[Biojava-l] Help

[Schreiber, Mark]

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
> > >
> >
> >
> >
> 
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================