SequenceIndexer (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.binseq.indexer.SequenceIndexer<T>

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

Constructor Summary

Constructors
Constructor Description

SequenceIndexer(SubsequenceComparator<T> subsequenceComparator)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`add(java.util.Collection<T> sequences)`	Add a collection of sequences
`int`	`add(T sequence)`	Add a sequence to this index
`int`	`compare(java.lang.Long reference1, java.lang.Long reference2)`	Compare two references
`T`	`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

Methods inherited from interface java.util.Comparator
equals, reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Constructor Detail
  - SequenceIndexer
```
public SequenceIndexer(SubsequenceComparator<T> subsequenceComparator)
```
- Method Detail
  - add
```
public void add(java.util.Collection<T> sequences)
```
    Add a collection of sequences
    
    Parameters:
    
    sequences -
  - 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)
  - compare
```
public int compare(java.lang.Long reference1,
                   java.lang.Long reference2)
```
    Compare two references
    
    Specified by:
    
    compare in interface java.util.Comparator<T extends BinarySequence>
    
    Parameters:
    
    reference1 -
    
    reference2 -
    
    Returns:
  - get
```
public T get(int idx)
```
    Get sequence in entry number 'idx'
    
    Parameters:
    
    idx -
    
    Returns:
  - iterator
```
public java.util.Iterator<T> iterator()
```
    Specified by:
    
    iterator in interface java.lang.Iterable<T extends BinarySequence>
  - size
```
public int size()
```
    Number of sequences in this index
    
    Returns: