OpenMS
InspectInfile.h
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34 
35 #pragma once
36 
38 
39 #include <map>
40 
41 namespace OpenMS
42 {
50  class OPENMS_DLLAPI InspectInfile
51  {
52 public:
53 
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 
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 
131  void setPrecursorMassTolerance(float precursor_mass_tolerance);
132 
138  float getPeakMassTolerance() const;
139  void setPeakMassTolerance(float peak_mass_tolerance);
140 
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 
159 
161 
163 
165 
168 
169  float maxptmsize_;
170 
172 
174 
177 
179 
181 
182  std::map<String, std::vector<String> > PTMname_residues_mass_type_;
183 
184  };
185 
186 } // namespace OpenMS
187 
Inspect input file adapter.
Definition: InspectInfile.h:51
Int getTagCount() const
Number of tags to generate.
void setBlind(UInt blind)
String instrument_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:178
void handlePTMs(const String &modification_line, const String &modifications_filename, const bool monoisotopic)
void setDb(const String &db)
InspectInfile()
default constructor
Int modifications_per_peptide_
allowed number of modifications per peptide
Definition: InspectInfile.h:164
InspectInfile(const InspectInfile &inspect_infile)
copy constructor
void setPeakMassTolerance(float peak_mass_tolerance)
UInt blind_
Definition: InspectInfile.h:166
UInt getBlind() const
run Inspect in a blind mode
void setMaxPTMsize(float maxptmsize)
const std::map< String, std::vector< String > > & getModifications() const
return the modifications (the modification names map to the affected residues, the mass change and th...
float getPrecursorMassTolerance() const
Specifies the parent mass tolerance, in Daltons.
float getMaxPTMsize() const
the maximum modification size (in Da) to consider in a blind search
float precursor_mass_tolerance_
Specifies the parent mass tolerance, in Daltons. A candidate's flanking mass can differ from the tag'...
Definition: InspectInfile.h:171
String db_
Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein ...
Definition: InspectInfile.h:160
void store(const String &filename)
Int tag_count_
Number of tags to generate. <0 is not set.
Definition: InspectInfile.h:180
void setSpectra(const String &spectra)
String enzyme_
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
Definition: InspectInfile.h:162
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
Int getModificationsPerPeptide() const
Number of PTMs permitted in a single peptide.
const String & getInstrument() const
If set to QTOF, uses a QTOF-derived fragmentation model, and does not attempt to correct the parent m...
void setEnzyme(const String &enzyme)
float maxptmsize_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:169
InspectInfile & operator=(const InspectInfile &inspect_infile)
assignment operator
const String & getSpectra() const
Specifies a spectrum file to search.
void setMulticharge(UInt multicharge)
void setTagCount(Int TagCount)
UInt multicharge_
Definition: InspectInfile.h:175
const String & getEnzyme() const
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
void setPrecursorMassTolerance(float precursor_mass_tolerance)
UInt getMulticharge() const
If set to true, attempt to guess the precursor charge and mass, and consider multiple charge states i...
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
virtual ~InspectInfile()
destructor
float getPeakMassTolerance() const
How far b and y peaks can be shifted from their expected masses.
void setModificationsPerPeptide(Int modifications_per_peptide)
bool operator==(const InspectInfile &inspect_infile) const
equality operator
String spectra_
Specifies a spectrum file to search.
Definition: InspectInfile.h:158
void setInstrument(const String &instrument)
const String & getDb() const
Specifies the name of a database (.trie file) to search.
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48