| OpenMS 2.5.0

InspectInfile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/String.h>
38
39 #include <map>
40
41 namespace OpenMS
42 {
50 class OPENMS_DLLAPI InspectInfile
51 {
52 public:
53
55 InspectInfile();
56
58 InspectInfile(const InspectInfile& inspect_infile);
59
61 virtual ~InspectInfile();
62
64 InspectInfile& operator=(const InspectInfile& inspect_infile);
65
67 bool operator==(const InspectInfile& inspect_infile) const;
68
73 void store(const String& filename);
74
83 void handlePTMs(const String& modification_line, const String& modifications_filename, const bool monoisotopic);
84
90 const String& getSpectra() const;
91 void setSpectra(const String& spectra);
92
98 const String& getDb() const;
99 void setDb(const String& db);
100
102 const String& getEnzyme() const;
103 void setEnzyme(const String& enzyme);
104
106 Int getModificationsPerPeptide() const;
107 void setModificationsPerPeptide(Int modifications_per_peptide);
108
114 UInt getBlind() const;
115 void setBlind(UInt blind);
116
122 float getMaxPTMsize() const;
123 void setMaxPTMsize(float maxptmsize);
124
130 float getPrecursorMassTolerance() const;
131 void setPrecursorMassTolerance(float precursor_mass_tolerance);
132
138 float getPeakMassTolerance() const;
139 void setPeakMassTolerance(float peak_mass_tolerance);
140
142 UInt getMulticharge() const;
143 void setMulticharge(UInt multicharge);
144
146 const String& getInstrument() const;
147 void setInstrument(const String& instrument);
148
150 Int getTagCount() const;
151 void setTagCount(Int TagCount);
152
154 const std::map<String, std::vector<String> >& getModifications() const;
155
156 private:
157
158 String spectra_;
159
160 String db_;
161
162 String enzyme_;
163
164 Int modifications_per_peptide_;
165
166 UInt blind_;
167
169 float maxptmsize_;
170
171 float precursor_mass_tolerance_;
172
173 float peak_mass_tolerance_;
174
175 UInt multicharge_;
176
178 String instrument_;
179
180 Int tag_count_;
181
182 std::map<String, std::vector<String> > PTMname_residues_mass_type_;
183
184 };
185
186 } // namespace OpenMS
187
OpenMS::InspectInfile::enzyme_
String enzyme_
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values...
Definition: InspectInfile.h:162
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::InspectInfile
Inspect input file adapter.
Definition: InspectInfile.h:50
OpenMS::InspectInfile::precursor_mass_tolerance_
float precursor_mass_tolerance_
Specifies the parent mass tolerance, in Daltons. A candidate&#39;s flanking mass can differ from the tag&#39;...
Definition: InspectInfile.h:171
OpenMS::InspectInfile::multicharge_
UInt multicharge_
Definition: InspectInfile.h:175
OpenMS::InspectInfile::spectra_
String spectra_
Specifies a spectrum file to search.
Definition: InspectInfile.h:158
OpenMS::InspectInfile::maxptmsize_
float maxptmsize_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:169
OpenMS::InspectInfile::instrument_
String instrument_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:178
OpenMS::InspectInfile::blind_
UInt blind_
Definition: InspectInfile.h:166
OpenMS::InspectInfile::db_
String db_
Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein ...
Definition: InspectInfile.h:160
String.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::InspectInfile::peak_mass_tolerance_
float peak_mass_tolerance_
How far b and y peaks can be shifted from their expected masses. Default is 0.5. Higher values produc...
Definition: InspectInfile.h:173
OpenMS::InspectInfile::PTMname_residues_mass_type_
std::map< String, std::vector< String > > PTMname_residues_mass_type_
the modification names map to the affected residues, the mass change and the type ...
Definition: InspectInfile.h:182
int
OpenMS::InspectInfile::modifications_per_peptide_
Int modifications_per_peptide_
allowed number of modifications per peptide
Definition: InspectInfile.h:164
OpenMS::InspectInfile::tag_count_
Int tag_count_
Number of tags to generate. <0 is not set.
Definition: InspectInfile.h:180
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806