meme
Class MemeR

java.lang.Object
  meme.MemeR

public class MemeR

extends java.lang.Object

Main, wRapper for meme geared toward processing multiple rounds of selex data. This is a major revision of MemeR, I've equipped it for mass data processing. Multiple files can be submitted. Each is searched for the presence of motifs using UCSD's meme program. These motifs are stored and then used to search the the sequences in each file for the presence of the motif, hits above a user defined cut off. Multiple results and summary tables are printed and saved. The program works by first firing the main method in MemeR which in turn creates a MemeResults object that will hold most of the data generated by the program. User inputs are processed asking for: 1)parsed selex multi-FASTA files separated by a comma 2)meme command line arguments 3)a meme cutoff score 4)a directory to save the result files 5) a basename to use in naming the result files. UCSD's meme is then fired for each file entered. A MemeParser is created to parse the meme output, a MemeMotif is created for each motif parsed from the meme output. Once the motifs have been created. A MotifScanner object is created from a motif and a fasta file and executes a search for motif hits. A MotifSearchResult object is used to hold the results from this search. If there were any hits, these are stored as an array of MotifHit objects in the MotifSearchResult object. So here's the flow MemeR->MemeParser->MemeMotif(s) MemeMotif->MotifScanner->MotifSearchResult->MotifHit(s) Lastly, several MemeResults methods are called from MemeR to print various reports/ summaries to the screen and also write them to file. These include a summary of the motifs identified, a summary table of motif hits in each file, and a crude printed graph showing the percentage of sequences in each multi-fasta file that contained each motif. nix@uclink.berkeley.edu 22 Oct 2004 MemeR(0.2.1)

Constructor Summary

MemeR()

Method Summary

void	fireMeme()
void	getUserInputs() Uses JOptionPane dialog input boxes to get user inputs
static void	main(java.lang.String[] args)
static java.lang.String	makeInputDialog(java.lang.String title, java.lang.String comment, java.lang.String suggestion)
void	searchDataFiles()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MemeR

public MemeR()

Method Detail

main

public static void main(java.lang.String[] args)

fireMeme

public void fireMeme()

searchDataFiles

public void searchDataFiles()

getUserInputs

public void getUserInputs()

Uses JOptionPane dialog input boxes to get user inputs

makeInputDialog

public static java.lang.String makeInputDialog(java.lang.String title,
                                               java.lang.String comment,
                                               java.lang.String suggestion)