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// BCSequence.h
// BioCocoa
//
// Created by Koen van der Drift on 12/14/2004.
// 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 biological sequence (DNA, protein, etc.).
*/
#import <Foundation/Foundation.h>
#import "BCFoundationDefines.h"
@class BCSymbol;
@class BCSymbolSet;
@class BCAnnotation;
/*!
@class BCSequence
@abstract Class that holds a biological sequence (DNA, protein, etc.)
@discussion This class is used for all types of sequences. The sequence type
* is determined by the symbolset, which defines the BCSymbols that are allowed
* to be in the sequence. Compare this to NSString, where the encoding determines the
* type of string that is inside the NSString object.
*/
@interface BCSequence : NSObject <NSCopying>
{
NSData *sequenceData; // holds a char array with the sequence string
BCSymbolSet *symbolSet; // determines the BCSymbols that can be in this sequence
NSArray *symbolArray; // array of BCSymbol objects to represent the sequence
NSMutableDictionary *annotations; // annotations fot this sequence
BCSequenceType sequenceType; // defines the sequence type
}
#if 0
#pragma mark == INITIALIZATION METHODS ==
#endif
/*!
@method initWithSymbolArray:symbolSet:
@abstract initializes a BCSequence object by passing it an NSArray of BCSymbol.
@discussion
* The method scans the passed array for all BCSymbol objects, and creates
* a new BCSequence using them. The symbol set is used to filter the passed symbols.
* The symbol set instance should be the same sequence type as the sequence, e.g. should
* contain DNA symbols if used to initialize a DNA sequence. If not the right sequence type,
* or if the symbolSet is nil, then the implementation guesses the most likely
* symbolSet based on the symbols in the array.
*/
- (id)initWithSymbolArray:(NSArray *)anArray symbolSet:(BCSymbolSet *)aSet;
/*!
@method initWithData:symbolSet:
@abstract initializes a BCSequence object by passing it an NSData of symbols.
@discussion
* The method scans the passed data for all BCSymbol objects, and creates
* a new BCSequence using them. The symbol set is used to filter the passed symbols.
* The symbol set instance should be the same sequence type as the sequence, e.g. should
* contain DNA symbols if used to initialize a DNA sequence. If not the right sequence type,
* or if the symbolSet is nil, then the implementation guesses the most likely
* symbolSet based on the symbols in the array.
*/
- (id)initWithData:(NSData *)aData symbolSet:(BCSymbolSet *)aSet;
/*!
@method initWithSymbolArray:
@abstract initializes a BCSequence object by passing it an NSArray of BCSymbol.
@discussion This method calls '-initWithSymbolArray:symbolSet'
* using the default symbol set for the class.
* The method scans the passed array for all BCSymbol objects compatible with the
* type of sequence being created.
*/
- (id)initWithSymbolArray:(NSArray *)anArray;
/*!
@method initWithString:symbolSet:
@abstract initializes a BCSequence object by passing it an NSString.
@discussion This is the designated initializer.
* This method will attempt to create an array of BCSymbols using the
* characters found in the string.
* The BCSymbols created will depend on the symbol set passed as argument.
*/
- (id)initWithString:(NSString *)aString symbolSet:(BCSymbolSet *)aSet;
/*!
@method initWithString:
@abstract initializes a BCSequence object by passing it an NSString.
@discussion This method calls initWithString:symbolSet:
* using the default symbol set of the class as argument.
* The method should only be called on a concrete subclass.
* This method will create an array of BCSymbols using the
* characters found in the string. The type of BCSymbols created
* will depend on the the sequence type, e.g. a DNA sequence
* will only use DNA bases.
*/
- (id)initWithString:(NSString*)aString;
/*!
@method initWithString:range:
@abstract initializes a BCSequence object by passing it an NSString and a range.
@discussion This method calls '-initWithString:'. Note that the range is 0-based.
*/
- (id)initWithString:(NSString*)aString range:(NSRange)aRange;
/*!
@method initWithString:symbolSet:
@abstract initializes sequence object with the string passed as argument
@discussion This method calls 'initWithString:symbolSet:'.
*/
- (id)initWithString:(NSString*)aString range:(NSRange)aRange symbolSet:(BCSymbolSet *)aSet;
/*!
@method initWithThreeLetterString:symbolSet:
@abstract initializes sequence object with a three-letter code string passed as argument
*/
- (id)initWithThreeLetterString:(NSString*)aString symbolSet:(BCSymbolSet *)aSet;
/*!
@method sequenceWithString:
@abstract creates and returns an autoreleased sequence object initialized with the string passed as argument
@discussion This method calls 'initWithString:'
*/
+ (BCSequence *)sequenceWithString:(NSString *)aString;
/*!
