experiments
Class ExpTypSeq

java.lang.Object
  experiments.Exp
      experiments.ExpTypSeq

public class ExpTypSeq
extends Exp

This class represents an experiment in which typical sequences are computed. It contains a Genome variable called gen (inherited from Exp) and four other fields: INPUTS: double[] tol (Frequence tolerance [tolIni,tolFin,tolStep]), int[] minLen (Window Min Length [minLenIni,minLenFin,minLenStep]), int[] jump (jump between analyzed sequences ([jumpIni,jumpFin,jumpStep]) OUTPUTS: Vector typSeqs (Typical sequence results (n-uples), each double[]: 0 -> tol, 1 -> minLen, 2 -> jump, 3 -> foundLen, 4 ->foundOccurrences In order to be launched an experiment must have set the genome and fields tol, minLen and jump.

Field Summary

Fields inherited from class experiments.Exp

gen

Constructor Summary

ExpTypSeq()
Empty constructor

ExpTypSeq(java.io.File f)
Constructs an ExpTypSeq experiment having genome set to the genome sequence in file f (fasta format)

ExpTypSeq(java.io.File f, double[] tolIn, int[] minLenIn, int[] jumpIn)
Generates an experiment for typical sequences

ExpTypSeq(Genome g, double[] tolIn, int[] minLenIn, int[] jumpIn)
Generates an experiment for typical sequences starting from a preloaded Genome object

Method Summary

int[]	getJump()
int[]	getMinLen()
double[]	getTol()
java.util.Vector<double[]>	getTypSeqs()
void	setJump(int[] jump)
void	setMinLen(int[] minLen)
void	setTol(double[] tol)
void	setTypSeqs(java.util.Vector<double[]> typSeqs)

Methods inherited from class experiments.Exp

getGen, setGen

Methods inherited from class java.lang.Object

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

Constructor Detail

ExpTypSeq

public ExpTypSeq()

Empty constructor

ExpTypSeq

public ExpTypSeq(java.io.File f)

Constructs an ExpTypSeq experiment having genome set to the genome sequence in file f (fasta format)

ExpTypSeq

public ExpTypSeq(java.io.File f,
                 double[] tolIn,
                 int[] minLenIn,
                 int[] jumpIn)

Generates an experiment for typical sequences

ExpTypSeq

public ExpTypSeq(Genome g,
                 double[] tolIn,
                 int[] minLenIn,
                 int[] jumpIn)

Generates an experiment for typical sequences starting from a preloaded Genome object

Method Detail

getTol

public double[] getTol()

Returns:

the tol

setTol

public void setTol(double[] tol)

Parameters:

tol - the tol to set

getMinLen

public int[] getMinLen()

Returns:

the minLen

setMinLen

public void setMinLen(int[] minLen)

Parameters:

minLen - the minLen to set

getJump

public int[] getJump()

Returns:

the jump

setJump

public void setJump(int[] jump)

Parameters:

jump - the jump to set

getTypSeqs

public java.util.Vector<double[]> getTypSeqs()

Returns:

the typSeqs

setTypSeqs

public void setTypSeqs(java.util.Vector<double[]> typSeqs)

Parameters:

typSeqs - the typSeqs to set