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// BCNucleotide.h
// BioCocoa
//
// Created by John Timmer on 2/25/05.
// 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 in-memory representations of nucleotides.
*/
#import <Foundation/Foundation.h>
#import "BCSymbol.h"
/*!
@class BCNucleotide
@abstract Nucleotide specific symbols.
@discussion This class provides in-memory representations of nucleotides.
*/
@interface BCNucleotide : BCSymbol {
BCSymbol *complement;
NSSet *complements;
}
///////////////////////////////////////////////////////////
// COMPLEMENTATION METHODS
///////////////////////////////////////////////////////////
/*!
@method complement
@abstract Returns a reference to the symbol the complements the receiver
@discussion When called on adenosine, this method will return a reference to thyidine.
* For ambiguous symbol, it returns the single most complete complement - when called on purine,
* it will return only pyrimidine. For amino acids, this will return nil.
*/
- (BCNucleotide *)complement;
/*!
@method complements
@abstract Returns references all symbols that may complement the receiver in an array
@discussion When called on adenosine, this method will return an array containing references
* to thyidine, weak, any, etc. For amino acids, this will return nil.
*/
- (NSSet *)complements;
/*!
@method complementsSymbol: (BCSymbol *)entry;
@abstract Evaluates whether the receiver complements the entry
@discussion When called on adenosine, this method will return YES if the entry is thymidine,
* weak, any base, etc. For amino acids, this will return nil.
*/
- (BOOL) complementsSymbol: (BCNucleotide *)entry;
- (BOOL) isComplementOfSymbol: (BCNucleotide *)entry;
@end
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