[Biococoa-dev] New Structure for BioCocoa

Philipp Seibel biococoa at bioworxx.com
Sun Jul 3 08:06:18 EDT 2005

Am 03.07.2005 um 13:45 schrieb Koen van der Drift:

> On Jul 3, 2005, at 6:12 AM, Philipp Seibel wrote:
>>> I like the parser idea, particularly if it is already written by  
>>> you ;-)
>>> I won't be of any help with C++, though!
>> this is no problem, because there is no much need of c++ except  
>> from expression templates.
>> The parser isn't allready written by me sorry ;-), but i'm working  
>> on it.
>> I'd like to know the different sequence formats i should  
>> implement, that i can finish the parsers for the sequence io first.
> Check out BCSequenceReader and BCReader (deprecated, but still in  
> the project for reference) for some formats, just note that these  
> methods still need a lot of work, annotations and features are  
> still not completely implemented. Note that there a re already  
> various parsers out there that could be of help, eg lucegene,  
> bioperl and more.
> What I don't understand yet is why the sequence parser framework is  
> at the bottom of your picture. This implies to me that it is the  
> basis for all the other frameworks? Why not put BCFoundation with  
> BCSymbol and BCSequence there, that seems much more logical to me.

In terms of importance you are right, but i wanted to show that you  
can't use BCFoundation without BCParser, because the BCFoundation-IO  
depends on the parsers. The same with all other BCXXXFrameworks.

>> Very good summary of the discussion.
>> I think we should try to implement the string thing in different  
>> ways and test the performance, to see which one is the best.
> Maybe you can already post some sample code here, so we can get an  
> idea what you have in mind.

Just give me one more week. I started the project a couple of days  

Here is a short description:

The base class is a BCParser, that can be instantiated with NSData or  
contentsOfURL etc. (just like NSXMLParser). The parser has a event  
driven architecture, which means that it calls delegate methods  
whenever it founds specific information in the parsed data  
(NSXMLParser ;-)). Errors are reported with the NSError class. Here  
is a first unfinished example of the BCGenBankParser delegate methods:

@interface NSObject (BCGenBankParserDelegateMethods)

- (void)parserDidBeginSequence:(BCParser *)parser;

// General Information
- (void)parser:(BCParser *)parser foundDefinition:(NSString *) 
- (void)parser:(BCParser *)parser foundAccession:(NSString *)accession;
- (void)parser:(BCParser *)parser foundKeywords:(NSArray *)keywords;

// References
- (void)parser:(BCParser *)parser didBeginReferenceForRange:(NSRange) 
- (void)parser:(BCParser *)parser foundReferenceAuthors:(NSArray *) 
- (void)parser:(BCParser *)parser foundReferenceTitle:(NSString *)title;
- (void)parser:(BCParser *)parser foundReferenceJournal:(NSString *) 
- (void)parserDidEndReference:(BCParser *)parser;

- (void)parser:(BCParser *)parser foundSequence:(NSString *)sequence;

- (void)parserDidEndSequence:(BCParser *)parser;


thats it for the moment.
feel free to comment the concept.



> cheers,
> - Koen.

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