@method sequenceWithString:symbolSet:
@abstract creates and returns an autoreleased sequence object initialized with the string passed as argument
@discussion This method calls 'initWithString:symbolSet:'.
*/
+ (BCSequence *)sequenceWithString:(NSString *)aString symbolSet:(BCSymbolSet *)aSet;
/*!
@method sequenceWithThreeLetterString:symbolSet:
@abstract creates and returns an autoreleased sequence object initialized with a three-letter code string passed as argument
@discussion This method calls 'initWithString:symbolSet:'.
*/
+ (BCSequence *)sequenceWithThreeLetterString:(NSString *)aString symbolSet:(BCSymbolSet *)aSet;
/*!
@method sequenceWithSymbolArray:
@abstract creates and returns an autoreleased sequence object initialized with the array of BCSymbols passed as argument
@discussion This method calls 'initWithSymbolArray:'
*/
+ (BCSequence *)sequenceWithSymbolArray:(NSArray *)entry;
/*!
@method sequenceWithSymbolArray:
@abstract creates and returns an autoreleased sequence object initialized with the array of BCSymbols passed as argument
@discussion This method calls 'initWithSymbolArray:symbolSet'
*/
+ (BCSequence *)sequenceWithSymbolArray:(NSArray *)entry symbolSet: (BCSymbolSet *)aSet;
/*!
@method objectForSavedRepresentation:
@abstract Returns a BCSequence object representing the sequence submitted
@discussion all BC classes should implement a "savableRepresentation" and an
* "objectForSavedRepresentation" method to allow archiving/uncarchiving in
* .plist formatted files.
*/
+ (BCSequence *)objectForSavedRepresentation:(NSString *)sequence;
/*!
@method convertThreeLetterStringToOneLetterString:symbolSet:
@abstract Converts a 3-letter code string to a 1-letter code string
*/
- (NSString *)convertThreeLetterStringToOneLetterString:(NSString *)aString symbolSet: (BCSymbolSet *)aSet;
#if 0
#pragma mark == SEQUENCE TYPE DETERMINATION ==
#endif
/*!
@method sequenceTypeForString:
@abstract Returns the guessed sequence type of an arbitrary string.
*/
- (BCSequenceType)sequenceTypeForString:(NSString *)string;
/*!
@method sequenceTypeForData:
@abstract Returns the guessed sequence type from sequence data.
*/
- (BCSequenceType)sequenceTypeForData:(NSData *)aData;
/*!
@method sequenceTypeForSymbolArray:
@abstract Returns the guessed sequence type of an array of BCSymbols.
*/
- (BCSequenceType)sequenceTypeForSymbolArray:(NSArray *)anArray;
#if 0
#pragma mark == OBTAINING SEQUENCE INFORMATION ==
#endif
/*!
@method sequenceData
@abstract returns and NSData object containing the sequenceData
*/
- (NSData *) sequenceData;
/*!
@method bytes;
@abstract returns the raw bytes representing the sequence
*/
- (const unsigned char *) bytes;
/*!
@method symbolSet
@abstract returns the symbolSet associated with this sequence
*/
- (BCSymbolSet *) symbolSet;
/*!
@method setSymbolSet:
@abstract sets the symbolSet associated with this sequence
*/
- (void) setSymbolSet:(BCSymbolSet *)symbolSet;
/*!
@method sequenceType
@abstract returns the type of sequence
*/
- (BCSequenceType) sequenceType;
/*!
@method length
@abstract returns the length of the sequence
*/
- (unsigned int) length;
/*!
@method symbolAtIndex:
@abstract returns the BCSymbol object at index. Returns nil if index is out of bounds.
*/
- (BCSymbol *)symbolAtIndex: (int)theIndex;
/*!
@method containsAmbiguousSymbols
@abstract determines whether any symbols in the sequence are compound symbols.
*/
- (BOOL) containsAmbiguousSymbols;
/*!
@method sequenceString
@abstract returns the sequence string of the object.
@discussion returns an NSString containing a one letter-code string of the sequence.
* This method is useful when the sequence needs to be displayed in a view.
*/
- (NSString*)sequenceString;
/*!
@method symbolArray
@abstract returns a ponter to the array of BCSymbol objects that make up the sequence.
@discussion The array returned is the object used internally by BCSequence.
* The array obtained should only be used for reading, and should not be modified by the caller.
* To modify the sequence, instead use one of the
* convenience methods setSymbolArray, removeSymbolsInRange, removeSymbolsAtIndex,
* or insertSymbolsFromSequence:atIndex.
*/
- (NSArray *)symbolArray;
/*!
@method clearSymbolArray
@abstract clears the symbol array
@discussion Removes all symbols from the symbol array and sets the array to nil.
* Call this method first to re-generate the symbolArray after the sequence has been modified.
*/
- (void)clearSymbolArray;
/*!
