edu.uconn.mcb.lineageevolver
Class Recombiner

java.lang.Object
  edu.uconn.mcb.lineageevolver.Recombiner

Direct Known Subclasses:

DiagonalRecombiner

public abstract class Recombiner

extends java.lang.Object

Intermediary class encapsulating the recombination process between two genes.

Author:

Hasan Khalil

Nested Class Summary

class

Recombiner.NoRecombineRegion Exception thrown when no region suitable for recombination could be found.

Field Summary

(package private) Gene	_gneDestination The gene into which recombined material will be copied.
(package private) Gene	_gneSource The gene from which recombined material will be copied.
static int	DEFAULT_RECOMBINE_MEAN Default mean of recombination sequence length.
static int	DEFAULT_RECOMBINE_PADDING Default padding of acceptable recombination sequence.
static int	DEFAULT_RECOMBINE_STDEV Default standard deviation of recombination sequence length.
static java.util.Random	randomNumberGenerator Random number generator shared by all Recombiners.

Constructor Summary

Recombiner(Gene gneSource, Gene gneDestination)
Default constructor for objects of type Recombiner.

Method Summary

abstract void

recombine() Processes recombination between the source and destination genes.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_RECOMBINE_MEAN

public static final int DEFAULT_RECOMBINE_MEAN

Default mean of recombination sequence length.

See Also:

Constant Field Values

DEFAULT_RECOMBINE_STDEV

public static final int DEFAULT_RECOMBINE_STDEV

Default standard deviation of recombination sequence length.

See Also:

Constant Field Values

DEFAULT_RECOMBINE_PADDING

public static final int DEFAULT_RECOMBINE_PADDING

Default padding of acceptable recombination sequence. This is the number of amino acids that must match on either side of the recombination sequence in both origin and desination sequences.

See Also:

Constant Field Values

randomNumberGenerator

public static final java.util.Random randomNumberGenerator

Random number generator shared by all Recombiners.

_gneSource

Gene _gneSource

The gene from which recombined material will be copied.

_gneDestination

Gene _gneDestination

The gene into which recombined material will be copied.

Constructor Detail

Recombiner

public Recombiner(Gene gneSource,
                  Gene gneDestination)

Default constructor for objects of type Recombiner. Simply assigns the source and destination gene private data members as provided. All subclasses should make a call to this constructor with provided data.

Parameters:

gneSource - the gene from which recombined material will be copied

gneDestination - the gene into which recombined material will be copied

Method Detail

recombine

public abstract void recombine()
                        throws Recombiner.NoRecombineRegion

Processes recombination between the source and destination genes.

Throws:

Recombiner.NoRecombineRegion - If no regioin suitable for recombination was found.