Package org.snpeff.binseq.indexer

Class SuffixIndexerNmer<T extends BinarySequence>

  • Type Parameters:
    T -
    All Implemented Interfaces:
    java.lang.Iterable<T>, java.util.Comparator<java.lang.Long>
    public class SuffixIndexerNmer<T extends BinarySequence>
extends SequenceIndexer<T>
    Index all suffixes of all the sequences (it indexes using Nmers). Note: Under the current structure, only exact overlap matches are allowed
    Author:
    pcingola

    • Constructor Detail

      • SuffixIndexerNmer

        public SuffixIndexerNmer​(SubsequenceComparator<T> subsequenceComparator,
                         int nmerSize)

    • Method Detail

      • add

        public int add​(T sequence)
        Add a sequence to this index
        Overrides:
        add in class SequenceIndexer<T extends BinarySequence>
        Parameters:
        sequence -
        Returns:
        Index to this sequence (a number that can be used to retrieve this sequence)

      • findBestOverlap

        public OverlapRessult<T> findBestOverlap​(T sequence)
        Find best overlap for 'sequence'
        Parameters:
        sequence -
        Returns:
        An overlap result

      • overlap

        public boolean overlap​(T sequence)
        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

      • printSequences

        public void printSequences()

      • sanityCheck

        public void sanityCheck()
        Perform consistency checks

      • setOverlapFilter

        public void setOverlapFilter​(OverlapFilter<T> overlapFilter)

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • toStringSequences

        public java.lang.String toStringSequences()