[Biococoa-dev] BCSequence init methods

[Charles PARNOT]

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