[Biococoa-dev] strider and gck format

Alexander Griekspoor a.griekspoor at nki.nl
Mon Mar 13 05:10:17 EST 2006

Hi Koen,

Indeed hard-coding a path isn't very elegant ;-) I'm not sure whether  
we need the sequenceIOcontroller though.
I would let the app decide how to do the interface and obtain the  
file path/url, after that everything can be done in the reader/writer  
The reason is that 1) interfaces can be very different (i.e. metal or  
not), 2) implementations can be very different. An an example, in  
iRNAi i use the code that I included in previous emails, in EnzymeX 3  
I make use of the standard NSDocument routines. No need to do any  
panel at all, just subclassing the read/writeFileFromPath:ofType:  
methods, all the panel stuff is handled by NSDocument itself. It  
might even be nice to have one demo app use this approach and one the  
iRNAi type approach.

On 12-mrt-2006, at 14:52, Koen van der Drift wrote:

> On Mar 11, 2006, at 7:19 AM, Alexander Griekspoor wrote:
>> Just to make sure, you can also export DNA strider files in a  
>> ascii format, I've attached a native file for you to test that is  
>> in the default binary format.
>> Again, you can't use text, trying to read in a binary file as  
>> ascii text will destroy the header..
> Thanks Alex,
> I was struggling some more with the Translation demo to get your  
> sample file to work. Apparently hard-coding the path as we do now  
> is not a good approach (at least in my hands). So I was thinking to  
> add your openPanel code to the Translation demo. Or even better, we  
> could have an openPanel controller class in our BCAppKit that can  
> be used in various programs. It could then also be used to get  
> sequences using NSURL.
> Let me know what you guys think of this approach, so I can start  
> working on that class (BCSequenceIOController seems like a useful  
> name). I won't have much time today though, it's going to be > 25  
> ûC, so I don't feel like sitting behind my computer :)
> cheers,
> - Koen._______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
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                       ** Alexander Griekspoor **
                 The Netherlands Cancer Institute
                 Department of Tumorbiology (H4)
           Plesmanlaan 121, 1066 CX, Amsterdam
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                    AIM: mekentosj at mac.com
                     E-mail: a.griekspoor at nki.nl
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