[Biojava-l] Help

[Hailong Meng]

Hello, Mark and Matthew,

If Meme class works, it will help me a lot. But, I am sorry that I
still have some questions with this class. I think I can use following
code to get a list of motif matrix:
----------------------------------------
Meme meme = new Meme(is, symPaser);
List list = meme.getMotifs();
---------------------------------------

I guess 'is' is the input stream of Meme's output file in TEXT
format. But, what is symPaser? symPaser is a object of
SymbolTokenization. Why I need to input that in the instructor of Meme
and where I get it?

Thanks again!

Hailong
 --


On Tue, 29 Jul 2003, Schreiber, Mark wrote:

> 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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