Uses of Interface
org.utgenome.format.fasta.GenomeSequence

Packages that use GenomeSequence

org.utgenome.format.fasta	FASTA utilities
org.utgenome.util.aligner

Uses of GenomeSequence in org.utgenome.format.fasta

Classes in org.utgenome.format.fasta that implement GenomeSequence

class	CompactACGT Compact array for ACGT (and N) sequences
static class	FASTA.RawStringWrapper
class	Kmer K-mer integer representation of ACGT.

Methods in org.utgenome.format.fasta that return GenomeSequence

GenomeSequence	CompactFASTA.getSequence(String chr)
GenomeSequence	CompactFASTA.getSequence(String chr, int start)

Uses of GenomeSequence in org.utgenome.util.aligner

Classes in org.utgenome.util.aligner that implement GenomeSequence

static class

SmithWatermanAligner.StringWrapper

Methods in org.utgenome.util.aligner with type parameters of type GenomeSequence

<Seq1 extends GenomeSequence,Seq2 extends GenomeSequence> SmithWatermanAligner.Alignment	SmithWatermanAligner.align(Seq1 seq1, Seq2 seq2)
<Seq1 extends GenomeSequence,Seq2 extends GenomeSequence> SmithWatermanAligner.Alignment	SmithWatermanAligner.align(Seq1 seq1, Seq2 seq2)

Methods in org.utgenome.util.aligner that return GenomeSequence

static GenomeSequence

SmithWatermanAligner.wrap(String seq) Wrap the input string as GenomeSequence