Search Java Classes and Packages

Search Java Frameworks and Libraries

255581 classes and counting ...
Search Tips Index Status



# Classes and Interfaces in #BioJava - 1031 results found.
NameDescriptionTypePackageFramework
AAindexFactoryFactory class to get Providers for substitution matrices the are provided by the AAINDEX database.Classorg.biojava.nbio.core.alignment.matricesBioJava
AAIndexFileParserClassorg.biojava.nbio.core.alignment.matricesBioJava
AAIndexProviderInterfaceorg.biojava.nbio.core.alignment.matricesBioJava
AboutDialogClassorg.biojava.nbio.structure.align.guiBioJava
AbstractAlignmentJmolAn Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.Classorg.biojava.nbio.structure.align.gui.jmolBioJava
AbstractAnnotationA utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.Classorg.biojava.nbio.ontology.utilsBioJava
AbstractBeana generic class that implements the toString method for a beanAuthor:Andreas PrlicClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
AbstractCompoundClassorg.biojava.nbio.core.sequence.templateBioJava
AbstractCompoundSetClassorg.biojava.nbio.core.sequence.templateBioJava
AbstractCompoundTranslatorClassorg.biojava.nbio.core.sequence.templateBioJava
AbstractFeatureA feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the userClassorg.biojava.nbio.core.sequence.featuresBioJava
AbstractLocationBase abstraction of a location which encodes for the majority of important features about a location such as the start, end and strandClassorg.biojava.nbio.core.sequence.location.templateBioJava
AbstractMatrixAlignerClassorg.biojava.nbio.alignment.templateBioJava
AbstractNucleotideCompoundSetClassorg.biojava.nbio.core.sequence.templateBioJava
AbstractPairwiseSequenceAlignerClassorg.biojava.nbio.alignment.templateBioJava
AbstractProfileProfileAlignerClassorg.biojava.nbio.alignment.templateBioJava
AbstractScorerClassorg.biojava.nbio.alignment.templateBioJava
AbstractScoresCacheAbstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.Classorg.biojava.nbio.structure.align.multipleBioJava
AbstractSequenceThe base class for DNA, RNA and Protein sequences.Classorg.biojava.nbio.core.sequence.templateBioJava
AbstractStructureAlignmentClassorg.biojava.nbio.structure.alignBioJava
AbstractTermAbstract implementation of term This provides basic change-forwarding functionality fromClassorg.biojava.nbio.ontologyBioJava
AbstractUserArgumentProcessorBase class for a new structure alignment CLI.Classorg.biojava.nbio.structure.align.ceBioJava
AccesionedLocationA location which is bound to an AccessionID.Interfaceorg.biojava.nbio.core.sequence.location.templateBioJava
AccessionedInterfaceorg.biojava.nbio.core.sequence.templateBioJava
AccessionIDUsed in Sequences as the unique indentifier.Classorg.biojava.nbio.core.sequenceBioJava
AFPA class to represent a FATCAT AFPAuthor:Andreas PrlicSee Also:Serialized FormClassorg.biojava.nbio.structure.align.modelBioJava
AFPAlignmentDisplayClassorg.biojava.nbio.structure.align.utilBioJava
AFPCalculatora class that performs calculations on AFPCHainsAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.fatcat.calcBioJava
AFPChainA bean to contain the core of a structure alignment.Classorg.biojava.nbio.structure.align.modelBioJava
AFPChainCoordManagerClassorg.biojava.nbio.structure.align.gui.aligpanelBioJava
AFPChainera class to chain AFPs to an alignmentAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.fatcat.calcBioJava
AFPChainFlipperClassorg.biojava.nbio.structure.align.xmlBioJava
AFPChainScorerClassorg.biojava.nbio.structure.align.utilBioJava
AfpChainWriterA class to convert the data in an AfpChain object to various String outputs.Classorg.biojava.nbio.structure.align.modelBioJava
AFPChainXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJava
AFPChainXMLParserClassorg.biojava.nbio.structure.align.xmlBioJava
AFPFromFastaDemo displaying a structural alignment from a FASTA file using FastaAFPChainConverter.ClassdemoBioJava
AFPOptimizerClassorg.biojava.nbio.structure.align.fatcat.calcBioJava
AFPPostProcessordoes post processing after alignment chainginAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.fatcat.calcBioJava
AFPTwisterClassorg.biojava.nbio.structure.alignBioJava
AgScoreClassorg.biojava.nbio.survival.cox.statsBioJava
AligMatElClassorg.biojava.nbio.structure.align.helperBioJava
AlignableInterfaceorg.biojava.nbio.structure.align.pairwiseBioJava
AlignedPositionClassorg.biojava.nbio.structure.gui.utilBioJava
AlignedSequenceDefines a data structure for a Sequence within an alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
AlignerDefines an algorithm which computes an alignment Profile from a list of Sequences.Interfaceorg.biojava.nbio.alignment.templateBioJava
AlignerHelperStatic utility to construct alignment routines from a common library of methods.Classorg.biojava.nbio.alignment.routinesBioJava
AlignmentCalcA class that obtains two structures via DAS and aligns them This is done in a separate thread.Classorg.biojava.nbio.structure.align.guiBioJava
AlignmentCalcA class that obtains two structures via DAS and aligns them This is done in a separate thread.Classorg.biojava.nbio.structure.gui.utilBioJava
AlignmentCalcDBClassorg.biojava.nbio.structure.align.guiBioJava
AlignmentCalculationRunnableInterfaceorg.biojava.nbio.structure.align.guiBioJava
AlignmentGuiA JFrame that allows to trigger a pairwise structure alignment, either from files in a directory,Classorg.biojava.nbio.structure.align.guiBioJava
AlignmentGuiDemoGet an instance of the two alignment GUIs.ClassdemoBioJava
AlignmentPositionListenerInterfaceorg.biojava.nbio.structure.gui.eventsBioJava
AlignmentProgressListenerInterfaceorg.biojava.nbio.structure.align.eventsBioJava
AlignmentProgressListenerClassorg.biojava.nbio.structure.align.pairwiseBioJava
AlignmentResultA class to track the alignment results in a flat fileAuthor:andreasSee Also:Serialized FormClassorg.biojava.nbio.structure.align.pairwiseBioJava
AlignmentsStatic utility to easily run alignment routines.Classorg.biojava.nbio.alignmentBioJava
AlignmentTextPanelClassorg.biojava.nbio.structure.align.guiBioJava
AlignmentToolsMethods for analyzing and manipulating AFPChains and for other pairwise alignment utilities.Classorg.biojava.nbio.structure.align.utilBioJava
AligNPEClassorg.biojava.nbio.structure.align.pairwiseBioJava
AlignToolsClassorg.biojava.nbio.structure.align.helperBioJava
AligPanelA JPanel that can display an AFPChain in a nice way and interact with Jmol.Classorg.biojava.nbio.structure.align.gui.aligpanelBioJava
AligPanelMouseMotionListenerClassorg.biojava.nbio.structure.align.gui.aligpanelBioJava
AligUIManagerClassorg.biojava.nbio.structure.align.webstartBioJava
AllChemCompProviderA ChemComp provider that downloads and caches the components.Classorg.biojava.nbio.structure.io.mmcifBioJava
AlreadyExistsExceptionThrown to indicate that a term or triple can't be added to an ontology because it is already present.Classorg.biojava.nbio.ontologyBioJava
AltAligComparatora comparator to sort AlternativeAlignments based on their number of equivalent residuesAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.pairwiseBioJava
AlternativeAlignment Alternative alignments arise from different seed alignments or seed FPairs.Classorg.biojava.nbio.structure.align.pairwiseBioJava
AlternativeAlignmentFramea frame showing the alternative alignments, which are the result of a structure superimpositionSince:1.Classorg.biojava.nbio.structure.gui.utilBioJava
AmbiguityDNACompoundSetClassorg.biojava.nbio.core.sequence.compoundBioJava
AmbiguityDNARNAHybridCompoundSetAmbiguity set for hybrid DNA/RNA sequences.Classorg.biojava.nbio.core.sequence.compoundBioJava
AmbiguityRNACompoundSetClassorg.biojava.nbio.core.sequence.compoundBioJava
AminoAcid A Group that represents an AminoAcid.Interfaceorg.biojava.nbio.structureBioJava
AminoAcidCompositionClassorg.biojava.nbio.aaproperties.xmlBioJava
AminoAcidCompositionTableClassorg.biojava.nbio.aaproperties.xmlBioJava
AminoAcidCompoundUsed to describe an Amino Acid.Classorg.biojava.nbio.core.sequence.compoundBioJava
AminoAcidCompoundSetSet of proteinogenic amino acids.Classorg.biojava.nbio.core.sequence.compoundBioJava
AminoAcidImplAminoAcid inherits most from Hetatom.Classorg.biojava.nbio.structureBioJava
AnchoredPairwiseSequenceAlignerThis algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment producedClassorg.biojava.nbio.alignment.routinesBioJava
AngleOrderDetectorPlusGuesses an order of rotational symmetry from the angle.Classorg.biojava.nbio.structure.symmetry.internalBioJava
AngleOutlierJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
AnnotatableIndicates that an object has an associated annotation.Interfaceorg.biojava.nbio.ontology.utilsBioJava
Annotation Arbitrary annotation associated with one or more objects.Interfaceorg.biojava.nbio.ontology.utilsBioJava
AppClassorg.biojava.nbio.genomeBioJava
AppClassorg.biojava.nbio.ontologyBioJava
ArrayListProxySequenceReaderClassorg.biojava.nbio.core.sequence.loaderBioJava
ArrayListSequenceReaderClassorg.biojava.nbio.core.sequence.storageBioJava
AsaCalculatorClass to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley.Classorg.biojava.nbio.structure.asaBioJava
AssertionFailureAn unchecked exception representing an Assertion failure.Classorg.biojava.nbio.ontology.utilsBioJava
AssignmentXMLSerializerClassorg.biojava.nbio.structure.domainBioJava
AstralProvides programmatic access to ASTRAL representative sets.Classorg.biojava.nbio.structure.scopBioJava
AtomA simple interface for an Atom.Interfaceorg.biojava.nbio.structureBioJava
AtomCacheA utility class that provides easy access to Structure objects.Classorg.biojava.nbio.structure.align.utilBioJava
AtomContactA pair of atoms that are in contactAuthor:duarte_jSee Also:Serialized FormClassorg.biojava.nbio.structure.contactBioJava
AtomContactSetA set of atom-atom contacts to hold the results of intra and inter-chain contact calculationsAuthor:duarte_jSee Also:Serialized FormClassorg.biojava.nbio.structure.contactBioJava
AtomIdentifierClassorg.biojava.nbio.structure.contactBioJava
AtomImpl currently the coordinates of an atom are represented by a double[3] array.Classorg.biojava.nbio.structureBioJava
AtomInfoThis class uniquely describes an atomAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.gui.jmolBioJava
AtomInfoParserClassorg.biojava.nbio.structure.align.gui.jmolBioJava
AtomIteratoran iterator over all atoms of a structure / group.Classorg.biojava.nbio.structureBioJava
AtomPositionMapA map from ResidueNumbers to ATOM record positions in a PDB file.Classorg.biojava.nbio.structureBioJava
AtomSiteClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
AuditAuthorClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
AugmentedResidueRangeCreated by douglas on 1/23/15.Classorg.biojava.nbio.structureBioJava
AuthorDescribes author attributes for author information in a PDB file.Classorg.biojava.nbio.structureBioJava
AutoSuggestProviderInterfaceorg.biojava.nbio.structure.align.gui.autosuggestBioJava
AxisAlignerClassorg.biojava.nbio.structure.symmetry.coreBioJava
BasicSequenceBare bones version of the Sequence object to be used sparingly.Classorg.biojava.nbio.core.sequenceBioJava
BerkeleyScopInstallation The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.Classorg.biojava.nbio.structure.scopBioJava
BetaBridgeContainer that represents a beta Bridge between two residues.Classorg.biojava.nbio.structure.secstrucBioJava
BioAssemblyIdentifierClassorg.biojava.nbio.structureBioJava
BioAssemblyInfoRepresentation of a Biological Assembly annotation as provided by the PDB.Classorg.biojava.nbio.structure.quaternaryBioJava
BioAssemblyToolsClassorg.biojava.nbio.structure.quaternaryBioJava
BioJavaAADemoCreated by andreas on 8/9/14.ClassdemoBioJava
BiojavaJmolA class that provides a simple GUI for JmolSince:1.Classorg.biojava.nbio.structure.guiBioJava
BioJavaStructureAlignmentWrapper for the BioJava Structure Alignment ImplementationAuthor:Andreas PrlicClassorg.biojava.nbio.structure.alignBioJava
BiologicalAssemblyBuilderReconstructs the quaternary structure of a protein from an asymmetric unitAuthor:Peter Rose, Andreas PrlicClassorg.biojava.nbio.structure.quaternaryBioJava
BiologicalAssemblyTransformationThe transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file.Classorg.biojava.nbio.structure.quaternaryBioJava
BioUnitDataProviderProvides access to the data that is needed in order to rebuild the correct biological assembly of a protein.Interfaceorg.biojava.nbio.structure.quaternary.ioBioJava
BioUnitDataProviderFactoryFactory to create BioUnitDataProvider instances.Classorg.biojava.nbio.structure.quaternary.ioBioJava
BitSequenceReaderAn implementation of the popular bit encodings.Classorg.biojava.nbio.core.sequence.storageBioJava
BlastAlignmentParameterEnumenum BlastAlignmentParameterEnumAlignment request parameters accepted by QBlast service.Classorg.biojava.nbio.ws.alignment.qblastBioJava
BlastClustReaderClassorg.biojava.nbio.structure.symmetry.utilsBioJava
BlastHitBuilderDesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.io.blastBioJava
BlastHomologyHitsClassorg.biojava.nbio.genome.homologyBioJava
BlastHspBuilderDesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.io.blastBioJava
BlastJobInformation about QBlast search jobAuthor:Gediminas RimsaClassorg.biojava.nbio.ws.alignment.qblastBioJava
BlastMatrixEnumenum BlastMatrixEnumEnum representing matrices supported by QBlastClassorg.biojava.nbio.ws.alignment.qblastBioJava
BlastOutputAlignmentFormatEnumenum BlastOutputAlignmentFormatEnumEnum representing available output alignment types.Classorg.biojava.nbio.ws.alignment.qblastBioJava
BlastOutputFormatEnumenum BlastOutputFormatEnumEnum representing available output formats.Classorg.biojava.nbio.ws.alignment.qblastBioJava
BlastOutputParameterEnumenum BlastOutputParameterEnumOutput parameters accepted by QBlast service.Classorg.biojava.nbio.ws.alignment.qblastBioJava
BlastProgramEnumenum BlastProgramEnumEnum representing available blast programs.Classorg.biojava.nbio.ws.alignment.qblastBioJava
BlastResultThis class models a Blast/Blast plus result.Classorg.biojava.nbio.core.search.io.blastBioJava
BlastResultBuilderDesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.io.blastBioJava
BlastTabularParserDesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.io.blastBioJava
BlastXMLParserRe-designed by Paolo Pavan on the footprint of: org.Classorg.biojava.nbio.core.search.io.blastBioJava
BlastXMLQueryClassorg.biojava.nbio.genome.queryBioJava
BlockA Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in aInterfaceorg.biojava.nbio.structure.align.multipleBioJava
BlockImplGeneral implementation of a Block that supports any type of sequential alignment with gaps.Classorg.biojava.nbio.structure.align.multipleBioJava
BlockSetA BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.Interfaceorg.biojava.nbio.structure.align.multipleBioJava
BlockSetImplA general implementation of a BlockSet to store a flexible part of a multiple alignment.Classorg.biojava.nbio.structure.align.multipleBioJava
BondA simple bond -- it stores information about two atoms as well as information about its bond order.Interfaceorg.biojava.nbio.structureBioJava
BondImplA simple bond -- it stores information about two atoms as well as information about its bond order.Classorg.biojava.nbio.structureBioJava
BondMakerAdds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component DictionaryClassorg.biojava.nbio.structure.ioBioJava
BondOutlierJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
BondTypeWork in progress - NOT final!Author:Jules Jacobsen Classorg.biojava.nbio.structureBioJava
BoundingBoxA bounding box for short cutting some geometrical calculations.Classorg.biojava.nbio.structure.contactBioJava
BravaisLatticeAn enum to represent the 7 Bravais latticesEnum Constant SummaryClassorg.biojava.nbio.structure.xtalBioJava
BridgeTypeA bridge is formed by two non-overlapping stretches of three residues each (i-1,i,i+1) and (j-1,j,j+1), where iClassorg.biojava.nbio.structure.secstrucBioJava
BrowserOpenerClassorg.biojava.nbio.structure.align.webstartBioJava
BufferedReaderBytesReadNeed to keep track of actual bytes read and take advantage of buffered reader performance.Classorg.biojava.nbio.core.sequence.ioBioJava
C2RotationSolverClassorg.biojava.nbio.structure.symmetry.coreBioJava
CachedRemoteScopInstallationAn extension of the RemoteScopInstallation that caches some of the data locally.Classorg.biojava.nbio.structure.scopBioJava
CacheFactoryprovides a SoftHashMap singleton.Classorg.biojava.nbio.structure.align.utilBioJava
CAConverterConverts full atom representations to Calpha only ones.Classorg.biojava.nbio.structure.ioBioJava
CalcUtility operations on Atoms, AminoAcids, etc.Classorg.biojava.nbio.structureBioJava
CalcBioAssemblySymmetryClassorg.biojava.nbio.structure.symmetry.analysisBioJava
CallablePairwiseSequenceAlignerClassorg.biojava.nbio.alignment.templateBioJava
CallablePairwiseSequenceScorerClassorg.biojava.nbio.alignment.templateBioJava
CallableProfileProfileAlignerClassorg.biojava.nbio.alignment.templateBioJava
CallableStructureAlignmentClassorg.biojava.nbio.structure.alignBioJava
CartesianProductA cartesian product between two lists A and B is the set of all ordered pairs of the elements of both sets.Classorg.biojava.nbio.structure.quaternaryBioJava
CaseFreeAminoAcidCompoundSetSet of proteinogenic amino acids.Classorg.biojava.nbio.aaproperties.xmlBioJava
CaseInsensitiveCompoundAttempts to wrap compounds so it is possible to view them in a case insensitive mannerClassorg.biojava.nbio.core.sequence.transcriptionBioJava
CasePreservingProteinSequenceCreatorA sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.Classorg.biojava.nbio.core.sequence.ioBioJava
CathCategoryThe categories found within CATH.Classorg.biojava.nbio.structure.cathBioJava
CathDatabaseGeneral API for interacting with CATH.Interfaceorg.biojava.nbio.structure.cathBioJava
CathDomainA class which represents a single CATH domain.Classorg.biojava.nbio.structure.cathBioJava
CathFactoryControls global CathDatabases being used.Classorg.biojava.nbio.structure.cathBioJava
CathFragmentClassorg.biojava.nbio.structure.cathBioJava
CathInstallationClassorg.biojava.nbio.structure.cathBioJava
CathNodeRepresents a node in the CATH hierarchy.Classorg.biojava.nbio.structure.cathBioJava
CathSegmentClassorg.biojava.nbio.structure.cathBioJava
CDSComparatorClassorg.biojava.nbio.core.sequenceBioJava
CDSSequenceRepresents a exon or coding sequence in a gene.Classorg.biojava.nbio.core.sequenceBioJava
CECalculatorThis is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.Classorg.biojava.nbio.structure.align.ceBioJava
CeCalculatorEnhancedThis is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.Classorg.biojava.nbio.structure.align.ceBioJava
CeCPMainA wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.Classorg.biojava.nbio.structure.align.ceBioJava
CECPParametersProvides parameters to CeCPMainAuthor:Spencer BlivenClassorg.biojava.nbio.structure.align.ceBioJava
CeCPUserArgumentProcessorClassorg.biojava.nbio.structure.align.ceBioJava
CellClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
CeMainThe main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I.Classorg.biojava.nbio.structure.align.ceBioJava
CensorStatusClassorg.biojava.nbio.survival.kaplanmeier.figureBioJava
CensorStatusSelectInterfaceorg.biojava.nbio.survival.kaplanmeier.figureBioJava
CeParametersContains the parameters that can be sent to CEAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.ceBioJava
CeSideChainMainClassorg.biojava.nbio.structure.align.ceBioJava
CeSideChainUserArgumentProcessorClassorg.biojava.nbio.structure.align.ceBioJava
CeSymmIdentify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment.Classorg.biojava.nbio.structure.symmetry.internalBioJava
CeSymmIterativeIterative version of CeSymm that aims at identifying all symmetry axis (internal or quaternary) of a particular structure.Classorg.biojava.nbio.structure.symmetry.internalBioJava
CESymmParametersProvides parameters to CeSymm.Classorg.biojava.nbio.structure.symmetry.internalBioJava
CeSymmResultThis Class stores all the relevant information of an internal symmetry result obtained with CeSymm.Classorg.biojava.nbio.structure.symmetry.internalBioJava
CeUserArgumentProcessorprocess the arguments from command lineAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.ceBioJava
Chain Defines the interface for a Chain.Interfaceorg.biojava.nbio.structureBioJava
ChainClustererClassorg.biojava.nbio.structure.symmetry.coreBioJava
ChainImplA Chain in a PDB file.Classorg.biojava.nbio.structureBioJava
ChainSignatureClassorg.biojava.nbio.structure.symmetry.miscBioJava
ChangeValueInterfaceorg.biojava.nbio.survival.dataBioJava
ChargeAdderClassorg.biojava.nbio.structure.ioBioJava
ChemCompA definition for a Chemical Component, as maintained by the wwPDB.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
ChemCompAtomstores these fields: _chem_comp_atom.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
ChemCompBondClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
ChemCompConsumerClassorg.biojava.nbio.structure.io.mmcifBioJava
ChemCompDescriptorContainer object for _pdbx_chem_comp_descriptorSince:3.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
ChemCompDistributionClassdemoBioJava
ChemCompGroupFactoryClassorg.biojava.nbio.structure.io.mmcifBioJava
ChemCompProviderInterface that is implemented by all classes that can provide ChemComp definitions.Interfaceorg.biojava.nbio.structure.io.mmcifBioJava
ChemCompToolsSome tools for working with chemical compounds.Classorg.biojava.nbio.structure.io.mmcif.chemBioJava
ChemicalComponentDictionaryA representation of the Chemical Component Dictionary.Classorg.biojava.nbio.structure.io.mmcifBioJava
ChiSqClassorg.biojava.nbio.survival.cox.statsBioJava
Cholesky2Classorg.biojava.nbio.survival.cox.statsBioJava
CholeskyDecompositionCholesky Decomposition.Classorg.biojava.nbio.structure.jamaBioJava
ChooseDirActionAsk the user to provide a directory containting PDB files.Classorg.biojava.nbio.structure.align.guiBioJava
ChromosomeSequenceA ChromosomeSequence is a DNASequence but keeps track of geneSequencesAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJava
Chsolve2Classorg.biojava.nbio.survival.cox.statsBioJava
ClashJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
ClasspathResourceThis object represents a classpath resource on the local system.Classorg.biojava.nbio.core.sequence.io.utilBioJava
ClinicalMetaDataOutcomeClassorg.biojava.nbio.survival.kaplanmeier.metadataBioJava
CliToolsUtilities for autoconfiguring javabeans based on command line arguments.Classorg.biojava.nbio.structure.align.utilBioJava
ClusterAltAligsA class that clusters alternative alignments according to theirSince:1.Classorg.biojava.nbio.structure.alignBioJava
ClusterDomainsClassorg.biojava.nbio.structure.domain.pdpBioJava
ClusterMergerMerges clusters based on their sequence identity.Classorg.biojava.nbio.structure.symmetry.coreBioJava
ClusterProteinChainsClusters the chains of one or two structures by sequence.Classorg.biojava.nbio.structure.symmetry.coreBioJava
CodonCompoundClassorg.biojava.nbio.core.sequence.compoundBioJava
CollectionToolsUtilities for working with collections.Classorg.biojava.nbio.structure.align.utilBioJava
ColorConverterClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
ColorInterpolatorInterfaceorg.biojava.nbio.structure.gui.util.colorBioJava
ColorUtilsClassorg.biojava.nbio.structure.gui.util.colorBioJava
CombinationGeneratorClassorg.biojava.nbio.structure.symmetry.utilsBioJava
CommandPromptClassorg.biojava.nbio.aapropertiesBioJava
CompactCharSequencehttp://www.Classorg.biojava.nbio.survival.dataBioJava
ComparisonThis class provides static methods for the calculation of the percentage of identity between two aligned sequences.Classorg.biojava.nbio.phyloBioJava
ComplementCompoundInterfaceorg.biojava.nbio.core.sequence.templateBioJava
ComplementSequenceViewFor a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlyingClassorg.biojava.nbio.core.sequence.viewsBioJava
Componentcontains information about a certain Component.Classorg.biojava.nbio.protmodBioJava
ComponentXMLConverterClassorg.biojava.nbio.protmod.ioBioJava
CompoundInterfaceorg.biojava.nbio.core.sequence.templateBioJava
CompoundAn object to contain the info from the PDB header for a Molecule.Classorg.biojava.nbio.structureBioJava
CompoundFinderHeuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure.Classorg.biojava.nbio.structure.ioBioJava
CompoundNotFoundExceptionClassorg.biojava.nbio.core.exceptionsBioJava
CompoundSetInterfaceorg.biojava.nbio.core.sequence.templateBioJava
CompoundTranslatorInterfaceorg.biojava.nbio.core.sequence.templateBioJava
ConcurrencyToolsStatic utility to easily share a thread pool for concurrent/parallel/lazy execution.Classorg.biojava.nbio.core.utilBioJava
ConfigPDBInstallPanelClassorg.biojava.nbio.structure.align.guiBioJava
ConfigStrucAligParamsInterfaceorg.biojava.nbio.structure.align.ceBioJava
ConfigurationExceptionClassorg.biojava.nbio.structure.align.utilBioJava
ConfigXMLHandlerClassorg.biojava.nbio.structure.align.webstartBioJava
ConstraintsThis class is used to support the implementation of properties stated in IPeptideProperties.Classorg.biojava.nbio.aapropertiesBioJava
ContinuousColorMapperProvides a mapping between real numbers and Colors.Interfaceorg.biojava.nbio.structure.gui.util.colorBioJava
ContinuousColorMapperTransformMaps colors by performing a transform of the input data and then passing the transformed value to a ContinuousColorMapper for rendering.Classorg.biojava.nbio.structure.gui.util.colorBioJava
Convert2ChargeClassorg.biojava.nbio.aaproperties.profeat.convertorBioJava
Convert2HydrophobicityClassorg.biojava.nbio.aaproperties.profeat.convertorBioJava
Convert2NormalizedVanDerWaalsVolumeClassorg.biojava.nbio.aaproperties.profeat.convertorBioJava
Convert2PolarityClassorg.biojava.nbio.aaproperties.profeat.convertorBioJava
Convert2PolarizabilityClassorg.biojava.nbio.aaproperties.profeat.convertorBioJava
Convert2SecondaryStructureClassorg.biojava.nbio.aaproperties.profeat.convertorBioJava
Convert2SolventAccessibilityClassorg.biojava.nbio.aaproperties.profeat.convertorBioJava
ConvertorClassorg.biojava.nbio.aaproperties.profeat.convertorBioJava
CookBookClassdemoBioJava
CookbookMSAClassdemoBioJava
CoordManagera class that manages the conversion of sequence coordinate system to JPanel drawing coordinatesClassorg.biojava.nbio.structure.gui.utilBioJava
CoreSuperimposerSuperimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
CountProgressListenerClassorg.biojava.nbio.structure.align.clientBioJava
CoxCCClassorg.biojava.nbio.survival.coxBioJava
CoxCoefficientClassorg.biojava.nbio.survival.coxBioJava
CoxComparatorInterfaceInterfaceorg.biojava.nbio.survival.cox.comparatorsBioJava
CoxHelperThe CoxHelper class is provided to start with a tab delimited file in a similar process in R and return the results as a CoxInfo class.Classorg.biojava.nbio.survival.coxBioJava
CoxInfoHolds the results of a cox analysis where calling dump(), toString() will give an output similar to RAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJava
CoxMartClassorg.biojava.nbio.survival.coxBioJava
CoxMethodClassorg.biojava.nbio.survival.coxBioJava
CoxRThis is a port of the R survival code used for doing Cox Regression.Classorg.biojava.nbio.survival.coxBioJava
CoxScoreClassorg.biojava.nbio.survival.coxBioJava
CoxVariablesClassorg.biojava.nbio.survival.coxBioJava
CoxVariablesOverallModelFitComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJava
CoxVariablesVariableComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJava
CRC64ChecksumUtility class that calculates a CRC64 checksum on a stream of bytes.Classorg.biojava.nbio.core.utilBioJava
CrystalBuilderA class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operatorsClassorg.biojava.nbio.structure.xtalBioJava
CrystalCellA crystal cell's parameters.Classorg.biojava.nbio.structure.xtalBioJava
CrystalTransformRepresentation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m)Classorg.biojava.nbio.structure.xtalBioJava
CutClassorg.biojava.nbio.structure.domain.pdpBioJava
CutDomainClassorg.biojava.nbio.structure.domain.pdpBioJava
CutSitesClassorg.biojava.nbio.structure.domain.pdpBioJava
CutValuesClassorg.biojava.nbio.structure.domain.pdpBioJava
CytobandClassorg.biojava.nbio.genome.parsers.cytobandBioJava
CytobandParserParses the cytoband (karyotype) file from UCSC.Classorg.biojava.nbio.genome.parsers.cytobandBioJava
DatabasePDBremarkClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
DatabasePDBrevClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
DatabasePdbrevRecordClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
DatabaseReferenceInterfaceIf a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s)Interfaceorg.biojava.nbio.core.sequence.featuresBioJava
DatasetClassorg.biojava.nbio.phosphositeBioJava
DataSource GenBank giClassorg.biojava.nbio.core.sequenceBioJava
DBRefA class to represent database cross references.Classorg.biojava.nbio.structureBioJava
DBReferenceInfoIf you have a uniprot ID then it is possible to get a collection of other id(s) that the protein is known by.Classorg.biojava.nbio.core.sequence.featuresBioJava
DBResultTableClassorg.biojava.nbio.structure.align.guiBioJava
DBSearchGUIClassorg.biojava.nbio.structure.align.guiBioJava
DefaultAAIndexProviderThe default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directoryAuthor:Andreas PrlicClassorg.biojava.nbio.core.alignment.matricesBioJava
DefaultAutoSuggestProviderClassorg.biojava.nbio.structure.align.gui.autosuggestBioJava
DefaultMatrixMapperColor Mapper which mimics the default coloring of JMatrixPanel pixels.Classorg.biojava.nbio.structure.gui.util.colorBioJava
DefaultOpsDefault implementation of OntologyOps.Classorg.biojava.nbio.ontologyBioJava
DemoAlignmentFromFastaDemo of how to use the FastaStructureParser class to read protein structures from a FASTA file.ClassdemoBioJava
DemoAlignProteinsClassdemoBioJava
DemoAsaClassdemoBioJava
DemoAtomCacheExample of how to load PDB files using the AtomCache class.ClassdemoBioJava
DemoBerkeleyScopA demo for how to use the Berkeley version of SCOP instead of the default UK-SCOPSince:3.ClassdemoBioJava
DemoCATHAn example for how to access CATH data.ClassdemoBioJava
DemoCEExample of how to run a structure alignment using the CE algorithm.ClassdemoBioJava
DemoCeSymmQuick demo of how to call CE-Symm programmatically.ClassdemoBioJava
DemoChangeChemCompProviderThis demo shows how to use an alternative ChemCompProvider.ClassdemoBioJava
DemoCommandLineStartupClassdemoBioJava
DemoContactsClassdemoBioJava
DemoCrystalInterfacesClassdemoBioJava
DemoDistanceTreeThis demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).ClassdemoBioJava
DemoDomainsplitClassdemoBioJava
DemoFATCATClassdemoBioJava
DemoLoadSecStrucDemonstration of how to load a Structure with the SS information, either from the PDB file annotation (Author's assignment) or from the DSSP file in theClassdemoBioJava
DemoLoadStructureExample for how to load protein structures (from PDB files).ClassdemoBioJava
DemoLoadSubstMaxClassdemoBioJava
DemoMMCIFReaderAn example of how to read MMcif filesAuthor:Andreas PrlicClassdemoBioJava
DemoMultipleMCDemo for running the MultipleMC Algorithm on a protein family.ClassdemoBioJava
DemoNWALignmentClassdemoBioJava
DemoOrientBioAssemblyCreated by ap3 on 02/04/2015.ClassdemoBioJava
DemoRotationAxisA demo for how to use RotationAxis to display the rotation for an alignment.ClassdemoBioJava
DemoSCOPA class demonstrating the use of the SCOP parsing toolsAuthor:Andreas PrlicClassdemoBioJava
DemoSecStrucCalcDemonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations andClassdemoBioJava
DemoShowBiolAssemblyClassdemoBioJava
DemoShowCATHDomainClassdemoBioJava
DemoShowLargeAssemblyClassdemoBioJava
DemoShowValidationResultsClassdemoBioJava
DemoSixFrameTranslationCreated by andreas on 8/10/15.ClassdemoBioJava
DemoStructureFromFastaDemo of how to use the FastaStructureParser class to read protein structures from a FASTA file.ClassdemoBioJava
DemoSW3DAlignerClassdemoBioJava
DiscreteQuantizerInterfaceInterfaceorg.biojava.nbio.survival.kaplanmeier.metadataBioJava
DisplayAFPA utility class for visualistion of structure alignmentsAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.guiBioJava
DistanceBoxClassorg.biojava.nbio.structure.symmetry.geometryBioJava
DistanceMatrixCalculatorThe DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).Classorg.biojava.nbio.phyloBioJava
DistanceTreeEvaluatorCheck the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.Classorg.biojava.nbio.phyloBioJava
DNACompoundSetClassorg.biojava.nbio.core.sequence.compoundBioJava
DNASequenceThis is class should model the attributes associated with a DNA sequenceAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJava
DNASequenceCreatorA helper class that allows different ways to read a string and create a DNA sequence.Classorg.biojava.nbio.core.sequence.ioBioJava
DNAToRNATranslatorPerforms the first stage of transcription by going from DNA to RNA.Classorg.biojava.nbio.core.sequence.transcriptionBioJava
DomainClassorg.biojava.nbio.structure.domain.pdpBioJava
DomainProviderInterfaceorg.biojava.nbio.structure.domainBioJava
DomainProviderFactoryClassorg.biojava.nbio.structure.domainBioJava
DotPlotPanelDisplays the dot plot trace for an alignment.Classorg.biojava.nbio.structure.align.guiBioJava
DownloadChemCompProviderThis provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.Classorg.biojava.nbio.structure.io.mmcifBioJava
DSSPParserClass to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure.Classorg.biojava.nbio.structure.secstrucBioJava
EcodDatabaseGeneral API for interacting with CATH.Interfaceorg.biojava.nbio.structure.ecodBioJava
EcodDomainClassorg.biojava.nbio.structure.ecodBioJava
EcodFactoryControls global CathDatabases being used.Classorg.biojava.nbio.structure.ecodBioJava
EcodInstallationProvides access to the Evolutionary Classification of Protein Domains (ECOD).Classorg.biojava.nbio.structure.ecodBioJava
EditInterface for carrying out edit operations on a Sequence.Interfaceorg.biojava.nbio.core.sequence.editsBioJava
EigenvalueDecompositionEigenvalues and eigenvectors of a real matrix.Classorg.biojava.nbio.structure.jamaBioJava
ElementClassorg.biojava.nbio.aaproperties.xmlBioJava
ElementElement is an enumeration of the elements of the periodic table.Classorg.biojava.nbio.structureBioJava
ElementTableClassorg.biojava.nbio.aaproperties.xmlBioJava
ElementTypeElementType is an enumeration of the types of elements found in the periodic table.Classorg.biojava.nbio.structureBioJava
EntityA simple class to represent Entity records in mmCif filesAuthor:Andreas PrlicClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
EntityPolySeqContainer for _entity_poly_seq recordsField Name mmCIF Data ItemClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
EntitySrcGenData items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in casesClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
EntitySrcNatData items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in casesClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
EntitySrcSynPDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
EntryJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
EqualsA set of helper methods which return true if the two parameters are equal to each other.Classorg.biojava.nbio.core.utilBioJava
ExonComparatorSort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction.Classorg.biojava.nbio.core.sequenceBioJava
ExonSequenceA gene contains a collection of Exon sequencesAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJava
ExperimentalTechniqueenum ExperimentalTechniqueAn enum to represent the experimental technique of a PDB structureClassorg.biojava.nbio.structureBioJava
ExpressionFigureClassorg.biojava.nbio.survival.kaplanmeier.figureBioJava
ExptlClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
FarmJobA job as it can be run on the farm.Classorg.biojava.nbio.structure.alignBioJava
FarmJobParametersClassorg.biojava.nbio.structure.align.clientBioJava
FarmJobRunnableContains the single thread for a job that can run multiple alignments.Classorg.biojava.nbio.structure.align.clientBioJava
FastaAFPChainConverterA collection of static utilities to convert between AFPChains and FastaSequences.Classorg.biojava.nbio.structure.ioBioJava
FastaGeneWriterA Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.Classorg.biojava.nbio.core.sequence.ioBioJava
FastaHeaderFormatInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJava
FastaReaderUse FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta filesClassorg.biojava.nbio.core.sequence.ioBioJava
FastaReaderHelperClassorg.biojava.nbio.core.sequence.ioBioJava
FastaSequenceA FASTA formatted sequence.Classorg.biojava.nbio.data.sequenceBioJava
FastaSequenceParserUsed to parse a stream of a fasta file to get the sequenceAuthor:Scooter Willis Classorg.biojava.nbio.core.sequence.ioBioJava
FastaStructureParserReads a protein sequence from a fasta file and attempts to match it to a 3D structure.Classorg.biojava.nbio.structure.ioBioJava
FastaWriterThe FastaWriter writes a collection of sequences to an outputStream.Classorg.biojava.nbio.core.sequence.ioBioJava
FastaWriterHelperThe class that should be used to write out fasta file of a sequence collectionAuthor:Scooter Willis Classorg.biojava.nbio.core.sequence.ioBioJava
FastqFASTQ formatted sequence.Classorg.biojava.nbio.sequencing.io.fastqBioJava
FastqBuilderFluent builder API for creating FASTQ formatted sequences.Classorg.biojava.nbio.sequencing.io.fastqBioJava
FastqReaderReader for FASTQ formatted sequences.Interfaceorg.biojava.nbio.sequencing.io.fastqBioJava
FastqToolsUtility methods for FASTQ formatted sequences.Classorg.biojava.nbio.sequencing.io.fastqBioJava
FastqVariantFASTQ sequence format variant.Classorg.biojava.nbio.sequencing.io.fastqBioJava
FastqWriterWriter for FASTQ formatted sequences.Interfaceorg.biojava.nbio.sequencing.io.fastqBioJava
FatCatClassorg.biojava.nbio.structure.align.fatcatBioJava
FatCatAlignerA class that does calculations on an AFPChainAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.fatcat.calcBioJava
FatCatFlexibleClassorg.biojava.nbio.structure.align.fatcatBioJava
FatCatParametersClassorg.biojava.nbio.structure.align.fatcat.calcBioJava
FatCatRigidClassorg.biojava.nbio.structure.align.fatcatBioJava
FatCatUserArgumentProcessorClassorg.biojava.nbio.structure.align.fatcatBioJava
FCAlignHelperClassorg.biojava.nbio.structure.align.fatcat.calcBioJava
FeatureA Feature corresponds to a single row in a GFF file.Classorg.biojava.nbio.genome.parsers.gffBioJava
FeatureDbReferenceInfoIt is DBReferenceInfo which implements FeatureInterface.Classorg.biojava.nbio.core.sequence.featuresBioJava
FeatureHelperClassorg.biojava.nbio.genome.parsers.gffBioJava
FeatureIA feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.Interfaceorg.biojava.nbio.genome.parsers.gffBioJava
FeatureInterfaceInterface class to handle describing arbitrary features.Interfaceorg.biojava.nbio.core.sequence.featuresBioJava
FeatureListA list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.Classorg.biojava.nbio.genome.parsers.gffBioJava
FeatureRetrieverIf a SequenceProxyReader implements this interface then that external source has a list featuresInterfaceorg.biojava.nbio.core.sequence.featuresBioJava
FeaturesKeyWordInterfaceModels the keywords that are annotated for a protein sequence at Uniprot.Interfaceorg.biojava.nbio.core.sequence.featuresBioJava
FileConvertMethods to convert a structure object into different file formats.Classorg.biojava.nbio.structure.ioBioJava
FileDownloadUtilsClassorg.biojava.nbio.structure.io.utilBioJava
FileParsingParametersA class that configures parameters that can be sent to the PDB file parsers setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.Classorg.biojava.nbio.structure.ioBioJava
FileProxyDNASequenceCreatorThis class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.Classorg.biojava.nbio.core.sequence.ioBioJava
FileProxyProteinSequenceCreatorThis class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily.Classorg.biojava.nbio.core.sequence.ioBioJava
FlatFileCacheProvides a cache for storing multiple small files in memory.Classorg.biojava.nbio.core.utilBioJava
ForesterWrapperThis class contains wrapper methods for communication between BioJava and forester (e.Classorg.biojava.nbio.phyloBioJava
FourBitSequenceReaderFour bit encoding of the bit formats.Classorg.biojava.nbio.core.sequence.storageBioJava
FractionalIdentityInProfileScorer Profile.Classorg.biojava.nbio.alignmentBioJava
FractionalIdentityScorer alignment columns which have identical Compounds.Classorg.biojava.nbio.alignmentBioJava
FractionalSimilarityInProfileScorer Profile.Classorg.biojava.nbio.alignmentBioJava
FractionalSimilarityScorer alignment columns which have similar Compounds.Classorg.biojava.nbio.alignmentBioJava
FragmentJoinerJoins the initial Fragments together to larger FragmentsSince:1.Classorg.biojava.nbio.structure.align.pairwiseBioJava
FragmentPaira pair of fragments of two protein structuresSince:1.Classorg.biojava.nbio.structure.align.pairwiseBioJava
FrameIndicates a way of translating a sequence.Classorg.biojava.nbio.core.sequence.transcriptionBioJava
FuzzyPointClassorg.biojava.nbio.core.sequence.locationBioJava
GapArrayClassorg.biojava.nbio.structure.align.helperBioJava
GapPenaltyDefines a data structure for the gap penalties used during a sequence alignment routine.Interfaceorg.biojava.nbio.alignment.templateBioJava
GCStatsClassorg.biojava.nbio.genome.parsers.gffBioJava
GenbankHeaderFormatInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJava
GenbankProxySequenceReaderClassorg.biojava.nbio.core.sequence.loaderBioJava
GenbankReaderUse GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank filesClassorg.biojava.nbio.core.sequence.ioBioJava
GenbankReaderHelperClassorg.biojava.nbio.core.sequence.ioBioJava
GenbankSequenceParserClassorg.biojava.nbio.core.sequence.ioBioJava
GenbankWriterClassorg.biojava.nbio.core.sequence.ioBioJava
GenbankWriterHelperClassorg.biojava.nbio.core.sequence.ioBioJava
GeneChromosomePositionClassorg.biojava.nbio.genome.parsers.genenameBioJava
GeneChromosomePositionParserA parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positionsAuthor:Andreas PrlicClassorg.biojava.nbio.genome.parsers.genenameBioJava
GeneFeatureHelperClassorg.biojava.nbio.genomeBioJava
GeneIDGFF2Readerhttp://www.Classorg.biojava.nbio.genome.parsers.gffBioJava
GeneIDXMLReaderClassorg.biojava.nbio.genome.parsers.geneidBioJava
GeneMarkGTFReaderhttp://www.Classorg.biojava.nbio.genome.parsers.gffBioJava
GeneNameA simple bean that contains gene name information as available from www.Classorg.biojava.nbio.genome.parsers.genenameBioJava
GeneNamesParserParses a file from the www.Classorg.biojava.nbio.genome.parsers.genenameBioJava
GenericFastaHeaderFormatWe store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file.Classorg.biojava.nbio.core.sequence.ioBioJava
GenericFastaHeaderParserThe default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifierClassorg.biojava.nbio.core.sequence.ioBioJava
GenericGenbankHeaderFormatClassorg.biojava.nbio.core.sequence.ioBioJava
GenericGenbankHeaderParserClassorg.biojava.nbio.core.sequence.ioBioJava
GenericInsdcHeaderFormatClassorg.biojava.nbio.core.sequence.ioBioJava
GeneSequenceClassorg.biojava.nbio.core.sequenceBioJava
GetDistanceMatrixClassorg.biojava.nbio.structure.domain.pdpBioJava
GetRepresentativesTODO Move this to Representatives.Classorg.biojava.nbio.structure.rcsbBioJava
GFF3FromUniprotBlastHitsClassorg.biojava.nbio.genome.homologyBioJava
GFF3Readerhttp://www.Classorg.biojava.nbio.genome.parsers.gffBioJava
GFF3WriterClassorg.biojava.nbio.genome.parsers.gffBioJava
GOParserSimple parser for the Gene Ontology (GO) flatfile format.Classorg.biojava.nbio.ontology.ioBioJava
Gotoha class to perform Gotoh algorithmSince:10:56:53 AMVersion:%I% %G%Author:Andreas Prlic (Java), Peter Lackner (original C code)Classorg.biojava.nbio.structure.align.pairwiseBioJava
GradientMapperMaps a set of real values onto a gradient.Classorg.biojava.nbio.structure.gui.util.colorBioJava
GradientPanelClassorg.biojava.nbio.structure.gui.util.colorBioJava
GraphComponentOrderDetectorThe GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components.Classorg.biojava.nbio.structure.symmetry.internalBioJava
GraphComponentRefinerThe GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components.Classorg.biojava.nbio.structure.symmetry.internalBioJava
GridA grid to be used for calculating atom contacts through geometric hashing algorithm.Classorg.biojava.nbio.structure.contactBioJava
GridCellA grid cell to be used in contact calculation via geometric hashing algorithm.Classorg.biojava.nbio.structure.contactBioJava
GroupThis is the data structure for a single Group of atoms.Interfaceorg.biojava.nbio.structureBioJava
GroupAsaA class to store the results of ASA calculations, it can hold ASA values per atom present in GroupClassorg.biojava.nbio.structure.asaBioJava
GroupContactA pair of residues that are in contactAuthor:duarte_jSee Also:Serialized FormClassorg.biojava.nbio.structure.contactBioJava
GroupContactSetA set of residue-residue contacts.Classorg.biojava.nbio.structure.contactBioJava
GroupIteratorAn iterator over all groups of a structure.Classorg.biojava.nbio.structureBioJava
GroupResultsClassorg.biojava.nbio.survival.kaplanmeier.figureBioJava
GroupToSDFClassorg.biojava.nbio.structure.ioBioJava
GroupTypeThis contains basic categories for Group types.Classorg.biojava.nbio.structureBioJava
GuanUberbacherGuan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).Classorg.biojava.nbio.alignment.routinesBioJava
GUIAlignmentProgressListenera GUI that allows to watch progress as multiple alignments are being processed.Classorg.biojava.nbio.structure.align.guiBioJava
GuideTree GuideTree.Classorg.biojava.nbio.alignmentBioJava
GuideTreeNodeDefines a data structure for the node in a guide tree used during progressive multiple sequence alignment.Interfaceorg.biojava.nbio.alignment.templateBioJava
GUIFarmJobRunnableClassorg.biojava.nbio.structure.align.guiBioJava
GuiWrapperA class to wrap some of the strucutre.Classorg.biojava.nbio.structure.align.ceBioJava
HashcoderContains helper methods for generating a HashCode without having to resort to the commons lang hashcode builders.Classorg.biojava.nbio.core.utilBioJava
HasResultXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJava
HBondContainer that represents a hidrogen bond.Classorg.biojava.nbio.structure.secstrucBioJava
HeaderInfoClassorg.biojava.nbio.survival.dataBioJava
HelicalRepeatUnitClassorg.biojava.nbio.structure.symmetry.coreBioJava
HelixClassorg.biojava.nbio.structure.symmetry.coreBioJava
HelixAxisAlignerClassorg.biojava.nbio.structure.symmetry.coreBioJava
HelixExtenderClassorg.biojava.nbio.structure.symmetry.coreBioJava
HelixLayersClassorg.biojava.nbio.structure.symmetry.coreBioJava
HelixSolverClassorg.biojava.nbio.structure.symmetry.coreBioJava
HelpDialogClassorg.biojava.nbio.structure.align.guiBioJava
HetatomImplGeneric Implementation of a Group interface.Classorg.biojava.nbio.structureBioJava
HierarchicalClustererDefines a clustering algorithm that converts a distance matrix into a tree.Interfaceorg.biojava.nbio.alignment.templateBioJava
HitThis class models a search Hit.Classorg.biojava.nbio.core.search.ioBioJava
HmmerDemoThe cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 serviceSince:3.ClassdemoBioJava
HmmerDomainProvides the details of a domain hitSince:3.Classorg.biojava.nbio.ws.hmmerBioJava
HmmerResultThe results of a Hmmer search for a single sequenceSince:3.Classorg.biojava.nbio.ws.hmmerBioJava
HmmerScanInterface for performing Hmmscans on sequences.Interfaceorg.biojava.nbio.ws.hmmerBioJava
HspThis class models a search Hsp.Classorg.biojava.nbio.core.search.ioBioJava
HSVColorSpaceClassorg.biojava.nbio.structure.gui.util.colorBioJava
HTTPConnectionToolsa class that takes care about opening HttpURLConnections and sets the proper timeoutsSince:9:58:25 AMVersion:%I% %G%Author:Andreas PrlicClassorg.biojava.nbio.structure.align.utilBioJava
IcosahedralSamplerClassorg.biojava.nbio.structure.symmetry.geometryBioJava
IcosahedronClassorg.biojava.nbio.structure.symmetry.geometryBioJava
IdentifierA collection of utilities to create StructureIdentifiers.Classorg.biojava.nbio.structureBioJava
IdxComparatorClassorg.biojava.nbio.structure.align.helperBioJava
IlluminaFastqReaderReader for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJava
IlluminaFastqWriterWriter for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJava
IndexPairClassorg.biojava.nbio.structure.align.helperBioJava
InputStreamProviderA class that provides an InputStream from a File.Classorg.biojava.nbio.core.utilBioJava
InsdcLocationsA collection of locations which are used whenever we work with INSDC; some of which could be deprecated (from INSDC's point of view) yet appearClassorg.biojava.nbio.core.sequence.locationBioJava
InsdcParserParser for working with INSDC style locations.Classorg.biojava.nbio.core.sequence.locationBioJava
IntegerOntologyClassorg.biojava.nbio.ontologyBioJava
IntronSequenceClassorg.biojava.nbio.core.sequenceBioJava
InvalidTermExceptionThrown to indicate that an ontology term is not acceptable or appropriate in a given contextClassorg.biojava.nbio.ontologyBioJava
IOUtilsClassorg.biojava.nbio.core.sequence.io.utilBioJava
IPeptidePropertiesAn interface to generate some basic physico-chemical properties of protein sequences.Interfaceorg.biojava.nbio.aapropertiesBioJava
IProfeatPropertiesInterfaceorg.biojava.nbio.aaproperties.profeatBioJava
IsotopeClassorg.biojava.nbio.aaproperties.xmlBioJava
IUPACParserAvailable translations 1 - UNIVERSAL2 - VERTEBRATE_MITOCHONDRIAL3 - YEAST_MITOCHONDRIAL4 - MOLD_MITOCHONDRIAL5 - INVERTEBRATE_MITOCHONDRIAL6 - CILIATE_NUCLEAR9 - ECHINODERM_MITOCHONDRIAL10 - EUPLOTID_NUCLEAR11 - BACTERIAL12 - ALTERNATIVE_YEAST_NUCLEAR13 - ASCIDIAN_MITOCHONDRIAL14 - FLATWORM_MITOCHONDRIAL15 - BLEPHARISMA_MACRONUCLEAR16 - 2CHLOROPHYCEAN_MITOCHONDRIAL21 - TREMATODE_MITOCHONDRIAL23 - SCENEDESMUS_MITOCHONDRIALClassorg.biojava.nbio.core.sequence.ioBioJava
JAutoSuggestA JTextField that can make suggestions for auto-complete.Classorg.biojava.nbio.structure.align.gui.autosuggestBioJava
JFatCatClientClassorg.biojava.nbio.structure.align.clientBioJava
JMatrixPanela JPanel that can display a difference of distance matrix and paths that have been taken for the alignmentClassorg.biojava.nbio.structure.guiBioJava
JmolAlignedPositionListenerClassorg.biojava.nbio.structure.gui.eventsBioJava
JmolPanelClassorg.biojava.nbio.structure.align.gui.jmolBioJava
JmolSymmetryScriptGeneratorClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
JmolSymmetryScriptGeneratorC1Classorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
JmolSymmetryScriptGeneratorCnClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
JmolSymmetryScriptGeneratorDnClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
JmolSymmetryScriptGeneratorHClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
JmolSymmetryScriptGeneratorIClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
JmolSymmetryScriptGeneratorOClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
JmolSymmetryScriptGeneratorPointGroupClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
JmolSymmetryScriptGeneratorTClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJava
JmolToolsClassorg.biojava.nbio.structure.align.gui.jmolBioJava
JmolViewerImplClassorg.biojava.nbio.structure.guiBioJava
JNLPProxyClassorg.biojava.nbio.structure.align.webstartBioJava
JobKillExceptionClassorg.biojava.nbio.structure.align.clientBioJava
JoiningSequenceReaderThis reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence.Classorg.biojava.nbio.core.sequence.storageBioJava
JointFragmentsA utility class that defines which set of atoms are considered to be on equivalent positions.Classorg.biojava.nbio.structure.align.helperBioJava
JournalArticleClassorg.biojava.nbio.structureBioJava
JPrintPanelClassorg.biojava.nbio.structure.align.guiBioJava
JronnThis class gives public API to RONN functions.Classorg.biojava.nbio.ronnBioJava
KaplanMeierFigureClassorg.biojava.nbio.survival.kaplanmeier.figureBioJava
KeyedWeakReferenceSubclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has beenClassorg.biojava.nbio.ontology.utilsBioJava
KMFigureInfoClassorg.biojava.nbio.survival.kaplanmeier.figureBioJava
LadderA Ladder is a set of one or more consecutive bridges of identical type.Classorg.biojava.nbio.structure.secstrucBioJava
LightweightProfileDefines a minimal data structure for reading and writing a sequence alignment.Interfaceorg.biojava.nbio.core.sequence.templateBioJava
LinearColorInterpolatorClassorg.biojava.nbio.structure.gui.util.colorBioJava
ListStringWrapperClassorg.biojava.nbio.structure.scop.serverBioJava
LocalPDBDirectorySuperclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and MMCIFFileReader.Classorg.biojava.nbio.structure.ioBioJava
LocalProteinDomainParserProtein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.Classorg.biojava.nbio.structure.domainBioJava
LocalScopDatabaseClasses which implement ScopDatabase in a way which allows them to serve queries without accessing the internet should implement this interface instead.Interfaceorg.biojava.nbio.structure.scopBioJava
LocationSets of integers used to represent the location of features on sequence.Interfaceorg.biojava.nbio.core.sequence.location.templateBioJava
LocationA location on a sequence.Classorg.biojava.nbio.genome.parsers.gffBioJava
LocationHelperHelper methods for use with the Location classes.Classorg.biojava.nbio.core.sequence.locationBioJava
LocIteratorMove a sliding window over a Location.Classorg.biojava.nbio.genome.parsers.gffBioJava
LogColorMapperPerforms a log10 transform on input before passing the values off to another For instance, to map [10^0, 10^10] to a rainbow gradient, useClassorg.biojava.nbio.structure.gui.util.colorBioJava
LUDecomposition For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n unit lower triangular matrix L, an n-by-n upper triangular matrix U,Classorg.biojava.nbio.structure.jamaBioJava
MapToStringTransformerTransforms Map to String.Classorg.biojava.nbio.ws.alignment.qblastBioJava
MathsClassorg.biojava.nbio.structure.jamaBioJava
MatrixJama = Java Matrix class.Classorg.biojava.nbio.structure.jamaBioJava
Matrix*********************************************************************** Compilation: javac Matrix.Classorg.biojava.nbio.survival.cox.matrixBioJava
MatrixAlignerDefines an Aligner which builds a score matrix during computation.Interfaceorg.biojava.nbio.alignment.templateBioJava
MatrixListenerInterfaceorg.biojava.nbio.structure.align.ceBioJava
MeanModelComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJava
MeanQuantizerClassorg.biojava.nbio.survival.kaplanmeier.metadataBioJava
MemoryMonitorTracks Memory allocated & used, displayed in graph form.Classorg.biojava.nbio.structure.align.guiBioJava
MenuCreatorCreate the menus for structure alignment GUI windows (JFrames).Classorg.biojava.nbio.structure.align.guiBioJava
MenuCreatorCreate the menu for BiojavaJmolSince:1.Classorg.biojava.nbio.structure.gui.utilBioJava
MessagesClassorg.biojava.nbio.core.exceptionsBioJava
MetaDataInfoClassorg.biojava.nbio.survival.kaplanmeier.metadataBioJava
MmCifBiolAssemblyProviderClassorg.biojava.nbio.structure.quaternary.ioBioJava
MMcifConsumerAn interface for the events triggered by a MMcifParser.Interfaceorg.biojava.nbio.structure.io.mmcifBioJava
MMCIFFileReaderHow to parse an mmCif file:public static void main(String[] args) throws Exception {Classorg.biojava.nbio.structure.ioBioJava
MMCIFFileToolsSome tools for mmCIF file writing.Classorg.biojava.nbio.structure.io.mmcifBioJava
MMcifParserInterface that needs to be implemented by an MMcifParserSince:1.Interfaceorg.biojava.nbio.structure.io.mmcifBioJava
MmCifPDBBiolAssemblyProviderA provider for information about biological units for PDB files that is based on reading local MMcif files.Classorg.biojava.nbio.structure.quaternary.ioBioJava
ModelledSubgroupJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
ModelLoaderClass that loads data from the model files into ModelLoader.Classorg.biojava.nbio.ronnBioJava
ModificationCategoryenum ModificationCategorydefine modification categories.Classorg.biojava.nbio.protmodBioJava
ModificationConditionConditions of a protein modification, e.Interfaceorg.biojava.nbio.protmodBioJava
ModificationConditionImplClassorg.biojava.nbio.protmodBioJava
ModificationLinkageClassorg.biojava.nbio.protmodBioJava
ModificationOccurrenceTypeenum ModificationOccurrenceTypeSince:3.Classorg.biojava.nbio.protmodBioJava
ModifiedAminoAcidCompoundSetClassorg.biojava.nbio.aaproperties.xmlBioJava
ModifiedCompoundRoot interface for all modifications in structure.Interfaceorg.biojava.nbio.protmod.structureBioJava
ModifiedCompoundImplClassorg.biojava.nbio.protmod.structureBioJava
ModifiedCompoundXMLConverterClassorg.biojava.nbio.protmod.ioBioJava
MogAngleOutlierJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
MogBondOutlierJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
MomentsOfInertiaClassorg.biojava.nbio.structure.symmetry.geometryBioJava
MultipleAlignmentA MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.Interfaceorg.biojava.nbio.structure.align.multipleBioJava
MultipleAlignmentCalcA class that obtains structures via DAS and aligns them.Classorg.biojava.nbio.structure.align.guiBioJava
MultipleAlignmentCoordManagerGeneralization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.Classorg.biojava.nbio.structure.align.gui.aligpanelBioJava
MultipleAlignmentDisplayUtility functions to generalize the visualization of MultipleAlignments in molecular viewers.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
MultipleAlignmentEnsembleA MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm,Interfaceorg.biojava.nbio.structure.align.multipleBioJava
MultipleAlignmentEnsembleImplA general implementation of a MultipleAlignmentEnsemble.Classorg.biojava.nbio.structure.align.multipleBioJava
MultipleAlignmentGUIA JFrame that allows to trigger a multiple structure alignment, either from files in a directory or after manual upload.Classorg.biojava.nbio.structure.align.guiBioJava
MultipleAlignmentImplA general implementation of a MultipleAlignment.Classorg.biojava.nbio.structure.align.multipleBioJava
MultipleAlignmentJmolA class that provides a 3D visualization Frame in Jmol for MultipleAlignments.Classorg.biojava.nbio.structure.align.gui.jmolBioJava
MultipleAlignmentJmolDisplayUtility Class that provides helper methods for the visualization of MultipleAlignments.Classorg.biojava.nbio.structure.align.guiBioJava
MultipleAlignmentScorerUtility class for calculating common scores of MultipleAlignments.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
MultipleAlignmentToolsUtility functions for working with MultipleAlignment.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
MultipleAlignmentWriterThis class contains functions for the conversion of MultipleAlignment to various String outputs.Classorg.biojava.nbio.structure.align.multiple.utilBioJava
MultipleAlignmentXMLConverterHelper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format.Classorg.biojava.nbio.structure.align.xmlBioJava
MultipleAlignmentXMLParserParse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered.Classorg.biojava.nbio.structure.align.xmlBioJava
MultipleAligPanelA JPanel that can display the sequence alignment of a MultipleAlignment in a nice way and interact with Jmol byClassorg.biojava.nbio.structure.align.gui.aligpanelBioJava
MultipleAligPanelMouseMotionListenerMouse Motion Listener for the MultipleAligPanel, which provides methods to obtain positions of the mouseClassorg.biojava.nbio.structure.align.gui.aligpanelBioJava
MultipleMcMainMain class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm,Classorg.biojava.nbio.structure.align.multiple.mcBioJava
MultipleMcOptimizerThis class takes a MultipleAlignment seed previously generated and runs a Monte Carlo optimization in order to improve the overall score and highlightClassorg.biojava.nbio.structure.align.multiple.mcBioJava
MultipleMcParametersContains the parameters to be sent to the MC optimization.Classorg.biojava.nbio.structure.align.multiple.mcBioJava
MultipleSequenceAlignment structure in the alignment module provides additional functionality.Classorg.biojava.nbio.core.sequenceBioJava
MultipleStatusDisplayThis class provides information of the selected positions in the It has to be linked to a MultipleAligPanel in order to obtainClassorg.biojava.nbio.structure.align.gui.aligpanelBioJava
MultipleStructureAlignerInterface for the Multiple Structure Alignment Algorithms.Interfaceorg.biojava.nbio.structure.alignBioJava
MultipleSuperimposerInterface for Multiple Alignment superposition algorithms.Interfaceorg.biojava.nbio.structure.align.multiple.utilBioJava
MultiThreadedDBSearchPerforms a multi threaded database search for an input protein structureAuthor:Andreas PrlicClassorg.biojava.nbio.structure.alignBioJava
MutableAlignedSequenceDefines a mutable (editable) data structure for an AlignedSequence.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
MutableProfileDefines a mutable (editable) data structure for a Profile.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
MutableProfilePairDefines a mutable (editable) data structure for a ProfilePair.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
MutableSequencePairDefines a mutable (editable) data structure for the results of pairwise sequence alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
MutatorA class that can change one amino acid to another.Classorg.biojava.nbio.structureBioJava
MyAlignmentLoadListenerLoads an alignment in an XML format and displays its content in a new Jmol panel.Classorg.biojava.nbio.structure.align.guiBioJava
MyDistMaxListenerShows the interatomic Distance Matrices of all the Structures aligned in different Frames.Classorg.biojava.nbio.structure.align.guiBioJava
MyExportListenerClassorg.biojava.nbio.structure.align.guiBioJava
MyJmolStatusListenerClassorg.biojava.nbio.structure.align.gui.jmolBioJava
MyOpenPdbFileListenerClassorg.biojava.nbio.structure.align.guiBioJava
MySaveFileListenerSave an alignment to a specified File by the user.Classorg.biojava.nbio.structure.align.guiBioJava
MyTableRowSorterClassorg.biojava.nbio.structure.align.guiBioJava
MyValidationEventHandlerClassorg.biojava.nbio.aaproperties.xmlBioJava
Name2CountClassorg.biojava.nbio.aaproperties.xmlBioJava
NCBIQBlastAlignmentPropertiesThis class wraps a QBlast search request parameter Map by adding several convenient parameter addition methods.Classorg.biojava.nbio.ws.alignment.qblastBioJava
NCBIQBlastOutputPropertiesThis class wraps a QBlast output parameter Map by adding several convenient parameter addition methods.Classorg.biojava.nbio.ws.alignment.qblastBioJava
NCBIQBlastServiceProvides a simple way of submitting BLAST request to the QBlast service at NCBI.Classorg.biojava.nbio.ws.alignment.qblastBioJava
NCBIQBlastServiceDemoA simple demo showing NCBIQBlastService usageAuthor:Gediminas RimsaClassdemoBioJava
NeedlemanWunschNeedleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).Classorg.biojava.nbio.alignmentBioJava
NucleotideCompoundClassorg.biojava.nbio.core.sequence.compoundBioJava
NucleotideImplA nucleotide group is almost the same as a Hetatm group.Classorg.biojava.nbio.structureBioJava
NullOutputStreamThe stream that void its inputSince:3.Classorg.biojava.nbio.ronnBioJava
NumbersAtRiskPanelClassorg.biojava.nbio.survival.kaplanmeier.figureBioJava
ObjectFactoryThis object contains factory methods for each Java content interface and Java element interfaceClassorg.biojava.nbio.structure.validationBioJava
OboFileEventListeneran interface for events that occur during parsing of .Interfaceorg.biojava.nbio.ontology.oboBioJava
OboFileHandlerA file handler for .Classorg.biojava.nbio.ontology.oboBioJava
OboFileParserA class to parse the content of an OBO file.Classorg.biojava.nbio.ontology.oboBioJava
OboParser OboParser parser = new OboParser(); InputStream inStream = this.Classorg.biojava.nbio.ontology.ioBioJava
OctahedronClassorg.biojava.nbio.structure.symmetry.geometryBioJava
Ontology This is just a set of Term objects, and a set of Triple objects describing relationships between these terms.Interfaceorg.biojava.nbio.ontologyBioJava
OntologyExceptionThrown to indicate an error in an Ontology objectSince:1.Classorg.biojava.nbio.ontologyBioJava
OntologyFactoryA factory for Ontology instances.Interfaceorg.biojava.nbio.ontologyBioJava
OntologyOpsThis is an interface for optimizing ontology operators.Interfaceorg.biojava.nbio.ontologyBioJava
OntologyTermA term in an ontology which identifies another ontology.Interfaceorg.biojava.nbio.ontologyBioJava
OntoToolsTools for manipulating ontologies.Classorg.biojava.nbio.ontologyBioJava
OperatorResolverClassorg.biojava.nbio.structure.quaternaryBioJava
OptimalCECPMainA wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.Classorg.biojava.nbio.structure.align.ceBioJava
OptimalCECPParametersContains the parameters that can be sent to CEAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.ceBioJava
OrderDetectorA method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm.Interfaceorg.biojava.nbio.structure.symmetry.internalBioJava
OrderedPairAn ordered pair represents a component of a cartesian product.Classorg.biojava.nbio.structure.quaternaryBioJava
ORonnFully re-factored and enhanced version of RONN.Classorg.biojava.nbio.ronnBioJava
ORonnModelFully re-factored version of RONN model.Classorg.biojava.nbio.ronnBioJava
OutputHitsGFFClassorg.biojava.nbio.genome.queryBioJava
PairA Pair of objects.Classorg.biojava.nbio.structure.contactBioJava
PairInProfileScorerDefines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.Interfaceorg.biojava.nbio.alignment.templateBioJava
PairwiseAlignmentClassorg.biojava.nbio.structure.symmetry.coreBioJava
PairwiseSequenceAlignerDefines an Aligner for a pair of Sequences.Interfaceorg.biojava.nbio.alignment.templateBioJava
PairwiseSequenceScorerDefines an algorithm which computes a score for a pair of sequences.Interfaceorg.biojava.nbio.alignment.templateBioJava
ParameterGUIUI for ConfigStrucAligParams, for the AlignmentGUI.Classorg.biojava.nbio.structure.align.guiBioJava
ParseFastaFileDemoCreated by andreas on 6/17/15.ClassdemoBioJava
ParseGOClassdemoBioJava
ParseListenerLow-level event based parser callback.Interfaceorg.biojava.nbio.sequencing.io.fastqBioJava
ParserExceptionGeneral abstraction of different parsing errorsAuthor:Scooter Willis See Also:Serialized FormClassorg.biojava.nbio.core.exceptionsBioJava
PartitionRefinerDefines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.Interfaceorg.biojava.nbio.alignment.templateBioJava
PassthroughIdentifierA stub StructureIdentifier, representing the full structure in all cases.Classorg.biojava.nbio.structureBioJava
PDBBioAssemblyParserParses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unitClassorg.biojava.nbio.structure.ioBioJava
PDBBioUnitDataProviderA BioUnitDataProvider that extracts the necessary info from PDB filesAuthor:Andreas PrlicClassorg.biojava.nbio.structure.quaternary.ioBioJava
PDBCrystallographicInfoA class to hold crystallographic information about a PDB structure.Classorg.biojava.nbio.structureBioJava
PDBDirPanelA class to define where a structure for the alignment is coming fromSince:1.Classorg.biojava.nbio.structure.gui.utilBioJava
PDBDomainProviderClass to fetch domains through the RCSB's REST API.Classorg.biojava.nbio.structure.domainBioJava
PDBFileParserThis class implements the actual PDB file parsing.Classorg.biojava.nbio.structure.ioBioJava
PDBFileReader The wrapper class for parsing a PDB file.Classorg.biojava.nbio.structure.ioBioJava
PDBHeaderA class that contains PDB Header information.Classorg.biojava.nbio.structureBioJava
PdbIdListsUtility classes for retrieving lists of PDB IDs.Classorg.biojava.nbio.structure.rcsbBioJava
PdbPairA pair for structure alignmentAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.clientBioJava
PdbPairsMessageClassorg.biojava.nbio.structure.align.xmlBioJava
PdbPairXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJava
PDBParseExceptionAn exception during the parsing of a PDB file.Classorg.biojava.nbio.structure.ioBioJava
PDBRecordAn interface implemented by all classes that represent PDB recordsSince:1.Interfaceorg.biojava.nbio.structureBioJava
PDBServerPanelA class to define where a structure for the alignment is coming fromSince:1.Classorg.biojava.nbio.structure.gui.utilBioJava
PDBStatusMethods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure.Classorg.biojava.nbio.structureBioJava
PDBTemporaryStorageUtilsInternal use only.Classorg.biojava.nbio.structure.io.utilBioJava
PDBUploadPanelA JPanel to upload 2 custom PDB files.Classorg.biojava.nbio.structure.gui.utilBioJava
PdbxChemCompDescriptorClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxChemCompIdentifier_pdbx_chem_comp_identifier.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxEntityNonPolyA bean for the Pdbx_entity_nonpoly category.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxNonPolySchemeA bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxPolySeqSchemeA bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxStructAssemblyClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxStructAssemblyGenClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxStructAssemblyGenXMLContainerClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxStructAssemblyXMLContainerClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxStructOperListClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
PdbxStructOperListXMLContainerClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
PDPDistanceMatrixClassorg.biojava.nbio.structure.domain.pdpBioJava
PDPDomainClassorg.biojava.nbio.structure.domainBioJava
PDPParametersClassorg.biojava.nbio.structure.domain.pdpBioJava
PDPProviderDecomposes a structure into representative PDP domains.Interfaceorg.biojava.nbio.structure.domainBioJava
PeptidePropertiesThis is an adaptor class which enable the ease of generating protein properties.Classorg.biojava.nbio.aapropertiesBioJava
PeptidePropertiesImplThis class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.Classorg.biojava.nbio.aapropertiesBioJava
PermutationGeneratorClassorg.biojava.nbio.structure.symmetry.utilsBioJava
PermutationGroupClassorg.biojava.nbio.structure.symmetry.coreBioJava
PersistentConfiga class to store the config using the Java Web StartAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.webstartBioJava
PlainFastaHeaderParserThe plain fasta header takes everything in the header as a single entity.Classorg.biojava.nbio.core.sequence.ioBioJava
PointInterfaceorg.biojava.nbio.core.sequence.location.templateBioJava
PolyhedronInterfaceorg.biojava.nbio.structure.symmetry.geometryBioJava
PolymerTypeEnumerates the classification of polymers.Classorg.biojava.nbio.structure.io.mmcif.chemBioJava
PositionInQueueXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJava
PredictDisorderClassdemoBioJava
PrettyXMLWriterClassorg.biojava.nbio.core.utilBioJava
PrismClassorg.biojava.nbio.structure.symmetry.geometryBioJava
ProfeatPropertiesThis is an adaptor class which enable the ease of generating profeat properties.Classorg.biojava.nbio.aaproperties.profeatBioJava
ProfeatPropertiesImplClassorg.biojava.nbio.aaproperties.profeatBioJava
ProfileDefines a data structure for the results of sequence alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
ProfilePairDefines a data structure for the results of the alignment of a pair of Profiles.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
ProfileProfileAlignerDefines an Aligner for a pair of Profiles.Interfaceorg.biojava.nbio.alignment.templateBioJava
ProfileProfileScorerDefines an algorithm which computes a score for a pairing of alignment profiles.Interfaceorg.biojava.nbio.alignment.templateBioJava
ProfileViewDefines a data structure for a view of sequence alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
ProgramJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
ProgramsJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
ProteinChainExtractorExtracts information about all the chains in a structure, including chain Ids, sequences, and atoms.Classorg.biojava.nbio.structure.symmetry.coreBioJava
ProteinComplexSignatureClassorg.biojava.nbio.structure.symmetry.miscBioJava
ProteinModificationThis interface defines information about a specific proteinSince:3.Interfaceorg.biojava.nbio.protmodBioJava
ProteinModificationIdentifierIdentify attachment modification in a 3-D structure.Classorg.biojava.nbio.protmod.structureBioJava
ProteinModificationImplThis class contains information about a specific proteinSince:3.Classorg.biojava.nbio.protmodBioJava
ProteinModificationRegistryThis class serves as a instance registry by maintaining a pool of ProteinModification instances.Classorg.biojava.nbio.protmodBioJava
ProteinModificationXmlReaderClassorg.biojava.nbio.protmod.ioBioJava
ProteinSequenceThe representation of a ProteinSequenceAuthor:Scooter Willis, Paolo PavanClassorg.biojava.nbio.core.sequenceBioJava
ProteinSequenceClustererRepresents a set of non-identical protein sequences.Classorg.biojava.nbio.structure.symmetry.coreBioJava
ProteinSequenceCreatorUsed to create a ProteinSequence from a String to allow for details about the location of the sequence etc.Classorg.biojava.nbio.core.sequence.ioBioJava
ProxySequenceReaderInterfaceorg.biojava.nbio.core.sequence.templateBioJava
QRDecomposition For an m-by-n matrix A with m >= n, the QR decomposition is an m-by-n orthogonal matrix Q and an n-by-n upper triangular matrix R so thatClassorg.biojava.nbio.structure.jamaBioJava
QualifierClassorg.biojava.nbio.core.sequence.featuresBioJava
QualityFeatureDNA Sequences produced by modern sequencers usually have quality informaion attached to them.Classorg.biojava.nbio.core.sequence.featuresBioJava
QuantityFeatureIt is common to have a numerical value or values associated with a feature.Classorg.biojava.nbio.core.sequence.featuresBioJava
QuatSuperpositionScorerClassorg.biojava.nbio.structure.symmetry.coreBioJava
QuatSymmetryDetectorDetects global and local quaternary protein structure symmetry in a structure.Classorg.biojava.nbio.structure.symmetry.coreBioJava
QuatSymmetryParametersClassorg.biojava.nbio.structure.symmetry.coreBioJava
QuatSymmetryResultsHolds the results of quaternary symmetry perception.Classorg.biojava.nbio.structure.symmetry.coreBioJava
QuatSymmetryScoresClassorg.biojava.nbio.structure.symmetry.coreBioJava
QuatSymmetrySolverInterfaceorg.biojava.nbio.structure.symmetry.coreBioJava
RasmolCommandListenera utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.gui.jmolBioJava
RasmolCommandListenera utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas PrlicClassorg.biojava.nbio.structure.guiBioJava
RawBioUnitDataProviderDefines the methods that have to be implemented by a class that provides the data that is necessary to recreate the correct biological assembly of a protein.Interfaceorg.biojava.nbio.structure.quaternary.ioBioJava
RCSBDescriptionCorresponds to the wrapper element in an RCSB describeMol XML file.Classorg.biojava.nbio.structure.rcsbBioJava
RCSBDescriptionFactoryFetches information from RCSB's RESTful Web Service Interface.Classorg.biojava.nbio.structure.rcsbBioJava
RCSBLigandCorresponds to a ligand in a ligandInfo XML file.Classorg.biojava.nbio.structure.rcsbBioJava
RCSBLigandsCorresponds to the wrapper element "ligandInfo" in an RCSB ligandInfo XML file.Classorg.biojava.nbio.structure.rcsbBioJava
RCSBLigandsFactoryFetches information from RCSB's RESTful Web Service Interface.Classorg.biojava.nbio.structure.rcsbBioJava
RCSBMacromoleculeCorresponds to a macromolecule in an RCSB describeMol XML file.Classorg.biojava.nbio.structure.rcsbBioJava
RCSBPolymerCorresponds to a polymer in a describeMol XML file.Classorg.biojava.nbio.structure.rcsbBioJava
RCSBTaxonomyCorresponds to a taxonomy in a describeMol XML file.Classorg.biojava.nbio.structure.rcsbBioJava
RCSBUpdatesClassorg.biojava.nbio.structure.rcsbBioJava
ReadUtilsPackage-level static utilities for parsing XML.Classorg.biojava.nbio.structure.rcsbBioJava
RectangularPrismClassorg.biojava.nbio.structure.symmetry.geometryBioJava
ReducedChemCompProviderUnlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions.Classorg.biojava.nbio.structure.io.mmcifBioJava
ReferenceSuperimposerSuperimposes each structure in a MultipleAlignment onto a reference Performs a global superposition of the MultipleAlignment in caseClassorg.biojava.nbio.structure.align.multiple.utilBioJava
RefineClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
RefinerFailedExceptionRefinement of the self-alignment failed.Classorg.biojava.nbio.structure.symmetry.internalBioJava
RemoteBioUnitDataProviderClassorg.biojava.nbio.structure.quaternary.ioBioJava
RemoteDomainProviderA DomainProvider that uses a mixture of SCOP and PDP domains.Classorg.biojava.nbio.structure.domainBioJava
RemoteHmmerScanMakes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.Classorg.biojava.nbio.ws.hmmerBioJava
RemotePairwiseAlignmentOutputPropertiesRemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.Interfaceorg.biojava.nbio.ws.alignmentBioJava
RemotePairwiseAlignmentPropertiesRemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties.Interfaceorg.biojava.nbio.ws.alignmentBioJava
RemotePairwiseAlignmentServiceThis interface specifies minimal information needed to execute a pairwise alignment on a remote service.Interfaceorg.biojava.nbio.ws.alignmentBioJava
RemotePDPProviderA class that provided PDP assignments that are loaded from a remote web serverAuthor:Andreas PrlicClassorg.biojava.nbio.structure.domainBioJava
RemoteRawBioUnitDataProviderA BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDBAuthor:Andreas PrlicClassorg.biojava.nbio.structure.quaternary.ioBioJava
RemoteScopInstallationA class that fetches information about SCOP from a remote data-source.Classorg.biojava.nbio.structure.scopBioJava
RemoteTermA term in another ontology.Interfaceorg.biojava.nbio.ontologyBioJava
RenderStyleClassorg.biojava.nbio.structure.guiBioJava
RepresentativeXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJava
RescoreRefinerInterfaceorg.biojava.nbio.alignment.templateBioJava
ResidualsCoxphClassorg.biojava.nbio.survival.coxBioJava
ResidueGroupA ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.Classorg.biojava.nbio.structure.symmetry.internalBioJava
ResidueNumberEverything that is needed to uniquely describe a residue positionAuthor:Andreas PrlicSee Also:Serialized FormClassorg.biojava.nbio.structureBioJava
ResidueRangeA chain, a start residue, and an end residue.Classorg.biojava.nbio.structureBioJava
ResidueRangeAndLengthA chain, a start residue, and an end residue.Classorg.biojava.nbio.structureBioJava
ResidueTypeEnumerates the possible classifications of residues.Classorg.biojava.nbio.structure.io.mmcif.chemBioJava
ResourceManagerA class that manages the Strings that are defined in the spice.Classorg.biojava.nbio.structure.align.utilBioJava
ResultThis class models a search result.Classorg.biojava.nbio.core.search.ioBioJava
ResultFactoryDesigned by Paolo Pavan.Interfaceorg.biojava.nbio.core.search.ioBioJava
ReversedSequenceViewFor a given sequence this class will return the base at the reversed position i.Classorg.biojava.nbio.core.sequence.viewsBioJava
RiskInfoClassorg.biojava.nbio.survival.coxBioJava
RNACompoundSetClassorg.biojava.nbio.core.sequence.compoundBioJava
RNASequenceRNASequence where RNACompoundSet are the allowed valuesAuthor:Scooter Willis Classorg.biojava.nbio.core.sequenceBioJava
RNASequenceCreatorUsed to create a RNA sequenceAuthor:Scooter Willis Classorg.biojava.nbio.core.sequence.ioBioJava
RnaSequenceViewClassorg.biojava.nbio.core.sequence.viewsBioJava
RNAToAminoAcidTranslatorTakes a Sequence of NucleotideCompound which should represent an RNA sequence (RNASequence is good for this) and returns a list ofClassorg.biojava.nbio.core.sequence.transcriptionBioJava
RonnConstraintA collection of various constrain values used by RONNSince:3.Classorg.biojava.nbio.ronnBioJava
RotationClassorg.biojava.nbio.structure.symmetry.coreBioJava
RotationAxisCalculates the rotation axis for an alignment A superposition of two structures is generally represented as a rotationClassorg.biojava.nbio.structure.align.utilBioJava
RotationAxisAlignerClassorg.biojava.nbio.structure.symmetry.coreBioJava
RotationGroupClassorg.biojava.nbio.structure.symmetry.coreBioJava
RotationSolverClassorg.biojava.nbio.structure.symmetry.coreBioJava
SandboxStyleStructureProviderThe "Sandbox" style of organizing files is to have a directory structure like below, i.Classorg.biojava.nbio.structure.ioBioJava
SangerFastqReaderReader for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJava
SangerFastqWriterWriter for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJava
ScaleableMatrixPanelA JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm.Classorg.biojava.nbio.structure.guiBioJava
ScaledSubstitutionMatrixThe biojava-alignment module represents substitution matrices with short values.Classorg.biojava.nbio.core.alignment.matricesBioJava
ScanSymmetryClassorg.biojava.nbio.structure.symmetry.analysisBioJava
SchemaGeneratorClassorg.biojava.nbio.aaproperties.xmlBioJava
SCOPAutoSuggestProviderClassorg.biojava.nbio.structure.align.gui.autosuggestBioJava
ScopCategoryThe various categories provided by SCOP.Classorg.biojava.nbio.structure.scopBioJava
ScopDatabaseGeneral API how to interact with SCOPSince:3.Interfaceorg.biojava.nbio.structure.scopBioJava
ScopDescription dir.Classorg.biojava.nbio.structure.scopBioJava
ScopDescriptionsClassorg.biojava.nbio.structure.scop.serverBioJava
ScopDomainContainer for the information for a domain.Classorg.biojava.nbio.structure.scopBioJava
ScopDomainsClassorg.biojava.nbio.structure.scop.serverBioJava
ScopFactoryControls the global ScopDatabase being used.Classorg.biojava.nbio.structure.scopBioJava
ScopInstallationThis class provides access to the SCOP protein structure classification.Classorg.biojava.nbio.structure.scopBioJava
ScopInstallationInstanceClassorg.biojava.nbio.structure.gui.utilBioJava
ScopIOExceptionIndicates that an I/O error occurred with SCOP lazy initialization.Classorg.biojava.nbio.structure.scopBioJava
ScopMirrorHelper class to store paths to the four SCOP files The string "%s" is replaced with the version number.Classorg.biojava.nbio.structure.scopBioJava
ScopNodeClassorg.biojava.nbio.structure.scopBioJava
ScopNodesClassorg.biojava.nbio.structure.scop.serverBioJava
ScopSelectPanelClassorg.biojava.nbio.structure.gui.utilBioJava
ScorerDefines an algorithm which computes a score.Interfaceorg.biojava.nbio.alignment.templateBioJava
ScoresCacheInterface for classes which implement a temporary cache for various numeric scores, e.Interfaceorg.biojava.nbio.structure.align.multipleBioJava
SearchIODesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.ioBioJava
SecStrucCalcCalculate and assign the secondary structure (SS) to the Groups of a Structure object.Classorg.biojava.nbio.structure.secstrucBioJava
SecStrucElementA secondary structure element (SSE) is an object representing a block of sequential residues that share the same secondary structure type.Classorg.biojava.nbio.structure.secstrucBioJava
SecStrucInfoContainer for the secondary structure information of a single residue.Classorg.biojava.nbio.structure.secstrucBioJava
SecStrucStateThis class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm.Classorg.biojava.nbio.structure.secstrucBioJava
SecStrucToolsThis class contains methods for obtaining and converting secondary structure information from BioJava Structures.Classorg.biojava.nbio.structure.secstrucBioJava
SecStrucTypeThis enum contains all of the secondary structure types found in the DSSP output.Classorg.biojava.nbio.structure.secstrucBioJava
SegmentClassorg.biojava.nbio.structure.domain.pdpBioJava
SegmentComparatorClassorg.biojava.nbio.structure.domain.pdpBioJava
SelectionInterfaceorg.biojava.nbio.structure.guiBioJava
SelectionImplClassorg.biojava.nbio.structure.guiBioJava
SelectMultiplePanelA Text Panel that allows the user to specify multiple structure identifiers, space separated.Classorg.biojava.nbio.structure.gui.utilBioJava
SelectPDBPanelA Panel that allows user to specify PDB & chain ID, as well as sub-rangesAuthor:AndreasSee Also:Serialized FormClassorg.biojava.nbio.structure.align.guiBioJava
SeqMisMatchCreated by andreas on 9/11/15.Interfaceorg.biojava.nbio.structureBioJava
SeqMisMatchImplCreated by andreas on 9/11/15.Classorg.biojava.nbio.structureBioJava
SeqRes2AtomAlignerAligns the SEQRES residues to the ATOM residues.Classorg.biojava.nbio.structure.ioBioJava
SequenceMain interface for defining a collection of Compounds and accessing them using biological indexesInterfaceorg.biojava.nbio.core.sequence.templateBioJava
SequenceAlignmentClusterClassorg.biojava.nbio.structure.symmetry.coreBioJava
SequenceAsStringHelperThis is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data.Classorg.biojava.nbio.core.sequence.storageBioJava
SequenceComparatorUsed to sort sequencesAuthor:Scooter Willis Classorg.biojava.nbio.core.sequenceBioJava
SequenceCreatorInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJava
SequenceDisplayA sequence display that can show the results of a protein structure alignment.Classorg.biojava.nbio.structure.guiBioJava
SequenceFileProxyLoaderThis class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence.Classorg.biojava.nbio.core.sequence.loaderBioJava
SequenceFunctionOrderDetectorCalls Spencer's method for determining order.Classorg.biojava.nbio.structure.symmetry.internalBioJava
SequenceFunctionRefinerCreates a refined alignment with the CE-Symm alternative self-alignment.Classorg.biojava.nbio.structure.symmetry.internalBioJava
SequenceHeaderParserInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJava
SequenceLocationA location in a sequence that keeps a reference to its parent sequenceAuthor:Scooter Willis , Paolo PavanSee Also:Serialized FormClassorg.biojava.nbio.core.sequence.locationBioJava
SequenceMixinProvides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way.Classorg.biojava.nbio.core.sequence.templateBioJava
SequenceMouseListenera mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriateClassorg.biojava.nbio.structure.gui.utilBioJava
SequenceOptimizationHintsA static class that provides optimization hints for memory or performance handling of sequence data.Classorg.biojava.nbio.core.sequenceBioJava
SequencePairDefines a data structure for the results of pairwise sequence alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
SequenceParserInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJava
SequenceProxyViewClassorg.biojava.nbio.core.sequence.templateBioJava
SequenceReaderInterfaceorg.biojava.nbio.core.sequence.templateBioJava
SequenceScalePanelA class that draws a Sequence as a rectangle, a scale display over it.Classorg.biojava.nbio.structure.gui.utilBioJava
SequenceToolsClassorg.biojava.nbio.core.utilBioJava
SequenceUtilUtility class for operations on sequencesSince:3.Classorg.biojava.nbio.data.sequenceBioJava
SequenceViewInterfaceorg.biojava.nbio.core.sequence.templateBioJava
SerializableCacheA class that provides all that is necessary to create a Serializable CacheSince:3.Classorg.biojava.nbio.structure.domainBioJava
ShortSegmentRemoverClassorg.biojava.nbio.structure.domain.pdpBioJava
ShowPDBIDListenerClassorg.biojava.nbio.structure.align.guiBioJava
ShowStructureInJmolDemo how to load and display a structure in JmolAuthor:Andreas PrlicClassdemoBioJava
SiftsChainEntryAn entry in the chain-level SIFTS mapping between UniProt and the PDB.Classorg.biojava.nbio.structure.io.siftsBioJava
SiftsChainToUniprotMappingA mapping between UniProt entries and PDB chains.Classorg.biojava.nbio.structure.io.siftsBioJava
SiftsEntityClassorg.biojava.nbio.structure.io.siftsBioJava
SiftsMappingProviderClassorg.biojava.nbio.structure.io.siftsBioJava
SiftsResidueClassorg.biojava.nbio.structure.io.siftsBioJava
SiftsSegmentClassorg.biojava.nbio.structure.io.siftsBioJava
SiftsXMLParserClassorg.biojava.nbio.structure.io.siftsBioJava
SigEvaClassorg.biojava.nbio.structure.align.fatcat.calcBioJava
SimpleAlignedSequenceClassorg.biojava.nbio.core.alignmentBioJava
SimpleGapPenaltyClassorg.biojava.nbio.alignmentBioJava
SimpleLocationVery basic implementation of the Location interface which defines a series of simple constructors.Classorg.biojava.nbio.core.sequence.locationBioJava
SimpleMMcifConsumerA MMcifConsumer implementation that builds an in-memory representation of the content of a mmcif file as a BioJava Structure object.Classorg.biojava.nbio.structure.io.mmcifBioJava
SimpleMMcifParserA simple mmCif file parserString file = "path/to/mmcif/file";Classorg.biojava.nbio.structure.io.mmcifBioJava
SimplePointBasic implementation of the Point interface.Classorg.biojava.nbio.core.sequence.locationBioJava
SimpleProfileClassorg.biojava.nbio.core.alignmentBioJava
SimpleProfilePairClassorg.biojava.nbio.core.alignmentBioJava
SimpleProfileProfileAligner NeedlemanWunsch pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score.Classorg.biojava.nbio.alignmentBioJava
SimpleSequencePairClassorg.biojava.nbio.core.alignmentBioJava
SimpleSubstitutionMatrix Compound in a sequence for another.Classorg.biojava.nbio.core.alignment.matricesBioJava
SingleCompoundSequenceReaderAn implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a StringClassorg.biojava.nbio.core.sequence.storageBioJava
SingleLinkageClustererAn implementation of a single linkage clusterer See http://en.Classorg.biojava.nbio.core.utilBioJava
SingularValueDecompositionSingular Value Decomposition.Classorg.biojava.nbio.structure.jamaBioJava
SiteCreated by ap3 on 31/10/2014.Classorg.biojava.nbio.phosphositeBioJava
SiteHolds the data of sites presented in PDB files.Classorg.biojava.nbio.structureBioJava
SmallAnnotationAnnotation that is optimized for memory usage.Classorg.biojava.nbio.ontology.utilsBioJava
SmallMapLightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.Classorg.biojava.nbio.ontology.utilsBioJava
SmithWatermanSmith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).Classorg.biojava.nbio.alignmentBioJava
SmithWaterman3Dalignerprovides a 3D superimposition based on the sequence alignmentAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.seqBioJava
SmithWaterman3DParametersClassorg.biojava.nbio.structure.align.seqBioJava
SmithWatermanUserArgumentProcessorClassorg.biojava.nbio.structure.align.seqBioJava
SoftHashMapA in memory cache using soft references.Classorg.biojava.nbio.core.utilBioJava
SolexaFastqReaderReader for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJava
SolexaFastqWriterWriter for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJava
SpaceGroupA crystallographic space group.Classorg.biojava.nbio.structure.xtalBioJava
SpaceGroupMapElementsClassorg.biojava.nbio.structure.xtal.ioBioJava
SpaceGroupMapRootClassorg.biojava.nbio.structure.xtal.ioBioJava
SparseSquareMatrixA sparse, square matrix, implementing using two arrays of sparse vectors, one representation for the rows and one for the columns.Classorg.biojava.nbio.structure.mathBioJava
SparseVectorA sparse vector, implemented using a symbol table.Classorg.biojava.nbio.structure.mathBioJava
SphereSamplerClassorg.biojava.nbio.structure.symmetry.geometryBioJava
SplitFastaUtility to write each Fasta entry to a unique fileAuthor:Scooter Willis Classorg.biojava.nbio.genome.utilBioJava
SqrtColorMapperPerforms a sqrt transform on input before passing the values off to another For instance, to map [0^2, 10^2] to a rainbow gradient, useClassorg.biojava.nbio.structure.gui.util.colorBioJava
SSBondImplA simple bean to store disulfide bridge information, the SSBOND records in the PDB files.Classorg.biojava.nbio.structure.ioBioJava
StainTypeClassorg.biojava.nbio.genome.parsers.cytobandBioJava
StandardAminoAcidA class that provides a set of standard amino acids.Classorg.biojava.nbio.structureBioJava
StandardRescoreRefinerClassorg.biojava.nbio.alignmentBioJava
StartCodonSequenceUsed to map the start codon feature on a geneAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJava
StartupParametersa simple bean that contains the parameters that can get set at startupAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.ceBioJava
StaticMemberPlaceHolderClassorg.biojava.nbio.ontology.utilsBioJava
StatusDisplayClassorg.biojava.nbio.structure.align.gui.aligpanelBioJava
StdArrayIOStandard array IO.Classorg.biojava.nbio.survival.cox.matrixBioJava
StockholmFileAnnotationStores all the content parsed from the #=GF linesSince:3.Classorg.biojava.nbio.alignment.ioBioJava
StockholmFileParserStockholm file parser.Classorg.biojava.nbio.alignment.ioBioJava
StockholmStructureStores all the content of a Stockholm file.Classorg.biojava.nbio.alignment.ioBioJava
StopCodonSequenceUsed to map the stop codon sequence on a geneAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJava
StrandProvides a way of representing the strand of a sequence, locationEnum Constant SummaryClassorg.biojava.nbio.core.sequenceBioJava
StrataInfoInformation needed to represent a survival curveAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJava
StrCompAlignmentClassorg.biojava.nbio.structure.align.pairwiseBioJava
StreamListenerEvent based parser callback.Interfaceorg.biojava.nbio.sequencing.io.fastqBioJava
StringManipulationHelperA utility class for common String manipulation tasks.Classorg.biojava.nbio.core.utilBioJava
StringProxySequenceReaderAn example of a ProxySequenceReader that is created from a String.Classorg.biojava.nbio.core.sequence.loaderBioJava
StrucAligParametersA class that contains all the parameters of the structure alignment algorithm.Classorg.biojava.nbio.structure.alignBioJava
Structa bean to contain the data of the _struct linesAuthor:Andreas PrlicClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructAsymContains the data for _struct_asymSince:1.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructConnClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructKeywordsClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructNcsOperClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructRefA class to containt the _struct_ref field dataAuthor:Andreas PrlicClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructRefSeqClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructRefSeqDifClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructSiteCreated by Matt on 11/1/2015.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructSiteGenCreated by Matt on 10/31/2015.Classorg.biojava.nbio.structure.io.mmcif.modelBioJava
StructureInterface for a structure object.Interfaceorg.biojava.nbio.structureBioJava
StructureAlignmentInterfaceorg.biojava.nbio.structure.alignBioJava
StructureAlignmentDisplayClassorg.biojava.nbio.structure.align.guiBioJava
StructureAlignmentFactoryClassorg.biojava.nbio.structure.alignBioJava
StructureAlignmentJmolA class that provides a simple GUI for JmolSince:1.Classorg.biojava.nbio.structure.align.gui.jmolBioJava
StructureAlignmentOptimizerClassorg.biojava.nbio.structure.align.fatcat.calcBioJava
StructureAtomEverything that is needed to uniquely describe a atom.Classorg.biojava.nbio.protmod.structureBioJava
StructureAtomLinkageClassorg.biojava.nbio.protmod.structureBioJava
StructureAtomXMLConverterClassorg.biojava.nbio.protmod.ioBioJava
StructureExceptionAn exception during the parsing of a PDB file.Classorg.biojava.nbio.structureBioJava
StructureGroupInformation of a group (residue or ligand) involved in a modification.Classorg.biojava.nbio.protmod.structureBioJava
StructureGroupXMLConverterClassorg.biojava.nbio.protmod.ioBioJava
StructureIdentifierAn identifier that uniquely identifies a whole Structure or arbitrary substructure.Interfaceorg.biojava.nbio.structureBioJava
StructureImpl provides the data contained in a PDB file.Classorg.biojava.nbio.structureBioJava
StructureInterfaceAn interface between 2 molecules (2 sets of atoms).Classorg.biojava.nbio.structure.contactBioJava
StructureInterfaceClusterClassorg.biojava.nbio.structure.contactBioJava
StructureInterfaceListA list of interfaces between 2 molecules (2 sets of atoms)Author:duarte_jSee Also:Serialized FormClassorg.biojava.nbio.structure.contactBioJava
StructureIOA class that provides static access methods for easy lookup of protein structure related componentsSince:3.Classorg.biojava.nbio.structureBioJava
StructureIOFileStructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.Interfaceorg.biojava.nbio.structure.ioBioJava
StructureLoaderThreadClassorg.biojava.nbio.structure.align.guiBioJava
StructureNameA utility class that makes working with names of structures, domains and ranges easier.Classorg.biojava.nbio.structure.align.clientBioJava
StructurePairAlignerPerform a pairwise protein structure superimposition.Classorg.biojava.nbio.structure.alignBioJava
StructurePairSelectorTo be implemented by JPanels that are part of the GUI to trigger structure aligmnents.Interfaceorg.biojava.nbio.structure.gui.utilBioJava
StructureProviderA class that can provide a protein structure object from somewhere.Interfaceorg.biojava.nbio.structure.ioBioJava
StructureSequenceMatcherA utility class with methods for matching ProteinSequences withAuthor:Spencer BlivenClassorg.biojava.nbio.structure.ioBioJava
StructureToolsA class that provides some tool methods.Classorg.biojava.nbio.structureBioJava
StructureUtilClassorg.biojava.nbio.protmod.structureBioJava
StructureViewerInterfaceorg.biojava.nbio.structure.guiBioJava
SubstitutionMatrixDefines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.Interfaceorg.biojava.nbio.core.alignment.templateBioJava
SubstitutionMatrixHelperStatic utility to access substitution matrices that come bundled with BioJava.Classorg.biojava.nbio.core.alignment.matricesBioJava
SubstitutionMatrixScorerScores using a substitution matrix.Classorg.biojava.nbio.alignmentBioJava
SubstructureIdentifierThis is the canonical way to identify a part of a structure.Classorg.biojava.nbio.structureBioJava
SubunitGraphClassorg.biojava.nbio.structure.symmetry.coreBioJava
SubunitsA bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment.Classorg.biojava.nbio.structure.symmetry.coreBioJava
SuperPositionClassorg.biojava.nbio.structure.symmetry.geometryBioJava
SuperPositionQCPClassorg.biojava.nbio.structure.symmetry.geometryBioJava
SurvFitInfoContains info for graphing km figuresAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJava
SurvFitKMPorted from survfitKM.Classorg.biojava.nbio.survival.kaplanmeier.figureBioJava
SurvivalInfoData class to represent a single sample where time and event/censor status is required Additionally each variable and data associated with that variable.Classorg.biojava.nbio.survival.coxBioJava
SurvivalInfoComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJava
SurvivalInfoHelperUsed to work with SurvivalInfoAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJava
SurvivalInfoIndexNot used and probably should be deletedAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJava
SurvivalInfoValueComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJava
SVDSuperimposerA class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class.Classorg.biojava.nbio.structureBioJava
SymbolTableSorted symbol table implementation using a java.Classorg.biojava.nbio.structure.mathBioJava
SymmClashJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
SymmetryClassorg.biojava.nbio.structure.io.mmcif.modelBioJava
SymmetryAxesData Structure that stores all the symmetry axis that describe the symmetry of a structure.Classorg.biojava.nbio.structure.symmetry.internalBioJava
SymmetryCalcCalculates a symmetry analysis and displays the results.Classorg.biojava.nbio.structure.symmetry.guiBioJava
SymmetryDisplayClass that provides visualizations methods for symmetry alignments.Classorg.biojava.nbio.structure.symmetry.guiBioJava
SymmetryGuiA JFrame that allows to trigger a symmetry analysis, either from files in a directory or after manual uploadClassorg.biojava.nbio.structure.symmetry.guiBioJava
SymmetryListenerAction Listener for the symmetry menu.Classorg.biojava.nbio.structure.symmetry.guiBioJava
SymmetryRefinerInterface for all symmetry refinement implementations.Interfaceorg.biojava.nbio.structure.symmetry.internalBioJava
SymmetryToolsUtility methods for the internal symmetry identification and manipulation.Classorg.biojava.nbio.structure.symmetry.utilsBioJava
SymmOptimizerOptimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.Classorg.biojava.nbio.structure.symmetry.internalBioJava
SymoplibParserA class containing static methods to parse the symop.Classorg.biojava.nbio.structure.xtalBioJava
SynchronizedOutFileClassorg.biojava.nbio.structure.align.utilBioJava
SynonymClassorg.biojava.nbio.ontologyBioJava
SystematicSolverClassorg.biojava.nbio.structure.symmetry.coreBioJava
SystemInfoClassorg.biojava.nbio.structure.align.guiBioJava
TabDelimParserParse tab-delimited ontology files into Ontology objects.Classorg.biojava.nbio.ontology.ioBioJava
TableProvides a way of separating us from the specific IUPACParser.Interfaceorg.biojava.nbio.core.sequence.transcriptionBioJava
TaxonomyIDA sequence can be associated with a species or Taxonomy IDAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJava
TermA term in an ontology.Interfaceorg.biojava.nbio.ontologyBioJava
TestDNANeedlemanWunschClassdemoBioJava
TetrahedronClassorg.biojava.nbio.structure.symmetry.geometryBioJava
TextFeatureA implmentation of AbstractFeatureAuthor:Scooter Willis Classorg.biojava.nbio.core.sequence.featuresBioJava
TimerA simple timer, calculates the time interval between two events.Classorg.biojava.nbio.ronnBioJava
TranscriptionEngineUsed as a way of encapsulating the data structures required to parse DNA to a In order to build one look at @ TranscriptionEngine.Classorg.biojava.nbio.core.sequence.transcriptionBioJava
TranscriptSequenceThis is the sequence if you want to go from a gene sequence to a protein sequence.Classorg.biojava.nbio.core.sequenceBioJava
TransfAlgebraicAdapterClassorg.biojava.nbio.structure.xtal.ioBioJava
TransformTypeClassorg.biojava.nbio.structure.xtalBioJava
TranslationExceptionThrown from AbstractCompundTranslatorAuthor:Andy YatesSee Also:Serialized FormClassorg.biojava.nbio.core.exceptionsBioJava
TreeConstructorThe TreeConstructor uses the forester library to build different types of phylogenetic trees.Classorg.biojava.nbio.phyloBioJava
TreeConstructorTypeenum TreeConstructorTypeThe TreeConstructorType specifies the aligorithm used to construct the treeClassorg.biojava.nbio.phyloBioJava
TreeMapSpaceGroupWrapperClassorg.biojava.nbio.structure.xtal.ioBioJava
TreeSetStringWrapperClassorg.biojava.nbio.structure.scop.serverBioJava
TreeTypeThe TreeType specifies the optimization criteria used to generate the tree.Classorg.biojava.nbio.phyloBioJava
TripleA triple in an ontology.Interfaceorg.biojava.nbio.ontologyBioJava
TwoBitParserdownloaded from http://storage.Classorg.biojava.nbio.genome.parsers.twobitBioJava
TwoBitSequenceReader 0 - T1 - C2 - A3 - G We also do not support case sensitive encodings therefore if you pass aClassorg.biojava.nbio.core.sequence.storageBioJava
UncompressInputStreamThis class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).Classorg.biojava.nbio.core.utilBioJava
UniprotProxySequenceReaderPass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot.Classorg.biojava.nbio.core.sequence.loaderBioJava
UniprotToFastaClassorg.biojava.nbio.genome.uniprotBioJava
UniqueSequenceListBean for a single sequence.Classorg.biojava.nbio.structure.symmetry.coreBioJava
UnitCellBoundingBoxClassorg.biojava.nbio.structure.xtalBioJava
URLIdentifierRepresents a structure loaded from a URL (including a file URL) A few custom query parameters are supported:Classorg.biojava.nbio.structureBioJava
UserArgumentProcessorInterfaceorg.biojava.nbio.structure.align.ceBioJava
UserConfigurationA container to persist config to the file systemAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.utilBioJava
UtilsThis is a utility class that contains utility methods which will facilitates the coding of other methodsSince:3.Classorg.biojava.nbio.aapropertiesBioJava
VariableInterfaceorg.biojava.nbio.ontologyBioJava
WaldTestClassorg.biojava.nbio.survival.coxBioJava
WaldTestInfoClassorg.biojava.nbio.survival.coxBioJava
WeakValueHashMapMap implementation which keeps weak references to values.Classorg.biojava.nbio.ontology.utilsBioJava
WebStartClientDemoClassdemoBioJava
WebStartDBSearchA Web Start wrapper for a FarmJobRunnable.Classorg.biojava.nbio.structure.align.webstartBioJava
WebStartDBSearchResultsClassorg.biojava.nbio.structure.align.webstartBioJava
WebStartMainClassorg.biojava.nbio.structure.align.webstartBioJava
WindowedSequenceA sliding window view of a sequence which does not implement any interfaces like Sequence because they do not fit how this works.Classorg.biojava.nbio.core.sequence.viewsBioJava
WorkSheetNeed to handle very large spreadsheets of expression data so keep memoryAuthor:Scooter Willis Classorg.biojava.nbio.survival.dataBioJava
WwPDBValidationInformationJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJava
XMLHelperClassorg.biojava.nbio.core.utilBioJava
XMLUtilUtility classes for the XML serialization and de-serialization of SCOP.Classorg.biojava.nbio.structure.scop.serverBioJava
XMLWriterSimple interface for building XML documents.Interfaceorg.biojava.nbio.core.utilBioJava
ZipChemCompProviderThis chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction.Classorg.biojava.nbio.structure.io.mmcifBioJava