Matrix Science Mascot Parser toolkit
 
Loading...
Searching...
No Matches
ms_mascotresults_params.hpp
1/*
2##############################################################################
3# file: ms_mascotresults_params.hpp #
4# 'msparser' toolkit #
5# Parameter storage for ms_peptidesummary and ms_proteinsummary #
6##############################################################################
7# COPYRIGHT NOTICE #
8# Copyright 1998-2018 Matrix Science Limited All Rights Reserved. #
9# #
10##############################################################################
11# $Author: robertog@matrixscience.com $ #
12# $Date: 2022-07-13 15:01:20 +0100 $ #
13# $Revision: 01fae171ab6047ffa9ea37b0bdc76a78e10877a7 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
14# $NoKeywords:: $ #
15##############################################################################
16*/
17
18#ifndef MS_MASCOTRESULTS_PARAMS_HPP
19#define MS_MASCOTRESULTS_PARAMS_HPP
20
21namespace matrix_science {
27 class ms_mascotresults;
28 class ms_peptidesummary;
29
31 class MS_MASCOTRESFILE_API ms_mascotresults_params
32 {
33 public:
35 ms_mascotresults_params(const unsigned int flags = ms_mascotresults::MSRES_GROUP_PROTEINS,
36 double minProbability = 0.05,
37 int maxHitsToReport = 0,
38 const char * unigeneIndexFile = 0,
39 double ignoreIonsScoreBelow = 0.0,
40 int minPepLenInPepSummary = 0,
41 const char * singleHit = 0,
42 const unsigned int flags2 = ms_peptidesummary::MSPEPSUM_NONE);
43
44 virtual ~ms_mascotresults_params();
45
47 ms_mascotresults_params(const ms_mascotresults_params & src);
48
49#ifndef SWIG
51 ms_mascotresults_params& operator=(const ms_mascotresults_params & right);
52#endif
53
55 void copyFrom(const ms_mascotresults_params * right);
56
58 void setFlags(const unsigned int flags);
59
61 void setFlag(const ms_mascotresults::FLAGS flag, bool enabled);
62
64 unsigned int getFlags() const;
65
67 void setFlags2(const unsigned int flags2);
68
70 void setFlag2(const ms_peptidesummary::MSPEPSUM flag, bool enabled);
71
73 unsigned int getFlags2() const;
74
76 double getMinProbability() const;
77
79 void setMinProbability(const double minProbability);
80
82 double getTargetFDR() const;
83
85 void setTargetFDR(double fdr);
86
88 ms_mascotresults::DECOY_STATS_COUNT_TYPE getTargetFDRType() const;
89
91 void setTargetFDRType(ms_mascotresults::DECOY_STATS_COUNT_TYPE fdrType);
92
94 double getIgnoreIonsScoreBelow() const;
95
97 void setIgnoreIonsScoreBelow(const double ignoreIonsScoreBelow);
98
100 int getMinNumSigUniqueSequences() const;
101
103 void setMinNumSigUniqueSequences(const int n);
104
106 int getMaxHitsToReport() const;
107
109 void setMaxHitsToReport(const int maxHitsToReport);
110
112 int getMinPepLenInPeptideSummary() const;
113
115 void setMinPepLenInPeptideSummary(const int minPepLenInPeptideSummary);
116
118 std::string getUnigeneIndexFile() const;
119
121 void setUnigeneIndexFile(const char* unigeneIndexFile);
122
124 std::string getSingleHit() const;
125
127 void setSingleHit(const char* singleHit);
128
130 bool isUsePeptideSummary() const;
131
133 void setUsePeptideSummary(const bool usePeptideSummary);
134
135 private:
136 unsigned int flags_;
137 double minProbability_;
138 double targetFDR_;
139 ms_mascotresults::DECOY_STATS_COUNT_TYPE targetFDRtype_;
140 int maxHitsToReport_;
141 double ignoreIonsScoreBelow_;
142 std::string unigeneIndexFile_;
143 int minPepLenInPepSummary_;
144 std::string singleHit_;
145 unsigned int flags2_;
146 bool usePeptideSummary_;
147
148 int minNumSigUniqueSeqs_;
149 };
150 // end of resfile_group
152} // matrix_science namespace
153
154#endif // MS_MASCOTRESULTS_PARAMS_HPP
155
156/*------------------------------- End of File -------------------------------*/
matrix_science::ms_mascotresults_params
Class which provides constructor parameters for either ms_peptidesummary or ms_proteinsummary.
Definition: ms_mascotresults_params.hpp:32
matrix_science::ms_mascotresults::DECOY_STATS_COUNT_TYPE
DECOY_STATS_COUNT_TYPE
Type of object counted by getNumHitsAboveIdentity() and friends.
Definition: ms_mascotresults.hpp:382
matrix_science::ms_mascotresults::FLAGS
FLAGS
Flags for the type of results.
Definition: ms_mascotresults.hpp:297
matrix_science::ms_peptidesummary::MSPEPSUM
MSPEPSUM
flags2 for ms_peptidesummary introduced in Mascot Parser 2.3.
Definition: ms_peptidesummary.hpp:140