//
//  BCSequenceDNABase.h
//  BioCocoa
//
//  Created by John Timmer on 8/11/04.
//  Copyright 2004 John Timmer. All rights reserved.
//

#import <Cocoa/Cocoa.h>

/*!
    @class BCSequenceDNABase
    @abstract    All DNA bases are handled through this single class
    @discussion  will be forthcoming.
*/




@interface BCSequenceDNABase : NSObject {
    NSDictionary *baseInfo;
    NSString *name;
    NSString *symbolString;
    unichar symbol;
    BOOL isSingleBase;
    BCSequenceDNABase *complement;
    NSArray *complements;
    NSArray *represents;
    NSArray *representedBy;
}


////////////////////////////////////////////////////////////////////////////
//  CLASS METHODS START HERE
#pragma mark â CLASS METHOS
////////////////////////////////////////////////////////////////////////////


+ (void) initBases;


/*!
    @method     baseForSymbol: (unichar)symbol
    @abstract   Returns a BCSequenceDNABase item representing the base submitted 
*/
+ (id) baseForSymbol: (unichar)symbol;


/*!
    @method     adenosine
    @abstract   Obtains a reference to the single adenosine representation
*/
+ (BCSequenceDNABase *) adenosine;

/*!
    @method     thymidine
    @abstract   Obtains a reference to the single thymidine representation
*/
+ (BCSequenceDNABase *) thymidine;


/*!
    @method     cytidine
    @abstract   Obtains a reference to the single cytidine representation
*/
+ (BCSequenceDNABase *) cytidine;


/*!
    @method     guanidine
    @abstract   Obtains a reference to the single guanidine representation
*/
+ (BCSequenceDNABase *) guanidine;


/*!
    @method     anyBase
    @abstract   Obtains a reference to the single N representation
*/
+ (BCSequenceDNABase *) anyBase;


+ (BCSequenceDNABase *) customBase: (NSString *)baseName;

////////////////////////////////////////////////////////////////////////////
//  OBJECT METHODS START HERE
//
#pragma mark â 
#pragma mark â OBJECT METHODS
#pragma mark â 
#pragma mark âINITIALIZATION METHODS
//
//  INITIALIZATION
////////////////////////////////////////////////////////////////////////////

- (BCSequenceDNABase *) initWithDictionary: (NSDictionary *)entry;

- (void) initializeBaseRelationships;








#pragma mark âBASE INFORMATION METHODS


- (NSString *) name;
- (unichar) symbol;
- (NSString *)symbolString;
- (BOOL) isSingleBase;
- (NSString *) savableRepresentation;
- (NSString *) description;



#pragma mark âBASE RELATIONSHIP METHODS

///////////////////////////////////////////////////////////
//  COMPLEMENTATION METHODS
///////////////////////////////////////////////////////////

- (BCSequenceDNABase  *)complement;
- (NSArray *)complements;
- (BOOL) complementsBase: (BCSequenceDNABase *)entry;


///////////////////////////////////////////////////////////
//  REPRESENTATION METHODS FOR AMBIGUOUS BASES
///////////////////////////////////////////////////////////

- (NSArray *) representedBases;
- (NSArray *) representingBases;
- (BOOL) representsBase: (BCSequenceDNABase *) entry;
- (BOOL) isRepresentedByBase: (BCSequenceDNABase *) entry;
- (NSCharacterSet *) symbolsOfRepresentedBases;



@end