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Packages that use org.biojava.bio | |
org.biojava.bio | The core classes that will be used throughout the bio packages. |
org.biojava.bio.alignment |
Implementation of the Alignment interface. |
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.gff | GFF manipulation. |
org.biojava.bio.program.hmmer | Tools for working with profile Hidden Markov Models from the HMMer package. |
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.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.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 into alternate coordinate systems. |
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. |
org.biojava.bio.taxa | Taxonomy object for representing species information. |
org.biojava.directory | Open Bio Sequence Database Access (OBDA) registry support. |
org.biojava.utils.math | Mathematical utility classes. |
Classes in org.biojava.bio used by org.biojava.bio | |
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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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 | |
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.chromatogram | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.dist | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.dp | |
Annotatable
Indicates that an object has an associated annotation. |
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Annotatable.AnnotationForwarder
A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one. |
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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 | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.dp.twohead | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.gui | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.molbio | |
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 | |
BioError
A nestable biological error. |
Classes in org.biojava.bio used by org.biojava.bio.program.das | |
Annotatable.AnnotationForwarder
A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one. |
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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.gff | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.hmmer | |
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.indexdb | |
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 | |
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.ssaha | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.program.ssbind | |
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 | |
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 | |
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 | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.proteomics | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.search | |
Annotatable
Indicates that an object has an associated annotation. |
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Annotatable.AnnotationForwarder
A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one. |
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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 | |
Annotatable
Indicates that an object has an associated annotation. |
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Annotatable.AnnotationForwarder
A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one. |
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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 | |
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 | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.db.biosql | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.db.flat | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.distributed | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.bio.seq.homol | |
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 | |
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 | |
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 | |
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 Map. |
Classes in org.biojava.bio used by org.biojava.bio.seq.io.filterxml | |
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. |
|
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 | |
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.ragbag | |
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.symbol | |
Annotatable
Indicates that an object has an associated annotation. |
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Annotatable.AnnotationForwarder
A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one. |
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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 | |
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 | |
BioException
A nestable biological exception. |
Classes in org.biojava.bio used by org.biojava.utils.math | |
BioException
A nestable biological exception. |
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