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root/BioCocoa/BioCocoa/trunk/BCFoundation/BCFoundationDefines.h
Revision: 350
Committed: Wed Aug 19 16:45:07 2015 UTC (4 years, 9 months ago) by schristley
File size: 4208 byte(s)
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1 //
2 // BCFoundationDefines.h
3 // BioCocoa
4 //
5 // Created by Alexander Griekspoor on 9/12/04.
6 // Copyright (c) 2003-2009 The BioCocoa Project.
7 // All rights reserved.
8 //
9 // Redistribution and use in source and binary forms, with or without
10 // modification, are permitted provided that the following conditions
11 // are met:
12 // 1. Redistributions of source code must retain the above copyright
13 // notice, this list of conditions and the following disclaimer.
14 // 2. Redistributions in binary form must reproduce the above copyright
15 // notice, this list of conditions and the following disclaimer in the
16 // documentation and/or other materials provided with the distribution.
17 // 3. The name of the author may not be used to endorse or promote products
18 // derived from this software without specific prior written permission.
19 //
20 // THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
21 // IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
22 // OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
23 // IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
24 // INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
25 // NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
26 // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
27 // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
28 // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
29 // THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
30
31 /*!
32 @header
33 @abstract Global macros, enumerations and data structure for BioCocoa Foundation.
34 @discussion This header declares global macros, enumerations and data structures
35 for the BioCocoa Foundation Framework. Import the top-level header
36 file BCFoundation.h to get these definitions as well as the BioCocoa
37 Foundation classes.
38 */
39
40 #import <Foundation/NSString.h>
41
42 #ifndef _BC_FOUNDATION_DEFINES_H_
43 #define _BC_FOUNDATION_DEFINES_H_
44
45 #if 0
46 #pragma mark == GLOBAL DEFINES ==
47 #endif
48
49 #define hydrogenMonoisotopicMass 1.00782503
50 #define oxygenMonoisotopicMass 15.99491463
51 #define hydrogenAverageMass 1.01
52 #define oxygenAverageMass 15.996
53
54 #if 0
55 #pragma mark == GLOBAL ENUMs ==
56 #endif
57
58 /*!
59 @enum BCSequenceType
60 @abstract A list of sequence types, for readability
61 @constant BCSequenceTypeOther something we haven't thought of yet
62 @constant BCSequenceTypeDNA DNA
63 @constant BCSequenceTypeRNA RNA
64 @constant BCSequenceTypeProtein Protein
65 @constant BCSequenceTypeCodon Codon
66 */
67 typedef enum BCSequenceType {
68 BCSequenceTypeOther = 0,
69 BCSequenceTypeDNA = 1,
70 BCSequenceTypeRNA = 2,
71 BCSequenceTypeProtein = 3,
72 BCSequenceTypeCodon = 4
73 } BCSequenceType;
74
75
76 /*!
77 @enum BCGeneticCodeName
78 @abstract Provides an ordered list of possible genetic codes. Allows for a lightweight, readable implementation.
79 */
80 typedef enum BCGeneticCodeName {
81 BCUniversalCode = 1,
82 BCVertebrateMitochondrial = 2
83
84 } BCGeneticCodeName;
85
86
87
88 /*!
89 @enum BCMassType
90 @abstract A list of mass types, for calculating molecular masses
91 @constant BCMonoisotopic
92 @constant BCAverage
93 */
94 typedef enum BCMassType {
95 BCMonoisotopic = 1,
96 BCAverage = 2
97 } BCMassType;
98
99
100 /*!
101 @enum BCHydropathyType
102 @abstract A list of hydropathy types, for calculating hydropathy values
103 @constant BCKyteDoolittle
104 @constant BCHoppWoods
105 */
106 typedef enum BCHydropathyType {
107 BCKyteDoolittle = 1,
108 BCHoppWoods = 2
109 } BCHydropathyType;
110
111 /*!
112 @enum BCSecondaryStructureType
113 @abstract A list of secondary structure types, for readability
114 @constant BCAnyStructure something we haven't thought of yet
115 @constant BCHelix Alpha helix
116 @constant BCSheet Beta sheet
117 @constant BCTurn Turn
118 */
119 typedef enum BCSecondaryStructureType {
120 BCAnyStructure = 0,
121 BCHelix = 1,
122 BCSheet = 2,
123 BCTurn = 3
124 } BCSecondaryStructureType;
125
126
127 #if 0
128 #pragma mark == GLOBAL STRING CONSTANTS ==
129 #endif
130
131 /*!
132 @constant BCSequenceID
133 @abstract Annotation key for the sequence id
134 */
135 extern NSString * const BCSequenceID;
136
137 #endif // _BC_FOUNDATION_DEFINES_H_