org.concord.biologica.engine
Interface IChromosome

All Known Implementing Classes:

SpeciesChromosome

public interface IChromosome

This interface represents a chromosome which all chromosomes implement.

Examples are SpeciesChromosome and OrganismChromosome.

Version:

$Revision: 1.1.1.1 $ $Date: 2001/04/28 00:39:13 $

Author:

$Author: ed $

Field Summary

static int	A_CHROMOSOME The "A" chromosome of a pair, sometimes of three.
static int	AUTOSOME Chromosome type - autosome (non-sex chromosome)
static int	B_CHROMOSOME The "B" chromosome of a pair, sometimes of three.
static int	C_CHROMOSOME The "C" chromosome of a pair, sometimes of three.
static int	NEXT_HIGHEST_AUTOSOME_NUMBER Next highest autosome number.
static int	SEX_CHROMOSOME Chromosome type - sex chromosome
static int	X_CHROMOSOME X chromosome - used as a "number type".
static java.lang.String	X_CHROMOSOME_STRING
static int	Y_CHROMOSOME Y chromosome - used as a "number type".
static java.lang.String	Y_CHROMOSOME_STRING

Method Summary

int	getChromosomeType() Get the chromosome type (autosome or sex chromosome).
int	getLengthInBases() Returns the length of chromosome in bases.
int	getLengthInCodons() Returns the length of the chromosome in codons, calculated by dividing the number of bases by 3, ignoring remainder.
int	getNumberType() Returns the number / type of this chromosome.
boolean	isSexChromosome() Returns whether the chromosome is a sex chromosome.

Field Detail

X_CHROMOSOME

public static final int X_CHROMOSOME

X chromosome - used as a "number type".

X_CHROMOSOME_STRING

public static final java.lang.String X_CHROMOSOME_STRING

Y_CHROMOSOME

public static final int Y_CHROMOSOME

Y chromosome - used as a "number type".

Y_CHROMOSOME_STRING

public static final java.lang.String Y_CHROMOSOME_STRING

A_CHROMOSOME

public static final int A_CHROMOSOME

The "A" chromosome of a pair, sometimes of three.

B_CHROMOSOME

public static final int B_CHROMOSOME

The "B" chromosome of a pair, sometimes of three.

C_CHROMOSOME

public static final int C_CHROMOSOME

The "C" chromosome of a pair, sometimes of three.

AUTOSOME

public static final int AUTOSOME

Chromosome type - autosome (non-sex chromosome)

SEX_CHROMOSOME

public static final int SEX_CHROMOSOME

Chromosome type - sex chromosome

NEXT_HIGHEST_AUTOSOME_NUMBER

public static final int NEXT_HIGHEST_AUTOSOME_NUMBER

Next highest autosome number.

Users should use this value when they want the new species chromosome to have the next highest chromosome value.

This is NOT a valid number type for most uses. It may only be used when constructing the species chromosome initially.

Method Detail

getLengthInBases

public int getLengthInBases()

Returns the length of chromosome in bases.

Returns:

int - length of this chromosome in bases

getLengthInCodons

public int getLengthInCodons()

Returns the length of the chromosome in codons, calculated by dividing the number of bases by 3, ignoring remainder.

Returns:

int - length of this chromosome in codons

getNumberType

public int getNumberType()

Returns the number / type of this chromosome.

Returns:

int - IChromosome.X_CHROMOSOME, IChromosome.Y_CHROMOSOME or an autosome number

isSexChromosome

public boolean isSexChromosome()

Returns whether the chromosome is a sex chromosome.

Returns:

boolean - true if sex chromosome, else false

getChromosomeType

public int getChromosomeType()

Get the chromosome type (autosome or sex chromosome).

Returns:

int - IChromosome.AUTOSOME or IChromosome.SEX_CHROMOSOME