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//
// BCSequenceCodon.h
// BioCocoa
//
// Created by John Timmer on 9/17/04.
// Copyright (c) 2003-2009 The BioCocoa Project.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions
// are met:
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// 3. The name of the author may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
// NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
// THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
/*!
@header
@abstract Provides in-memory representations of DNA or RNA based codons.
*/
#import <Foundation/Foundation.h>
#import "BCSequence.h"
/*!
@class BCSequenceCodon
@abstract Wrapper for an ordered array of BCCodons, either DNA- or RNA-based
@discussion A subclass of BCSequence, this class handles access to an ordered list
* of BCCodons. In addition to the usual BCSequence objects, it contains references to the
* genetic code used to generate the BCSequenceCodon, and the reading frame as a string
* (ie - +1, -2). Typically, BCCodonSequences are not created directly, but via the BCUtilTranslator
* class methods.
*/
@interface BCSequenceCodon : BCSequence {
BCGeneticCodeName usedCode;
NSString *readingFrame;
}
#if 0
#pragma mark == INITIALIZATION METHODS ==
#endif
/*!
@method initWithCodonArray:geneticCode:frame:
@abstract Designated class initializer. Arguments should be self explanatory.
@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.
*/
- (id)initWithCodonArray:(NSArray *)anArray geneticCode: (BCGeneticCodeName)codeType frame: (NSString *)theFrame;
/*!
@method initWithString:skippingUnknownSymbols:
@abstract initializes a BCSequenceCodon object by passing it an NSString.
@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:'
*/
- (id)initWithString:(NSString *)aString skippingUnknownSymbols:(BOOL)skipFlag;
///*!
// @method - (id)initWithSymbolArray:(NSArray *)anArray
// @abstract initializes a BCSequenceCodon object by passing it an NSArray of BCSymbol.
// @discussion The implementation overrides the superclass.
// * This method scans the passed array for all BCSymbol objects, and creates
// * a new BCSequence using them. Once a sequence is made, it sends it for translation,
// * and the returned codon array is sent to the designated initializer
// * 'initWithCodonArray:geneticCode:frame:'
//*/
//- (id)initWithSymbolArray:(NSArray *)anArray;
/*!
@method initWithCodonArray:
@abstract nitializes a BCSequenceCodon object by passing it an array of BCCodon objects
@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.
*/
- (id)initWithCodonArray:(NSArray *)anArray;
/*!
@method sequenceWithCodonArray:
@abstract creates and returns an autoreleased BCSequenceCodon object initialized with the codon array passed as argument
*/
+ (BCSequenceCodon *)sequenceWithCodonArray:(NSArray *)anArray;
- (BCSequence *)translate;
#if 0
#pragma mark == ORF/TRANSLATION METHODS ==
#endif
/*!
@method longestOpenReadingFrame
@abstract returns the longest stretch of codons that don't code for a stop or undefined aa.
*/
- (NSRange) longestOpenReadingFrame;
/*!
@method longestOpenReadingFrameUsingStartCodon:
@abstract returns the longest stretch of codons that starts with (codon) and doesn't contain a stop or undefined aa.
@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.
*/
- (NSRange) longestOpenReadingFrameUsingStartCodon: (id)codon;
/*!
@method openReadingFramesLongerThanCutoff:
@abstract returns all open reading frames longer than the supplied 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.
*/
- (NSArray *) openReadingFramesLongerThanCutoff: (unsigned int)cutoff;
/*!
@method openReadingFramesLongerThanCutoff:usingStartCodon:
@abstract behaves identically to "openReadingFramesLongerThanCutoff:", but requires a start codon to initiate the ORF
*/
- (NSArray *) openReadingFramesLongerThanCutoff: (unsigned int)cutoff usingStartCodon: (id)codon;
/*!
@method translationOfRange:
@abstract provides a protein sequence code for by the sub-sequence of codons within theRange
@discussion This method will terminate short of the end of theRange if a stop codon or an undefined codon
* is encountered
*/
- (BCSequence *) translationOfRange: (NSRange) theRange;
/*!
@method translationOfRange:usingStartCodon:
@abstract behaves identically to "translationOfRange:" but requires a start codon to initiate translation
*/
- (BCSequence *) translationOfRange: (NSRange) theRange usingStartCodon: (id)codon;
/*!
@method translationsLongerThanCutoff:
@abstract provides an array of BCSequences encoded by the receiver which are longer than cutoff
*/
- (NSArray *) translationsLongerThanCutoff: (unsigned int)cutoff;
/*!
@method translationsLongerThanCutoff:usingStartCodon:
@abstract behaves identically to "translationsLongerThanCutoff:", but requires a start codon to initiate translation
*/
- (NSArray *) translationsLongerThanCutoff: (unsigned int)cutoff usingStartCodon: (id)codon;
#if 0
#pragma mark == BASIC INFO ==
#endif
/*!
@method usedCode
@abstract returns the genetic code used to generate the codon sequence
*/
- (BCGeneticCodeName) usedCode;
/*!
@method readingFrame
@abstract returns the reading frame ("+2", "-1", etc.) used to generate the codon sequence
*/
- (NSString *)readingFrame;
/*!
@method convertRangeToOriginalSequence:
@abstract converts a range in the codon sequence to the equivalent range in the coding sequence
@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.
*/
- (NSRange) convertRangeToOriginalSequence: (NSRange)entry;
@end
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