//
//  BCCodon.h
//  BioCocoa
//
//  Created by John Timmer on 8/31/04.
//  Copyright (c) 2003-2009 The BioCocoa Project.
//  All rights reserved.
//
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//  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
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//  3. The name of the author may not be used to endorse or promote products
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//
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/*!
@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
