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)


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.