[Biococoa-dev] BCSequenceRecord

Koen van der Drift kvddrift at earthlink.net
Sat Jul 9 20:16:20 EDT 2005

On Jul 9, 2005, at 8:06 PM, Alexander Griekspoor wrote:

> About the implementation, even if we use single byte const chars, I 
> still like the idea a lot of Charles to use NSMutableData as the 
> internal datastore and provide an accessor to it. The NSData -bytes 
> method casted to const char will give you direct access to the c 
> array. Indeed the ivars can best be held read only as all editing 
> should occur through class methods that also do the syncing of 
> features/annotations. I would have absolutely no problem (certainly 
> for performance reasons) to just have the accessor be - (NSData 
> *)sequenceData; while internally it really is an NSMutableData. John 
> uses to be very picky about this one, but it is fair I think that the 
> user should respect that things only work for what we tell that we 
> hand him, not what he really gets. I know that also Apple does this, 
> their methods sometimes tell you you will get an NSArray, while in 
> fact it is a NSMutableArray. But don't blame them if you start editing 
> the array and things behave weird. 
> Again the main reason for going for NSMutableData instead of directly 
> using a char array is that we don't have to do the memory 
> allocation/management. For instance from the NSMutableData  documents:
> - (void)replaceBytesInRange:(NSRange)range withBytes:(const void 
> *)replacementBytes length:(unsigned)replacementLength
> Replaces the range within the contents of the receiver with 
> replacementBytes. If the length of range is not equal to 
> replacementLength, the receiver is resized to accommodate the new 
> bytes. Any bytes past range in the receiver are shifted to accommodate 
> the new bytes.
> This is just fantastic instead of having to do all malloc and pointer 
> shifting etc ourselves!

I like the NSData approach. So if we go for NSMutableData, we will have 
mutable sequences, correct? Are we aso going to add immutable 

> Ps. Any clues on the spam stuff, I think none of my 5 messages have 
> yet been posted to the list while you Koen for instance got the direct 
> one immediately so it seems. 

I saw 2 spam messages, and 3 messages from you Alex a few hours ago.

- Koen.

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