[Biococoa-dev] BCSequence init methods
Charles PARNOT
charles.parnot at stanford.edu
Wed Feb 9 03:06:27 EST 2005
Another framework-wide commit tonight, with what is described in my previous email (see below). I am very happy with the result. you get exactly the same functionality as before, but with much less code. I also corrected some weird mistakes in the BCSequenceCodon init methods.
Next task is to finally get BCSequence up and running. At that point, I will check the code of the examples to fully comply.
And then, later, I want to discuss the BCSeqenceCodon design. Get ready for some long emails ;-)
charles
At 5:03 PM -0800 2/3/05, Charles PARNOT wrote:
>Hi all!
>
>I commited last night (Pacific time...) the code with the new class 'BCAbstractSequence', the superclass, and changed the subclass header accordingly, and all the methods names etc.. in the framework (like I said before).
>
>In the process of writing the implementation for the BCSequence one-for-all placeholder class, I spent some time looking at the init and factory methods of the whole BCAbstractSequence class tree. I had a few questions, comments and/or suggestions:
>
>* I believe some of the factory methods in the subclasses are redundant; I am talking about the '+dnaSequenceWithString:' and equivalents; normally, defining a '+sequenceWithString' in the superclass is enough, because the type of the returned object is defined by the class used for the call, e.g.
>
> BCSequenceDNA *dna=[BCSequenceDna sequenceWithString:@"ATCGGGT"];
> BCSequenceProtein *prot=[BCSequenceProtein sequenceWithString:@"AOCOCOIB"];
>
> It would make the interface cleaner and more consistent, and reduce the amount of code by factoring it out to the superclass.
>
>* There is this concept of 'skippingNonBases' in the BCSequenceDNA, which could indeed be useful; but this could actually be useful for all the subclasses, proteins as well as DNA (the rationale is to handle pasting from output where there are numbers, spaces and other non-relevant characters); so I thought we could maybe put the code in the superclass and use something more generic like 'skippingUndefinedSymbols' (if you have a better shorter name, I'll take it); again, more consistent interface and more shared code in the superclass
>
>* I still don't know what to do with '-initWithSequence:' if the target and the argument are different sequence types; should we return an empty sequence unless they are the same type?; should we translate?; the latter might seem logical, but this innocent method name would then be hiding quite an important feature... I propose we drop that method (and +sequenceWithSequence), and let the user with 'copy', and then come up with a better name for a method that would do the tranformation of one sequence type into another.
>
>
>I put at the end of the email what I would propose as init and factory methods for the different subclasses. There are not many changes from the current status, in fact. I put some comments to indicate which methods will really need to be implemented in the subclass (well, the code is already done, anyway). This little 'cleaning' would be nice before we add the annotations stuff, what do you think?
>
>
>One more random thought: We probably don't need annotations in the init methods (or at least we can live without for a while). We would just need to set the ivar to nil at init and then alloc it at the first '-addAnnotation:'.
>
>Let me know what you think!
>
>Charles
>
>NB: I think Alex is still away, so I will wait also for his input...
>
>
>
>// ------------------
>// BCAbstractSequence
>// ------------------
>
> //designated initializer
> //override in subclasses
> - (id)initWithString:(NSString *)aString
> skippingUnknownSymbols:(BOOL)skipFlag;
>
> //another initializer
> //(that does not call the designated initializer)
> //(or should this one be the designated initializer?)
