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Packages that use org.biojava.bio.seq.io | |
org.biojava.bio.program | Java wrappers for interacting with external bioinformatics tools. |
org.biojava.bio.program.phred | Parser for Phred output |
org.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.seq.ragbag | The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. |
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
Classes in org.biojava.bio.seq.io used by org.biojava.bio.program | |
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 | |
ParseException
ParseException should be thrown to indicate that there was a problem with parsing sequence information. |
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SeqIOListener
Notification interface for objects which listen to a sequence stream parser. |
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SequenceFormat
Defines what a sequence format does. |
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StreamReader
Parses a stream into sequences. |
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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 | |
SeqIOListener
Notification interface for objects which listen to a sequence stream parser. |
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SequenceFormat
Defines what a sequence format does. |
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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 | |
ParseException
ParseException should be thrown to indicate that there was a problem with parsing sequence information. |
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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 | |
SequenceBuilderFactory
Simple factory for constructing new SequenceBuilder objects. |
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SequenceFormat
Defines what a sequence format does. |
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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 | |
AlignmentFormat
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FeatureTableParser
Simple parser for feature tables. |
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GenbankFileFormer
GenbankFileFormer performs the detailed formatting of
Genbank entries for writing to a PrintStream . |
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GenbankProcessor
Simple filter which handles attribute lines from a Genbank file |
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ParseException
ParseException should be thrown to indicate that there was a problem with parsing sequence information. |
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SeqFileFormer
Objects implementing the SeqFileFormer interface are
responsible for the detailed formatting of sequence data prior to
writing to a PrintStream . |
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SeqIOListener
Notification interface for objects which listen to a sequence stream parser. |
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SequenceBuilder
Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object. |
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SequenceBuilderBase
Basic SequenceBuilder implementation which accumulates all notified information. |
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SequenceBuilderFactory
Simple factory for constructing new SequenceBuilder objects. |
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SequenceBuilderFilter
Base-class for builders that pass filtered events onto another builder. |
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SequenceFormat
Defines what a sequence format does. |
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StreamParser
Parse a stream of characters into BioJava symbols. |
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SymbolReader
Encapsulate a stream of Symbols being parsed from some input stream. |
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SymbolTokenization
Encapsulate a mapping between BioJava Symbol objects and some string representation. |
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SymbolTokenization.TokenType
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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 | |
ParseException
ParseException should be thrown to indicate that there was a problem with parsing sequence information. |
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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 | |
StreamParser
Parse a stream of characters into BioJava symbols. |
Classes in org.biojava.bio.seq.io used by org.biojava.bio.seq.io.game12 | |
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.ragbag | |
ParseException
ParseException should be thrown to indicate that there was a problem with parsing sequence information. |
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SeqIOListener
Notification interface for objects which listen to a sequence stream parser. |
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SequenceBuilder
Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object. |
Classes in org.biojava.bio.seq.io used by org.biojava.bio.symbol | |
SymbolTokenization
Encapsulate a mapping between BioJava Symbol objects and some string representation. |
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