//
//  BCSequenceDNA.h
//  BioCocoa
//
//  Created by John Timmer on 8/12/04.
//  Copyright 2004 John Timmer. All rights reserved.
//

#import <Cocoa/Cocoa.h>
#import "BCSequenceDNABases.h"


@interface BCSequenceDNA : NSObject {

    NSMutableArray *theSequence;
}
/*

////////////////////////////////////////////////////////////////////////////
//  INITIALIZATION METHODS
////////////////////////////////////////////////////////////////////////////
- (BCSequenceDNA *) initWithSequenceString: (NSString *)entry skippingNonBases: (BOOL)skip; 
+ (BCSequenceDNA *) DNASequenceWithSequenceString: (NSString *)entry skippingNonBases: (BOOL)skip;
+ (BCSequenceDNA *) DNASequenceWithBaseArray: (NSArray *)entry;
+ (BCSequenceDNA *) DNASequenceWithSequence: (BCSequenceDNA *)entry;


////////////////////////////////////////////////////////////////////////////
//  OBTAINING INFORMATION ABOUT THE SEQUENCE
////////////////////////////////////////////////////////////////////////////
- (NSArray *) sequenceBaseArray;
- (int) length;
- (BOOL) containsNonBaseSymbols;
- (BOOL) containsAmbiguousBases;
- (BCSequenceDNABase *) baseAtIndex: (int)index;





////////////////////////////////////////////////////////////////////////////
//  ALTERING THE CONTENTS
////////////////////////////////////////////////////////////////////////////
- (void) setSequenceBaseArray: (NSArray *)entry;
- (void) removeBaseAtIndex: (int)index;
- (void) removeBasesInRange: (NSRange)entry;





////////////////////////////////////////////////////////////////////////////
//  DERIVING OTHER SEQUENCES
////////////////////////////////////////////////////////////////////////////
- (BCSequenceDNA *) complementOfSequence;
- (BCSequenceDNA *) reverseComplementOfSequence;
- (BCSequenceDNA *) sequenceInRange: (NSRange)entry;
*/

@end