[Biojava-l] Help

Schreiber, Mark mark.schreiber at agresearch.co.nz
Tue Jul 29 10:39:28 EDT 2003


Hi -

There is a class called Meme in org.biojava.bio.program that appears to
be able to read in Meme files and produce a List of WeightMatrices using
the getMotifs method. I haven't used it much so if you get any errors
let us know and we can fix them up.

- Mark


> -----Original Message-----
> From: Hailong Meng [mailto:hmeng at cise.ufl.edu] 
> Sent: Tuesday, 29 July 2003 4:46 a.m.
> To: Matthew Pocock
> Cc: Schreiber, Mark; biojava-l at biojava.org
> Subject: Re: [Biojava-l] Help
> 
> 
> Hi Mark,
> 
> But, how can I input the matrixes from the file to the class 
> WeightMatrix. Because I did not find any method in class 
> WeightMatrix which can do that.
> 
> Thanks again.
> 
> Hailong
> -- 
> 
> 
> On Mon, 28 Jul 2003, Matthew Pocock wrote:
> 
> > Hi Hailong,
> >
> > List is nicer than arrays - use something like this:
> >
> > List matricies = new ArrayList();
> >
> > ... loop that loads the next matrix in ...
> >    matricies.add(matrix);
> > ... end of matrix loading loop ...
> >
> > See java.util.List and java.util.Collection - also, 
> Iterator is your 
> > friend. The sun web site has a tutorial on collections.
> >
> > Matthew
> >
> >
> > Hailong Meng wrote:
> >
> > > Hi, Mark,
> > >
> > > Thank you very much for your suggestions! I am so excited when I 
> > > find BioJava. It is a wonderful place. Maybe I am new 
> here, it is a 
> > > little bit hard for me to find the classes I want to use. 
> Hopefully, 
> > > it will get better when I stay here a little longer.
> > >
> > > I have one more question. I plan to search a list of 
> motifs against 
> > > a list of sequences. I got motifs from MEME and put all the motif 
> > > matrixes to a file. I guess I need to put all these motif 
> matrixes 
> > > to a array of WeightMatrix. How can I do that?
> > >
> > > Thanks.
> > >
> > > Hailong
> > >
> >
> >
> >
> 
> 
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