Uses of Package
org.biojava.bio.seq
Packages that use org.biojava.bio.seq
Package
Description
Classes to generate and describe sequence alignments.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical displays of biological sequences and associated annotations.
Classes for the handling of the layout of a WrappedSequencePanel.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
FASTQ and variants sequence format I/O.
GFF manipulation.
Support for reading and writing GFF3.
Parser for Phred output
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Objects for representing Unigene clusters.
Event-driven parsing system for the Extensible Feature Format (XFF).
Utilities to aid in performing various physical analysis of proteins.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
Client for the OBDA BioFetch protocol.
General purpose Sequence storage in a relational database.
Support for OBDA flatfile databases.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Code for projecting Feature objects and systematically altering their
properties.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
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 used by org.biojava.bio.alignmentClassDescriptionExtension of GappedSymbolList which also projects features into the gapped coordinate system.A biological sequence.An iterator over a bag of sequences.
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Classes in org.biojava.bio.seq used by org.biojava.bio.dist
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Classes in org.biojava.bio.seq used by org.biojava.bio.dpClassDescriptionA biological sequence.An object which adds some additional information to a Sequence.
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Classes in org.biojava.bio.seq used by org.biojava.bio.gui.sequenceClassDescriptionA feature within a sequence, or nested within another feature.A filter for accepting or rejecting a feature.The interface for objects that contain features.The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.A biological sequence.Class to represent the 'strandedness' of a feature.
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Classes in org.biojava.bio.seq used by org.biojava.bio.gui.sequence.tracklayout
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Classes in org.biojava.bio.seq used by org.biojava.bio.molbioClassDescriptionA feature within a sequence, or nested within another feature.Template class for a plain feature.The interface for objects that contain features.A biological sequence.An object which adds some additional information to a Sequence.Adds the concept of 'strand' to features.Template class for parameterizing the creation of a new
StrandedFeature
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Classes in org.biojava.bio.seq used by org.biojava.bio.program.fastq
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Classes in org.biojava.bio.seq used by org.biojava.bio.program.gffClassDescriptionA feature within a sequence, or nested within another feature.A filter for accepting or rejecting a feature.A biological sequence.An object which adds some additional information to a Sequence.Class to represent the 'strandedness' of a feature.
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Classes in org.biojava.bio.seq used by org.biojava.bio.program.gff3
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Classes in org.biojava.bio.seq used by org.biojava.bio.program.phredClassDescriptionThe interface for objects that contain features.Interface for
FeatureHolder
objects which know how to instantiate new child Features.A biological sequence. -
Classes in org.biojava.bio.seq used by org.biojava.bio.program.ssbind
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Classes in org.biojava.bio.seq used by org.biojava.bio.program.unigene
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Classes in org.biojava.bio.seq used by org.biojava.bio.program.xffClassDescriptionA feature within a sequence, or nested within another feature.Template class for a plain feature.The interface for objects that contain features.A biological sequence.Template class for parameterizing the creation of a new
StrandedFeature
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Classes in org.biojava.bio.seq used by org.biojava.bio.proteomics
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Classes in org.biojava.bio.seq used by org.biojava.bio.searchClassDescriptionA biological sequence.Class to represent the 'strandedness' of a feature.
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Classes in org.biojava.bio.seq used by org.biojava.bio.seqClassDescriptionAn abstract implementation of FeatureHolder.A feature within a sequence, or nested within another feature.
ByLocationComparator
comparesFeature
s by the minimum base position of theirLocation
.Template class for a plain feature.A filter for accepting or rejecting a feature.A filter that returns all features that have an annotation bundle that is of a given annotation type.The interface for objects that contain features.Interface for translators which map from Feature.Template instances to real Feature objects.A named collection of Types.A type of feature.An object able to transform some FeatureFilter instances sytematically into others.Title: Frame.A singleton to hold the frame informationExtension of GappedSymbolList which also projects features into the gapped coordinate system.The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.Interface forFeatureHolder
objects which know how to instantiate new child Features.A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature.A biological sequence.Adds the concept of 'strand' to features.Class to represent the 'strandedness' of a feature.Template class for parameterizing the creation of a newStrandedFeature
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.dbClassDescriptionA filter for accepting or rejecting a feature.The interface for objects that contain features.A biological sequence.An object which adds some additional information to a Sequence.An iterator over a bag of sequences.
