Package org.snpeff.binseq.comparator

Class DnaSubsequenceComparator<T extends DnaSequence>

java.lang.Object

org.snpeff.binseq.comparator.SubsequenceComparator<T>

org.snpeff.binseq.comparator.DnaSubsequenceComparator<T>

public class DnaSubsequenceComparator<T extends DnaSequence>
extends SubsequenceComparator<T>

Compares two subsequences of DNA (DnaSequence)

Author:

pcingola

Constructor Summary

Constructors

Constructor	Description
DnaSubsequenceComparator(boolean differentLengthsAreEqual)
DnaSubsequenceComparator(boolean differentLengthsAreEqual, int maxDifferentBases)

Method Summary

Modifier and Type	Method	Description
int	compare(DnaSequence seq1, int index1, DnaSequence seq2, int index2)
int	score(DnaSequence seq1, int index1, DnaSequence seq2, int index2)
int	scoreSlow(DnaSequence seq1, int index1, DnaSequence seq2, int index2)	This method is used when none of the indexes is zero.

Methods inherited from class java.lang.Object

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

Constructor Detail

DnaSubsequenceComparator

public DnaSubsequenceComparator(boolean differentLengthsAreEqual)

DnaSubsequenceComparator

public DnaSubsequenceComparator(boolean differentLengthsAreEqual,
                                int maxDifferentBases)

Method Detail

compare

public int compare(DnaSequence seq1,
                   int index1,
                   DnaSequence seq2,
                   int index2)

Specified by:

compare in class SubsequenceComparator<T extends DnaSequence>

score

public int score(DnaSequence seq1,
                 int index1,
                 DnaSequence seq2,
                 int index2)

Specified by:

score in class SubsequenceComparator<T extends DnaSequence>

scoreSlow

public int scoreSlow(DnaSequence seq1,
                     int index1,
                     DnaSequence seq2,
                     int index2)

This method is used when none of the indexes is zero. Also used for debugging and comparison

Parameters:

seq1 -

index1 -

seq2 -

index2 -

Returns: