org.concord.biologica.engine
Class Branch

java.lang.Object
  |
  +--org.concord.biologica.engine.Branch

public class Branch

extends java.lang.Object

Constructor Summary

Branch(OrganismAllele[] PL_arr, java.awt.Color[] PL_Color, OrganismAllele[] PR_arr, java.awt.Color[] PR_Color, OrganismAllele[] QL_arr, java.awt.Color[] QL_Color, OrganismAllele[] QR_arr, java.awt.Color[] QR_Color)

Branch(OrganismAllele[] PL_arr, OrganismAllele[] PR_arr, OrganismAllele[] QL_arr, OrganismAllele[] QR_arr)

Branch(OrganismAllele[] PL_arr, OrganismAllele[] PR_arr, OrganismAllele[] QL_arr, OrganismAllele[] QR_arr, java.awt.Color color)

Branch(OrganismChromosome chr1)
This class is used to store the chromosome's alleles when the cross over happened,

Branch(OrganismChromosome chr1, java.awt.Color strandColor)

Method Summary

Branch[]	crossOverWith(Branch b)
java.lang.String	getAllelesAsString()
OrganismChromosome	getChromosome()
int	getnumberOfPStrandSegments()
int	getnumberOfQStrandSegments()
java.lang.String	getNumberTypeAsString()
OrganismAllele[]	getPLStrand()
java.awt.Color[]	getPLStrandColor()
OrganismAllele[]	getPRStrand()
java.awt.Color[]	getPRStrandColor()
OrganismAllele[]	getQLStrand()
java.awt.Color[]	getQLStrandColor()
OrganismAllele[]	getQRStrand()
java.awt.Color[]	getQRStrandColor()
void	setChromosome(OrganismChromosome chr)
void	setColors(int PStrandLength, int QStrandLength, java.awt.Color color)
void	setPLStrand(OrganismAllele[] array)
void	setPLStrandColor(java.awt.Color[] colorArr)
protected void	setPossibility(double po)
void	setPRStrand(OrganismAllele[] array)
void	setPRStrandColor(java.awt.Color[] colorArr)
void	setQLStrand(OrganismAllele[] array)
void	setQLStrandColor(java.awt.Color[] colorArr)
void	setQRStrand(OrganismAllele[] array)
void	setQRStrandColor(java.awt.Color[] colorArr)

Methods inherited from class java.lang.Object

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

Constructor Detail

Branch

public Branch(OrganismChromosome chr1)

This class is used to store the chromosome's alleles when the cross over happened,

Branch

public Branch(OrganismChromosome chr1,
              java.awt.Color strandColor)

Branch

public Branch(OrganismAllele[] PL_arr,
              java.awt.Color[] PL_Color,
              OrganismAllele[] PR_arr,
              java.awt.Color[] PR_Color,
              OrganismAllele[] QL_arr,
              java.awt.Color[] QL_Color,
              OrganismAllele[] QR_arr,
              java.awt.Color[] QR_Color)

Branch

public Branch(OrganismAllele[] PL_arr,
              OrganismAllele[] PR_arr,
              OrganismAllele[] QL_arr,
              OrganismAllele[] QR_arr)

Branch

public Branch(OrganismAllele[] PL_arr,
              OrganismAllele[] PR_arr,
              OrganismAllele[] QL_arr,
              OrganismAllele[] QR_arr,
              java.awt.Color color)

Method Detail

setColors

public void setColors(int PStrandLength,
                      int QStrandLength,
                      java.awt.Color color)

crossOverWith

public Branch[] crossOverWith(Branch b)

getAllelesAsString

public java.lang.String getAllelesAsString()

setPossibility

protected void setPossibility(double po)

setPLStrand

public void setPLStrand(OrganismAllele[] array)

getPLStrand

public OrganismAllele[] getPLStrand()

setQLStrand

public void setQLStrand(OrganismAllele[] array)

getQLStrand

public OrganismAllele[] getQLStrand()

setPRStrand

public void setPRStrand(OrganismAllele[] array)

getPRStrand

public OrganismAllele[] getPRStrand()

setQRStrand

public void setQRStrand(OrganismAllele[] array)

getQRStrand

public OrganismAllele[] getQRStrand()

getnumberOfPStrandSegments

public int getnumberOfPStrandSegments()

getnumberOfQStrandSegments

public int getnumberOfQStrandSegments()

getNumberTypeAsString

public java.lang.String getNumberTypeAsString()

getChromosome

public OrganismChromosome getChromosome()

setChromosome

public void setChromosome(OrganismChromosome chr)

setPLStrandColor

public void setPLStrandColor(java.awt.Color[] colorArr)

getPLStrandColor

public java.awt.Color[] getPLStrandColor()

setPRStrandColor

public void setPRStrandColor(java.awt.Color[] colorArr)

getPRStrandColor

public java.awt.Color[] getPRStrandColor()

setQLStrandColor

public void setQLStrandColor(java.awt.Color[] colorArr)

getQLStrandColor

public java.awt.Color[] getQLStrandColor()

setQRStrandColor

public void setQRStrandColor(java.awt.Color[] colorArr)

getQRStrandColor

public java.awt.Color[] getQRStrandColor()