BCCodonDNA

Provides codon functionality for translation of DNA sequences

Superclass: BCCodon
Declared In: BCCodonDNA.h

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.

Methods

-initWithDNASequenceString:andAminoAcidString:: designated class initilizer
-matchesTriplet:: returns yes only if every base of the entry is represented by the bases of the codon in the appropriate order.
-triplet: returns a BCSequence comprised of the appropriate bases
+unmatched: provides access to a singleton codon that represents a generic non-coding triplet

initWithDNASequenceString:andAminoAcidString:

designated class initilizer

- (BCCodonDNA *)initWithDNASequenceString: (NSString *)sequenceString 
        andAminoAcidString: (NSString *)aaString;

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.

matchesTriplet:

returns yes only if every base of the entry is represented by the bases of the codon in the appropriate order.

- (BOOL) matchesTriplet: (NSArray *)entry;

Discussion

implementation of this method accounts for ambiguous bases.

triplet

returns a BCSequence comprised of the appropriate bases

- (BCSequence *) triplet;

unmatched

provides access to a singleton codon that represents a generic non-coding triplet

+ (BCCodonDNA *)unmatched;