Uses of Package
org.biojavax.bio.seq
Packages that use org.biojavax.bio.seq
Package
Description
The Biojava extensions packages, classes that extend the core biojava
functionality
This package contains the interfaces that need to be implemented by discrete alignment services.
This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services
through the WWW.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
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.biojavax.bio.seq used by org.biojavaxClassDescriptionResolves a position that is fuzzy or covers a range of bases by converting it to a single base.Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.An interface for classes that know how to handle subsequence operations.
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Classes in org.biojavax.bio.seq used by org.biojavax.bio.alignmentClassDescriptionA rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
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Classes in org.biojavax.bio.seq used by org.biojavax.bio.alignment.blastClassDescriptionA rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
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Classes in org.biojavax.bio.seq used by org.biojavax.bio.dbClassDescriptionA rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Essentially the same as SequenceIterator.
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Classes in org.biojavax.bio.seq used by org.biojavax.bio.db.biosqlClassDescriptionDescribes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.This class represents a strand on which a location may lie.A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.An interface for classes that know how to handle subsequence operations.
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Classes in org.biojavax.bio.seq used by org.biojavax.bio.db.ncbiClassDescriptionA rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
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Classes in org.biojavax.bio.seq used by org.biojavax.bio.seqClassDescriptionAn implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.Holds info about base positions.Resolves a position that is fuzzy or covers a range of bases by converting it to a single base.Represents a feature that can be given name and rank and be moved from one sequence to another.Represents the relation between two features.Holds feature relationships.Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.This class represents a strand on which a location may lie.A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.An interface for classes that know how to handle subsequence operations.Essentially the same as SequenceIterator.A simple implementation of RichLocation.A simple implementation of RichSequence.
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Classes in org.biojavax.bio.seq used by org.biojavax.bio.seq.ioClassDescriptionRepresents a feature that can be given name and rank and be moved from one sequence to another.Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Stores a number of useful terms used across many sequence formats for consistency's sake.Essentially the same as SequenceIterator.