Package org.biojavax.bio.seq.io
package org.biojavax.bio.seq.io
Classes to support the I/O of RichSequence and Bioentry objects.
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ClassDescriptionThis is purely for debugging purposes.Format reader for EMBL files.Implements some EMBL-specific terms.Format reader for EMBLxml files.Implements some EMBLxml-specific terms.Format object representing FASTA files.This class is used by
FastaFormat
to determine which fields are in the fasta header.Format reader for GenBank files.Implements some GenBank-specific terms.Parses Genbank location strings into RichLocation objects.Iterates over a Fasta file that is kept in memory for optimized access.Format reader for INSDseq files.Implements some INSDseq-specific terms.This class implements all methods of RichSeqIOListener and takes no action.An interface for classes that listen to BioEntry or RichSequence I/O streams.An interface for objects that can build RichSequences.Simple factory for constructing new RichSequenceBuilder objects.Allows a file format to be read/written as RichSequences.Provides a basic format with simple things like line-widths precoded.Provides the basic implementation required for simple header/footer-less files such as Genbank.Parses a stream into sequences.Writes all of the sequences from a SequenceIterator to a stream with a particular format.Constructs BioEntry objects by listening to events.Generates RichSequenceBuilder objects.A class to describe events for alternative product comments.A class to describe protein-protein interactions.A class to describe isoforms for alternative product comments.A class to describe seq caution entries.Format reader for UniProt files.Implements some UniProt-specific terms.Parses UniProt location strings into RichLocation objects.Format reader for UniProtXML files.Implements some UniProtXML-specific terms.