Package org.snpeff.binseq.comparator

Class DnaQualSubsequenceComparator

java.lang.Object

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

org.snpeff.binseq.comparator.DnaQualSubsequenceComparator

public class DnaQualSubsequenceComparator
extends SubsequenceComparator<DnaAndQualitySequence>

Compares two subsequences of DNA (DnaAndQualitySequence)

Author:

pcingola

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
int	compare(DnaAndQualitySequence seq1, int index1, DnaAndQualitySequence seq2, int index2)
int	score(DnaAndQualitySequence seq1, int index1, DnaAndQualitySequence seq2, int index2)

Methods inherited from class java.lang.Object

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

Constructor Detail

DnaQualSubsequenceComparator

public DnaQualSubsequenceComparator(boolean differentLengthsAreEqual)

DnaQualSubsequenceComparator

public DnaQualSubsequenceComparator(boolean differentLengthsAreEqual,
                                    int maxDifferentBases)

Method Detail

compare

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

Specified by:

compare in class SubsequenceComparator<DnaAndQualitySequence>

score

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

Specified by:

score in class SubsequenceComparator<DnaAndQualitySequence>