Package com.hfg.bio.seq.format

Interface Summary

Interface	Description
ReadableSeqFormat<T extends BioSequence>	Interface for readable sequence formats.
SeqFormat	Created by taylora on 9/24/14.
WritableSeqFormat<T extends BioSequence>	Interface for writable sequence formats.

Class Summary

Class	Description
BufferedSeqReader<T extends BioSequence>	Buffered sequence reader.
EMBL<T extends BioSequence>	EMBL sequence format.
EMBL_DataClass	Enumerated list of EMBL data class.
FASTA<T extends BioSequence>	FASTA sequence format.
FASTQ<T extends NucleicAcid>	FASTQ sequence format encompassing sequences and their per-base sequencing quality scores.
GenBank<T extends BioSequence>	GenBank sequence format.
IlluminaFASTQ<T extends NucleicAcid>	FASTQ sequence format from Illumina.
ReadableSeqFormatBase<T extends BioSequence>	Base class for readable sequence formats.
SeqCitation	A citation with sequence location information.
WIPO_ST_25<T extends BioSequence>	Sequence format based on WIPO Standard ST.25.

Exception Summary

Exception	Description
SeqFormatException	Indicates an exception with the format of the sequence record being read.
SeqIOException	Indicates an exception during sequence I/O manipulation.