meme
Class MotifScanner

java.lang.Object
  meme.MotifScanner

public class MotifScanner

extends java.lang.Object

MotifScanner objects are used to scan sequences with a particular weight matrix and generate an array of MotifHit objects.

Constructor Summary

MotifScanner(double[][] logLikelihoodMatrix)

MotifScanner(double[][] logLikelihoodMatrix, MemeResults res)

Method Summary

static int	calculateMaxCluster(MotifHit[] hits, int window) Calculates the maximum number of hits that occur within a given window size.
double	findLowestScoringSeq(java.lang.String[] seqs) Returns the lowest score from scoring all the seqs.
double[]	getBaseScores()
java.util.ArrayList	getMotifHits()
int	scanEm(java.lang.String[] seqs, java.lang.String[] names, double cutOff) Scans a set of sequences for the motif, saves results in a MemeResults object.
void	scanPrintAllSequences(java.lang.String[] seqs, java.lang.String[] names) Scans a set of sequences for the motif, prints as it goes.
void	scanPrintSequences(java.lang.String[] seqs, java.lang.String[] names, double cutOff) Scans a set of sequences for the motif, prints as it goes.
void	scanSequence(java.lang.String seq) Scans a sequence for the motif, scores every window, forward and reverse complement, assigning the higher score to the center base.
MotifHit[]	scoreSequence(double cutOff, java.lang.String seq) Returns an array of MotifHits that are > or = to the loglikelihood cutOff.
double	scoreSubSeq(java.lang.String seq) ignores non GATC chars

Methods inherited from class java.lang.Object

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

Constructor Detail

MotifScanner

public MotifScanner(double[][] logLikelihoodMatrix,
                    MemeResults res)

MotifScanner

public MotifScanner(double[][] logLikelihoodMatrix)

Method Detail

getMotifHits

public java.util.ArrayList getMotifHits()

calculateMaxCluster

public static int calculateMaxCluster(MotifHit[] hits,
                                      int window)

Calculates the maximum number of hits that occur within a given window size. Assumes that the array hasn't been sorted and is ordered by position.

findLowestScoringSeq

public double findLowestScoringSeq(java.lang.String[] seqs)

Returns the lowest score from scoring all the seqs. Usefull in getting a cutOff score when the seqs are the seqs used to generate the matrix. All the seqs must be the same size as the matrix!

scanEm

public int scanEm(java.lang.String[] seqs,
                  java.lang.String[] names,
                  double cutOff)

Scans a set of sequences for the motif, saves results in a MemeResults object.

scanPrintSequences

public void scanPrintSequences(java.lang.String[] seqs,
                               java.lang.String[] names,
                               double cutOff)

Scans a set of sequences for the motif, prints as it goes.

scanPrintAllSequences

public void scanPrintAllSequences(java.lang.String[] seqs,
                                  java.lang.String[] names)

Scans a set of sequences for the motif, prints as it goes.

scoreSequence

public MotifHit[] scoreSequence(double cutOff,
                                java.lang.String seq)

Returns an array of MotifHits that are > or = to the loglikelihood cutOff. Set cutOff to a very negative number (ie -20*lengthOfMotif) if you want all the MotifHits. Will not score any non GATC containing sequences. Searches both strands but returns coordinates for either in forward direction. Also assigning the higher score to the center base for every window (baseWindow double[]) where index 0 in the double[] is base 1 in the seq. 0s will be found at the beginning and end. Scores < 0 are assigned 0.

scanSequence

public void scanSequence(java.lang.String seq)

Scans a sequence for the motif, scores every window, forward and reverse complement, assigning the higher score to the center base. Index 0 in the double[] is base 1 in the seq. 0s will be found at the beginning and end. Scores < 0 are assigned 0

scoreSubSeq

public double scoreSubSeq(java.lang.String seq)

ignores non GATC chars

getBaseScores

public double[] getBaseScores()