[Biococoa-dev] New Structure for BioCocoa

[Philipp Seibel]

Ok this will lead us to the structure of the diagram i sent arround,  
right ?
Or do you want to put the BCParser.framework also into the  
BCFoundation ?

I think it would be better to have the BCParser.framework separate,  
because one could use it to read the files in other structures than  
the bcfoundation structures.
This will of course cause a dependancy between bcfoundation and  
bcparser framework.

.... the next one please ;-)

Phil

Am 04.07.2005 um 11:23 schrieb Peter Schols:

> I fully agree with Alex. It seems most logical to me if IO would be  
> part of BCFoundation.
>
> peter
>
>
> On 04 Jul 2005, at 10:50, Alexander Griekspoor wrote:
>
>
>> About the IO discussion.
>> If we want a separate IO framework(s), I would suggest to keep all  
>> IO in one framework, the examples you give are all sequence  
>> related, so would depend only on the core framework (BCFoundation)  
>> right. If say the HMM framework would need some kind of special  
>> structure, than we can always opt to either define the structure  
>> in the foundation, but put all other stuff in the HMM framework,  
>> or place the HMM specific IO in the HMM framework as it is  
>> probably consists of only a few  methods anyway.
>> But my main question is whether we really want to separate the IO  
>> framework as being independent. BCFoundation is so much related  
>> with IO that I don't really see a need to separate them. Most  
>> important, I don't think the IO will be so much code that it will  
>> be a large framework, or that it will make the foundation so  
>> bloated. It's two files right now! So why don't we make  
>> BCFoundation contain the IO like it does now. And the HMM  
>> framework contains its IO etc.
>> IMHO a basic core that defines sequences and can IO them doesn't  
>> have to be separated in two, I see it as one core. Similar to the  
>> fact that NSString can also IO them without the need of an IO  
>> framework.
>> Cheers,
>> Alex
>>
>>
>>
>> On 4-jul-2005, at 1:20, Koen van der Drift wrote:
>>
>>
>>>
>>> On Jul 3, 2005, at 3:12 PM, Philipp Seibel wrote:
>>>
>>>
>>>
>>>> Sorry, but i got lost :-). I just meant that we can't put all io  
>>>> of all Frameworks in one IOFramework, because this IOFramework  
>>>> will then depend on all Frameworks ( Foundation ,HMM,  
>>>> Phylogenetics, etc.) because it will use the structure classes  
>>>> of all of them. To solve this problem, we will need a seperate  
>>>> IOFramework for each of the Frameworks.
>>>>
>>>>
>>>>
>>>
>>> Aha, but now I understand :) I didn't realize that you were  
>>> assuming different data structures for each data format.  Maybe  
>>> we should put some effort in creating a general internal data  
>>> format that will also allow easy  exchange between the various  
>>> formats.
>>>
>>> cheers,
>>>
>>> - Koen.
>>>
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>>>
>>
>> *********************************************************
>>                       ** Alexander Griekspoor **
>> *********************************************************
>>                 The Netherlands Cancer Institute
>>                 Department of Tumorbiology (H4)
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