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
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
|
//
// 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 "BCCodonDNA.h"
#import "BCSequence.h"
#import "BCAminoAcid.h"
#import "BCSymbol.h"
#import "BCNucleotideDNA.h"
static BCCodonDNA *unmatchedCodon = nil;
@implementation BCCodonDNA
- (BCCodonDNA *)initWithDNASequenceString: (NSString *)sequenceString andAminoAcidString: (NSString *)aaString {
self = [super init];
if ( self == nil )
return self;
if ( ![aaString isEqualToString: @"stop"] )
codedAminoAcid = [BCAminoAcid performSelector: NSSelectorFromString( aaString )];
else
codedAminoAcid = nil;
if ( [sequenceString length] != 3)
return nil;
firstBase = [BCNucleotideDNA symbolForChar: [sequenceString characterAtIndex: 0]];
if ( firstBase == nil || firstBase == [BCNucleotideDNA undefined] )
return nil;
secondBase = [BCNucleotideDNA symbolForChar: [sequenceString characterAtIndex: 1]];
if ( secondBase == nil || secondBase == [BCNucleotideDNA undefined] )
return nil;
wobbleBase = [BCNucleotideDNA symbolForChar: [sequenceString characterAtIndex: 2]];
if ( wobbleBase == nil || wobbleBase == [BCNucleotideDNA undefined] )
return nil;
return self;
}
- (BCCodon *) init {
return nil;
}
//- (void) dealloc {
//
// [super release];
//}
+ (BCCodonDNA *)unmatched {
if ( unmatchedCodon == nil)
unmatchedCodon = [[BCCodonDNA alloc] initWithDNASequenceString: @"---" andAminoAcidString: @"undefined"];
return unmatchedCodon;
}
- (BOOL) matchesTriplet: (NSArray *)entry {
if ( ![(BCNucleotideDNA *)[entry objectAtIndex: 0] isRepresentedBySymbol: (BCNucleotideDNA *)firstBase] )
return NO;
if ( ![(BCNucleotideDNA *)[entry objectAtIndex: 1] isRepresentedBySymbol: (BCNucleotideDNA *)secondBase] )
return NO;
if ( ![(BCNucleotideDNA *)[entry objectAtIndex: 2] isRepresentedBySymbol: (BCNucleotideDNA *)wobbleBase] )
return NO;
return YES;
}
- (BCSequence *) triplet {
NSArray *tempArray = [NSArray arrayWithObjects: firstBase, secondBase, wobbleBase, nil];
return [BCSequence sequenceWithSymbolArray: tempArray];
}
@end
|
