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org.biojava.bio.structure
Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align
Classes for the alignment of structures.
org.biojava.bio.structure.align.ce
Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.bio.structure.align.client
This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.bio.structure.align.events
org.biojava.bio.structure.align.fatcat
Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.bio.structure.align.fatcat.calc
org.biojava.bio.structure.align.gui
org.biojava.bio.structure.align.gui.aligpanel
org.biojava.bio.structure.align.gui.autosuggest
org.biojava.bio.structure.align.gui.jmol
Utility methods for better interaction with Jmol.
org.biojava.bio.structure.align.helper
Helper classes for structural alignment.
org.biojava.bio.structure.align.model
org.biojava.bio.structure.align.pairwise
Classes for the pairwise alignment of structures.
org.biojava.bio.structure.align.seq
org.biojava.bio.structure.align.util
org.biojava.bio.structure.align.webstart
Classes related to Java Web Start
org.biojava.bio.structure.align.xml
Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.bio.structure.domain
org.biojava.bio.structure.domain.pdp
org.biojava.bio.structure.gui
A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.bio.structure.gui.events
Some event classes for the protein structure GUIs.
org.biojava.bio.structure.gui.util
Some utility classes for the protein structure GUIs.
org.biojava.bio.structure.gui.util.color
org.biojava.bio.structure.io
Input and Output of Structures
org.biojava.bio.structure.io.mmcif
Input and Output of mmcif files
org.biojava.bio.structure.io.mmcif.chem
org.biojava.bio.structure.io.mmcif.model
Datamodel objects used for processing mmcif files.
org.biojava.bio.structure.io.sifts
org.biojava.bio.structure.io.util
org.biojava.bio.structure.jama
Matrix package for from
JAMA
org.biojava.bio.structure.scop
Parsers and API for
SCOP, Structural Classification of Proteins
.
org.biojava.bio.structure.scop.server
org.biojava.bio.structure.secstruc
org.biojava.bio.structure.server
classes for easier management of PDB installations As of BioJava 3.0.2 this package is deprecated.
org.biojava3.aaproperties
Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava3.aaproperties.profeat
Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
org.biojava3.aaproperties.profeat.convertor
Set of classes that enable the conversion protein sequences into various attributes.
org.biojava3.aaproperties.xml
Set of classes that handles the reading and writing of xml files.
org.biojava3.alignment
org.biojava3.alignment.aaindex
org.biojava3.alignment.routines
org.biojava3.alignment.template
org.biojava3.core.exceptions
org.biojava3.core.sequence
org.biojava3.core.sequence.compound
org.biojava3.core.sequence.edits
org.biojava3.core.sequence.features
org.biojava3.core.sequence.io
org.biojava3.core.sequence.io.template
org.biojava3.core.sequence.io.util
org.biojava3.core.sequence.loader
org.biojava3.core.sequence.location
org.biojava3.core.sequence.location.template
org.biojava3.core.sequence.storage
org.biojava3.core.sequence.template
org.biojava3.core.sequence.transcription
org.biojava3.core.sequence.views
org.biojava3.core.util
org.biojava3.data.sequence
Set of classes that responsible for data handling.
org.biojava3.genome
org.biojava3.genome.homology
org.biojava3.genome.parsers.geneid
org.biojava3.genome.parsers.gff
org.biojava3.genome.query
org.biojava3.genome.uniprot
org.biojava3.genome.util
org.biojava3.phylo
org.biojava3.protmod
org.biojava3.protmod.io
org.biojava3.protmod.structure
org.biojava3.ronn
BioJava provide a module biojava3-protein-disorder for prediction disordered regions from a protein sequence.
org.biojava3.sequencing.io.fastq
FASTQ and variants sequence format I/O.
org.biojava3.structure.gui
New MVC interface for structure-gui
org.biojava3.ws.alignment
This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava3.ws.alignment.qblast
org.biojava3.ws.hmmer
org.forester.application
org.forester.archaeopteryx
org.forester.archaeopteryx.phylogeny.data
org.forester.archaeopteryx.webservices
org.forester.datastructures
org.forester.development
org.forester.go
org.forester.go.etc
org.forester.io.parsers
org.forester.io.parsers.nexus
org.forester.io.parsers.nhx
org.forester.io.parsers.phyloxml
org.forester.io.parsers.phyloxml.phylogenydata
org.forester.io.parsers.tol
org.forester.io.writers
org.forester.pccx
org.forester.phylogeny
org.forester.phylogeny.data
org.forester.phylogeny.factories
org.forester.phylogeny.iterators
org.forester.phylogenyinference
org.forester.sdi
org.forester.surfacing
org.forester.test
org.forester.tools
org.forester.util
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