Package org.biojava.bio.seq.io
package org.biojava.bio.seq.io
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.
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ClassDescription
AlignIOConstants
contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing alignments.Implementation of SymbolTokenization which binds symbols to strings of characters.Implementation of SymbolTokenization which binds symbols to single unicode characters.class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.Tokenization for cross-product alphabets.Deprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io.EMBLFormat insteadDeprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io framework insteadFactory which wraps SequenceBuilders in an EmblProcessorThis class implements the AlignmentFormat interface to read FASTA alignments.Deprecated.Use org.biojavax.bio.seq.io.FastaFormatFactory which wraps SequenceBuilders in a FastaDescriptionLineParserDeprecated.Use org.biojavax.bio.seq.io.FastaFormatDeprecated.Use org.biojavax.bio.seq.io framework insteadA rudimentary read-only GAME 1.2 Format object.Deprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io.GenbankFormatDeprecated.Use org.biojavax.bio.seq.io framework insteadFactory which wraps sequence builders in a GenbankProcessorDeprecated.Use org.biojavax.bio.seq.io.INSDseqFormatDeprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io framework insteadSimple implementation of SymbolTokenization which uses the `name' field of the symbols.Deprecated.Use org.biojavax.bio.taxa framework insteadFactory which wraps SequenceBuilders in an OrganismParser.ParseException should be thrown to indicate that there was a problem with parsing sequence information.Deprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io framework insteadFactory which wraps sequence builders in a ProteinRefSeqProcessorDeprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io framework insteadAdapter class for SeqIOListener that has empty methods.SeqIOConstants
contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing sequences.Deprecated.Use org.biojavax.bio.seq.io framework insteadBase-class for listeners that pass filtered events onto another listener.Notification interface for objects which listen to a sequence stream parser.Deprecated.use org.biojavax.bio.seq.RichSequence.IOToolsInterface for objects which accumulate state via SeqIOListener, then construct a Sequence object.Basic SequenceBuilder implementation which accumulates all notified information.Simple factory for constructing new SequenceBuilder objects.Base-class for builders that pass filtered events onto another builder.This SequenceBuilder has a variety of modes of operation.Defines what a sequence format does.Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.Parse a stream of characters into BioJava symbols.Parses a stream into sequences.Writes all of the sequences from a SequenceIterator to a stream with a particular format.Deprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io framework insteadFactory which wraps SequenceBuilders in a SwissprotProcessorSymbolListCharSequence
is aCharSequence
implementation which wraps aSymbolList
.Encapsulate a stream of Symbols being parsed from some input stream.Encapsulate a mapping between BioJava Symbol objects and some string representation.Base class for tokenizations which accept whitespace-separated `words'.