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// BCSymbol.h
// BioCocoa
//
// Created by Koen van der Drift on Sun Aug 15 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 symbol representation of individual sequence elements (nucleotide, amino acid, etc.).
*/
#import <Foundation/Foundation.h>
#import "BCFoundationDefines.h"
@class BCSymbolSet;
/*!
@class BCSymbol
@abstract Superclass of all individual sequence elements (nucleotide, amino acid, etc.)
@discussion This class should not be instantiated, but acts to provide some common methods
* and variables that are used by all subclasses.
*/
@interface BCSymbol : NSObject <NSCopying>
{
unsigned char symbolChar;
NSString *name;
NSString *symbolString;
NSDictionary *symbolInfo;
NSSet *represents;
NSSet *representedBy;
float monoisotopicMass;
float averageMass;
}
#if 0
#pragma mark == INITIALIZATION METHODS ==
#endif
/*!
@method initWithSymbolChar:
@abstract initializes a BCSymbol object using a single character.
@discussion This method does nothing else, it only sets the symbol.
* It's the subclass responsibility to setup all other variables
*/
- (id)initWithSymbolChar:(unsigned char)aChar;
/*!
@method initializeSymbolRelationships
@abstract converts string-based selectors to symbol references
@discussion After the initialization above, internal references to other symbols
* (complement, representations, etc.) remain in string-based selector form. The first time
* the actual reference is needed, this method will use the selectors to generate the actual
* references to the symbols.
*/
- (void) initializeSymbolRelationships;
#if 0
#pragma mark == OBJECT METHODS ==
#endif
/*!
@method name
@abstract returns the chemical name of the object.
@discussion returns the common chemical name for the represented object.
* For a nucleotide with a symbol of 'A', this will return "Adenosine", while
* for an amino acid with that symbol, it will return "Alanine".
*/
- (NSString *)name;
/*!
@method symbolChar
@abstract returns the one letter symbol for the object
@discussion Provides a unicode character symbol that represents the object.
* These are the standard representations: nucleotides are ATCGNYR etc., amino acids
* are ACDEF etc. Stop codons are represented with *, and gaps are represented with -.
* If non-symbol items are allowed, they are represented by a ?.
*/
- (unsigned char) symbolChar;
/*!
@method symbolString
@abstract returns the symbol as a single character string.
@discussion The behavior is identical to that for the "symbol" method above, except the
* value returned is an NSString, and so can be readily saved, appended to strings, etc.
*/
- (NSString *)symbolString;
/*!
@method savableRepresentation
@abstract Returns the symbol string of the object.
@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. Subclasses should provide a method of converting this information
* back into the appropriate Symbol object.
*/
- (NSString *) savableRepresentation;
/*!
@method description
@abstract Overrides NSObject's description - describes the object in string form
@discussion In the default implementation, returns the name of the object. Useful primarily
* for debugging.
*/
- (NSString *) description;
/*!
@method symbolInfo
@abstract Returns the dictionary that was used to initialize the symbol information
@discussion The default set of symbols (bases and amino acids) are generated from information stored in a .plist
* file in dictionary form. Upon initialization, each symbol retrieves and retains this dictionary, which is
* accessible by this method. Use of this method should be avoided; rather, use "valueForKey" to retrieve information
* about a symbol from this dictionary.
*/
- (NSDictionary *) symbolInfo;
/*!
@method valueForKey:
@abstract Retrieves a value from the symbolInfo dictionary
@discussion The default set of symbols (bases and amino acids) are generated from information stored in dictionary form
* in a .plist file. Upon initialization, each symbol retrieves and retains this dictionary. Most, if not all,
* of the values in this dictionary (ie - monoisotopicMass) are accessible through defined methods. This method may
* be used to retrieve those values which do not have specified methods. It returns nil if the key is not used.
* For a list of valid keys and their defined equivalents, check the file "BCStringDefinitions" or the .plist files
* in the "Symbol Templates" folder.
*
* This method is primarily designed to allow rapid addition of features to the symbols which are the foundation of
* BioCocoa via editing of the included .plist files (in the "Symbol Templates" folder), rather than by code.
*
* NB - the valid keys in this dictionary may vary between releases of BioCocoa, and returned values should not be
* assumed to be non-nil.
*/
- (id) valueForKey: (NSString *)aKey;
/*!
