experiments
Class ExpTypSeqProf

java.lang.Object
  experiments.Exp
      experiments.ExpTypSeqProf

public class ExpTypSeqProf
extends Exp

This class represents an experiment in which typical sequence profiles are computed. It contains a Genome variable called gen (inherited from Exp) and five other fields: INPUTS: double[] tol (Frequence tolerance [tolIni,tolFin,tolStep]), int nLens (Number of lengths to test), int[] lens (Lengths to test [lenIni, lenfin,lenStep]) OUTPUTS: int[] lengths (Lengths to test: [len1, len2, len3, ...], Vector tests (Output vector containing tolerance value and related vector of couples (len-nOccur))). In order to be launched an experiment must have set the genome, the field tol and either the field nLens or the field lens.

Field Summary

Fields inherited from class experiments.Exp

gen

Constructor Summary

ExpTypSeqProf()
Empty constructor

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

ExpTypSeqProf(java.io.File f, double[] tolIn, int nLensIn)
Generates an experiment for typical sequences profiles in which the number of lengths to be tested are defined in field nLensIn.

ExpTypSeqProf(java.io.File f, double[] tolIn, int[] lengthsIn)
Generates an experiment for typical sequences profiles in which the lengths to be tested are defined in field lengthsIn (lenIni, lenfin, lenStep).

ExpTypSeqProf(Genome g, double[] tolIn, int nLensIn)
Generates an experiment for typical sequences profiles starting from a preloaded Genome object.

ExpTypSeqProf(Genome g, double[] tolIn, int[] lengthsIn)
Generates an experiment for typical sequences profiles starting from a preloaded Genome object.

Method Summary

int[]	getLengths()
int[]	getLens()
int	getnLens()
java.util.Vector<TolTest>	getTests()
double[]	getTol()
void	setLengths(int[] lengths)
void	setLens(int[] lens)
void	setnLens(int nLens)
void	setTests(java.util.Vector<TolTest> tests)
void	setTol(double[] tol)

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

ExpTypSeqProf

public ExpTypSeqProf()

Empty constructor

ExpTypSeqProf

public ExpTypSeqProf(java.io.File f)

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

ExpTypSeqProf

public ExpTypSeqProf(java.io.File f,
                     double[] tolIn,
                     int nLensIn)

Generates an experiment for typical sequences profiles in which the number of lengths to be tested are defined in field nLensIn. Tested lengths span from 3 to the genome lengths and they are nLensIn (uniform steps).

ExpTypSeqProf

public ExpTypSeqProf(Genome g,
                     double[] tolIn,
                     int nLensIn)

Generates an experiment for typical sequences profiles starting from a preloaded Genome object. The number of lengths to be tested are defined in field nLensIn. Tested lengths span from 3 to the genome lengths and they are nLensIn (uniform steps)

ExpTypSeqProf

public ExpTypSeqProf(java.io.File f,
                     double[] tolIn,
                     int[] lengthsIn)

Generates an experiment for typical sequences profiles in which the lengths to be tested are defined in field lengthsIn (lenIni, lenfin, lenStep).

ExpTypSeqProf

public ExpTypSeqProf(Genome g,
                     double[] tolIn,
                     int[] lengthsIn)

Generates an experiment for typical sequences profiles starting from a preloaded Genome object. The lengths to be tested are defined in field lengthsIn (lenIni, lenfin, lenStep)

Method Detail

getTol

public double[] getTol()

Returns:

the tol

getLengths

public int[] getLengths()

Returns:

the lengths

getTests

public java.util.Vector<TolTest> getTests()

Returns:

the tests

getnLens

public int getnLens()

Returns:

the nLens

getLens

public int[] getLens()

Returns:

the lens

setTol

public void setTol(double[] tol)

Parameters:

tol - the tol to set

setnLens

public void setnLens(int nLens)

Parameters:

nLens - the nLens to set

setLens

public void setLens(int[] lens)

Parameters:

lens - the lens to set

setLengths

public void setLengths(int[] lengths)

Parameters:

lengths - the lengths to set

setTests

public void setTests(java.util.Vector<TolTest> tests)

Parameters:

tests - the tests to set