *
const qname,
const xercesc::Attributes & attributes)
override;
85 double getMinScore()
const;
91 double getMaxScore()
const;
97 UInt getNumberOfHits()
const;
100 virtual void writeTo(std::ostream& os)
override;
141 const std::vector<ProteinIdentification>*
cpro_id_;
142 const std::vector<PeptideIdentification>*
cpep_id_;
187 inline void extractDateTime_(
const String & xquest_datetime_string,
DateTime & date_time);
202 void getLinkPosition_(
const xercesc::Attributes & attributes, std::pair<SignedSize, SignedSize> & pair);
std::vector< PeptideIdentification > current_spectrum_search_
The current spectrum search.
Definition: XQuestResultXMLHandler.h:177
int spectrum_index_heavy_
Definition: XQuestResultXMLHandler.h:133
Base class for XML handlers.
Definition: XMLHandler.h:151
StringList ms_run_path_
Definition: XQuestResultXMLHandler.h:173
UInt min_precursor_charge_
Definition: XQuestResultXMLHandler.h:161
A more convenient string class.
Definition: String.h:58
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
String cross_linker_name_
Definition: XQuestResultXMLHandler.h:134
double min_score_
Definition: XQuestResultXMLHandler.h:147
double rt_light_
Definition: XQuestResultXMLHandler.h:165
Database for enzymes that digest proteins (proteases)
Definition: ProteaseDB.h:52
String spectrum_input_file_
Definition: XQuestResultXMLHandler.h:174
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
double rt_heavy_
Definition: XQuestResultXMLHandler.h:166
int spectrum_index_light_
Definition: XQuestResultXMLHandler.h:132
double mz_light_
Definition: XQuestResultXMLHandler.h:169
const std::vector< ProteinIdentification > * cpro_id_
Definition: XQuestResultXMLHandler.h:141
std::map< String, DataValue > peptide_id_meta_values_
Stores the attributes of a record (peptide identification)
Definition: XQuestResultXMLHandler.h:180
double max_score_
Definition: XQuestResultXMLHandler.h:148
std::set< UInt > charges_
Keeps track of the charges of the hits.
Definition: XQuestResultXMLHandler.h:160
UInt max_precursor_charge_
Definition: XQuestResultXMLHandler.h:162
static std::map< String, UInt > months
Maps String encoding month to the numeric value.
Definition: XQuestResultXMLHandler.h:58
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
static std::map< Size, String > enzymes
Maps enzyme_num in xQuest result file to the enzyme name used by OpenMS.
Definition: XQuestResultXMLHandler.h:55
std::vector< ProteinIdentification > * prot_ids_
Definition: XQuestResultXMLHandler.h:138
UInt n_hits_
Total no. of hits found in the result XML file.
Definition: XQuestResultXMLHandler.h:144
XMLHandler for the result files of XQuest.
Definition: XQuestResultXMLHandler.h:49
bool is_openpepxl_
Whether or not current xquest result tag comes from OpenPepXL (xQuest otherwise)
Definition: XQuestResultXMLHandler.h:151
std::set< String > accessions_
Set of all protein accessions that are within the ProteinHits.
Definition: XQuestResultXMLHandler.h:154
ProteaseDB * enzymes_db_
The enzyme database for enzyme lookup.
Definition: XQuestResultXMLHandler.h:157
double mz_heavy_
Definition: XQuestResultXMLHandler.h:170
const std::vector< PeptideIdentification > * cpep_id_
Definition: XQuestResultXMLHandler.h:142
std::vector< PeptideIdentification > * pep_ids_
Definition: XQuestResultXMLHandler.h:137
DateTime Class.
Definition: DateTime.h:54
Representation of a peptide hit.
Definition: PeptideHit.h:54