Package javagene.seq

Sequences, features on sequences, and the locations of features.

See:
Description

Interface Summary

FeatureI	A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.
SeqI	A sequence of either nucleotides or amino acids.

Class Summary

AminoAcid	An amino acid object with codon/residue utility methods.
Feature	A Feature corresponds to a single row in a GFF file.
FeatureList	A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
Location	A location on a sequence.
LocIterator	Move a sliding window over a Location.
Nucleotide	A nucleotide object, with Dna/Rna utility methods.
SeqBig	A SeqI implementation capable of handling large sequences that do not fit into memory.
SeqFast	A SeqI implementation that keeps the entire sequence in memory.
SeqStranded	A SeqI wrapper that presents a stranded coordinate system mapped to an underlying SeqI object.

Enum Summary

Nucleotide.Type

Sequence type: DNA or RNA.

Package javagene.seq Description

Sequences, features on sequences, and the locations of features.