Uses of Package
org.biojava.bio.seq.io
Packages that use org.biojava.bio.seq.io
Package
Description
Java wrappers for interacting with external bioinformatics tools.
Parser for Phred output
SSAHA sequence searching API.
Event-driven parsing system for the Extensible Feature Format (XFF).
Collections of biological sequence data.
Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Representation of the Symbols that make up a sequence, and locations within
them.
Tools for loading and saving ontologies.
Classes to support the I/O of Nexus files.
Classes to support the reading and writing of PHYLIP format.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.programClassDescriptionEncapsulate a mapping between BioJava Symbol objects and some string representation.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.program.phredClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.Notification interface for objects which listen to a sequence stream parser.Defines what a sequence format does.Parses a stream into sequences.Encapsulate a mapping between BioJava Symbol objects and some string representation.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.program.ssahaClassDescriptionNotification interface for objects which listen to a sequence stream parser.Defines what a sequence format does.Encapsulate a mapping between BioJava Symbol objects and some string representation.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.program.xffClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.Notification interface for objects which listen to a sequence stream parser.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.dbClassDescriptionSimple factory for constructing new SequenceBuilder objects.Defines what a sequence format does.Encapsulate a mapping between BioJava Symbol objects and some string representation.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.ioClassDescriptionDeprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io framework insteadDeprecated.Use org.biojavax.bio.seq.io.GenbankFormatDeprecated.Use org.biojavax.bio.seq.io framework insteadParseException should be thrown to indicate that there was a problem with parsing sequence information.Deprecated.Use org.biojavax.bio.seq.io framework insteadNotification interface for objects which listen to a sequence stream parser.Interface 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.Defines what a sequence format does.Parse a stream of characters into BioJava symbols.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'.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io.agaveClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.Notification interface for objects which listen to a sequence stream parser.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io.gameClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.Notification interface for objects which listen to a sequence stream parser.Parse a stream of characters into BioJava symbols.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io.game12ClassDescriptionNotification interface for objects which listen to a sequence stream parser.
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Classes in org.biojava.bio.seq.io used by org.biojava.bio.symbolClassDescriptionNotification interface for objects which listen to a sequence stream parser.Parse a stream of characters into BioJava symbols.Encapsulate a mapping between BioJava Symbol objects and some string representation.
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Classes in org.biojava.bio.seq.io used by org.biojava.ontology.ioClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.
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Classes in org.biojava.bio.seq.io used by org.biojava.ontology.oboClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.
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Classes in org.biojava.bio.seq.io used by org.biojavax.bio.phylo.io.nexusClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.
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Classes in org.biojava.bio.seq.io used by org.biojavax.bio.phylo.io.phylipClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.
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Classes in org.biojava.bio.seq.io used by org.biojavax.bio.seqClassDescriptionEncapsulate a mapping between BioJava Symbol objects and some string representation.
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Classes in org.biojava.bio.seq.io used by org.biojavax.bio.seq.ioClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.Notification interface for objects which listen to a sequence stream parser.Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object.Simple factory for constructing new SequenceBuilder objects.Defines what a sequence format does.Encapsulate a mapping between BioJava Symbol objects and some string representation.
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Classes in org.biojava.bio.seq.io used by org.biojavax.bio.taxa.ioClassDescriptionParseException should be thrown to indicate that there was a problem with parsing sequence information.