Package org.snpeff.overlap

Class OverlapDnaSeq

java.lang.Object

org.snpeff.overlap.Overlap<DnaSequence>

org.snpeff.overlap.OverlapDnaSeq

public class OverlapDnaSeq
extends Overlap<DnaSequence>

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	debug

Constructor Summary

Constructors

Constructor	Description
OverlapDnaSeq()

Method Summary

Modifier and Type	Method	Description
int	getMinOverlap()
int	overlap(DnaSequence seq1, DnaSequence seq2)	Calculate the best overlap between two sequences
void	setMinOverlap(int minOverlap)

Methods inherited from class org.snpeff.overlap.Overlap

getBestOffset, getBestScore

Methods inherited from class java.lang.Object

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

Field Detail

debug

public static boolean debug

Constructor Detail

OverlapDnaSeq

public OverlapDnaSeq()

Method Detail

getMinOverlap

public int getMinOverlap()

overlap

public int overlap(DnaSequence seq1,
                   DnaSequence seq2)

Description copied from class: Overlap

Calculate the best overlap between two sequences

Specified by:

overlap in class Overlap<DnaSequence>

Returns:

setMinOverlap

public void setMinOverlap(int minOverlap)