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// BCCodon.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 codon functionality.
*/
#import <Foundation/Foundation.h>
@class BCSymbol, BCAminoAcid;
/*!
@class BCCodon
@abstract Provides codon functionality.
@discussion A codon is a composite object, consisting of three bases and a corresponding amino acid. This class
* provides the equivalent functionality in code form. You will typically not create these items, but rather access
* them via methods in BCGeneticCode.
*/
@interface BCCodon : NSObject {
BCSymbol *firstBase;
BCSymbol *secondBase;
BCSymbol *wobbleBase;
BCAminoAcid *codedAminoAcid;
}
/*!
@method codedAminoAcid
@abstract returns the BCAminoAcid encoded by the reciever. Returns nil for stop codons.
*/
- (BCAminoAcid *) codedAminoAcid;
/*!
@method aminoAcidSymbolString
@abstract returns the symbol string of the amino acid encoded by the receiver. Returns "*" for stop codons.
*/
- (NSString *) aminoAcidSymbolString;
/*!
@method tripletString
@abstract returns a string representing the three bases of the codon.
@discussion calls "symbolString" on each base of the codon, appending the results to generate a single string
*/
- (NSString *) tripletString;
- (NSString *)symbolString;
/*!
@method description
@abstract returns the tripletString
*/
- (NSString *) description;
/*!
@method copyWithZone:
@abstract returns self to keep the codon a singleton. This may be dangerous, but i don't entirely understand memory zones.
*/
- (id)copyWithZone:(NSZone *)zone;
@end
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