[Biococoa-dev] strider and gck format

Alexander Griekspoor a.griekspoor at nki.nl
Sat Mar 11 07:19:02 EST 2006

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..

On 11-mrt-2006, at 13:14, Koen van der Drift wrote:

> On Mar 11, 2006, at 4:44 AM, Alexander Griekspoor wrote:
>> Both the GCK and the Strider files are inherited from the good old  
>> MacOS9 period. In those days you would identify files using a type/ 
>> creator code, and that's what I check for in this code. You will  
>> never see these 4 character codes unless you use a program like  
>> resedit, and they are not the same as file extensions, in fact  
>> under MacOS9 you would never use file extensions unless you wanted  
>> your Windows buddies to open your word file as well. So  
>> NSHFSTypeOfFile is not the same as [filepath pathExtension].
>> The problem is that both filetypes are in binary format compared  
>> to the other formats which are ASCII based. Trying to read in the  
>> file as a string with ascii encoding creates some garbage which is  
>> impossible to interpret, let alone determine the filetype from. So  
>> the options were to either read all files in as data and check if  
>> it would fit the header of either filetype, and try to make  
>> anything out of that (quite tricky!) or simply to the filetype  
>> check. As a result I changed the code to have it pass the filepath  
>> instead of the raw text to the reader class. It better isolates  
>> code (no more reading at all in the delegate class), but we  
>> sacrifice the possibility to work with remote files. Guess this  
>> could be easily added to through a readFileFromURL method.
>> Now that I think of it, perhaps we should also check for the file  
>> extensions that are added to GCK files if you create them on the  
>> windows platform. I'm not sure if in those files the creator/type  
>> codes are added, I could check that on monday...
>> Hope this clears things up?
> Yes, thanks!  I was trying to test your code in the framework using  
> the Translation example. So I found some strider test file and read  
> that in with the current code in Translation. The file works fine  
> with your demo app. However in Translation it doesn't. Right now I  
> use:
> BCSequenceArray *sequenceArray = [sequenceReader readFileUsingText:  
> [[NSBundle mainBundle] pathForResource: @"Strider" ofType:@"seq"]];
> But that doesn't work. Maybe that should be changed to:
> BCSequenceArray *sequenceArray = [sequenceReader readFileUsingPath:  
> [[NSBundle mainBundle] pathForResource: @"Strider" ofType:@"seq"]];
> I agree with you that passing the filepath is a better way of doing  
> things. I will look into that this weekend.
> cheers,
> - Koen.
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Mek (Alexander Griekspoor)
Web: http://www.mekentosj.com
Mail:  mek at mekentosj.com

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