net.maizegenetics.analysis.rna

Class FindMatchByWordHash

net.maizegenetics.analysis.rna.FindMatchByWordHash

public class FindMatchByWordHash

Find Match by Words using a simple hashmap of fixed length word (kmers) to determine most similar sequence.

Method Detail

totalNumberOfTags

public int totalNumberOfTags()

Total number of tags (reference sequences)

getTags

public java.util.List<net.maizegenetics.dna.tag.Tag> getTags()

Returns a unmodifiable list of the tags (reference sequences)

match

public net.maizegenetics.analysis.rna.FindMatchByWordHash.Match match(java.lang.String seq)

Return the first unique kmer match found starting at the 5' end of the sequence.

Parameters:

seq - query sequence - usually the reads

Returns:

org.jetbrains.dokka.NodeRenderContent@d81a0e6: matching sequence

toString

public java.lang.String toString()

calcIdentity

public static Tuple<java.lang.Integer,java.lang.Integer> calcIdentity(java.lang.String querySeq,
                                                                      java.lang.String refSeq)

LevenshteinDistance

public static int LevenshteinDistance(kotlin.Array[] s,
                                      kotlin.Array[] t)

getBuilder

public static net.maizegenetics.analysis.rna.FindMatchByWordHash.Builder getBuilder(java.util.Set<net.maizegenetics.dna.tag.Tag> tagSet)