Package org.snpeff.binseq.indexer
Class SequenceIndexer<T extends BinarySequence>
java.lang.Object
org.snpeff.binseq.indexer.SequenceIndexer<T>
- All Implemented Interfaces:
Iterable<T>
,Comparator<Long>
- Direct Known Subclasses:
SuffixIndexerNmer
public class SequenceIndexer<T extends BinarySequence>
extends Object
implements Comparator<Long>, Iterable<T>
A collection of sequences that are indexed using some algorithm
Note: The ID is just the position in the array. That is why the array
should not change the order of the elements (only append new ones or
replace old ones).
- Author:
- pcingola
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, 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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SequenceIndexer
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Method Details
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add
Add a collection of sequences- Parameters:
sequences
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add
Add a sequence to this index- Parameters:
sequence
-- Returns:
- Index to this sequence (a number that can be used to retrieve this sequence)
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compare
Compare two references- Specified by:
compare
in interfaceComparator<T extends BinarySequence>
- Parameters:
reference1
-reference2
-- Returns:
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get
Get sequence in entry number 'idx'- Parameters:
idx
-- Returns:
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iterator
- Specified by:
iterator
in interfaceIterable<T extends BinarySequence>
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size
public int size()Number of sequences in this index- Returns:
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