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// BCCodonDNA.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 for translation of DNA sequences.
*/
#import <Foundation/Foundation.h>
#import "BCCodon.h"
@class BCSequence;
/*!
@class BCCodonDNA
@abstract Provides codon functionality for translation of DNA sequences
@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. The common (amino acid) portion of the class is implemented
* by the superclass, BCCodon. The DNA specific form provides a designated initilization
* routine and methods for querying its base component. You will typically not create these items, but rather access
* them via methods in BCGeneticCode.
*/
@interface BCCodonDNA : BCCodon {
}
/*!
@method unmatched
@abstract provides access to a singleton codon that represents a generic non-coding triplet
*/
+ (BCCodonDNA *)unmatched;
/*!
@method initWithDNASequenceString:andAminoAcidString:
@abstract designated class initilizer
@discussion takes the supplied strings and uses them to get references to the corresponding BCSymbol objects. Will return
* nil if any of these objects cannot be created with the given strings, or the strings are malformed.
*/
- (BCCodonDNA *)initWithDNASequenceString: (NSString *)sequenceString andAminoAcidString: (NSString *)aaString;
/*!
@method triplet
@abstract returns a BCSequence comprised of the appropriate bases
*/
- (BCSequence *) triplet;
/*!
@method matchesTriplet:
@abstract returns yes only if every base of the entry is represented by the bases of the codon in the appropriate order.
@discussion implementation of this method accounts for ambiguous bases.
*/
- (BOOL) matchesTriplet: (NSArray *)entry;
@end
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