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//
// BCUtilStringDNA.h
//
// Created by John Timmer on Fri Jul 16 2004.
// Copyright (c) 2004 The BioCocoa Project. All rights reserved.
//
#import <Foundation/Foundation.h>
@interface BCUtilStringDNA : NSObject {
NSDictionary *baseComplements;
NSCharacterSet *strictBaseSet;
NSCharacterSet *normalBaseSet;
NSCharacterSet *looseBaseSet;
NSDictionary *basesAndReplacements;
}
//////////////////////////////////////////////////////////////////////////////////
// A note on usage -
// Most of these methods require the use of character sets and dictionaries.
// To save a bit of energy, we create a single shared instance, so we only make
// them once. Use "sharedDNAUtilObject" to get it.
//////////////////////////////////////////////////////////////////////////////////
// creation of this object
- (BCUtilStringDNA *) init;
+ (BCUtilStringDNA *) sharedDNAUtilObject;
//////////////////////////////////////////////////////////////////////////////////
// A note on the strings returned -
// These methods handle differences in case by uppercasing everything, so the
// string returned will be uppercase.
// This should be an invitation for someone to write a case preserving version!
//////////////////////////////////////////////////////////////////////////////////
// handling the composition of a string in terms of valid DNA characters
// the strict methods allow ATCGN
// the others allow the full spectrum: ATCGNMKRYWSHVDB
- (BOOL) hasNonDNACharacters: (NSString *)entry;
- (BOOL) hasNonDNACharacters_Strict: (NSString *)entry;
- (NSString *) stripNonDNACharacters: (NSString *)entry;
- (NSString *) stripNonDNACharacters_Strict: (NSString *)entry;
// complementing DNA sequences
- (NSString *) complementOfSequence: (NSString *)entry;
- (NSString *) reverseComplementOfSequence: (NSString *)entry;
// building a list of all possible sequences from a sequence with ambiguous bases
- (NSArray *) getAllSitesForSequence: (NSString *) entry;
// finding ORFs
- (NSRange) findLongestORFInSequence: (NSString *)entry startingWithATG: (BOOL)atgStart inBothDirections: (BOOL)bothDirections;
@end
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