NCBI C++ ToolKit
Delta_ext.hpp
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1 /* $Id: Delta_ext.hpp 63181 2014-06-05 13:07:19Z gotvyans $
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27 
28 /// @file Delta_ext.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: Delta_ext_.hpp
37 
38 
39 #ifndef OBJECTS_SEQ_DELTA_EXT_HPP
40 #define OBJECTS_SEQ_DELTA_EXT_HPP
41 
42 
43 // generated includes
45 #include <objects/seq/Seq_data.hpp>
46 #include <objects/seq/Seq_inst.hpp>
48 
49 // generated classes
50 
52 
53 BEGIN_objects_SCOPE // namespace ncbi::objects::
54 
55 class CDelta_seq;
56 class CSeq_id;
57 
58 /////////////////////////////////////////////////////////////////////////////
60 {
62 public:
63  // constructor
64  CDelta_ext(void);
65  // destructor
66  ~CDelta_ext(void);
67 
68  /// add a literal segment at the end
69  /// this variant adds a gap literal
71 
72  /// add a literal segment at the end
73  /// this variant adds a non-gap literal
74  CDelta_seq& AddLiteral(const CTempString& iupac_seq, CSeq_inst::EMol mol,
75  bool do_pack = true);
76 
77  /// add a chunk of sequence, splitting it as necessary for the
78  /// sake of compactness (isolating ambiguous portions and optionally gaps)
79  void AddAndSplit(const CTempString& src, CSeq_data::E_Choice format,
80  TSeqPos length /* in residues */, bool gaps_ok = false,
81  bool allow_packing = true);
82 
83  /// add a segment that refers to another segment
84  CDelta_seq& AddSeqRange(const CSeq_id& id, TSeqPos from, TSeqPos to,
85  ENa_strand strand = eNa_strand_plus);
86 
87 private:
88  // Prohibit copy constructor and assignment operator
91 
92 };
93 
94 /////////////////// CDelta_ext inline methods
95 
96 // constructor
97 inline
99 {
100 }
101 
102 
103 /////////////////// end of CDelta_ext inline methods
104 
105 
106 END_objects_SCOPE // namespace ncbi::objects::
107 
109 
110 #endif // OBJECTS_SEQ_DELTA_EXT_HPP
111 /* Original file checksum: lines: 94, chars: 2559, CRC32: 732ab450 */
Data storage class.
CDelta_ext_Base –.
Definition: Delta_ext_.hpp:77
CDelta_ext(const CDelta_ext &value)
CDelta_ext_Base Tparent
Definition: Delta_ext.hpp:61
CDelta_ext & operator=(const CDelta_ext &value)
CDelta_ext(void)
Definition: Delta_ext.hpp:98
CDelta_seq –.
Definition: Delta_seq.hpp:66
CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...
Definition: tempstr.hpp:65
char value[7]
Definition: config.c:431
void AddLiteral(CSeq_inst &inst, const string &seq, CSeq_inst::EMol mol_class)
unsigned int TSeqPos
Type for sequence locations and lengths.
Definition: ncbimisc.hpp:875
#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
ENa_strand
strand of nucleic acid
Definition: Na_strand_.hpp:64
@ eNa_strand_plus
Definition: Na_strand_.hpp:66
E_Choice
Choice variants.
Definition: Seq_data_.hpp:102
EMol
molecule class in living organism
Definition: Seq_inst_.hpp:108
int len
static Format format
Definition: njn_ioutil.cpp:53
Modified on Thu Feb 29 12:20:10 2024 by modify_doxy.py rev. 669887