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

  • Constructor Details

  • Method Details

    • add

      public void add(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(Long reference1, Long reference2)
      Compare two references
      Specified by:
      compare in interface 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 Iterator<T> iterator()
      Specified by:
      iterator in interface Iterable<T extends BinarySequence>

    • size

      public int size()
      Number of sequences in this index
      Returns: