edu.uconn.mcb.lineageevolver
Class DiagonalRecombiner

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

public class DiagonalRecombiner

extends Recombiner

Description of type goes here.

Author:

Hasan Khalil, Lina Pezzella

Nested Class Summary

Nested classes inherited from class edu.uconn.mcb.lineageevolver.Recombiner

Recombiner.NoRecombineRegion

Field Summary

Fields inherited from class edu.uconn.mcb.lineageevolver.Recombiner

_gneDestination, _gneSource, DEFAULT_RECOMBINE_MEAN, DEFAULT_RECOMBINE_PADDING, DEFAULT_RECOMBINE_STDEV, randomNumberGenerator

Constructor Summary

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

Method Summary

private int	findEnd(int target) Searches for matching regions between source and destination genes within a reasonable distance of the provided target region.
private int	findStart(int start, int end) Searches the source and destination genes between given start and end points for a matching region of length 6.
private boolean	isIdentical(int start, int distance) Determines if a given region is identical between both source and destination Genes.
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

Constructor Detail

DiagonalRecombiner

public DiagonalRecombiner(Gene gneSource,
                          Gene gneDestination)

Default constructor for objects of type DiagonalRecombiner.

See Also:

Recombiner.Recombiner(Gene, Gene)

Method Detail

recombine

public void recombine()
               throws Recombiner.NoRecombineRegion

Description copied from class: Recombiner

Processes recombination between the source and destination genes.

Specified by:

recombine in class Recombiner

Throws:

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

See Also:

Recombiner.recombine()

findStart

private int findStart(int start,
                      int end)

Searches the source and destination genes between given start and end points for a matching region of length 6.

Parameters:

start - the start point of the search.

end - the end point of the search.

Returns:

the start end point of the matching region of length 6, of -1 if none was found.

findEnd

private int findEnd(int target)

Searches for matching regions between source and destination genes within a reasonable distance of the provided target region.

Parameters:

target - the desired center for a matching sequence to be found.

Returns:

the start position of a matching segment of length DEFAULT_RECOMBINE_PADDING, or -1 if none was found within reasonable boundaries.

See Also:

Recombiner.DEFAULT_RECOMBINE_PADDING, Recombiner.DEFAULT_RECOMBINE_STDEV

isIdentical

private boolean isIdentical(int start,
                            int distance)

Determines if a given region is identical between both source and destination Genes.

Parameters:

start - the location to start checking identicality.

distance - the distance from the start location to stop checking identicality.

Returns:

true if both genes are identical for the specified stretch, false otherwise.