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
|
//
// BCToolTranslatorDNA.m
// BioCocoa
//
// Created by John Timmer on 8/29/04.
// 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 "BCToolTranslatorDNA.h"
#import "BCNucleotideDNA.h"
#import "BCAminoAcid.h"
#import "BCSequenceCodon.h"
#import "BCCodonDNA.h"
#import "BCGeneticCode.h"
@implementation BCToolTranslatorDNA
+ (BCToolTranslatorDNA *) dnaTranslatorToolWithSequence: (BCSequence *) list
{
BCToolTranslatorDNA *translatorTool = [[BCToolTranslatorDNA alloc] initWithSequence: list];
return [translatorTool autorelease];
}
/*
+ (BCSequenceCodon *) translateSequence: (BCSequence*) entry usingGeneticCode: (BCGeneticCodeName) codeName
{
return nil;
}
*/
- (NSArray *)translateDNASequence
{
return [BCToolTranslatorDNA translateDNASequence: [self sequence] usingGeneticCode: [self codeName]];
}
- (BCGeneticCodeName) codeName
{
return codeName;
}
- (void)setCodeName: (BCGeneticCodeName)aName
{
codeName = aName;
}
+ (id) translateSequence: (BCSequence*) entry usingGeneticCode: (BCGeneticCodeName) codeName {
return nil;
}
+ (NSArray *) translateDNASequence: (BCSequence *) entry usingGeneticCode: (BCGeneticCodeName) codeName {
NSArray *theCode = [BCGeneticCode universalGeneticCodeDNA];
if ( theCode == nil )
return nil;
int codonCount = [theCode count];
int loopCounter, innerCounter;
NSArray *theSequenceArray = [entry symbolArray];
NSMutableArray *returnArray = [NSMutableArray array];
NSArray *tempCodon;
BCCodonDNA *aCodon;
BOOL oneMatch;
for ( loopCounter = 0 ; loopCounter + 2 < [entry length] ; loopCounter = loopCounter + 3 ) {
tempCodon = [theSequenceArray subarrayWithRange: NSMakeRange( loopCounter, 3 ) ];
oneMatch = NO;
for ( innerCounter = 0 ; innerCounter < codonCount ; innerCounter++ ) {
aCodon = [theCode objectAtIndex: innerCounter];
if ( [aCodon matchesTriplet: tempCodon] ) {
[returnArray addObject: aCodon];
oneMatch = YES;
break;
}
}
if ( !oneMatch )
[returnArray addObject: [BCCodonDNA unmatched]];
}
return [[returnArray copy] autorelease];
}
@end
|
