Fwd: [Biococoa-dev] Sequence Structure

[Alexander Griekspoor]

To long for the list, so here's the relevant part...

Begin forwarded message:

> From: Alexander Griekspoor <mek at mekentosj.com>
> Date: 13 juli 2005 15:44:06 GMT+02:00
> To: Koen van der Drift <kvddrift at earthlink.net>
> Cc: Charles Parnot <charles.parnot at gmail.com>, BioCocoa-dev  
> <biococoa-dev at bioinformatics.org>
> Subject: Re: [Biococoa-dev] Sequence Structure
>
>
> Just a quick remark:
>
> I thought that the idea was to have the NSData be the char array,  
> so no separate const char*, that IS the NSData object already.
> So to go over the list
>> BCSequence
>>     const char *sequence;
>  -> is NSData so this one goes away, if you want access to the  
> data, you would do: [sequenceData bytes]; which gives you the pointer
>>     NSData *sequenceData;
>>     NSArray *symbolArray;
>  -> this one only if we decide to cache it, otherwise, this would  
> be a method only. So what was the consensus again on this?
>>    BCSymbolSet *symbolSet;
>
> Cheers,
> Alex
>
>
> On 13-jul-2005, at 15:19, Koen van der Drift wrote:
>
>> Hi,
>>
>> After all the talking in the last week or so, I felt like coding  
>> again was playing last night with a possible new BCSequence-only  
>> structure. It will also include the char string and NSData ivars.  
>> For starters, I want to do just the immutable version, of course  
>> we can add stuff for the mutable sequence too later.  I need to  
>> read the chat log again to see if you guys came up with a good  
>> solution for that.
>>
>> However, so far I have:
>>
>> BCSequence
>>     const char *sequence;
>>     NSData *sequenceData;
>>     NSArray *symbolArray;
>>     BCSymbolSet *symbolSet;
>>
>> We can re-use most of the methods that are now in BCSequence and  
>> BCAbstractSequence, including the code that guesses the sequence  
>> type if there is no symbolset defined.  I am not sure if we also  
>> should add the BCSequenceType back in there. I think the symbolset  
>> is enough.
>>
>> Let me know what you guys think of this, and if this is a good way  
>> forward.  In order not to screw up the project I won't commit  
>> anything until we all agree on this (or another) approach. I will  
>> make some code availabe for download, though.
>>
>> cheers,
>>
>> - Koen.
>>

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