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// BCNucleotideDNA.h
// BioCocoa
//
// Created by John Timmer on 8/11/04.
// 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.
/*!
@header
@abstract Provides in-memory representations of DNA bases.
*/
#import <Foundation/Foundation.h>
#import "BCNucleotide.h"
@class BCNucleotideRNA;
/*!
@class BCNucleotideDNA
@abstract All DNA bases are handled through this single class
@discussion This class provides in-memory representations of DNA bases.
* Through class methods and static variables, single application wide representations
* of each individual base and the ambiguous base representations are provided to all
* BioCocoa applications. Access to an individual base is provided by methods such as:
* [BCNucleotideDNA adenine];
* [BCNucleotideDNA purine];
* Repesentations of a non-base and gap characters (for alignments) are also available.
* Typically, bases are not handled directly, but rather through their container objects,
* BCSequence subclasses.
*
* Why not use strings?
* Unicode characters are 16bit, while pointers on MacOS-X are (currently) 32 bit. In
* the overall picture, memory differences are not significant. In return, each base provides
* detailed information about complements, ambiguity, etc. which would otherwise need to be coded
* by hand.
*
* Initialization of base data
* Details of base information and relationships are read from the "nucleotides.plist" file
* within the Framework bundle. Loss or alteration of this file will cause all DNA-based programs
* to fail. References to other bases (ie - the complement) are retained as string-formatted selectors
* until they are needed, at which point they are used to generate pointers to the other bases.
* Custom bases can be generated using this file as an example - they remain stored in an NSDictionary.
*
* Individual bases are obtained using their named class method, or by sending an appropriate symbol to the
* "symbolForChar:" class method.
*/
@interface BCNucleotideDNA : BCNucleotide
{
}
#if 0
#pragma mark == CLASS METHODS ==
#endif
/*!
@method initBases
@abstract Used internaly to generate the full set of base objects.
*/
+ (void) initBases;
/*!
@method symbolForChar:
@abstract Returns a BCNucleotideDNA item representing the base submitted
*/
+ (id) symbolForChar: (unsigned char)symbol;
/*!
@method objectForSavedRepresentation:
@abstract Returns a BCNucleotideDNA object representing the base submitted
@discussion all BC classes should implement a "savableRepresentation" and an
* "objectForSavedRepresentation" method to allow archiving/uncarchiving in
* .plist formatted files.
*/
+ (id) objectForSavedRepresentation: (NSString *)aSymbol;
/*!
@method adenosine
@abstract Obtains a reference to the single adenosine representation
*/
+ (BCNucleotideDNA *) adenosine;
/*!
@method thymidine
@abstract Obtains a reference to the single thymidine representation
*/
+ (BCNucleotideDNA *) thymidine;
/*!
@method cytidine
@abstract Obtains a reference to the single cytidine representation
*/
+ (BCNucleotideDNA *) cytidine;
/*!
@method guanidine
@abstract Obtains a reference to the single guanidine representation
*/
+ (BCNucleotideDNA *) guanidine;
/*!
@method anyBase
@abstract Obtains a reference to the single N representation
*/
+ (BCNucleotideDNA *) anyBase;
/*!
@method purine
@abstract Obtains a reference to the single purine representation
*/
+ (BCNucleotideDNA *) purine;
/*!
@method pyrimidine
@abstract Obtains a reference to the single pyrimidine representation
*/
+ (BCNucleotideDNA *) pyrimidine;
/*!
@method strong
@abstract Obtains a reference to the single strong-bond representation
*/
+ (BCNucleotideDNA *) strong;
/*!
@method weak
@abstract Obtains a reference to the single weak-bond representation
*/
+ (BCNucleotideDNA *) weak;
/*!
@method M
@abstract Obtains a reference to the single M (A, C) representation
*/
+ (BCNucleotideDNA *) amino;
/*!
@method K
@abstract Obtains a reference to the single K (A, C) representation
*/
+ (BCNucleotideDNA *) keto;
/*!
@method H
@abstract Obtains a reference to the single H (A, C, T) representation
*/
+ (BCNucleotideDNA *) H;
/*!
@method V
@abstract Obtains a reference to the single V (A, C, G) representation
*/
+ (BCNucleotideDNA *) V;
/*!
@method D
@abstract Obtains a reference to the single D (A, G, T) representation
*/
+ (BCNucleotideDNA *) D;
/*!
@method B
@abstract Obtains a reference to the single D (C, G, T) representation
*/
+ (BCNucleotideDNA *) B;
/*!
@method gap
@abstract Obtains a reference to the single representation of a gap, for alignments
*/
+ (BCNucleotideDNA *) gap;
/*!
@method undefined
@abstract Obtains a reference to the single representation of any non-base character
*/
+ (BCNucleotideDNA *) undefined;
/*!
@method customBase:
@abstract Obtains a reference to a user-defined base
*/
+ (BCNucleotideDNA *) customBase: (NSString *)baseName;
#if 0
#pragma mark == OBJECT METHODS ==
#endif
#if 0
#pragma mark == INITIALIZATION METHODS ==
#endif
/*!
@method initWithSymbolChar:
@abstract designated initialization method
@discussion Given a symbol, this method generates the appropriate Nucleotide representation using
* information in the bundle's "nucleotides.plist" file.
*/
- (id)initWithSymbolChar:(unsigned char)aChar;
#if 0
#pragma mark == BASE INFORMATION METHODS ==
#endif
/*!
@method isBase
@abstract Returns NO if the receiver is a gap or undefined
*/
- (BOOL) isBase;
#if 0
#pragma mark == BASE RELATIONSHIP METHODS ==
#endif
- (BCNucleotideRNA *) RNABaseEquivalent;
@end
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