OpenMS  3.0.0
DBSearchParam.h
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32 // $Authors: Hendrik Weisser $
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34 
35 #pragma once
36 
40 
41 namespace OpenMS
42 {
43  namespace IdentificationDataInternal
44  {
48  {
51 
55 
56  std::set<Int> charges;
57 
58  std::set<String> fixed_mods;
59  std::set<String> variable_mods;
60 
65 
66  // allow for either "DigestionEnzymeProtein" or "DigestionEnzymeRNA":
72 
80  {
81  }
82 
83  DBSearchParam(const DBSearchParam& other) = default;
84 
85  bool operator<(const DBSearchParam& other) const
86  {
87  return (std::tie(molecule_type, mass_type,
94  std::tie(other.molecule_type, other.mass_type,
95  other.database, other.database_version, other.taxonomy,
96  other.charges, other.fixed_mods, other.variable_mods,
100  other.min_length, other.max_length));
101  }
102 
103  bool operator==(const DBSearchParam& other) const
104  {
105  return (std::tie(molecule_type, mass_type, database,
111  std::tie(other.molecule_type, other.mass_type,
112  other.database, other.database_version, other.taxonomy,
113  other.charges, other.fixed_mods, other.variable_mods,
119  other.missed_cleavages,
120  other.min_length, other.max_length));
121  }
122  };
123 
124  typedef std::set<DBSearchParam> DBSearchParams;
126  typedef std::map<ProcessingStepRef, SearchParamRef> DBSearchSteps;
127 
128  }
129 }
OpenMS::EnzymaticDigestion::Specificity
Specificity
when querying for valid digestion products, this determines if the specificity of the two peptide end...
Definition: EnzymaticDigestion.h:70
OpenMS::IdentificationDataInternal::MoleculeType
MoleculeType
Definition: MetaData.h:65
OpenMS::IdentificationDataInternal::MassType
MassType
Definition: MetaData.h:73
OpenMS::IdentificationDataInternal::DBSearchParam::fragment_mass_tolerance
double fragment_mass_tolerance
Definition: DBSearchParam.h:62
EnzymaticDigestion.h
OpenMS::IdentificationDataInternal::DBSearchParam::operator<
bool operator<(const DBSearchParam &other) const
Definition: DBSearchParam.h:85
OpenMS::IdentificationDataInternal::DBSearchParam::fragment_tolerance_ppm
bool fragment_tolerance_ppm
Definition: DBSearchParam.h:64
MetaData.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IdentificationDataInternal::DBSearchParams
std::set< DBSearchParam > DBSearchParams
Definition: DBSearchParam.h:124
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:66
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IdentificationDataInternal::PROTEIN
Definition: MetaData.h:67
OpenMS::IdentificationDataInternal::DBSearchParam::mass_type
enum MassType mass_type
Definition: DBSearchParam.h:50
OpenMS::IdentificationDataInternal::DBSearchParam::precursor_tolerance_ppm
bool precursor_tolerance_ppm
Definition: DBSearchParam.h:63
OpenMS::IdentificationDataInternal::DBSearchParam::database
String database
Definition: DBSearchParam.h:52
OpenMS::IdentificationDataInternal::DBSearchParam
Parameters specific to a database search step.
Definition: DBSearchParam.h:47
OpenMS::IdentificationDataInternal::DBSearchParam::operator==
bool operator==(const DBSearchParam &other) const
Definition: DBSearchParam.h:103
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::IdentificationDataInternal::SearchParamRef
IteratorWrapper< DBSearchParams::iterator > SearchParamRef
Definition: DBSearchParam.h:125
OpenMS::IdentificationDataInternal::DBSearchParam::enzyme_term_specificity
EnzymaticDigestion::Specificity enzyme_term_specificity
Definition: DBSearchParam.h:68
OpenMS::IdentificationDataInternal::DBSearchParam::digestion_enzyme
const DigestionEnzyme * digestion_enzyme
Definition: DBSearchParam.h:67
OpenMS::IdentificationDataInternal::DBSearchSteps
std::map< ProcessingStepRef, SearchParamRef > DBSearchSteps
Definition: DBSearchParam.h:126
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::IdentificationDataInternal::IteratorWrapper
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:45
OpenMS::IdentificationDataInternal::DBSearchParam::variable_mods
std::set< String > variable_mods
Definition: DBSearchParam.h:59
OpenMS::IdentificationDataInternal::DBSearchParam::max_length
Size max_length
Definition: DBSearchParam.h:71
OpenMS::IdentificationDataInternal::DBSearchParam::charges
std::set< Int > charges
Definition: DBSearchParam.h:56
OpenMS::IdentificationDataInternal::DBSearchParam::min_length
Size min_length
Definition: DBSearchParam.h:70
OpenMS::IdentificationDataInternal::DBSearchParam::missed_cleavages
Size missed_cleavages
Definition: DBSearchParam.h:69
OpenMS::DigestionEnzyme
Base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
OpenMS::IdentificationDataInternal::DBSearchParam::precursor_mass_tolerance
double precursor_mass_tolerance
Definition: DBSearchParam.h:61
OpenMS::IdentificationDataInternal::DBSearchParam::taxonomy
String taxonomy
Definition: DBSearchParam.h:54
OpenMS::IdentificationDataInternal::MONOISOTOPIC
Definition: MetaData.h:75
DigestionEnzyme.h
OpenMS::IdentificationDataInternal::DBSearchParam::database_version
String database_version
Definition: DBSearchParam.h:53
OpenMS::IdentificationDataInternal::DBSearchParam::DBSearchParam
DBSearchParam()
Definition: DBSearchParam.h:73
OpenMS::IdentificationDataInternal::DBSearchParam::fixed_mods
std::set< String > fixed_mods
Definition: DBSearchParam.h:58
OpenMS::IdentificationDataInternal::DBSearchParam::molecule_type
enum MoleculeType molecule_type
Definition: DBSearchParam.h:49