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:[EMAIL PROTECTED] > > Sent: Tuesday, 29 July 2003 4:46 a.m. > > To: Matthew Pocock > > Cc: Schreiber, Mark; [EMAIL PROTECTED] > > 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. > ======================================================================= > > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
