Package org.biojava.bio.seq.io

Classes and interfaces for processing and producing flat-file representations of sequences.

See:
          Description

Interface Summary
AlignmentFormat  
FastaDescriptionReader Converts the description line of a fasta entry into useful information.
FeatureBuilder Factory for new latent features.
SequenceFormat Defines what a sequence format does.
 

Class Summary
DefaultDescriptionReader Assumes that the description is of the form 'id\s*desc'.
EmblFormat Format reader for EMBL files.
FastaFormat Format for Fasta files.
GenbankFormat Format reader for EMBL files.
SimpleFeatureBuilder Simple FeatureBuilder implementation.
StreamReader Parses a stream into sequences.
StreamReader.Context Encapsulate a stream for reading sequence data.
StreamWriter Writes all of the sequences from a SequenceIterator to a stream with a particular format.
 

Package org.biojava.bio.seq.io Description

Classes and interfaces for processing and producing flat-file representations of sequences.

These interfaces define how to read and write arbitrary file formats. The file format is decoupled from the type of sequence that will be produced or written. For example, you could read in entries from a Fasta database and generate ACeDB sequences within an ACeDB database for each entry just by configuring a StreamReader with a FastaFormat and an AceSequenceFactory.