1 /* $Id: Seq_interval.hpp 256179 2011-03-02 18:19:45Z vasilche $
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
12 * Government have not placed any restriction on its use or reproduction.
13 *
14 * Although all reasonable efforts have been taken to ensure the accuracy
15 * and reliability of the software and data, the NLM and the U.S.
16 * Government do not and cannot warrant the performance or results that
17 * may be obtained by using this software or data. The NLM and the U.S.
18 * Government disclaim all warranties, express or implied, including
19 * warranties of performance, merchantability or fitness for any particular
20 * purpose.
21 *
22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Author: .......
27 *
28 * File Description:
29 * .......
30 *
31 * Remark:
32 * This code was originally generated by application DATATOOL
33 * using specifications from the ASN data definition file
34 * 'seqloc.asn'.
35 */
36
37 #ifndef OBJECTS_SEQLOC_SEQ_INTERVAL_HPP
38 #define OBJECTS_SEQLOC_SEQ_INTERVAL_HPP
39
40
41 // generated includes
42 #include <objects/seqloc/Seq_interval_.hpp>
43
44 // generated classes
45
46 BEGIN_NCBI_SCOPE
47
48 BEGIN_objects_SCOPE // namespace ncbi::objects::
49
50 class NCBI_SEQLOC_EXPORT CSeq_interval : public CSeq_interval_Base
51 {
52 typedef CSeq_interval_Base Tparent;
53 public:
54 // See also related function in util/sequence.hpp:
55 //
56 // bool IsValid(const CSeq_interval&, CScope*)
57 //
58
59 // constructor
60 CSeq_interval(void);
61 CSeq_interval(TId& id, TFrom from, TTo to, TStrand strand = eNa_strand_unknown);
62
63 // destructor
64 ~CSeq_interval(void);
65
66 // Get the length of the interval
67 TSeqPos GetLength(void) const;
68
69 // check start or stop end of location for e_Lim fuzz
70 bool IsPartialStart(ESeqLocExtremes ext) const;
71 bool IsPartialStop (ESeqLocExtremes ext) const;
72
73 // set / remove e_Lim fuzz on start or stop end
74 void SetPartialStart(bool val, ESeqLocExtremes ext);
75 void SetPartialStop (bool val, ESeqLocExtremes ext);
76
77 /// check if parts of the seq-loc are missing
78 bool IsTruncatedStart(ESeqLocExtremes ext) const;
79 bool IsTruncatedStop (ESeqLocExtremes ext) const;
80
81 /// set / remove e_Lim fuzz on start or stop
82 /// (tl/tr - indicating removed parts of the seq-loc)
83 void SetTruncatedStart(bool val, ESeqLocExtremes ext);
84 void SetTruncatedStop (bool val, ESeqLocExtremes ext);
85
86 TSeqPos GetStart(ESeqLocExtremes ext) const;
87 TSeqPos GetStop (ESeqLocExtremes ext) const;
88
89 // Flip the strand (e.g. plus to minus)
90 void FlipStrand(void);
91
92 private:
93 // Prohibit copy constructor & assignment operator
94 CSeq_interval(const CSeq_interval&);
95 CSeq_interval& operator= (const CSeq_interval&);
96
97 bool x_IsMinusStrand(void) const;
98 };
99
100
101
102 /////////////////// CSeq_interval inline methods
103
104 // constructor
105 inline
CSeq_interval(void)106 CSeq_interval::CSeq_interval(void)
107 {
108 }
109
110
111 inline
CSeq_interval(TId & id,TFrom from,TTo to,TStrand strand)112 CSeq_interval::CSeq_interval(TId& id, TFrom from, TTo to, TStrand strand)
113 {
114 SetId(id);
115 SetFrom(from);
116 SetTo(to);
117 if ( strand != eNa_strand_unknown ) {
118 SetStrand(strand);
119 }
120 }
121
122
123 // length return
124 inline
GetLength(void) const125 TSeqPos CSeq_interval::GetLength(void) const
126 {
127 return GetTo() >= GetFrom() ? ((GetTo() - GetFrom()) + 1) : 0;
128 }
129
130 /////////////////// end of CSeq_interval inline methods
131
132
133 END_objects_SCOPE // namespace ncbi::objects::
134
135 END_NCBI_SCOPE
136
137
138 #endif // OBJECTS_SEQLOC_SEQ_INTERVAL_HPP
139