1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
|
//
// BCCodon.m
// BioCocoa
//
// Created by John Timmer on 8/31/04.
// Copyright (c) 2003-2009 The BioCocoa Project.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions
// are met:
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// 3. The name of the author may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
// NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
// THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#import "BCCodon.h"
#import "BCSequence.h"
#import "BCAminoAcid.h"
#import "BCSymbol.h"
@implementation BCCodon
- (BCAminoAcid *) codedAminoAcid {
return codedAminoAcid;
}
- (BCSequence *) triplet {
NSArray *tempArray = [NSArray arrayWithObjects: firstBase, secondBase, wobbleBase, nil];
return [BCSequence sequenceWithSymbolArray: tempArray];
}
- (NSString *) aminoAcidSymbolString {
if ( codedAminoAcid == nil )
return @"*";
else
return [codedAminoAcid symbolString];
}
- (NSString *) tripletString {
NSMutableString *returnString = [NSMutableString stringWithString: [firstBase symbolString]];
[returnString appendString: [secondBase symbolString]];
[returnString appendString: [wobbleBase symbolString]];
return [[returnString copy] autorelease];
}
- (NSString *)symbolString {
return [[self aminoAcidSymbolString] stringByAppendingString: [NSString stringWithFormat: @"(%@)", [self tripletString]]];
}
- (NSString *) description {
return [self tripletString];
}
- (id)copyWithZone:(NSZone *)zone {
return self;
}
@end
|