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.db.biofetch
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.db.biosqlClassDescriptionA filter for accepting or rejecting a feature.The interface for objects that contain features.A biological sequence.An iterator over a bag of sequences.
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.db.flat
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.distributedClassDescriptionA filter for accepting or rejecting a feature.The interface for objects that contain features.A biological sequence.
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.filterClassDescriptionA filter for accepting or rejecting a feature.A filter that returns all features accepted by both child filter.Filter by applying a nested
FeatureFilter
to all ancestor features.Filter by applying a nestedFeatureFilter
to the child features.Filter by applying a nestedFeatureFilter
to all descendant features.Filter by applying a nestedFeatureFilter
to the parent feature.A filter that returns all features not accepted by a child filter.Accepts features where all immediate children meet the supplied filter.Accepts features where all descendants meet the supplied filter.A filter that returns all features accepted by at least one child filter. -
Classes in org.biojava.bio.seq used by org.biojava.bio.seq.homolClassDescriptionA feature within a sequence, or nested within another feature.Template class for a plain feature.The interface for objects that contain features.Adds the concept of 'strand' to features.Template class for parameterizing the creation of a new
StrandedFeature
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.implClassDescriptionFeature which represents a component in an assembly (contig).A feature within a sequence, or nested within another feature.Template class for a plain feature.A filter for accepting or rejecting a feature.The interface for objects that contain features.Interface for translators which map from Feature.Template instances to real Feature objects.An object able to transform some FeatureFilter instances sytematically into others.Title: Frame.Title: FramedFeature.A singleton to hold the frame informationExtension of GappedSymbolList which also projects features into the gapped coordinate system.Interface for
FeatureHolder
objects which know how to instantiate new child Features.A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature.A biological sequence.Deprecated.use org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilderA no-frills implementation of FeatureHolder.Adds the concept of 'strand' to features.Class to represent the 'strandedness' of a feature.Template class for parameterizing the creation of a newStrandedFeature
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.ioClassDescriptionFeature which represents a component in an assembly (contig).Template for constructing a new ComponentFeature.A feature within a sequence, or nested within another feature.Template class for a plain feature.A biological sequence.An iterator over a bag of sequences.Class to represent the 'strandedness' of a feature.
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.io.agaveClassDescriptionA feature within a sequence, or nested within another feature.Template class for a plain feature.The interface for objects that contain features.A biological sequence.Class to represent the 'strandedness' of a feature.
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.io.filterxml
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.io.gameClassDescriptionTemplate class for a plain feature.Class to represent the 'strandedness' of a feature.
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Classes in org.biojava.bio.seq used by org.biojava.bio.seq.projectionClassDescriptionAn abstract implementation of FeatureHolder.A feature within a sequence, or nested within another feature.Template class for a plain feature.A filter for accepting or rejecting a feature.The interface for objects that contain features.An object able to transform some FeatureFilter instances sytematically into others.A biological sequence.Class to represent the 'strandedness' of a feature.
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Classes in org.biojava.bio.seq used by org.biojavax.bio.dbClassDescriptionA filter for accepting or rejecting a feature.The interface for objects that contain features.A biological sequence.An iterator over a bag of sequences.
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Classes in org.biojava.bio.seq used by org.biojavax.bio.db.biosqlClassDescriptionA feature within a sequence, or nested within another feature.A filter for accepting or rejecting a feature.The interface for objects that contain features.
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Classes in org.biojava.bio.seq used by org.biojavax.bio.seqClassDescriptionA feature within a sequence, or nested within another feature.Template class for a plain feature.A filter for accepting or rejecting a feature.The interface for objects that contain features.A biological sequence.An iterator over a bag of sequences.Adds the concept of 'strand' to features.Class to represent the 'strandedness' of a feature.
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Classes in org.biojava.bio.seq used by org.biojavax.bio.seq.ioClassDescriptionTemplate class for a plain feature.A biological sequence.An iterator over a bag of sequences.