NCBI C++ ToolKit
Seq_data.cpp
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1 /* $Id: Seq_data.cpp 33815 2007-05-04 17:18:18Z kazimird $
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 data definition file
34  * 'seq.asn'.
35  */
36 
37 // standard includes
38 
39 // generated includes
40 #include <ncbi_pch.hpp>
41 #include <objects/seq/Seq_data.hpp>
42 
43 // additional includes
44 #include <objects/seq/IUPACaa_.hpp>
45 #include <objects/seq/IUPACna.hpp>
46 #include <objects/seq/NCBI2na_.hpp>
47 #include <objects/seq/NCBI4na_.hpp>
48 #include <objects/seq/NCBI8aa_.hpp>
49 #include <objects/seq/NCBI8na_.hpp>
50 #include <objects/seq/NCBIeaa_.hpp>
51 #include <objects/seq/NCBIpaa_.hpp>
52 #include <objects/seq/NCBIpna_.hpp>
54 #include <corelib/ncbiexpt.hpp>
55 
56 // generated classes
57 
59 
60 BEGIN_objects_SCOPE // namespace ncbi::objects::
61 
62 // constructor
63 CSeq_data::CSeq_data(const string& value, E_Choice index)
64 {
65 
66 
67  // Does value have to be validated
68  // create seq type data holder
69  switch (index) {
70  case e_Iupacna:
71  case e_Iupacaa:
72  case e_Ncbieaa:
73  DoConstruct (value, index);
74  break;
75 
76  case e_Ncbi2na:
77  case e_Ncbi4na:
78  case e_Ncbi8na:
79  case e_Ncbipna:
80  case e_Ncbi8aa:
81  case e_Ncbipaa:
82  case e_Ncbistdaa:
83  {
84  vector< char > v;
85  v.resize (value.size());
86  memcpy(&v[0], value.c_str(), value.size());
87  DoConstruct (v, index);
88  break;
89  }
90  default:
91  // throw error
93  "CSeq_data constructor: Invalid E_Choice index");
94  }
95 }
96 
97 CSeq_data::CSeq_data(const vector< char >& value, E_Choice index)
98 {
99  // Does value have to be validated
100  // create seq type data holder
101  switch (index) {
102  case e_Iupacna:
103  case e_Iupacaa:
104  case e_Ncbieaa:
105  {
106  string s;
107  s.assign (&value[0], value.size());
108  DoConstruct (s, index);
109  break;
110  }
111  case e_Ncbi2na:
112  case e_Ncbi4na:
113  case e_Ncbi8na:
114  case e_Ncbipna:
115  case e_Ncbi8aa:
116  case e_Ncbipaa:
117  case e_Ncbistdaa:
118  DoConstruct (value, index);
119  break;
120 
121  default:
122  // throw error
124  "CSeq_data constructor: Invalid E_Choice index");
125  }
126 }
127 
128 // destructor
130 {
131 }
132 
133 void CSeq_data::DoConstruct(const string& value, E_Choice index)
134 {
135 
136  switch (index) {
137  case e_Iupacna:
139  break;
140  case e_Iupacaa:
142  break;
143  case e_Ncbieaa:
145  break;
146  default:
147  // throw an error
149  "CSeq_data::DoConstruct: Invalid E_Choice index");
150  }
151 }
152 
153 void CSeq_data::DoConstruct(const vector< char >& value, E_Choice index)
154 {
155  switch (index) {
156  case e_Ncbi2na:
157  SetNcbi2na().Set() = value;
158  break;
159  case e_Ncbi4na:
160  SetNcbi4na().Set() = value;
161  break;
162  case e_Ncbi8na:
163  SetNcbi8na().Set() = value;
164  break;
165  case e_Ncbipna:
166  SetNcbipna().Set() = value;
167  break;
168  case e_Ncbi8aa:
169  SetNcbi8aa().Set() = value;
170  break;
171  case e_Ncbipaa:
172  SetNcbipaa().Set() = value;
173  break;
174  case e_Ncbistdaa:
175  SetNcbistdaa().Set() = value;
176  break;
177  default:
178  // throw an error
180  "CSeq_data::DoConstruct: Invalid E_Choice index");
181  }
182 }
183 
184 END_objects_SCOPE // namespace ncbi::objects::
185 
187 
188 /* Original file checksum: lines: 64, chars: 1872, CRC32: 4f4e2fd */
Data storage class.
User-defined methods of the data storage class.
Data storage class.
Data storage class.
Data storage class.
Data storage class.
Data storage class.
Data storage class.
Data storage class.
Data storage class.
CIUPACaa –.
Definition: IUPACaa.hpp:66
CIUPACna –.
Definition: IUPACna.hpp:66
CNCBIeaa –.
Definition: NCBIeaa.hpp:66
void DoConstruct(const string &value, E_Choice index)
Definition: Seq_data.cpp:133
CSeq_data(void)
Definition: Seq_data.hpp:79
~CSeq_data(void)
Definition: Seq_data.cpp:129
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
Definition: ncbiexpt.hpp:704
TPrim & Set(void)
Definition: serialbase.hpp:351
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
TNcbipna & SetNcbipna(void)
Select the variant.
Definition: Seq_data_.hpp:617
TNcbi8aa & SetNcbi8aa(void)
Select the variant.
Definition: Seq_data_.hpp:637
TNcbipaa & SetNcbipaa(void)
Select the variant.
Definition: Seq_data_.hpp:677
TNcbieaa & SetNcbieaa(void)
Select the variant.
Definition: Seq_data_.hpp:657
E_Choice
Choice variants.
Definition: Seq_data_.hpp:102
TIupacna & SetIupacna(void)
Select the variant.
Definition: Seq_data_.hpp:517
TNcbi8na & SetNcbi8na(void)
Select the variant.
Definition: Seq_data_.hpp:597
TNcbistdaa & SetNcbistdaa(void)
Select the variant.
Definition: Seq_data_.hpp:697
TNcbi2na & SetNcbi2na(void)
Select the variant.
Definition: Seq_data_.hpp:557
TNcbi4na & SetNcbi4na(void)
Select the variant.
Definition: Seq_data_.hpp:577
TIupacaa & SetIupacaa(void)
Select the variant.
Definition: Seq_data_.hpp:537
@ e_Ncbipna
nucleic acid probabilities
Definition: Seq_data_.hpp:109
@ e_Ncbieaa
extended ASCII 1 letter aa codes
Definition: Seq_data_.hpp:111
@ e_Ncbistdaa
consecutive codes for std aas
Definition: Seq_data_.hpp:113
@ e_Ncbi2na
2 bit nucleic acid code
Definition: Seq_data_.hpp:106
@ e_Iupacna
IUPAC 1 letter nuc acid code.
Definition: Seq_data_.hpp:104
@ e_Ncbipaa
amino acid probabilities
Definition: Seq_data_.hpp:112
@ e_Ncbi8na
8 bit extended nucleic acid code
Definition: Seq_data_.hpp:108
@ e_Ncbi4na
4 bit nucleic acid code
Definition: Seq_data_.hpp:107
@ e_Iupacaa
IUPAC 1 letter amino acid code.
Definition: Seq_data_.hpp:105
@ e_Ncbi8aa
8 bit extended amino acid codes
Definition: Seq_data_.hpp:110
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
Defines NCBI C++ exception handling.
Modified on Fri Jun 14 16:48:29 2024 by modify_doxy.py rev. 669887