OpenMS
DBSearchParam.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
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34 
35 #pragma once
36 
40 
41 namespace OpenMS
42 {
43  namespace IdentificationDataInternal
44  {
48  {
50  enum MassType mass_type;
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 }
Base class for digestion enzymes.
Definition: DigestionEnzyme.h:53
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:64
Specificity
when querying for valid digestion products, this determines if the specificity of the two peptide end...
Definition: EnzymaticDigestion.h:68
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
A more convenient string class.
Definition: String.h:60
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::map< ProcessingStepRef, SearchParamRef > DBSearchSteps
Definition: DBSearchParam.h:126
std::set< DBSearchParam > DBSearchParams
Definition: DBSearchParam.h:124
IteratorWrapper< DBSearchParams::iterator > SearchParamRef
Definition: DBSearchParam.h:125
MoleculeType
Definition: MetaData.h:66
@ PROTEIN
Definition: MetaData.h:67
MassType
Definition: MetaData.h:74
@ MONOISOTOPIC
Definition: MetaData.h:75
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Parameters specific to a database search step.
Definition: DBSearchParam.h:48
bool fragment_tolerance_ppm
Definition: DBSearchParam.h:64
String database_version
Definition: DBSearchParam.h:53
EnzymaticDigestion::Specificity enzyme_term_specificity
Definition: DBSearchParam.h:68
std::set< Int > charges
Definition: DBSearchParam.h:56
String taxonomy
Definition: DBSearchParam.h:54
std::set< String > variable_mods
Definition: DBSearchParam.h:59
std::set< String > fixed_mods
Definition: DBSearchParam.h:58
bool operator<(const DBSearchParam &other) const
Definition: DBSearchParam.h:85
bool precursor_tolerance_ppm
Definition: DBSearchParam.h:63
String database
Definition: DBSearchParam.h:52
enum MassType mass_type
Definition: DBSearchParam.h:50
double fragment_mass_tolerance
Definition: DBSearchParam.h:62
bool operator==(const DBSearchParam &other) const
Definition: DBSearchParam.h:103
Size min_length
Definition: DBSearchParam.h:70
double precursor_mass_tolerance
Definition: DBSearchParam.h:61
enum MoleculeType molecule_type
Definition: DBSearchParam.h:49
Size max_length
Definition: DBSearchParam.h:71
DBSearchParam(const DBSearchParam &other)=default
const DigestionEnzyme * digestion_enzyme
Definition: DBSearchParam.h:67
Size missed_cleavages
Definition: DBSearchParam.h:69
DBSearchParam()
Definition: DBSearchParam.h:73
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:46