Package org.snpeff.binseq.indexer
Class SequenceIndexer<T extends BinarySequence>
- java.lang.Object
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- org.snpeff.binseq.indexer.SequenceIndexer<T>
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- All Implemented Interfaces:
java.lang.Iterable<T>
,java.util.Comparator<java.lang.Long>
- Direct Known Subclasses:
SuffixIndexerNmer
public class SequenceIndexer<T extends BinarySequence> extends java.lang.Object implements java.util.Comparator<java.lang.Long>, java.lang.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 Constructor Description SequenceIndexer(SubsequenceComparator<T> subsequenceComparator)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(java.util.Collection<T> sequences)
Add a collection of sequencesint
add(T sequence)
Add a sequence to this indexint
compare(java.lang.Long reference1, java.lang.Long reference2)
Compare two referencesT
get(int idx)
Get sequence in entry number 'idx'java.util.Iterator<T>
iterator()
int
size()
Number of sequences in this index-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Constructor Detail
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SequenceIndexer
public SequenceIndexer(SubsequenceComparator<T> subsequenceComparator)
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Method Detail
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add
public void add(java.util.Collection<T> sequences)
Add a collection of sequences- Parameters:
sequences
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add
public int add(T sequence)
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
public int compare(java.lang.Long reference1, java.lang.Long reference2)
Compare two references- Specified by:
compare
in interfacejava.util.Comparator<T extends BinarySequence>
- Parameters:
reference1
-reference2
-- Returns:
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get
public T get(int idx)
Get sequence in entry number 'idx'- Parameters:
idx
-- Returns:
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iterator
public java.util.Iterator<T> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<T extends BinarySequence>
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size
public int size()
Number of sequences in this index- Returns:
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