NCBI C++ ToolKit
Seq_gap.hpp
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1 /* $Id: Seq_gap.hpp 71421 2016-03-03 18:29:40Z gotvyans $
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27 
28 /// @file Seq_gap.hpp
29 /// User-defined methods of the data storage class.
30 ///
31 /// This file was originally generated by application DATATOOL
32 /// using the following specifications:
33 /// 'seq.asn'.
34 ///
35 /// New methods or data members can be added to it if needed.
36 /// See also: Seq_gap_.hpp
37 
38 
39 #ifndef OBJECTS_SEQ_SEQ_GAP_HPP
40 #define OBJECTS_SEQ_SEQ_GAP_HPP
41 
42 
43 // generated includes
44 #include <objects/seq/Seq_gap_.hpp>
45 
47 
48 // generated classes
49 
50 
52 
53 template <class KeyType, class ValueType, class KeyCompare >
54 class CStaticArrayMap;
55 
56 BEGIN_objects_SCOPE // namespace ncbi::objects::
57 
58 /////////////////////////////////////////////////////////////////////////////
60 {
62 public:
63  // constructor
64  CSeq_gap(void);
65  // destructor
66  ~CSeq_gap(void);
67 
68  void ChangeType(TType linkage_type);
71  bool AddLinkageEvidence(CLinkage_evidence::TType evidence_type);
72 
73  /// indicates which linkage-evidences a given gap-type
74  /// can accept, if any
75  enum ELinkEvid {
76  /// only the "unspecified" linkage-evidence is allowed
78  /// no linkage-evidence is allowed
80  /// any linkage-evidence is allowed, and at least one is required
82  };
83  /// Holds information about a given gap-type string
84  struct SGapTypeInfo {
85  /// The underlying type that the string corresponds to
87  /// Indicates what linkage-evidences are compatible with this
89  };
90  /// Map a gap-type string to its information
91  /// Note that PCase_CStr, which means direct lookup is
92  /// NOT insensitive to case, etc.
94 
95  /// From a gap-type string, get the SGapTypeInfo,
96  /// insensitive to case, etc. This is NOT quite the same as calling
97  /// find on the TGapTypeMap.
98  ///
99  /// @returns NULL if not found
100  static const SGapTypeInfo * NameToGapTypeInfo(const CTempString & sName);
101  /// This is for if the user needs to get the gap-type string
102  /// to SGapTypeInfo info directly (For example, to iterate through
103  /// all possible types).
104  static const TGapTypeMap & GetNameToGapTypeInfoMap(void);
105 
106 
107 private:
108  // Prohibit copy constructor and assignment operator
111 
112 };
113 
114 /////////////////// CSeq_gap inline methods
115 
116 // constructor
117 inline
119 {
120 }
121 
122 
123 /////////////////// end of CSeq_gap inline methods
124 
125 
126 END_objects_SCOPE // namespace ncbi::objects::
127 
129 
130 
131 #endif // OBJECTS_SEQ_SEQ_GAP_HPP
132 /* Original file checksum: lines: 86, chars: 2354, CRC32: 25e00c0f */
User-defined methods of the data storage class.
Data storage class.
CSeq_gap_Base –.
Definition: Seq_gap_.hpp:77
CSeq_gap(void)
Definition: Seq_gap.hpp:118
ELinkEvid
indicates which linkage-evidences a given gap-type can accept, if any
Definition: Seq_gap.hpp:75
@ eLinkEvid_UnspecifiedOnly
only the "unspecified" linkage-evidence is allowed
Definition: Seq_gap.hpp:77
@ eLinkEvid_Forbidden
no linkage-evidence is allowed
Definition: Seq_gap.hpp:79
@ eLinkEvid_Required
any linkage-evidence is allowed, and at least one is required
Definition: Seq_gap.hpp:81
CSeq_gap(const CSeq_gap &value)
CStaticArrayMap< const char *, SGapTypeInfo, PCase_CStr > TGapTypeMap
Map a gap-type string to its information Note that PCase_CStr, which means direct lookup is NOT insen...
Definition: Seq_gap.hpp:93
CSeq_gap_Base Tparent
Definition: Seq_gap.hpp:61
CSeq_gap & operator=(const CSeq_gap &value)
class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...
Definition: static_map.hpp:175
CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...
Definition: tempstr.hpp:65
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define NCBI_SEQ_EXPORT
Definition: ncbi_export.h:825
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
void SetLinkageTypeScaffold(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)
SetLinkageTypeScaffold A special case of SetLinkageType.
void SetLinkageTypeLinkedRepeat(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)
void AddLinkageEvidence(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)
AddLinkageEvidence A function to add linkage evidence for gaps in a delta sequence.
Holds information about a given gap-type string.
Definition: Seq_gap.hpp:84
CSeq_gap::EType m_eType
The underlying type that the string corresponds to.
Definition: Seq_gap.hpp:86
ELinkEvid m_eLinkEvid
Indicates what linkage-evidences are compatible with this.
Definition: Seq_gap.hpp:88
Modified on Wed Apr 17 13:08:46 2024 by modify_doxy.py rev. 669887