[Biojava-dev] Parser backwards compatibility

[P. Troshin]

> So what you're looking for is something like this?
> FastaParser fasta = ParserFactory.fasta("example.fasta");
> FastqParser fastq = ParserFactory.fastq("example.fastq");

Yes, only that I expect to construct a parser from an InputStream as well.
I agree with Hannes that having a factory you could guess the input
format and instantiate an appropriate parser. However, I do not see
this as a particularly important feature because in the real life you
usually know which format you work with.

Regards,
Peter


On 14 April 2012 14:50, David Felty <davfelty at gmail.com> wrote:
> Michael Heuer wrote:
>> Open source projects should projects should provide room for
>> both evolutionary and revolutionary changes
>
> Thanks for all the info, very useful!
>
>
> P. Troshin wrote:
>> I think you just need to make a common entry point for them.
>> E.g a factory class which would contain functions to
>> instantiate various parsers.
>
> So what you're looking for is something like this?
> FastaParser fasta = ParserFactory.fasta("example.fasta");
> FastqParser fastq = ParserFactory.fastq("example.fastq");
>
> Scooter Willis wrote:
>> Can you give some examples of what you are trying to do for
>> the common set of interfaces?
>
> I gave this example in my proposal at
> http://www.google-melange.com/gsoc/proposal/review/google/gsoc2012/dfelt/2001
>
> for (BasicSequence seq : SeqIO.parse(inStream, SeqFormat.FASTA) {
>     System.out.println(seq.getSequenceAsString());
> }
>
> But I think Troshin's idea would be easier to implement, given
> the current BioJava parsers.
>
> On Apr 13, 2012 1:31 PM, "P. Troshin" <to.petr at gmail.com> wrote:
>>
>> Hi David,
>>
>> > In order to fit BioJava's parsers into a shared API, I would like to
>> > wrap them under a common set of interfaces.
>>
>> I think you just need to make a common entry point for them. E.g. a
>> factory class which would contain functions to instantiate various
>> parsers.
>> You only need a common interface for the same parsers, e.g. Fasta
>> parsers. However, I'd be inclined to converge all Fasta parsers in
>> BioJava to one parser. So I am not sure you'd need a common interface
>> in the end.
>>
>> >However, I foresee that
>> > some of the parsers will resist being wrapped, and will need to either
>> > be modified or rewritten.
>>
>> You'll need to choose the best parser and implement features that a
>> lacking from it. Other parsers then can be retired.
>>
>>
>> >However, this would mean that two different
>> > copies of the same parsers would exist in BioJava, which I think is
>> > kind of ugly.
>>
>> Yes, that would be scary for the languages like Perl or Python, but
>> Java is compiled language, so you'll see most of the problems as
>> compilation errors. You will also need to write unit tests for
>> existing parsers and then for your new parser to make sure that
>> rewrite were successful.
>>
>> >However, this would mean that two different
>> > copies of the same parsers would exist in BioJava, which I think is
>> > kind of ugly.
>>
>> The whole idea of this project is to get rid of this ugliness, and
>> provide a streamline API for the users as well as the powerful
>> parsers.
>>
>> Hope that helps.
>> Regards,
>> Peter
>>
>>
>> On 13 April 2012 14:47, David Felty <davfelty at gmail.com> wrote:
>> > In order to fit BioJava's parsers into a shared API, I would like to
>> > wrap them under a common set of interfaces. However, I foresee that
>> > some of the parsers will resist being wrapped, and will need to either
>> > be modified or rewritten. So my question is, should I keep the
>> > original versions these problematic parsers around for backwards
>> > compatibility, or can I freely modify them to fit into the new API?
>> > I'm afraid that the latter would break existing code, so I'm more
>> > inclined to do the former. However, this would mean that two different
>> > copies of the same parsers would exist in BioJava, which I think is
>> > kind of ugly. Any thoughts?
>> >
>> > Thanks,
>> > David
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