[Biococoa-dev] BCSymbolSet problem

[Koen van der Drift]

On Nov 16, 2004, at 8:24 PM, Koen van der Drift wrote:

>  Hi,
>
> I am having some trouble getting to populate a BCSymbolSet. I am using 
> the code that was originally committed by Alex, and changed it so that 
> BCSymbolSet now is a subclass of NSMutableSet.  To populate a set, I 
> put some code into the dnaStrictSymbolSet and initwithString methods. 
> I also added two lines in the translation demo. You need to uncomment 
> them to debug the symbolset code. Everytime I reach the line 
> addSymbol, the program raises an exception.
>
> I have no idea why this is happening, so if you see what I am doing 
> wrong, let me know!
>
> There is another problem with the current approach. initWithString is 
> now hardcoded to create a BCNucleotideDNA, but what  if the method is 
> called for RNA or a protein? Not sure yet how to solve this. We might 
> need to take a different approach after all.
>


The following solves the second problem:

+ (BCSymbolSet *)dnaStrictSymbolSet
{
	BCSymbolSet *symbolSet = [[BCSymbolSet alloc] init];
	
	NSMutableArray	*symbolArray = [NSMutableArray	array];

	[symbolArray addObject: [BCNucleotideDNA baseForSymbol: 'A']];
	[symbolArray addObject: [BCNucleotideDNA baseForSymbol: 'C']];
	[symbolArray addObject: [BCNucleotideDNA baseForSymbol: 'G']];
	[symbolArray addObject: [BCNucleotideDNA baseForSymbol: 'T']];

	[symbolSet addObjectsFromArray: symbolArray];
	
	return [symbolSet autorelease];
}


But I still crash when I hit the line [symbolSet addObjectsFromArray: 
symbolArray];

 From the debugger I see this:

(gdb) po symbolSet
<object raised exception generating description>

So even if I initialized the object, it causes an error.  But it did do 
something during the initialization:

(gdb) po [symbolSet class]
BCSymbolSet
(gdb) po [symbolSet superclass]
NSMutableSet


A possible solution could be to not subclass NSMutableSet, but let 
BCSymbolSet have a member NSMutableSet.

Any ideas?

cheers,

- Koen.