Package org.snpeff.binseq.comparator
Class DnaSubsequenceComparator<T extends DnaSequence>
- java.lang.Object
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- org.snpeff.binseq.comparator.SubsequenceComparator<T>
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- org.snpeff.binseq.comparator.DnaSubsequenceComparator<T>
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public class DnaSubsequenceComparator<T extends DnaSequence> extends SubsequenceComparator<T>
Compares two subsequences of DNA (DnaSequence)- Author:
- pcingola
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Constructor Summary
Constructors Constructor Description DnaSubsequenceComparator(boolean differentLengthsAreEqual)
DnaSubsequenceComparator(boolean differentLengthsAreEqual, int maxDifferentBases)
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Method Summary
All Methods Instance Methods Concrete Methods 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.
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Method Detail
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compare
public int compare(DnaSequence seq1, int index1, DnaSequence seq2, int index2)
- Specified by:
compare
in classSubsequenceComparator<T extends DnaSequence>
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score
public int score(DnaSequence seq1, int index1, DnaSequence seq2, int index2)
- Specified by:
score
in classSubsequenceComparator<T extends DnaSequence>
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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:
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