Package org.snpeff.binseq.indexer

Class SuffixIndexerNmer<T extends BinarySequence>

java.lang.Object
org.snpeff.binseq.indexer.SequenceIndexer<T>
org.snpeff.binseq.indexer.SuffixIndexerNmer<T>
Type Parameters:
T -
All Implemented Interfaces:
Iterable<T>, Comparator<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 Details

  • Method Details

    • 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

    • getOverlapFilter

      public OverlapFilter<T> getOverlapFilter()

    • iterator

      public Iterator<T> iterator()
      Specified by:
      iterator in interface Iterable<T extends BinarySequence>
      Overrides:
      iterator in class SequenceIndexer<T extends BinarySequence>

    • 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 String toString()
      Overrides:
      toString in class Object

    • toStringSequences

      public String toStringSequences()