edu.uconn.mcb.lineageevolver
Class Recombiner

java.lang.Object
  extended byedu.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.