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
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
|
//
// BCSymbolSet.h
// BioCocoa
//
// Created by Alexander Griekspoor on Fri Sep 10 2004.
// 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.
/*!
@header
@abstract A collection of BCSymbols of the same type.
*/
#import <Foundation/Foundation.h>
#import "BCFoundationDefines.h"
@class BCSymbol;
/*!
@class BCSymbolSet
@abstract A collection of BCSymbols of the same type
@discussion BCSymbolSet objects provide a lot of flexibility for the user
* of the framework when creating and manipulating sequence objects.
* They can be thought of as filters, by restricting a sequence object
* to a certain set of symbols. For instance, a dna sequence could be
* created that will only accept the non-ambiguous bases A, T, G, C
* but not the compound symbols like P and Y.
*
* BCSymbolSet objects are immutable. The class object provides a number
* of factory methods for prebuilt symbol sets such as
* '+ (BCSymbolSet *)dnaSymbolSet' and '+ (BCSymbolSet *)dnaStrictSymbolSet'.
* It is recommanded to use these methods when creating a symbol set
* supported by the class. For other cases, a new BCSymbolSet can easily
* be created from an array of symbols, or by combining existing symbol sets.
* Because BCSymbolSet are immutable, new objects have to be created to
* modify existing symbol sets.
*/
@interface BCSymbolSet : NSObject <NSCopying>
{
NSSet *symbolSet;
BCSequenceType sequenceType;
}
#if 0
#pragma mark == INITIALIZATION METHODS ==
#endif
/*!
@method initWithArray:sequenceType:
@abstract initialize symbol set with an array of symbols and a sequence type
@discussion Designated initializer.
*/
- (id)initWithArray:(NSArray *)symbols sequenceType:(BCSequenceType)type;
/*!
@method initWithArray:
@abstract initialize symbol set with an array of symbols
@discussion Decides the sequence type based on the first symbol in the passed array.
*/
- (id)initWithArray:(NSArray *)symbols;
/*!
@method initWithString:sequenceType:
@abstract initialize symbol set with an array of symbols and a sequence type
@discussion Initializes the symbol sets using a string, by scanning the characters
and generating symbols of the right sequence type
e.g. A --> Adenosine if sequence type is DNA, Alanine if protein
*/
- (id)initWithString:(NSString *)stringOfCharacters sequenceType:(BCSequenceType)type;
//factory methods - return an autoreleased object
+ (BCSymbolSet *)symbolSetWithArray:(NSArray *)symbols;
+ (BCSymbolSet *)symbolSetWithArray:(NSArray *)symbols sequenceType:(BCSequenceType)type;
+ (BCSymbolSet *)symbolSetWithString:(NSString *)aString sequenceType:(BCSequenceType)type;
+ (BCSymbolSet *)symbolSetForSequenceType:(BCSequenceType)type;
#if 0
#pragma mark == FACTORY METHODS FOR PREBUILT SETS ==
#endif
+ (BCSymbolSet *)dnaSymbolSet;
+ (BCSymbolSet *)dnaStrictSymbolSet;
+ (BCSymbolSet *)rnaSymbolSet;
+ (BCSymbolSet *)rnaStrictSymbolSet;
+ (BCSymbolSet *)proteinSymbolSet;
+ (BCSymbolSet *)proteinStrictSymbolSet;
+ (BCSymbolSet *)unknownSymbolSet;
+ (BCSymbolSet *)unknownAndGapSymbolSet;
#if 0
#pragma mark == GENERAL METHODS ==
#endif
- (NSSet *)symbolSet;
- (NSArray *)allSymbols;
- (NSCharacterSet *)characterSetRepresentation;
- (NSString *)stringRepresentation;
- (BCSequenceType)sequenceType;
- (BOOL)containsCharactersFromString: (NSString *) aString;
- (BOOL)containsSymbol:(BCSymbol *)aSymbol; // aSymbol=W and contains A --> no
- (BOOL)containsSymbolRepresentedBy:(BCSymbol *)aSymbol; // aSymbol=W and contains A --> yes
- (BOOL)containsAllSymbolsRepresentedBy:(BCSymbol *)aSymbol; // aSymbol=W and contains A,T --> yes
- (BOOL)containsSymbolRepresenting:(BCSymbol *)aSymbol; // aSymbol=A and contains W --> yes
//creating new symbol sets from existing ones
- (BCSymbolSet *)symbolSetByFormingUnionWithSymbolSet:(BCSymbolSet *)otherSet;
- (BCSymbolSet *)symbolSetByFormingIntersectionWithSymbolSet:(BCSymbolSet *)otherSet;
/* TO DO (or not to do?)
- (BCSymbolSet *)complementSet;
- (BCSymbolSet *)expandedSet; // ambigous symbols expanded
*/
- (BOOL)isSupersetOfSet:(BCSymbolSet *)theOtherSet;
//filtering an array of symbols
//returned array = without the unknown symbols
- (NSArray *)arrayByRemovingUnknownSymbolsFromArray:(NSArray *)anArray;
- (NSString *)stringByRemovingUnknownCharsFromString:(NSString *)aString;
- (NSData *)dataByRemovingUnknownCharsFromData:(NSData *)aData;
//returns nil if symbol unknown
- (BCSymbol *)symbolForChar:(unsigned char)aChar;
//NSCopying formal protocol
- (id)copyWithZone:(NSZone *)zone;
//BCSymbolSet is immutable
//Keep this for a future BCMutableSymbolSet, if ever needed
/*
////////////////////////////////////////////////////////////////////////////
//
#pragma mark
#pragma mark MUTABILITY METHODS
//
// MUTABILITY METHODS
////////////////////////////////////////////////////////////////////////////
- (void)addSymbol:(BCSymbol *)symbol;
- (void)addSymbols:(NSArray *)symbols;
- (void)addSymbolsInString:(NSString *)aString;
- (void)removeSymbol:(BCSymbol *)symbol;
- (void)removeSymbols:(NSArray *)symbols;
- (void)removeSymbolsInString:(NSString *)aString;
- (void)formUnionWithSymbolSet:(BCSymbolSet *)otherSet;
- (void)formIntersectionWithSymbolSet:(BCSymbolSet *)otherSet;
- (void)makeComplementary;
*/
@end
|
