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Packages that use org.biojava.bio | |
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org.biojava.bio | The core classes that will be used throughout the bio packages. |
org.biojava.bio.alignment | Classes to generate and describe sequence alignments. |
org.biojava.bio.annodb | Databases of generic structured data (annotation) objects. |
org.biojava.bio.chromatogram | Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment. |
org.biojava.bio.dist | Probability distributions over Alphabets. |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.dp.onehead | |
org.biojava.bio.dp.twohead | |
org.biojava.bio.gui | Graphical interfaces for biojava objects. |
org.biojava.bio.molbio | The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR. |
org.biojava.bio.program.abi | ABI Trace Handling. |
org.biojava.bio.program.das | Development client for the Distributed Annotation System. |
org.biojava.bio.program.das.dasalignment | request alignments via DAS |
org.biojava.bio.program.formats | Experimental parsers using the tagvalue framework. |
org.biojava.bio.program.gff | GFF manipulation. |
org.biojava.bio.program.gff3 | Support for reading and writing GFF3. |
org.biojava.bio.program.hmmer | Tools for working with profile Hidden Markov Models from the HMMer package. |
org.biojava.bio.program.homologene | Support classes for Homologene data. |
org.biojava.bio.program.indexdb | A flat-file ascii index of ascii flat files as per the OBDA specification. |
org.biojava.bio.program.phred | Parser for Phred output |
org.biojava.bio.program.sax.blastxml | Parsers for the XML output from NCBI blast. |
org.biojava.bio.program.ssaha | SSAHA sequence searching API. |
org.biojava.bio.program.ssbind | Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. |
org.biojava.bio.program.tagvalue | Process files as streams of records, each with tags with values. |
org.biojava.bio.program.unigene | Objects for representing Unigene clusters. |
org.biojava.bio.program.xff | Event-driven parsing system for the Extensible Feature Format (XFF). |
org.biojava.bio.proteomics | Utilities to aid in performing various physical analysis of proteins. |
org.biojava.bio.proteomics.aaindex | Classes and interfaces to load Amino Acid Index database files. |
org.biojava.bio.search | Interfaces and classes for representing sequence similarity search results. |
org.biojava.bio.seq | Classes and interfaces for defining biological sequences and informatics objects. |
org.biojava.bio.seq.db | Collections of biological sequence data. |
org.biojava.bio.seq.db.biofetch | Client for the OBDA BioFetch protocol. |
org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database. |
org.biojava.bio.seq.db.flat | Support for OBDA flatfile databases. |
org.biojava.bio.seq.distributed | Sequences and SequenceDBs which are composed from data taken from a number of data sources. |
org.biojava.bio.seq.homol | The classes and interfaces for defining sequence similarity and honology. |
org.biojava.bio.seq.impl | Standard in-memory implementations of Sequence and
Feature . |
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.filterxml | Tools for reading and writing an XML representation of BioJava's FeatureFilter language. |
org.biojava.bio.seq.projection | Code for projecting Feature objects and systematically altering their properties. |
org.biojava.bio.structure | Interfaces and classes for protein structure (PDB). |
org.biojava.bio.structure.io | Input and Output of Structures |
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
org.biojava.bio.taxa | Taxonomy object for representing species information. |
org.biojava.directory | Open Bio Sequence Database Access (OBDA) registry support. |
org.biojava.ontology | A general-purpose API for ontologies. |
org.biojava.utils.automata | |
org.biojava.utils.math | Mathematical utility classes. |
org.biojava.utils.regex | This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets. |
org.biojava.utils.walker | |
org.biojavax | The Biojava extensions packages, classes that extend the core biojava functionality |
org.biojavax.bio | Classes to represent biological entities and their relationships. |
org.biojavax.bio.db | Interactions between biojavax objects and a DB. |
org.biojavax.bio.db.biosql | Interface between biojava and biosql databases |
org.biojavax.bio.db.ncbi | Interfaces to NCBI data. |
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.ontology | Extensions to the biojava ontology model that represent BioSQL ontology. |
Classes in org.biojava.bio used by org.biojava.bio | |
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AbstractAnnotation
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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AnnotationType
A set of constraints on the data contained in an Annotation . |
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AnnotationType.Abstract
An abstract base class useful for implementing AnnotationType instances. |
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CollectionConstraint
Used by AnnotationType to represent the constraint on
the collection of values in a property-slot. |
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EcNumber
An ec (enzyme classification) number. |
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EcNumber.Impl
A simple implementation of EcNumber. |
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PropertyConstraint
PropertyConstraint s describes a constraint applied
to the members of an annotation bundle. |
Classes in org.biojava.bio used by org.biojava.bio.alignment | |
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BioError
A nestable biological error. |
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BioException
A nestable biological exception. |
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BioRuntimeException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.annodb | |
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AnnotationType
A set of constraints on the data contained in an Annotation . |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.chromatogram | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.dist | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.dp | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.dp.onehead | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.dp.twohead | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.gui | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.molbio | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.abi | |
