Thanks for all the comments, it should get me started. I do not intend to write a file-format guesser (out of my scope) but I would like to make an RFE for it here and now. I think many people would benefit from it.
Cheers, .../Ola On Tue, 2005-11-29 at 14:34, Kalle Näslund wrote: > Ola Spjuth wrote: > > >Hi, > > > >I am investigating the usefulness of BioJava as a backend for sequence > >management in Bioclipse (www.bioclipse.net). As a total newbie to > >Biojava, I have read the tutorial, BIA examples, glanced at the API, > >read my first FASTA-sequence and have come up with a few questions: > > > >1) Is it possible to search the Biojava-l archives without having to > >manually browse by month? > > > >2) Is there a wrapper for SequenceIO.fileToBiojava(..) that > >automatically detects file formats or is it necessary to distinguish > >sequence formats externally, i.e. with different file-extensions? If so, > >does anyone know of a complete list of file-extensions that could be > >mapped to a format? > > > > > There is a deprecated piece of code available, that quite many people > actualy use > in their code still. Even though it might not be the greatest thing to > try to auto > guess file format, its the desireable thing to do in many cases. > If i just look at people in my lab, they want to open the file, they > dont want to keep > track of what file format that particular sequence was in, and so on. > > So, even if file format guessing is bad, people are going to write it, > and imho its > better to have one centralised good, known to work file guesser, then > several > different implementations that differ in each persons own application. > > So, my suggestion is to start with using the deprecated version thats in > biojava, if > it gets removed you can easily just copy that small part of the code > into your own > application, or as an external little jarfile. > > >3) How robust are the I/O-classes for different formats? The > >test-library provided is rather short in my opinion and my first test > >broke since there was a space in the wrong position... > > > >4) What are the capabilities for multiple sequence alignment in Biojava? > >Is it limited to parse results into Biojava objects (as in BIA) or does > >it contain any stable MSA-implementations? Due to BioJavas size it is > >not easy to get an overview of the current capabilities and the standard > >of different parts. > > > > > > There is some support for multiple alignments in biojava. The Alignment > interface > and implementations happily handle multiple alignments. And you can > choose how > to interpret it, either as SymbolList over a crossproduct alphabet, or > as individual > sequences accessable by some label. > > There is a basic framework for handling multiple alignment formats in > the biojava > org.biojava.bio.seq.io package. It currently only implements two > formats, FASTA > and MSF. Most programs seem to be able to generate multiple alignment > output > into either FASTA or MSF format so you should be able to get the results > into > biojava. > > >5) As a novice, has anyone implemented BLAST or CLUSTALW in Java? Any > >public web-services running for this? > > > > > > > I have been told by greater deities that implementing BLAST in java is > hard, because > the blast algorithm makes heavy use of low level data structures, > pointers ? and similar > things that are very hard to implement and controll in java. So the > resulting implementation > would most likely run pretty darn slow, and not do what you want. > > Depending on what you want to do with BLAST, the biojava SSAHA > implementation > might be something you can use instead ( it works pretty ok on quite > conserved sequences, > but its not realy suited for more divergent sequences ) > > When it comes to webservices i just know of a few things, i have not > used any of these > to an large extent, so i cant comment on how well they work for large > sequences, big > jobs and so on. > > http://www.ebi.ac.uk/Tools/webservices/services.html > http://xml.ddbj.nig.ac.jp/wsdl/index.jsp > > Sadly they all use their own data encoding and service invocation setup, > so its pretty darn > annoying to use. > > > >6) Is there some example-code on how to use DAS (as a client)? > > > >7) How can I submit an RFE? > > > >Sorry for so many questions in one post; I have a lot of catching up to > >do and was hoping for some guidance. Some answers have probably already > >been answered in earlier posts but I have not been able to search the > >archives. > > > >Cheers, > > > > .../Ola > > > > > > > > > >_______________________________________________ > >Biojava-l mailing list - Biojava-l@biojava.org > >http://biojava.org/mailman/listinfo/biojava-l > > > > -- Ola Spjuth <[EMAIL PROTECTED]> _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
