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// BCGeneticCode.h
// 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.
/*!
@header
@abstract Provides an interface for obtaining the codons of different genetic codes.
*/
#import <Foundation/Foundation.h>
#import "BCFoundationDefines.h"
@class BCSequence, BCCodonRNA, BCCodonDNA, BCCodon, BCNucleotideDNA, BCNucleotideRNA, BCAminoAcid;
// @class BCSequence, BCSequenceRNA
/*!
@class BCGeneticCode
@abstract Provides an interface for obtaining the codons of different genetic codes.
@discussion Genetic codes are essentially a translation dictionary implemented in BCCodons.
* This class does not get implemented, but rather creates and allows access to NSArrays that
* contain the appropriate set of codons for a given genetic code. Individual codes can be
* accessed either by their BCGeneticCodeName, or via appropriately named class methods.
*/
@interface BCGeneticCode : NSObject {
}
+ (NSArray *) geneticCode: (BCGeneticCodeName)codeType forSequenceType: (BCSequenceType)seqType;
+ (BCCodon *) codon: (BCSequence*)aCodon inGeneticCode: (BCGeneticCodeName)codeType;
+ (NSArray *) universalGeneticCodeDNA;
+ (NSArray *) universalGeneticCodeRNA;
+ (void) initUniversalGeneticCode;
+ (NSArray *) vertebrateMitochondrialGeneticCodeDNA;
+ (NSArray *) vertebrateMitochondrialGeneticCodeRNA;
+ (void) initVertebrateMitochondrialGeneticCode;
@end
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