35 #ifndef OPENMS_METADATA_PROTEINIDENTIFICATION_H
36 #define OPENMS_METADATA_PROTEINIDENTIFICATION_H
46 class PeptideIdentification;
100 static const std::string NamesOfPeakMassType[SIZE_OF_PEAKMASSTYPE];
111 SIZE_OF_DIGESTIONENZYME
114 static const std::string NamesOfDigestionEnzyme[SIZE_OF_DIGESTIONENZYME];
159 const std::vector<ProteinHit> & getHits()
const;
162 std::vector<ProteinHit> & getHits();
171 void setHits(
const std::vector<ProteinHit> & hits);
174 std::vector<ProteinHit>::iterator findHit(
const String & accession);
177 const std::vector<ProteinGroup> & getProteinGroups()
const;
179 std::vector<ProteinGroup> & getProteinGroups();
184 const std::vector<ProteinGroup> & getIndistinguishableProteins()
const;
186 std::vector<ProteinGroup> & getIndistinguishableProteins();
188 void insertIndistinguishableProteins(
const ProteinGroup & group);
191 double getSignificanceThreshold()
const;
193 void setSignificanceThreshold(
double value);
195 const String & getScoreType()
const;
197 void setScoreType(
const String & type);
199 bool isHigherScoreBetter()
const;
201 void setHigherScoreBetter(
bool higher_is_better);
213 Size computeCoverage(
const std::vector<PeptideIdentification> & pep_ids);
218 const DateTime & getDateTime()
const;
221 void setDateTime(
const DateTime & date);
223 void setSearchEngine(
const String & search_engine);
225 const String & getSearchEngine()
const;
227 void setSearchEngineVersion(
const String & search_engine_version);
229 const String & getSearchEngineVersion()
const;
235 const String & getIdentifier()
const;
237 void setIdentifier(
const String &
id);
263 #endif // OPENMS_METADATA_PROTEINIDENTIFICATION_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
String db
The used database.
Definition: ProteinIdentification.h:120
A more convenient string class.
Definition: String.h:57
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:125
String db_version
The database version.
Definition: ProteinIdentification.h:121
double probability
Probability of this group.
Definition: ProteinIdentification.h:74
String search_engine_version_
Definition: ProteinIdentification.h:245
ProteinHit HitType
Hit type definition.
Definition: ProteinIdentification.h:66
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Search parameters of the DB search.
Definition: ProteinIdentification.h:117
String taxonomy
The taxonomy restriction.
Definition: ProteinIdentification.h:122
std::vector< ProteinHit > protein_hits_
Definition: ProteinIdentification.h:254
String protein_score_type_
Definition: ProteinIdentification.h:252
double protein_significance_threshold_
Definition: ProteinIdentification.h:258
std::vector< String > accessions
Accessions of (indistinguishable) proteins that belong to the same group.
Definition: ProteinIdentification.h:77
String id_
Definition: ProteinIdentification.h:243
double precursor_tolerance
Mass tolerance of precursor ions (Dalton)
Definition: ProteinIdentification.h:130
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:128
std::vector< ProteinGroup > protein_groups_
Definition: ProteinIdentification.h:255
String search_engine_
Definition: ProteinIdentification.h:244
double peak_mass_tolerance
Mass tolerance of fragment ions (Dalton)
Definition: ProteinIdentification.h:129
Representation of a protein hit.
Definition: ProteinHit.h:54
bool higher_score_better_
Definition: ProteinIdentification.h:253
DateTime date_
Definition: ProteinIdentification.h:247
DateTime Class.
Definition: DateTime.h:55
std::vector< ProteinGroup > indistinguishable_proteins_
Indistinguishable proteins: accessions[0] is "group leader", probability is meaningless.
Definition: ProteinIdentification.h:257
DigestionEnzyme enzyme
The enzyme used for cleavage.
Definition: ProteinIdentification.h:127
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:124
SearchParameters search_parameters_
Definition: ProteinIdentification.h:246
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:123
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:71
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:126