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BioError
A nestable biological error. |
Classes in org.biojava.bio used by org.biojava.bio.program.das | |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.das.dasalignment | |
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Annotation
Arbitrary annotation associated with one or more objects. |
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AnnotationType
A set of constraints on the data contained in an Annotation . |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.formats | |
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AnnotationType
A set of constraints on the data contained in an Annotation . |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.gff | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.gff3 | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.hmmer | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
Classes in org.biojava.bio used by org.biojava.bio.program.homologene | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.indexdb | |
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Annotation
Arbitrary annotation associated with one or more objects. |
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AnnotationType
A set of constraints on the data contained in an Annotation . |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.phred | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.sax.blastxml | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.ssaha | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.ssbind | |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.tagvalue | |
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Annotation
Arbitrary annotation associated with one or more objects. |
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AnnotationType
A set of constraints on the data contained in an Annotation . |
Classes in org.biojava.bio used by org.biojava.bio.program.unigene | |
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Annotatable
Indicates that an object has an associated annotation. |
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AnnotationType
A set of constraints on the data contained in an Annotation . |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.xff | |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.proteomics | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.proteomics.aaindex | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.search | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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AnnotationType
A set of constraints on the data contained in an Annotation . |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.db | |
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BioException
A nestable biological exception. |
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BioRuntimeException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.db.biofetch | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.db.biosql | |
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BioException
A nestable biological exception. |
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BioRuntimeException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.db.flat | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.distributed | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.homol | |
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Annotatable
Indicates that an object has an associated annotation. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.impl | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.io | |
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AbstractAnnotation
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map. |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.io.agave | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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SimpleAnnotation
A no-frills implementation of Annotation that is just a wrapper around a LinkedHashMap . |
Classes in org.biojava.bio used by org.biojava.bio.seq.io.filterxml | |
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AnnotationType
A set of constraints on the data contained in an Annotation . |
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CollectionConstraint
Used by AnnotationType to represent the constraint on
the collection of values in a property-slot. |
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PropertyConstraint
PropertyConstraint s describes a constraint applied
to the members of an annotation bundle. |
Classes in org.biojava.bio used by org.biojava.bio.seq.projection | |
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Annotatable
Indicates that an object has an associated annotation. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.structure | |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.structure.io | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.symbol | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.taxa | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.directory | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.ontology | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
Classes in org.biojava.bio used by org.biojava.utils.automata | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.utils.math | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.utils.regex | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.utils.walker | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojavax | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
Classes in org.biojava.bio used by org.biojavax.bio | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojavax.bio.db | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojavax.bio.db.biosql | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojavax.bio.db.ncbi | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojavax.bio.seq | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojavax.bio.seq.io | |
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BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojavax.ontology | |
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Annotatable
Indicates that an object has an associated annotation. |
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Annotation
Arbitrary annotation associated with one or more objects. |
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