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
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
|
//
// BCToolTranslator.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 "BCToolTranslator.h"
#import "BCNucleotideDNA.h"
#import "BCAminoAcid.h"
#import "BCSequence.h"
#import "BCSequenceCodon.h"
#import "BCCodonDNA.h"
#import "BCGeneticCode.h"
@implementation BCToolTranslator
- (BCToolTranslator *) initWithSequence: (BCSequence *)list {
self = [super initWithSequence: list];
// set some defaults
if ( self != nil ) {
readingFrame = 1;
codeName = BCUniversalCode;
}
return self;
}
- (int) readingFrame {
return readingFrame;
}
- (void) setReadingFrame: (int)theFrame {
// this has got to be between -3 and 3, skipping 0.
// we default to 1
if ( theFrame > 3 || theFrame == 0 )
readingFrame = 1;
else if ( theFrame < -3 )
readingFrame = -1;
else
readingFrame = theFrame;
}
- (BCGeneticCodeName) codeName {
return codeName;
}
- (void)setCodeName: (BCGeneticCodeName)aName {
codeName = aName;
}
+ (BCToolTranslator *) translatorToolWithSequence: (BCSequence *)list {
BCToolTranslator *translatorTool = [[BCToolTranslator alloc] initWithSequence: list];
return [translatorTool autorelease];
}
- (BCSequenceCodon *) codonTranslation {
// check for the right kind of sequence
if ( [sequence sequenceType] != BCSequenceTypeDNA && [sequence sequenceType] != BCSequenceTypeRNA )
return nil;
// next, grab the genetic code
NSArray *theCode = [BCGeneticCode geneticCode: codeName forSequenceType: [sequence sequenceType]];
if ( theCode == nil || [theCode count] == 0 )
return nil;
// adjust the sequence to reflect the desired frame
BCSequence *tempSequence;
if ( readingFrame < 0 )
tempSequence = [sequence reverse];
else tempSequence = sequence;
NSArray *theSequenceArray;
if ( abs( readingFrame ) == 1 )
theSequenceArray = [tempSequence symbolArray];
else if ( abs( readingFrame ) == 2 )
theSequenceArray = [tempSequence subSymbolArrayInRange: NSMakeRange( 1, [sequence length] - 1) ];
else
theSequenceArray = [tempSequence subSymbolArrayInRange: NSMakeRange( 2, [sequence length] - 2) ];
int codonCount = [theCode count];
int loopCounter, innerCounter;
NSMutableArray *returnArray = [NSMutableArray array];
NSArray *tempCodon;
BCCodonDNA *aCodon;
BOOL oneMatch;
for ( loopCounter = 0 ; loopCounter + 2 < [sequence 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]];
}
NSString *frameRep;
if ( readingFrame > 0 )
frameRep = [NSString stringWithFormat: @"+%i", readingFrame];
else
frameRep = [NSString stringWithFormat: @"-%i", readingFrame];
return [[[BCSequenceCodon alloc] initWithCodonArray: returnArray geneticCode: codeName frame: frameRep] autorelease];
}
- (NSDictionary *) allCodonTranslations {
// we hang onto the frame that's set because we're going to change it repeatedly
int holdingInt = readingFrame;
int loopCounter = -4;
NSMutableDictionary *theReturn = [NSMutableDictionary dictionary];
BCSequenceCodon *codonSequence;
while ( loopCounter < 3) {
loopCounter++;
if ( loopCounter == 0 )
loopCounter++;
readingFrame = loopCounter;
codonSequence = [self codonTranslation];
[theReturn setObject: codonSequence forKey: [codonSequence readingFrame]];
}
readingFrame = holdingInt;
return theReturn;
}
@end
|
