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See:
Description
Interface Summary | |
---|---|
AlignmentFormat | |
SeqFileFormer | Deprecated. Use org.biojavax.bio.seq.io framework instead |
SeqIOListener | Notification interface for objects which listen to a sequence stream parser. |
SequenceBuilder | Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object. |
SequenceBuilderFactory | Simple factory for constructing new SequenceBuilder objects. |
SequenceFormat | Defines what a sequence format does. |
StreamParser | Parse a stream of characters into BioJava symbols. |
SymbolReader | Encapsulate a stream of Symbols being parsed from some input stream. |
SymbolTokenization | Encapsulate a mapping between BioJava Symbol objects and some string representation. |
Class Summary | |
---|---|
AlignIOConstants | AlignIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing alignments. |
AlternateTokenization | Implementation of SymbolTokenization which binds symbols to strings of characters. |
CharacterTokenization | Implementation of SymbolTokenization which binds symbols to single unicode characters. |
ChunkedSymbolListFactory | class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves. |
CrossProductTokenization | Tokenization for cross-product alphabets. |
DoubleTokenization | |
EmblFileFormer | Deprecated. Use org.biojavax.bio.seq.io framework instead |
EmblLikeFormat | Deprecated. Use org.biojavax.bio.seq.io.EMBLFormat instead |
EmblLikeLocationParser | Deprecated. Use org.biojavax.bio.seq.io framework instead |
EmblProcessor | Deprecated. Use org.biojavax.bio.seq.io framework instead |
EmblProcessor.Factory | Factory which wraps SequenceBuilders in an EmblProcessor |
EmblReferenceComparator | |
FastaAlignmentFormat | This class implements the AlignmentFormat interface to read FASTA alignments. |
FastaDescriptionLineParser | Deprecated. Use org.biojavax.bio.seq.io.FastaFormat |
FastaDescriptionLineParser.Factory | Factory which wraps SequenceBuilders in a FastaDescriptionLineParser |
FastaFormat | Deprecated. Use org.biojavax.bio.seq.io.FastaFormat |
FeatureTableParser | Deprecated. Use org.biojavax.bio.seq.io framework instead |
GAMEFormat | A rudimentary read-only GAME 1.2 Format object. |
GenbankFileFormer | Deprecated. Use org.biojavax.bio.seq.io framework instead |
GenbankFormat | Deprecated. Use org.biojavax.bio.seq.io.GenbankFormat |
GenbankProcessor | Deprecated. Use org.biojavax.bio.seq.io framework instead |
GenbankProcessor.Factory | Factory which wraps sequence builders in a GenbankProcessor |
GenbankXmlFormat | Deprecated. Use org.biojavax.bio.seq.io.INSDseqFormat |
GenEmblFeatureComparator | Deprecated. Use org.biojavax.bio.seq.io framework instead |
GenEmblPropertyComparator | Deprecated. Use org.biojavax.bio.seq.io framework instead |
GenpeptFormat | Deprecated. Use org.biojavax.bio.seq.io framework instead |
IntegerTokenization | |
MSFAlignmentFormat | |
NameTokenization | Simple implementation of SymbolTokenization which uses the `name' field of the symbols. |
OrganismParser | Deprecated. Use org.biojavax.bio.taxa framework instead |
OrganismParser.Factory | Factory which wraps SequenceBuilders in an OrganismParser. |
ProteinRefSeqFileFormer | Deprecated. Use org.biojavax.bio.seq.io framework instead |
ProteinRefSeqProcessor | Deprecated. Use org.biojavax.bio.seq.io framework instead |
ProteinRefSeqProcessor.Factory | Factory which wraps sequence builders in a ProteinRefSeqProcessor |
ReferenceAnnotation | Deprecated. Use org.biojavax.bio.seq.io framework instead |
SeqIOAdapter | Adapter class for SeqIOListener that has empty methods. |
SeqIOConstants | SeqIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing sequences. |
SeqIOEventEmitter | Deprecated. Use org.biojavax.bio.seq.io framework instead |
SeqIOFilter | Base-class for listeners that pass filtered events onto another listener. |
SeqIOTools | Deprecated. use org.biojavax.bio.seq.RichSequence.IOTools |
SequenceBuilderBase | Basic SequenceBuilder implementation which accumulates all notified information. |
SequenceBuilderFilter | Base-class for builders that pass filtered events onto another builder. |
SequenceDBSequenceBuilder | This SequenceBuilder has a variety of modes of operation. |
SimpleAssemblyBuilder | Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly. |
SimpleSequenceBuilder | Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence. |
SmartSequenceBuilder | Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence. |
StreamReader | Parses a stream into sequences. |
StreamWriter | Writes all of the sequences from a SequenceIterator to a stream with a particular format. |
SubIntegerTokenization | |
SwissprotFileFormer | Deprecated. Use org.biojavax.bio.seq.io framework instead |
SwissprotProcessor | Deprecated. Use org.biojavax.bio.seq.io framework instead |
SwissprotProcessor.Factory | Factory which wraps SequenceBuilders in a SwissprotProcessor |
SymbolListCharSequence | SymbolListCharSequence is a CharSequence
implementation which wraps a SymbolList . |
SymbolTokenization.TokenType | |
WordTokenization | Base class for tokenizations which accept whitespace-separated `words'. |
Exception Summary | |
---|---|
ParseException | ParseException should be thrown to indicate that there was a problem with parsing sequence information. |
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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