edu.mssm.crover.tools.tm
Class tmMotif

java.lang.Object
  |
  +--edu.mssm.crover.tools.tm.tmMotif

public class tmMotif

extends java.lang.Object

Finds motifs given by the user in specified TM domains, or loop segments, or returns the TM domain or loop segment that the motif is found in.

Constructor Summary

tmMotif()

Method Summary

static int[]	getGenStart()
static java.lang.String	getInputFile(java.lang.String[] args) get name of input file with sequences
static java.lang.String	getMotif(java.lang.String[] args) get the motif with which to search
static void	main(java.lang.String[] args)
static Sequence[]	parseSeqs(SequenceReaderFactoryImpl sr, java.lang.String seqfile) Reads the sequences from the file into the Sequence array.
static void	printHelpFile()

Methods inherited from class java.lang.Object

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

Constructor Detail

tmMotif

public tmMotif()

Method Detail

getGenStart

public static int[] getGenStart()

getInputFile

public static java.lang.String getInputFile(java.lang.String[] args)

get name of input file with sequences

getMotif

public static java.lang.String getMotif(java.lang.String[] args)

get the motif with which to search

parseSeqs

public static Sequence[] parseSeqs(SequenceReaderFactoryImpl sr,
                                   java.lang.String seqfile)
                            throws java.io.FileNotFoundException,
                                   java.io.IOException

Reads the sequences from the file into the Sequence array.

java.io.FileNotFoundException

java.io.IOException

printHelpFile

public static void printHelpFile()

main

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