@method subSequenceStringInRange:
@abstract returns a subsequence in string form
@discussion returns an NSString containing a subsequence specified by aRange (0-based).
* Returns nil if any part of aRange is out of bounds.
*/
- (NSString *)subSequenceStringInRange:(NSRange)aRange;
/*!
@method sequenceStringFromSymbolArray:
@abstract returns an NSString representation of a symbolArray
*/
- (NSString *)sequenceStringFromSymbolArray:(NSArray *)anArray;
/*!
@method subSymbolArrayInRange:
@abstract returns a sub-symbolarray form
@discussion returns an NSArray containing a subsequence specified by aRange (0-based).
* Returns nil if any part of aRange is out of bounds.
*/
- (NSArray *)subSymbolArrayInRange:(NSRange)aRange;
/*!
@method subSequenceInRange:
@abstract returns a sub-symbollist
@discussion returns an BCSequence containing a sub-symbollist specified by aRange (0-based).
* Returns nil if any part of aRange is out of bounds.
*/
- (BCSequence *)subSequenceInRange:(NSRange)aRange;
/*!
@method savableRepresentation
@abstract Returns the sequenceString for saving.
@discussion All BCSymbol classes implement this method to provide a standard way of
* accessing their data in a format that can be stored in Apple .plist files within
* arrays or dictionaries.
*/
- (NSString *) savableRepresentation;
/*!
@method description
@abstract Overrides NSObject's description - describes the object in string form
@discussion In the default implementation, returns the sequence string. Useful primarily
* for debugging.
*/
- (NSString *) description;
/*!
@method addAnnotation:
@abstract Add a BCAnnotation object to the annotations dictionary
*/
- (void) addAnnotation:(BCAnnotation *)annotation;
/*!
@method addAnnotation:forKey:
@abstract Add an annotation to the annotations dictionary
@discussion Using two strings for the key and value, this method adds an annotation
*/
- (void) addAnnotation:(NSString *)annotation forKey: (NSString *) key;
/*!
@method annotationForKey:
@abstract Get the annpotation for a specific key
@discussion Returns the annotation for a given key, which is passed as an NSString
*/
- (id) annotationForKey: (NSString *) key;
/*!
@method annotations
@abstract Returns the annotations dictionary
*/
- (NSMutableDictionary *) annotations;
/*!
@method setAnnotations:
@abstract Set the annotations dictionary
@discussion This will completely replace the current annotations dictaionry. All key-value pairs will be lost
* and replaced by those in the new dictionary.
*/
//- (void)setAnnotations:(NSMutableDictionary *)aDict;
#if 0
#pragma mark == MANIPULATING THE SEQUENCE ==
#endif
/*!
@method setSymbolArray:
@abstract sets the symbollist as an array of BCSymbol objects.
*/
- (void)setSymbolArray:(NSArray *)anArray;
/*!
@method removeSymbolsInRange:
@abstract deletes a sub-symbollist.
@discussion deletes the BCSymbols in the sub-symbollist specified by aRange (0-based).
*/
- (void)removeSymbolsInRange:(NSRange)aRange;
/*!
@method removeSymbolAtIndex:
@abstract deletes one symbol.
@discussion deletes a BCSymbol located at index (0-based).
*/
- (void)removeSymbolAtIndex:(int)index;
/*!
@method insertSymbolsFromSequence:atIndex:
@abstract inserts a BCSequence into the current symbolarray, starting at index (0-based)
@discussion inserts the BCSequence that is in the first argument in the current BCSequence.
*/
- (void)insertSymbolsFromSequence:(BCSequence *)seq atIndex:(int)index;
#if 0
#pragma mark == DERIVING RELATED SEQUENCES ==
#endif
/*!
@method reverse
@abstract returns a BCSequence that is the reverse of the one queried.
*/
- (BCSequence *) reverse;
/*!
@method complement
@abstract returns a BCSequence that is the complement of the one queried.
@discussion This is a convenience method that calls BCToolComplement.
*/
- (BCSequence *) complement;
/*!
@method reverseComplement
@abstract returns a BCSequence that is the reverse complement of the one queried.
@discussion This is a convenience method that calls BCToolComplement.
*/
- (BCSequence *) reverseComplement;
#if 0
#pragma mark == FINDING SUBSEQUENCES ==
#endif
- (NSArray *) findSequence: (BCSequence *) entry;
- (NSArray *) findSequence: (BCSequence *) entry usingStrict: (BOOL) strict;
- (NSArray *) findSequence: (BCSequence *) entry usingStrict: (BOOL) strict firstOnly: (BOOL) firstOnly;
- (NSArray *) findSequence: (BCSequence *) entry usingStrict: (BOOL) strict firstOnly: (BOOL) firstOnly usingSearchRange: (NSRange) range;
@end
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