ee.ut.ga.util
Class PwmUtil

java.lang.Object
  ee.ut.ga.util.PwmUtil

public class PwmUtil

extends java.lang.Object

Field Summary

static org.apache.log4j.Logger

log

Constructor Summary

PwmUtil()

Method Summary

static int	getLength(java.util.Map matrix)
static int	getMotifSetLength(java.util.Map pam)
private static int	getPam(java.util.Map pam, java.lang.String nucleotide, int position)
static java.lang.String	getPattern(java.util.Map pwm, int length)
static java.util.Map	getPwm(java.util.Map pam, java.util.Map priors, int length)
private static double	getPwm(java.util.Map pwm, java.lang.String nucleotide, int position)
static java.math.BigDecimal	getValue(java.util.Map pwm, java.lang.String motif)

Methods inherited from class java.lang.Object

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

Field Detail

log

public static org.apache.log4j.Logger log

Constructor Detail

PwmUtil

public PwmUtil()

Method Detail

getValue

public static java.math.BigDecimal getValue(java.util.Map pwm,
                                            java.lang.String motif)

Returns:

weight of the given motif with specified Position-Weigth-Matrix

getPwm

public static java.util.Map getPwm(java.util.Map pam,
                                   java.util.Map priors,
                                   int length)

Returns:

Position-Weigth-Matrix (Map), calculated using Position-Align-Matrix

getPattern

public static java.lang.String getPattern(java.util.Map pwm,
                                          int length)

Returns:

approximate pattern of Position-Weight-Matrix.

getLength

public static int getLength(java.util.Map matrix)

Returns:

number of columns in matrix (aka length of pattern)

getMotifSetLength

public static int getMotifSetLength(java.util.Map pam)

Returns:

quantity of DNA sequencies used to calculate matrixes.

getPwm

private static double getPwm(java.util.Map pwm,
                             java.lang.String nucleotide,
                             int position)

Returns:

value of Position-Weight-Matrix in specified row and column.

getPam

private static int getPam(java.util.Map pam,
                          java.lang.String nucleotide,
                          int position)

Returns:

value of Position-Align-Matrix in specified row and column.