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