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