util.bio.calc
Class Alignment

java.lang.Object
  util.bio.calc.Alignment

public class Alignment

extends java.lang.Object

Methods associated with alignments, pvalues, blast.

Constructor Summary

Alignment()

Method Summary

static int[]	calculateEffectiveMandN(double m, double n, double K, double H) Calculates effective m and n using BLAST parameters, returning int[m', n']
static java.lang.String	calculateEValue(double lambdaNats, double K, int rawS, double effectiveN, double effectiveM) Calculates an E value given a variety of alignment parameters
static double	convertBitScoreToRaw(double lambdaNats, double K, double bitS) Converts a nat bit score to raw S.
static double	convertRawScoreToBit(double lambdaNats, double K, double rawS) Converts a raw S score to a bit score given lambda (in nats) and K
static double	estimatePValue(double z) Calculates the standard normal cumulative distribution given a z-ratio.
static double[]	fetchBLASTParams(int match, int misMatch) Returns Lambda, K, H or null for a given match and misMatch from BLASTN.
static int	ScoreDNAAlignment(java.lang.String seq1, java.lang.String seq2, int match, int misMatch, int gapCreate, int gapExtend) Will score a DNA alignment given the two sequences, and scoring parameters.
static double	transform10Log10(double num) Calculates a -10Log10(number) transformation

Methods inherited from class java.lang.Object

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

Constructor Detail

Alignment

public Alignment()

Method Detail

estimatePValue

public static double estimatePValue(double z)

Calculates the standard normal cumulative distribution given a z-ratio. AKA The area under the curve in the tail. Returns 0 or 1 if z>6 or Z<-6, respectively. Taken from http://finance.bi.no/~bernt/gcc_prog/recipes/recipes/node23.html

transform10Log10

public static double transform10Log10(double num)

Calculates a -10Log10(number) transformation

convertRawScoreToBit

public static double convertRawScoreToBit(double lambdaNats,
                                          double K,
                                          double rawS)

Converts a raw S score to a bit score given lambda (in nats) and K

convertBitScoreToRaw

public static double convertBitScoreToRaw(double lambdaNats,
                                          double K,
                                          double bitS)

Converts a nat bit score to raw S.

calculateEValue

public static java.lang.String calculateEValue(double lambdaNats,
                                               double K,
                                               int rawS,
                                               double effectiveN,
                                               double effectiveM)

Calculates an E value given a variety of alignment parameters

calculateEffectiveMandN

public static int[] calculateEffectiveMandN(double m,
                                            double n,
                                            double K,
                                            double H)

Calculates effective m and n using BLAST parameters, returning int[m', n']

fetchBLASTParams

public static double[] fetchBLASTParams(int match,
                                        int misMatch)

Returns Lambda, K, H or null for a given match and misMatch from BLASTN. Some combinations of match/misMatch are not computed by BLASTN!

ScoreDNAAlignment

public static int ScoreDNAAlignment(java.lang.String seq1,
                                    java.lang.String seq2,
                                    int match,
                                    int misMatch,
                                    int gapCreate,
                                    int gapExtend)

Will score a DNA alignment given the two sequences, and scoring parameters.