Class MotifSearch

java.lang.Object
  MotifSearch

Direct Known Subclasses:

EM_MotifSearch

public class MotifSearch
extends java.lang.Object

An instance of the MotifSearch class represents a search for a motif common to a set of genomic sequences.

Field Summary

protected java.util.Vector<java.lang.Integer>	instanceLocations A collection of integers where each integer represents the index of the start location of a motif instance in a genomic sequence
protected double[][]	matrix A 2D array corresponding to a position-specific scoring matrix (PSSM) that is a model of the motif being searched for
protected int	motifLength The length of the motif being search for
protected int	numSequences The number of genomic sequences
protected java.util.Vector<java.lang.String>	sequences A collection of genomic sequences

Constructor Summary

MotifSearch(java.lang.String fileName, int motifLength)
Creates an initially empty MotifSearch.

Method Summary

void	addPseudocountsToMatrix() Replaces values of 0.0 in the matrix (motif model) with small pseudocount values (0.0001).
java.lang.String	getConsensusSequence() Returns the consensus sequence for the motif.
java.util.Vector<java.lang.Integer>	getInstanceLocations() Returns a copy of the indices of start locations of motif instances in the sequences.
double[][]	getMatrix() Returns a copy of the matrix that models the motif.
double	getNucleotideContent(char c) Returns a double representing the frequency that the specified nucleotide character occurs in the genomic sequences.
static void	main(java.lang.String[] args) The main method creates an initially empty MotifSearch for a motif of the specified length in the genomic sequences found in the specified FASTA file.
java.lang.String	matrixToString() Returns a String representation of the matrix that models the motif.
java.lang.String	motifInstancesToString() Returns a String representation of motif instances found in the genomic sequences.

Methods inherited from class java.lang.Object

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

Field Detail

sequences

protected java.util.Vector<java.lang.String> sequences

A collection of genomic sequences

numSequences

protected int numSequences

The number of genomic sequences

motifLength

protected int motifLength

The length of the motif being search for

matrix

protected double[][] matrix

A 2D array corresponding to a position-specific scoring matrix (PSSM) that is a model of the motif being searched for

instanceLocations

protected java.util.Vector<java.lang.Integer> instanceLocations

A collection of integers where each integer represents the index of the start location of a motif instance in a genomic sequence

Constructor Detail

MotifSearch

public MotifSearch(java.lang.String fileName,
                   int motifLength)

Creates an initially empty MotifSearch.

A set of genomic sequences is determined from the specified String representing the name of a file. Genomic sequences are read-in from the FASTA file. The integer parameter represents the desired length of the motif being searched for. Initially, the constructed MotifSearch is empty.

Parameters:

fileName - the name of a FASTA file containing one or more genomic sequences

motifLength - the length of the desired motif

Method Detail

matrixToString

public java.lang.String matrixToString()

Returns a String representation of the matrix that models the motif.

Returns:

a String represenation of the matrix modeling the motif

motifInstancesToString

public java.lang.String motifInstancesToString()

Returns a String representation of motif instances found in the genomic sequences.

Returns:

a String represenation of motif instances found in the genomic sequences

addPseudocountsToMatrix

public void addPseudocountsToMatrix()

Replaces values of 0.0 in the matrix (motif model) with small pseudocount values (0.0001).

getNucleotideContent

public double getNucleotideContent(char c)

Returns a double representing the frequency that the specified nucleotide character occurs in the genomic sequences.

Parameters:

c - a nucleotide character (e.g., A or C or G or T)

Returns:

a double representing the frequency that c occurs in the sequences

getMatrix

public double[][] getMatrix()

Returns a copy of the matrix that models the motif.

Returns:

a 2D array represenation of the matrix modeling the motif

getInstanceLocations

public java.util.Vector<java.lang.Integer> getInstanceLocations()

Returns a copy of the indices of start locations of motif instances in the sequences.

Returns:

a collection of indices of start locations of motif instances in the sequences

getConsensusSequence

public java.lang.String getConsensusSequence()

Returns the consensus sequence for the motif. IUPAC symbols are used as the alphabet for the consensus sequence.

Returns:

a String representing the consensus sequence for the motif

main

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

The main method creates an initially empty MotifSearch for a motif of the specified length in the genomic sequences found in the specified FASTA file.

Parameters:

args - an array of Strings representing any command line arguments