35 #ifndef OPENMS_METADATA_PROTEINIDENTIFICATION_H
36 #define OPENMS_METADATA_PROTEINIDENTIFICATION_H
46 class PeptideIdentification;
79 probability(0.0), accessions()
98 static const std::string NamesOfPeakMassType[SIZE_OF_PEAKMASSTYPE];
109 SIZE_OF_DIGESTIONENZYME
112 static const std::string NamesOfDigestionEnzyme[SIZE_OF_DIGESTIONENZYME];
135 mass_type(MONOISOTOPIC),
136 fixed_modifications(),
137 variable_modifications(),
138 enzyme(UNKNOWN_ENZYME),
140 peak_mass_tolerance(0.0),
141 precursor_tolerance(0.0)
147 return db == rhs.
db &&
162 return !(*
this == rhs);
186 const std::vector<ProteinHit> & getHits()
const;
189 std::vector<ProteinHit> & getHits();
193 void setHits(
const std::vector<ProteinHit> & hits);
195 std::vector<ProteinHit>::iterator findHit(
const String & accession);
198 const std::vector<ProteinGroup> & getProteinGroups()
const;
200 std::vector<ProteinGroup> & getProteinGroups();
202 void insertProteinGroup(
const ProteinGroup & group);
205 const std::vector<ProteinGroup> & getIndistinguishableProteins()
const;
207 std::vector<ProteinGroup> & getIndistinguishableProteins();
209 void insertIndistinguishableProteins(
const ProteinGroup & group);
214 void setSignificanceThreshold(
DoubleReal value);
216 const String & getScoreType()
const;
218 void setScoreType(
const String & type);
220 bool isHigherScoreBetter()
const;
222 void setHigherScoreBetter(
bool higher_is_better);
234 Size computeCoverage(
const std::vector<PeptideIdentification> & pep_ids);
239 const DateTime & getDateTime()
const;
242 void setDateTime(
const DateTime & date);
244 void setSearchEngine(
const String & search_engine);
246 const String & getSearchEngine()
const;
248 void setSearchEngineVersion(
const String & search_engine_version);
250 const String & getSearchEngineVersion()
const;
252 void setSearchParameters(
const SearchParameters & search_parameters);
254 const SearchParameters & getSearchParameters()
const;
256 const String & getIdentifier()
const;
258 void setIdentifier(
const String &
id);
284 #endif // OPENMS_METADATA_PROTEINIDENTIFICATION_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
bool operator!=(const SearchParameters &rhs) const
Definition: ProteinIdentification.h:160
String db
The used database.
Definition: ProteinIdentification.h:118
A more convenient string class.
Definition: String.h:56
bool operator==(const SearchParameters &rhs) const
Definition: ProteinIdentification.h:145
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:123
String db_version
The database version.
Definition: ProteinIdentification.h:119
bool operator==(const ProteinGroup rhs) const
Definition: ProteinIdentification.h:82
DoubleReal probability
Probability of this group.
Definition: ProteinIdentification.h:74
Definition: ProteinIdentification.h:94
Definition: ProteinIdentification.h:103
ProteinGroup()
Definition: ProteinIdentification.h:78
String search_engine_version_
Definition: ProteinIdentification.h:266
Definition: ProteinIdentification.h:107
ProteinHit HitType
Hit type definition.
Definition: ProteinIdentification.h:66
Definition: ProteinIdentification.h:104
Definition: ProteinIdentification.h:105
Search parameters of the DB search.
Definition: ProteinIdentification.h:115
DoubleReal peak_mass_tolerance
Mass tolerance of fragment ions (Dalton)
Definition: ProteinIdentification.h:127
String taxonomy
The taxonomy restriction.
Definition: ProteinIdentification.h:120
PeakMassType
Peak mass type.
Definition: ProteinIdentification.h:91
StringList accessions
Accessions of (indistinguishable) proteins that belong to the same group.
Definition: ProteinIdentification.h:76
DigestionEnzyme
Definition: ProteinIdentification.h:101
std::vector< ProteinHit > protein_hits_
Definition: ProteinIdentification.h:275
DoubleReal protein_significance_threshold_
Definition: ProteinIdentification.h:279
String protein_score_type_
Definition: ProteinIdentification.h:273
DoubleReal precursor_tolerance
Mass tolerance of precursor ions (Dalton)
Definition: ProteinIdentification.h:128
String id_
Definition: ProteinIdentification.h:264
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:126
std::vector< ProteinGroup > protein_groups_
Definition: ProteinIdentification.h:276
String search_engine_
Definition: ProteinIdentification.h:265
Definition: ProteinIdentification.h:108
Representation of a protein hit.
Definition: ProteinHit.h:54
bool higher_score_better_
Definition: ProteinIdentification.h:274
DateTime date_
Definition: ProteinIdentification.h:268
Definition: ProteinIdentification.h:106
Definition: ProteinIdentification.h:93
String list.
Definition: StringList.h:56
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
DateTime Class.
Definition: DateTime.h:55
std::vector< ProteinGroup > indistinguishable_proteins_
Indistinguishable proteins: accessions[0] is "group leader", probability is meaningless.
Definition: ProteinIdentification.h:278
SearchParameters()
Definition: ProteinIdentification.h:130
DigestionEnzyme enzyme
The enzyme used for cleavage.
Definition: ProteinIdentification.h:125
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:122
SearchParameters search_parameters_
Definition: ProteinIdentification.h:267
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:121
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:71
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:124