@method setValue:forKey:
@abstract Non-functional method present for key-value coding compliance.
@discussion The symbolInfo dictionary with which symbols are initialized is non-mutable in order to maintain these
* objects in an internally consistent state. Therefore, this method cannot actually change values in this
* dictionary. It is included only to allow Symbols to be key-value coding compliant.
*/
- (void) setValue: (id)aValue forKey: (NSString *)theKey;
/*!
@method monoisotopicMass
@abstract Returns a float value containing the monoisotopic mass for this BCSymbol
@discussion The monoisotopic mass is the mass calculated using the first
* isotope of each element (eg 12C, 14N, 16O, etc)
*/
- (float)monoisotopicMass;
/*!
@method setMonoisotopicMass:
@abstract Set the monoisotopic mass for this BCSymbol.
@discussion The monoisotopic mass is the mass calculated using the first
* isotope of each element (eg 12C, 14N, 16O, etc)
*/
- (void)setMonoisotopicMass:(float)value;
/*!
@method averageMass
@abstract Returns a float value containing the average mass for this BCSymbol
@discussion The average mass is the mass calculated averaging over all
* isotopes of each element.
*/
- (float)averageMass;
/*!
@method setAverageMass:
@abstract Set the average mass for this BCSymbol.
@discussion The average mass is the mass calculated averaging over all
* isotopes of each element.
*/
- (void)setAverageMass:(float)value;
/*!
@method massUsingType:
@abstract Returns the mass of this BCSymbol
@discussion aType defines if either the monoisotopic or average mass is returned
*/
- (float)massUsingType:(BCMassType) aType;
/*!
@method minMassUsingType:
@abstract Returns the minimum mass for this BCSymbol
@discussion This is used for ambiguous symbols which have a mass range, because they are represented
* by different BCSymbols, each with their own mass. It will return the mass of the BCSymbol
* with the lowest mass.
* aType defines if either the monoisotopic or average mass is returned
*/
- (float)minMassUsingType:(BCMassType) aType;
/*!
@method maxMassUsingType:
@abstract Returns the maximum mass for this BCSymbol
@discussion This is used for ambiguous symbols which have a mass range, because they are represented
* by different BCSymbols, each with their own mass. It will return the mass of the BCSymbol
* with the highest mass.
* aType defines if either the monoisotopic or average mass is returned
*/
- (float)maxMassUsingType:(BCMassType) aType;
#if 0
#pragma mark == SYMBOL RELATIONSHIP METHODS ==
#endif
/*!
@method isCompoundSymbol
@abstract indicates if symbol is a compound symbol
*/
- (BOOL)isCompoundSymbol;
- (BOOL)isEqualToSymbol:(BCSymbol *)aSymbol;
/*!
@method representedSymbols
@abstract returns an array containing all symbols represented by the receiver
@discussion For instance, when called on adenosine, this method will return an array with a single item, adenosine.
* When called on purine, it will return an array with adenosine and guanidine.
*/
- (NSSet *) representedSymbols;
/*!
@method representingSymbols
@abstract returns an array with all symbols that may represent the receiver
@discussion For instance, when called on adenosine, this method will return adenosine,
* weak, any base, etc.
*/
- (NSSet *) representingSymbols;
/*!
@method representsSymbol:
@abstract Evaluates whether the receiver represents the entry
@discussion For instance, when called on adenosine, this method will return YES if the entry is adenosine,
* It will return NO for anything else.
* When called on weak, will return YES for adenosine and thymidine, but NO for anything else.
*/
- (BOOL) representsSymbol: (BCSymbol *) entry;
/*!
@method isRepresentedBySymbol:
@abstract Evaluates whether the receiver is represented by the entry
@discussion For instance, when called on adenosine, this method will return YES if the entry is adenosine,
* weak, any base, etc.
*/
- (BOOL) isRepresentedBySymbol: (BCSymbol *) entry;
/*!
@method symbolSetWithRepresentedSymbols
@abstract Returns a symbol set containing the symbols of all the symbols that are represented by the receiver.
*/
- (BCSymbolSet *)symbolSetOfRepresentedSymbols;
/*!
@method symbolSetWithRepresentedSymbols
@abstract Returns a symbol set containing the symbols of all the symbols that represent by the receiver.
*/
- (BCSymbolSet *)symbolSetOfRepresentingSymbols;
@end
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