DnaSubsequenceComparator (SnpEff 5.2 API)

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 Details
- DnaSubsequenceComparator
  
  public DnaSubsequenceComparator(boolean differentLengthsAreEqual)
- DnaSubsequenceComparator
  
  public DnaSubsequenceComparator(boolean differentLengthsAreEqual, int maxDifferentBases)
Method Details
- 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: