| 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 |
|
| 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 |
|