| OpenMS 2.5.0

MoleculeParentMatch.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/METADATA/ID/ParentMolecule.h>
38
39 namespace OpenMS
40 {
41 namespace IdentificationDataInternal
42 {
45 struct MoleculeParentMatch: public MetaInfoInterface
46 {
47 // in extraordinary cases (e.g. database searches that allow insertions/
48 // deletions), the length of the identified molecule may differ from the
49 // length of the subsequence in the parent; therefore, store "end_pos":
50 Size start_pos, end_pos;
51
52 // String instead of char so modified residues can be represented:
53 String left_neighbor, right_neighbor; // neighboring sequence elements
54
55 static constexpr Size UNKNOWN_POSITION = Size(-1);
56 static constexpr char UNKNOWN_NEIGHBOR = 'X';
57 static constexpr char LEFT_TERMINUS = '[';
58 static constexpr char RIGHT_TERMINUS = ']';
59
60 explicit MoleculeParentMatch(Size start_pos = UNKNOWN_POSITION,
61 Size end_pos = UNKNOWN_POSITION,
62 String left_neighbor = UNKNOWN_NEIGHBOR,
63 String right_neighbor = UNKNOWN_NEIGHBOR):
64 start_pos(start_pos), end_pos(end_pos), left_neighbor(left_neighbor),
65 right_neighbor(right_neighbor)
66 {
67 }
68
69 bool operator<(const MoleculeParentMatch& other) const
70 {
71 // positions determine neighbors - no need to compare those:
72 return (std::tie(start_pos, end_pos) <
73 std::tie(other.start_pos, other.end_pos));
74 }
75
76 bool operator==(const MoleculeParentMatch& other) const
77 {
78 // positions determine neighbors - no need to compare those:
79 return (std::tie(start_pos, end_pos) ==
80 std::tie(other.start_pos, other.end_pos));
81 }
82
83 bool hasValidPositions(Size molecule_length = 0, Size parent_length = 0) const
84 {
85 if ((start_pos == UNKNOWN_POSITION) || (end_pos == UNKNOWN_POSITION))
86 {
87 return false;
88 }
89 if (end_pos < start_pos) return false;
90 if (molecule_length && (end_pos - start_pos + 1 != molecule_length))
91 {
92 return false;
93 }
94 if (parent_length && (end_pos >= parent_length)) return false;
95 return true;
96 }
97 };
98
100 typedef std::map<ParentMoleculeRef,
101 std::set<MoleculeParentMatch>> ParentMatches;
102
103 }
104 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IdentificationDataInternal::MoleculeParentMatch::start_pos
Size start_pos
Definition: MoleculeParentMatch.h:50
OpenMS::IdentificationDataInternal::MoleculeParentMatch::hasValidPositions
bool hasValidPositions(Size molecule_length=0, Size parent_length=0) const
Definition: MoleculeParentMatch.h:83
OpenMS::IdentificationDataInternal::MoleculeParentMatch::MoleculeParentMatch
MoleculeParentMatch(Size start_pos=UNKNOWN_POSITION, Size end_pos=UNKNOWN_POSITION, String left_neighbor=UNKNOWN_NEIGHBOR, String right_neighbor=UNKNOWN_NEIGHBOR)
Definition: MoleculeParentMatch.h:60
ParentMolecule.h
OpenMS::IdentificationDataInternal::MoleculeParentMatch::UNKNOWN_NEIGHBOR
static constexpr char UNKNOWN_NEIGHBOR
Definition: MoleculeParentMatch.h:56
OpenMS::IdentificationDataInternal::MoleculeParentMatch::UNKNOWN_POSITION
static constexpr Size UNKNOWN_POSITION
Definition: MoleculeParentMatch.h:55
OpenMS::IdentificationDataInternal::MoleculeParentMatch::RIGHT_TERMINUS
static constexpr char RIGHT_TERMINUS
Definition: MoleculeParentMatch.h:58
OpenMS::IdentificationDataInternal::MoleculeParentMatch::end_pos
Size end_pos
Definition: MoleculeParentMatch.h:50
OpenMS::IdentificationDataInternal::MoleculeParentMatch::left_neighbor
String left_neighbor
Definition: MoleculeParentMatch.h:53
OpenMS::IdentificationDataInternal::ParentMatches
std::map< ParentMoleculeRef, std::set< MoleculeParentMatch > > ParentMatches
mapping: parent molecule -> match information
Definition: MoleculeParentMatch.h:101
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::IdentificationDataInternal::MoleculeParentMatch
Meta data for the association between an identified molecule (e.g. peptide) and a parent molecule (e...
Definition: MoleculeParentMatch.h:45
OpenMS::IdentificationDataInternal::MoleculeParentMatch::right_neighbor
String right_neighbor
Definition: MoleculeParentMatch.h:53
OpenMS::IdentificationDataInternal::ParentMoleculeRef
IteratorWrapper< ParentMolecules::iterator > ParentMoleculeRef
Definition: ParentMolecule.h:100
OpenMS::IdentificationDataInternal::MoleculeParentMatch::operator<
bool operator<(const MoleculeParentMatch &other) const
Definition: MoleculeParentMatch.h:69
OpenMS::IdentificationDataInternal::MoleculeParentMatch::LEFT_TERMINUS
static constexpr char LEFT_TERMINUS
Definition: MoleculeParentMatch.h:57
OpenMS::IdentificationDataInternal::MoleculeParentMatch::operator==
bool operator==(const MoleculeParentMatch &other) const
Definition: MoleculeParentMatch.h:76
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127