edu.mssm.crover.util
Class MotifFinder

java.lang.Object
  |
  +--edu.mssm.crover.util.MotifFinder

public class MotifFinder

extends java.lang.Object

Constructor Summary

MotifFinder()

MotifFinder(boolean logged)

Method Summary

java.util.Collection	findMotif(java.lang.String motif, java.lang.String sequence, boolean multiple) Finds the given motif string in the given sequence string, if it exists, and returns the start position of the motif in the sequence.
java.lang.String	getMotifInSeq()
int	getMotifLength()
java.lang.String	getMotifResiduePositions()
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Constructor Detail

MotifFinder

public MotifFinder()

MotifFinder

public MotifFinder(boolean logged)

Method Detail

findMotif

public java.util.Collection findMotif(java.lang.String motif,
                                      java.lang.String sequence,
                                      boolean multiple)
                               throws InvalidMotifException

Finds the given motif string in the given sequence string, if it exists, and returns the start position of the motif in the sequence. If a start position of -1 is returned, the motif was not found. The motif must be in the form "R-[IP]-X-N-[YHS]-T", i.e., with dashes between each position, where X can represent any residue. The {} (optional) residue finder has not yet been implemented.

InvalidMotifException

getMotifInSeq

public java.lang.String getMotifInSeq()

getMotifLength

public int getMotifLength()

getMotifResiduePositions

public java.lang.String getMotifResiduePositions()

main

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