Uses of Package
org.biojava.nbio.core.sequence.template

Packages that use org.biojava.nbio.core.sequence.template

Package	Description
org.biojava.nbio.aaproperties.xml	Set of classes that handles the reading and writing of xml files.
org.biojava.nbio.alignment
org.biojava.nbio.alignment.io
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.matrices
org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.search.io
org.biojava.nbio.core.search.io.blast
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.compound
org.biojava.nbio.core.sequence.edits
org.biojava.nbio.core.sequence.features
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.io.template
org.biojava.nbio.core.sequence.io.util
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.location
org.biojava.nbio.core.sequence.location.template
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.transcription
org.biojava.nbio.core.sequence.views
org.biojava.nbio.core.util
org.biojava.nbio.genome.io.fastq	FASTQ and variants sequence format I/O.
org.biojava.nbio.phylo
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.ws.alignment	This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava.nbio.ws.alignment.qblast

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.aaproperties.xml

Class and Description
CompoundSet
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.alignment

Class and Description
Compound
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.alignment.io

Class and Description
AbstractCompound The details of a Compound
AbstractSequence The base class for DNA, RNA and Protein sequences.

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.alignment.routines

Class and Description
Compound
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.alignment.template

Class and Description
Compound
CompoundSet
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.alignment

Class and Description
Accessioned Indicates an entity is accessioned
Compound
CompoundSet
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes
SequenceView

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.alignment.matrices

Class and Description
Compound
CompoundSet

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.alignment.template

Class and Description
Accessioned Indicates an entity is accessioned
Compound
CompoundSet
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.search.io

Class and Description
Compound
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.search.io.blast

Class and Description
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence

Class and Description
AbstractSequence The base class for DNA, RNA and Protein sequences.
Accessioned Indicates an entity is accessioned
Compound
CompoundSet
LightweightProfile Defines a minimal data structure for reading and writing a sequence alignment.
LightweightProfile.StringFormat List of output formats.
ProxySequenceReader
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes
SequenceReader
SequenceView

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.compound

Class and Description
AbstractCompound The details of a Compound
AbstractCompoundSet
AbstractNucleotideCompoundSet
ComplementCompound
Compound
CompoundSet
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.edits

Class and Description
Compound
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.features

Class and Description
AbstractSequence The base class for DNA, RNA and Protein sequences.
Compound

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.io

Class and Description
AbstractSequence The base class for DNA, RNA and Protein sequences.
Compound
CompoundSet
ProxySequenceReader
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.io.template

Class and Description
AbstractSequence The base class for DNA, RNA and Protein sequences.
Compound
ProxySequenceReader
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.io.util

Class and Description
Compound
CompoundSet
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.loader

Class and Description
AbstractSequence The base class for DNA, RNA and Protein sequences.
Accessioned Indicates an entity is accessioned
Compound
CompoundSet
ProxySequenceReader
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes
SequenceReader
SequenceView

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.location

Class and Description
AbstractSequence The base class for DNA, RNA and Protein sequences.
Accessioned Indicates an entity is accessioned
Compound

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.location.template

Class and Description
Accessioned Indicates an entity is accessioned
Compound
ProxySequenceReader
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.storage

Class and Description
Accessioned Indicates an entity is accessioned
Compound
CompoundSet
ProxySequenceReader
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes
SequenceReader
SequenceView

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.template

Class and Description
AbstractCompoundSet
AbstractSequence The base class for DNA, RNA and Protein sequences.
AbstractSequence.AnnotationType
Accessioned Indicates an entity is accessioned
ComplementCompound
Compound
CompoundSet
CompoundTranslator
LightweightProfile.StringFormat List of output formats.
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes
SequenceReader
SequenceView

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.transcription

Class and Description
AbstractCompoundTranslator
Compound
CompoundSet
CompoundTranslator
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.sequence.views

Class and Description
Accessioned Indicates an entity is accessioned
ComplementCompound
Compound
CompoundSet
ProxySequenceReader
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes
SequenceProxyView
SequenceReader
SequenceView

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.core.util

Class and Description
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.genome.io.fastq

Class and Description
AbstractSequence The base class for DNA, RNA and Protein sequences.

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.phylo

Class and Description
Compound
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.structure

Class and Description
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.structure.io

Class and Description
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.ws.alignment

Class and Description
Compound
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes

Classes in org.biojava.nbio.core.sequence.template used by org.biojava.nbio.ws.alignment.qblast

Class and Description
Compound
Sequence Main interface for defining a collection of Compounds and accessing them using biological indexes