NCBI C++ ToolKit
pepxml.hpp
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5  * National Center for Biotechnology Information
6  *
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26  * Author: Douglas J. Slotta
27  *
28  * File Description:
29  * Code for converting OMSSA to PepXML
30  *
31  */
32 
33 #ifndef PEPXML_HPP
34 #define PEPXML_HPP
35 
38 #include "msmerge.hpp"
39 
42 BEGIN_SCOPE(omssa)
43 
44 
46 
48 
49 public:
50 
51  // constructor
52  CPepXML(void) {}
53  // destructor
54  ~CPepXML(void) {}
55 
56  /**
57  * convert OMSSA to PepXML
58  *
59  * @param inOMSSA the ASN.1 structure to search to be copied
60  */
61  void ConvertFromOMSSA(CMSSearch& inOMSSA, CRef <CMSModSpecSet> Modset, string basename, string newname);
62 
63 private:
64  // Prohibit copy constructor and assignment operator
67 
68  string ConvertDouble(double n);
69  char ConvertAA(char in);
70  CRef<CModification_info> ConvertModifications(CRef<CMSHits> msHits, CRef<CMSModSpecSet> Modset, set<int>& vModSet,
71  CMSSearch& inOMSSA);
72  void ConvertModSetting(CRef<CSearch_summary> sSum, CRef<CMSModSpecSet> Modset, int modnum, bool fixed);
73  void ConvertScanID(CRef<CSpectrum_query> sQuery, string SpecID, int query, int charge);
74  string GetProteinName(CRef<CMSPepHit> pHit);
75  void ConvertMSHitSet(CRef<CMSHitSet> pHitSet, CMsms_run_summary::TSpectrum_query& sQueries, CRef<CMSModSpecSet> Modset, set<int>& variableMods, CMSSearch& inOMSSA);
76 
77  typedef pair<char, double> TAminoAcidMassPair;
79 
82 
83  float m_scale;
84  int m_index;
85 };
86 
87 
88 END_SCOPE(omssa)
91 
92 #endif // MSMERGE_HPP
CMsms_pipeline_analysis –.
TAminoAcidMassMap m_aaMassMap
Definition: pepxml.hpp:80
CPepXML & operator=(const CPepXML &value)
float m_scale
Definition: pepxml.hpp:83
CPepXML(void)
Definition: pepxml.hpp:52
~CPepXML(void)
Definition: pepxml.hpp:54
map< char, double > TAminoAcidMassMap
Definition: pepxml.hpp:78
int m_index
Definition: pepxml.hpp:84
CPepXML(const CPepXML &value)
pair< char, double > TAminoAcidMassPair
Definition: pepxml.hpp:77
CMsms_pipeline_analysis Tparent
Definition: pepxml.hpp:47
set< char > m_staticModSet
Definition: pepxml.hpp:81
#define basename(path)
Definition: replacements.h:116
string GetProteinName(const CBioseq_Handle &seq)
Return protein name from corresponding Prot-ref feature.
Definition: sequence.cpp:356
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
#define NCBI_XOMSSA_EXPORT
Definition: ncbi_export.h:1355
list< CRef< CSpectrum_query > > TSpectrum_query
yy_size_t n
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
std::istream & in(std::istream &in_, double &x_)
static string query
Modified on Wed Apr 24 14:11:29 2024 by modify_doxy.py rev. 669887