Uses of Package
org.biojava.bio.seq.io
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Packages that use org.biojava.bio.seq.io Package Description org.biojava.bio.program Java wrappers for interacting with external bioinformatics tools.org.biojava.bio.program.phred Parser for Phred outputorg.biojava.bio.program.ssaha SSAHA sequence searching API.org.biojava.bio.program.xff Event-driven parsing system for the Extensible Feature Format (XFF).org.biojava.bio.seq.db Collections of biological sequence data.org.biojava.bio.seq.io Classes and interfaces for processing and producing flat-file representations of sequences.org.biojava.bio.seq.io.agave Classes for converting between AGAVE XML and BioJava objects.org.biojava.bio.seq.io.game Event-driven parsing system for the Gene Annotation Markup Elements (GAME).org.biojava.bio.seq.io.game12 Event-driven parsing system for the Gene Annotation Markup Elements (GAME).org.biojava.bio.symbol Representation of the Symbols that make up a sequence, and locations within them.org.biojava.ontology.io Tools for loading and saving ontologies.org.biojava.ontology.obo org.biojavax.bio.phylo.io.phylip Classes to support the reading and writing of PHYLIP format.org.biojavax.bio.seq Rich implementations of Sequences, Locations and Features.org.biojavax.bio.seq.io Classes to support the I/O of RichSequence and Bioentry objects.org.biojavax.bio.taxa.io -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.program Class Description SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation. -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.program.phred Class Description ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information.SeqIOListener Notification interface for objects which listen to a sequence stream parser.SequenceFormat Defines what a sequence format does.StreamReader Parses a stream into sequences.SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation. -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.program.ssaha Class Description SeqIOListener Notification interface for objects which listen to a sequence stream parser.SequenceFormat Defines what a sequence format does.SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation. -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.program.xff Class Description ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information.SeqIOListener Notification interface for objects which listen to a sequence stream parser. -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.db Class Description SequenceBuilderFactory Simple factory for constructing new SequenceBuilder objects.SequenceFormat Defines what a sequence format does.SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation. -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io Class Description AlignmentFormat FeatureTableParser Deprecated.Use org.biojavax.bio.seq.io framework insteadGenbankFileFormer Deprecated.Use org.biojavax.bio.seq.io framework insteadGenbankFormat Deprecated.Use org.biojavax.bio.seq.io.GenbankFormatGenbankProcessor Deprecated.Use org.biojavax.bio.seq.io framework insteadParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information.SeqFileFormer Deprecated.Use org.biojavax.bio.seq.io framework insteadSeqIOListener 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.SequenceBuilderBase Basic SequenceBuilder implementation which accumulates all notified information.SequenceBuilderFactory Simple factory for constructing new SequenceBuilder objects.SequenceBuilderFilter Base-class for builders that pass filtered events onto another builder.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.SymbolTokenization.TokenType WordTokenization Base class for tokenizations which accept whitespace-separated `words'. -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io.agave Class Description ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information.SeqIOListener Notification interface for objects which listen to a sequence stream parser. -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io.game Class Description ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information.SeqIOListener Notification interface for objects which listen to a sequence stream parser.StreamParser Parse a stream of characters into BioJava symbols. -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io.game12 Class Description SeqIOListener Notification interface for objects which listen to a sequence stream parser. -
Classes in org.biojava.bio.seq.io used by org.biojava.bio.symbol Class Description SeqIOListener Notification interface for objects which listen to a sequence stream parser.StreamParser Parse a stream of characters into BioJava symbols.SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation.SymbolTokenization.TokenType -
Classes in org.biojava.bio.seq.io used by org.biojava.ontology.io Class Description ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information. -
Classes in org.biojava.bio.seq.io used by org.biojava.ontology.obo Class Description ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information. -
Classes in org.biojava.bio.seq.io used by org.biojavax.bio.phylo.io.phylip Class Description ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information. -
Classes in org.biojava.bio.seq.io used by org.biojavax.bio.seq Class Description SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation. -
Classes in org.biojava.bio.seq.io used by org.biojavax.bio.seq.io Class Description ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information.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.SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation. -
Classes in org.biojava.bio.seq.io used by org.biojavax.bio.taxa.io Class Description ParseException ParseException should be thrown to indicate that there was a problem with parsing sequence information.