[Biojava-dev] Code Update

[Andy Yates]

Talking about code updates I've got DNA -> RNA -> Peptide working  
quite well. It's about a day or two of tinkering away from being  in a  
sensible state. There's also some utilities I've gone & created;  
they've gone into org.biojava3.core.util ... anyone got any better  
suggestions as to where they should live?

Andy

On 26 Jan 2010, at 18:45, Andreas Prlic wrote:

> the cookbook approach seems to work quite well. You could start a new
> "Chapter" in the book and make it clear that this will be only
> available once biojava 3 has been released (or via SVN checkout)
>
> Andreas
>
> On Tue, Jan 26, 2010 at 10:09 AM, Scooter Willis  
> <HWillis at scripps.edu> wrote:
>>
>> I checked in updates with test cases for Fasta fileparsing where  
>> the main focus is on the fasta header.  The test cases are based on  
>> the wikipedia examples so results will vary with actual files. It  
>> is very easy now to do a custom header parser so we have lots of  
>> flexibility.  I also started the code for the file pointer sequence  
>> proxy where the key usage is creating a sequence with the header  
>> and storing a reference to the file and offset in the file for the  
>> start of the sequence. When a method is called related to getting a  
>> sequence/subsequence the init() method is called to load the  
>> sequence data via RandomAccessFile with a seek to the offset. It  
>> turns out that none of the java io classes will actually return an  
>> offset index of the actual bytes read. This also gets complicated  
>> with the readline() methods where the CR and/or LF is stripped off  
>> when the string is returned so you can't keep track of it  
>> externally. I copied the BufferedReader.java class to  
>> BufferedReaderBytes!
>>  Read.java and keep track of the file pointer internally. This code  
>> still needs to be tested. This should be a great way to load large  
>> date sets with minimal memory. To complete this approach I will  
>> probably do a collection that is proxy aware that can go through  
>> and free up storage by returning a sequence to its proxy state.
>>
>> I will work this week on getting some wiki pages created to give  
>> examples on using the header parsing interface and proxy sequences.  
>> How do we want to organize wiki pages related to biojava3 work?
>>
>> Thanks
>>
>> Scooter
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>
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