Package org.snpeff.binseq.indexer
Class SuffixIndexerNmer<T extends BinarySequence>
java.lang.Object
org.snpeff.binseq.indexer.SequenceIndexer<T>
org.snpeff.binseq.indexer.SuffixIndexerNmer<T>
- Type Parameters:
T
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- All Implemented Interfaces:
Iterable<T>
,Comparator<Long>
Index all suffixes of all the sequences (it indexes using Nmers).
Note: Under the current structure, only exact overlap matches are allowed
- Author:
- pcingola
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Constructor Summary
ConstructorsConstructorDescriptionSuffixIndexerNmer
(SubsequenceComparator<T> subsequenceComparator, int nmerSize) -
Method Summary
Modifier and TypeMethodDescriptionint
Add a sequence to this indexfindBestOverlap
(T sequence) Find best overlap for 'sequence'iterator()
boolean
Find the best possible overlap and join the sequences or just add add the sequence to the indexvoid
void
Perform consistency checksvoid
setOverlapFilter
(OverlapFilter<T> overlapFilter) toString()
Methods inherited from class org.snpeff.binseq.indexer.SequenceIndexer
add, compare, get, size
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.util.Comparator
equals, reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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SuffixIndexerNmer
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Method Details
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add
Add a sequence to this index- Overrides:
add
in classSequenceIndexer<T extends BinarySequence>
- Parameters:
sequence
-- Returns:
- Index to this sequence (a number that can be used to retrieve this sequence)
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findBestOverlap
Find best overlap for 'sequence'- Parameters:
sequence
-- Returns:
- An overlap result
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getOverlapFilter
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iterator
- Specified by:
iterator
in interfaceIterable<T extends BinarySequence>
- Overrides:
iterator
in classSequenceIndexer<T extends BinarySequence>
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overlap
Find the best possible overlap and join the sequences or just add add the sequence to the index- Parameters:
sequence
-- Returns:
- true if an overlap was found and false if no overlap was found
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printSequences
public void printSequences() -
sanityCheck
public void sanityCheck()Perform consistency checks -
setOverlapFilter
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toString
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toStringSequences
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