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>
Compares two subsequences of DNA (DnaSequence)
- Author:
- pcingola
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Constructor Summary
ConstructorsConstructorDescriptionDnaSubsequenceComparator
(boolean differentLengthsAreEqual) DnaSubsequenceComparator
(boolean differentLengthsAreEqual, int maxDifferentBases) -
Method Summary
Modifier and TypeMethodDescriptionint
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.
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Constructor Details
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DnaSubsequenceComparator
public DnaSubsequenceComparator(boolean differentLengthsAreEqual) -
DnaSubsequenceComparator
public DnaSubsequenceComparator(boolean differentLengthsAreEqual, int maxDifferentBases)
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Method Details
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compare
- Specified by:
compare
in classSubsequenceComparator<T extends DnaSequence>
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score
- Specified by:
score
in classSubsequenceComparator<T extends DnaSequence>
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scoreSlow
This method is used when none of the indexes is zero. Also used for debugging and comparison- Parameters:
seq1
-index1
-seq2
-index2
-- Returns:
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