> //override in subclasses
> - (id)initWithSymbolArray:(NSArray *)anArray;
>
> //Call the designated initializer
> //do not override in the subclasses
> - (id)initWithString:(NSString *)aString;
> - (id)initWithString:(NSString *)aString
> range:(NSRange)aRange
> skippingUnknownSymbols:(BOOL)skipFlag;
>
> //Factory methods that call the init methods
> //do not override in the subclasses
> + (BCAbstractSequence *) sequenceWithString:(NSString *)aString;
> + (BCAbstractSequence *) sequenceWithString:(NSString *)aString
> skippingUnknownSymbols:(BOOL)skipFlag;
> + (BCAbstractSequence *) sequenceWithString:(NSString *)aString
> range:(NSRange)aRange
> skippingUnknownSymbols:(BOOL)skipFlag;
> + (BCAbstractSequence *) sequenceWithSymbolArray: (NSArray *)entry;
>
> //Call the designated initializer
> //do not override in subclasses
> //(these methods are a bit dangerous when using 2 different subclasses
> // probably better to forget that for now
> // and come up with a better name that clearly implies translation
> // may have to occur for the method to make sense)
> - (id)initWithSequence:(BCAbstractSequence *)entry;
> + (BCAbstractSequence *)sequenceWithSequence:(BCAbstractSequence *)entry;
>
>
>
>// ----------
>// BCSequence
>// ----------
>// placeholder subclass
>
>
> //methods to override
> - (id)initWithString:(NSString *)aString
> skippingUnknownSymbols:(BOOL)skipFlag;
> - (id)initWithSymbolArray:(NSArray *)anArray;
>
> //new methods
> - (id)initWithString:(NSString *)aString
> skippingUnknownSymbols:(BOOL)skipFlag;
> usingType:(BCSequenceType) type;
> + (BCSequence *)sequenceWithString:(NSString *)string
> skippingUnknownSymbols:(BOOL)skipFlag;
>
>usingType:(BCSequenceType) type;
> - (BCSequenceType)sequenceTypeForUntypedString:(NSString *)string;
>
> //automatically inherited methods
> - (id)initWithString:(NSString *)aString;
> - (id)initWithString:(NSString *)aString
> range:(NSRange)aRange
> skippingUnknownSymbols:(BOOL)skipFlag;
> +(BCAbstractSequence *)sequenceWithString:(NSString *)string;
> +(BCAbstractSequence *)sequenceWithString:(NSString *)string
> skippingUnknownSymbols:(BOOL)skipFlag;
> +(BCAbstractSequence *)sequenceWithString:(NSString *)string
> range:(NSRange)aRange
> skippingUnknownSymbols:(BOOL)skipFlag;
> +(BCAbstractSequence *)sequenceWithSymbolArray: (NSArray *)entry;
> - (id)initWithSequence:(BCAbstractSequence *)entry;
> + (BCAbstractSequence *)sequenceWithSequence:(BCAbstractSequence *)entry;
>
>
>
>// ------------
>// BCSequenceDNA
>/ ------------
>
> //methods to override
> - (id)initWithString:(NSString *)aString
> skippingUnknownSymbols:(BOOL)skipFlag;
> - (id)initWithSymbolArray:(NSArray *)anArray;
>
>
> //automatically inherited methods
> //...same as above...
>
>
>// ------------
>// BCSequenceRNA
>// ------------
>
> //methods to override
> - (id)initWithString:(NSString *)aString
> skippingUnknownSymbols:(BOOL)skipFlag;
> - (id)initWithSymbolArray:(NSArray *)anArray;
>
> //new methods
> - (id)initWithString:(NSString *)aString
> skippingUnknownSymbols:(BOOL)skipFlag
> convertingThymidines:(BOOL)convertFlag;
> + (BCSequenceRNA *)rnaSequenceWithString:(NSString *)string
> skippingUnknownSymbols:(BOOL)skipFlag;
> convertingThymidines:(BOOL)convertFlag;
>
> //automatically inherited methods
> //...same as above...
>
>
>
>// ---------------
>// BCSequenceCodon
>// ---------------
>
> //methods to override
> - (id)initWithString:(NSString *)aString
> skippingUnknownSymbols:(BOOL)skipFlag;
> - (id)initWithSymbolArray:(NSArray *)anArray;
>
> //new methods
> - (id)initWithCodonArray:(NSArray *)anArray
> geneticCode:(BCGeneticCodeName)codeType
> frame:(NSString *)theFrame;
> - (BCSequenceCodon *)codonSequenceWithCodonArray:(NSArray *)anArray
>
>geneticCode:(BCGeneticCodeName)codeType
> frame:(NSString *)theFrame;
>
> //automatically inherited methods
> //...same as above...
>
>
>
>// ------------
>// BCSequenceProtein
>// ------------
>
> //methods to override
> - (id)initWithString:(NSString *)aString
> skippingUnknownSymbols:(BOOL)skipFlag;
> - (id)initWithSymbolArray:(NSArray *)anArray;
>
>
> //automatically inherited methods
> //...same as above...
>
>--
>Help science go fast forward:
>http://cmgm.stanford.edu/~cparnot/xgrid-stanford/
>
>Charles Parnot
>charles.parnot at stanford.edu
>
>Room B157 in Beckman Center
>279, Campus Drive
>Stanford University
>Stanford, CA 94305 (USA)
>
>Tel +1 650 725 7754
>Fax +1 650 725 8021
>_______________________________________________
>Biococoa-dev mailing list
>Biococoa-dev at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/biococoa-dev
--
Help science go fast forward:
http://cmgm.stanford.edu/~cparnot/xgrid-stanford/
Charles Parnot
charles.parnot at stanford.edu
Room B157 in Beckman Center
279, Campus Drive
Stanford University
Stanford, CA 94305 (USA)
Tel +1 650 725 7754
Fax +1 650 725 8021
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