//
//  BCCodon.m
//  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.

#import "BCCodon.h"
#import "BCSequence.h"
#import "BCAminoAcid.h"
#import "BCSymbol.h"


@implementation BCCodon


- (BCAminoAcid *) codedAminoAcid {
    return codedAminoAcid;
}

- (BCSequence *) triplet {
    NSArray *tempArray = [NSArray arrayWithObjects: firstBase, secondBase, wobbleBase, nil];
    return [BCSequence sequenceWithSymbolArray: tempArray];
}


- (NSString *) aminoAcidSymbolString {
    if ( codedAminoAcid == nil )
        return @"*";
    else
        return [codedAminoAcid symbolString];
}
    
    
- (NSString *) tripletString {
    NSMutableString *returnString = [NSMutableString stringWithString: [firstBase symbolString]];
    [returnString appendString: [secondBase symbolString]];
    [returnString appendString: [wobbleBase symbolString]];

    return [[returnString copy] autorelease];
}

- (NSString *)symbolString {
	return [[self aminoAcidSymbolString] stringByAppendingString: [NSString stringWithFormat: @"(%@)", [self tripletString]]];
}


- (NSString *) description {
    return [self tripletString];
}

- (id)copyWithZone:(NSZone *)zone {
    return self;
}

@end
