Matrix Science Mascot Parser toolkit
 
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ms_ms1quant_match_component.hpp
1/*
2##############################################################################
3# file: ms_ms1quant_match_component.hpp
4# 'msparser' toolkit
5#
6##############################################################################
7# COPYRIGHT NOTICE
8# Copyright 1998-2014 Matrix Science Limited All Rights Reserved.
9#
10##############################################################################
11 * @(#)$Source: parser/inc/ms_ms1quant_match_component.hpp $
12 * @(#)$Revision: 81909fd23cef6d5183470d1ca2d9a4677bb0f755 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $
13 * @(#)$Date: 2022-03-28 14:50:02 +0100 $
14##############################################################################
15 */
16
17#ifndef MS_MS1QUANT_MATCH_COMPONENT_HPP
18#define MS_MS1QUANT_MATCH_COMPONENT_HPP
19
20
21// Includes from the standard template library
22#include <string>
23
24namespace matrix_science
25{
26 //=========================================================================
32 class ms_ms1quant_match_component_body;
33
35
38 class MS_MASCOTRESFILE_API ms_ms1quant_match_component :
39 public ms_handle
40 {
41 public:
43 ms_ms1quant_match_component();
44
46 ms_ms1quant_match_component(const ms_ms1quant_match_component_body & body);
47
48#ifndef SWIG
50 ms_ms1quant_match_component_body * body();
52 const ms_ms1quant_match_component_body * body() const;
53#endif
54
56 std::string getComponent() const;
57
59 int getNumFileIndexesMatched() const;
60
62 int getFileIndex(const int idx) const;
63
65 bool isComponentIdentified(const int file_index = -1) const;
66
68 double getRelativeMass() const;
69
71 double getMoverz() const;
72
74 std::string getVarModsStr() const;
75
77 std::string getSummedModsStr() const;
78
80 bool hasAbsoluteValue(const int file_index = -1) const;
81
83 double getAbsoluteValue(const int file_index = -1) const;
84
86 void setAbsoluteValue(double value);
87
89 void setAbsoluteValue(const int file_index, double value);
90
92 bool hasMatchedRho(const int file_index = -1) const;
93
95 double getMatchedRho(const int file_index = -1) const;
96
98 void setMatchedRho(const int file_index, double value);
99
101 bool hasMatchedFraction(const int file_index = -1) const;
102
104 double getMatchedFraction(const int file_index = -1) const;
105
107 void setMatchedFraction(const int file_index, double value);
108
109
111 ms_xic getXic(const int file_index = ms_quant_file_index::file_index_value_not_set) const;
112
114 ms_xic * getXicPtr(const int file_index = ms_quant_file_index::file_index_value_not_set);
115
117 int getNumRanges(const int file_index = ms_quant_file_index::file_index_value_not_set) const;
118
120 ms_ms1quant_match_range getRange(int index) const;
121
123 ms_ms1quant_match_range getRange(const int file_index, int index) const;
124
125 void setRanges(std::vector<ms_ms1quant_match_range> ranges);
126 void setRanges(const int file_index, std::vector<ms_ms1quant_match_range> ranges);
127
129 int getNumPeptides(const int file_index = ms_quant_file_index::file_index_value_not_set) const;
130#ifndef SWIG
132 void getPeptideKey(int index, int & q, int & p) const;
133
135 void getPeptideKey(const int file_index, int index, int & q, int & p) const;
136
138 void removePeptide(const int file_index, const int q, const int p);
139#else // SWIG Multiple return values
140 void getPeptideKey(int index, int & OUTPUT, int & OUTPUT) const;
141 void getPeptideKey(const int file_index, int index, int & OUTPUT, int & OUTPUT) const;
142#endif
143 protected:
145 std::size_t getIdxFromFileIndex(const int file_index) const;
146 };
147 // end of quantitation_group
149 //=========================================================================
150
151} // namespace matrix_science
152
153#ifndef SWIG
154namespace msparser_internal
155{
156 MS_PARSERINTERNAL_API double calcRelMassFromMz(double mz, long charge);
157 MS_PARSERINTERNAL_API double calcMzFromRelMass(double mr, long charge);
158}
159#endif
160
161#endif // MS_MS1QUANT_MATCH_COMPONENT_HPP
162
163/*------------------------------- End of File -------------------------------*/
matrix_science::ms_ms1quant_match_component
A component within a match.
Definition: ms_ms1quant_match_component.hpp:40
matrix_science::ms_ms1quant_match_range
A range for a component of a peptide match.
Definition: ms_ms1quant_match_range.hpp:37
matrix_science::ms_xic
An eXtracted Ion Chromatogram (XIC).
Definition: ms_xic.hpp:69