-convertRangeToOriginalSequence:
converts a range in the codon sequence to the equivalent range in the coding sequence
-initWithCodonArray:
nitializes a BCSequenceCodon object by passing it an array of BCCodon objects
-initWithCodonArray:geneticCode:frame:
Designated class initializer. Arguments should be self explanatory.
-initWithString:skippingUnknownSymbols:
initializes a BCSequenceCodon object by passing it an NSString.
-longestOpenReadingFrame
returns the longest stretch of codons that don't code for a stop or undefined aa.
-longestOpenReadingFrameUsingStartCodon:
returns the longest stretch of codons that starts with (codon) and doesn't contain a stop or undefined aa.
-openReadingFramesLongerThanCutoff:
returns all open reading frames longer than the supplied cutoff
-openReadingFramesLongerThanCutoff:usingStartCodon:
behaves identically to "openReadingFramesLongerThanCutoff:", but requires a start codon to initiate the ORF
-readingFrame
returns the reading frame ("+2", "-1", etc.) used to generate the codon sequence
+sequenceWithCodonArray:
creates and returns an autoreleased BCSequenceCodon object initialized with the codon array passed as argument
-translationOfRange:
provides a protein sequence code for by the sub-sequence of codons within theRange
-translationOfRange:usingStartCodon:
behaves identically to "translationOfRange:" but requires a start codon to initiate translation
-translationsLongerThanCutoff:
provides an array of BCSequences encoded by the receiver which are longer than cutoff
-translationsLongerThanCutoff:usingStartCodon:
behaves identically to "translationsLongerThanCutoff:", but requires a start codon to initiate translation
-usedCode
returns the genetic code used to generate the codon sequence

convertRangeToOriginalSequence:


converts a range in the codon sequence to the equivalent range in the coding sequence

- (NSRange) convertRangeToOriginalSequence: (NSRange)entry; 
Discussion

in many cases, the ranges of locations in a codon sequence (ie - ORF locations) need to be located in the coding sequence of DNA or RNA bases. This method should allow the ranges generated by methods in this class to be converted to the equivalent ranges for use with BCSequence or RNA classes. The method accounts for reading frame.


initWithCodonArray:


nitializes a BCSequenceCodon object by passing it an array of BCCodon objects

- (id)initWithCodonArray:(NSArray *)anArray; 
Discussion

Scans the provided array for BCSequenceCodons and adds them to the resulting sequence. If the first codon is RNA, it will assume a BCUnversalCodeRNA origin, otherwise the DNA version. The reading frame is assumed to be +1.


initWithCodonArray:geneticCode:frame:


Designated class initializer. Arguments should be self explanatory.

- (id)initWithCodonArray:(NSArray *)anArray geneticCode: (BCGeneticCodeName)codeType 
        frame: (NSString *)theFrame; 
Discussion

This is the designated initializer: other initializers call this method. The designated initializer is thus different from the superclass. It calls the designated initializer for the superclass.


initWithString:skippingUnknownSymbols:


initializes a BCSequenceCodon object by passing it an NSString.

- (id)initWithString:(NSString *)aString 
        skippingUnknownSymbols:(BOOL)skipFlag; 
Discussion

The implementation overrides the superclass. If skipFlag is YES, any character that cannot be converted to a BCNucleotideDNA object is eliminated from the final symbolArray. Otherwise, they are replaced by "undefined" symbols. As codons cannot be easily represented as single characters, this method attempts to determine if the sequence is likely to be RNA (no T's, U's present), and creates a BCSequenceRNA from it if so. If not, it creates a BCSequence. Once a sequence is made, it sends it for translation, and the returned codon array is sent to the designated initializer 'initWithCodonArray:geneticCode:frame:'


longestOpenReadingFrame


returns the longest stretch of codons that don't code for a stop or undefined aa.

- (NSRange) longestOpenReadingFrame; 


longestOpenReadingFrameUsingStartCodon:


returns the longest stretch of codons that starts with (codon) and doesn't contain a stop or undefined aa.

- (NSRange) longestOpenReadingFrameUsingStartCodon: (id)codon; 
Discussion

the start codon argument can be provided as a single BCCodon or as an array of codons, for situations/sepcies where there is more than one start codon.


openReadingFramesLongerThanCutoff:


returns all open reading frames longer than the supplied cutoff

- (NSArray *) openReadingFramesLongerThanCutoff: (unsigned int)cutoff; 
Discussion

The return array contains NSValues, coding for NSRanges. if no open reading frames are found, it will return an empty array. Note the BioCocoa provides a method in BCUtilValueAdditions that allows the sorting of these values based on the range length.


openReadingFramesLongerThanCutoff:usingStartCodon:


behaves identically to "openReadingFramesLongerThanCutoff:", but requires a start codon to initiate the ORF

- (NSArray *) openReadingFramesLongerThanCutoff: (unsigned int)cutoff 
        usingStartCodon: (id)codon; 


readingFrame


returns the reading frame ("+2", "-1", etc.) used to generate the codon sequence

- (NSString *)readingFrame; 


sequenceWithCodonArray:


creates and returns an autoreleased BCSequenceCodon object initialized with the codon array passed as argument

+ (BCSequenceCodon *)sequenceWithCodonArray:(NSArray *)anArray; 


translationOfRange:


provides a protein sequence code for by the sub-sequence of codons within theRange

- (BCSequence *) translationOfRange: (NSRange) theRange; 
Discussion

This method will terminate short of the end of theRange if a stop codon or an undefined codon is encountered


translationOfRange:usingStartCodon:


behaves identically to "translationOfRange:" but requires a start codon to initiate translation

- (BCSequence *) translationOfRange: (NSRange) theRange 
        usingStartCodon: (id)codon; 


translationsLongerThanCutoff:


provides an array of BCSequences encoded by the receiver which are longer than cutoff

- (NSArray *) translationsLongerThanCutoff: (unsigned int)cutoff; 


translationsLongerThanCutoff:usingStartCodon:


behaves identically to "translationsLongerThanCutoff:", but requires a start codon to initiate translation

- (NSArray *) translationsLongerThanCutoff: (unsigned int)cutoff 
        usingStartCodon: (id)codon; 


usedCode


returns the genetic code used to generate the codon sequence

- (BCGeneticCodeName) usedCode; 

© 2008 The BioCocoa Project.
Last Updated: Wednesday, October 01, 2008