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# Classes and Interfaces in #BioJava - 1031 results found.
NameDescriptionTypePackageFrameworkJavaDoc
AAindexFactoryFactory class to get Providers for substitution matrices the are provided by the AAINDEX database.Classorg.biojava.nbio.core.alignment.matricesBioJavajavadoc
AAIndexFileParserClassorg.biojava.nbio.core.alignment.matricesBioJavajavadoc
AAIndexProviderInterfaceorg.biojava.nbio.core.alignment.matricesBioJavajavadoc
AboutDialogClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
AbstractAlignmentJmolAn Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.Classorg.biojava.nbio.structure.align.gui.jmolBioJavajavadoc
AbstractAnnotationA utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.Classorg.biojava.nbio.ontology.utilsBioJavajavadoc
AbstractBeana generic class that implements the toString method for a beanAuthor:Andreas PrlicClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
AbstractCompoundClassorg.biojava.nbio.core.sequence.templateBioJavajavadoc
AbstractCompoundSetClassorg.biojava.nbio.core.sequence.templateBioJavajavadoc
AbstractCompoundTranslatorClassorg.biojava.nbio.core.sequence.templateBioJavajavadoc
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.featuresBioJavajavadoc
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.templateBioJavajavadoc
AbstractMatrixAlignerClassorg.biojava.nbio.alignment.templateBioJavajavadoc
AbstractNucleotideCompoundSetClassorg.biojava.nbio.core.sequence.templateBioJavajavadoc
AbstractPairwiseSequenceAlignerClassorg.biojava.nbio.alignment.templateBioJavajavadoc
AbstractProfileProfileAlignerClassorg.biojava.nbio.alignment.templateBioJavajavadoc
AbstractScorerClassorg.biojava.nbio.alignment.templateBioJavajavadoc
AbstractScoresCacheAbstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.Classorg.biojava.nbio.structure.align.multipleBioJavajavadoc
AbstractSequenceThe base class for DNA, RNA and Protein sequences.Classorg.biojava.nbio.core.sequence.templateBioJavajavadoc
AbstractStructureAlignmentClassorg.biojava.nbio.structure.alignBioJavajavadoc
AbstractTermAbstract implementation of term This provides basic change-forwarding functionality fromClassorg.biojava.nbio.ontologyBioJavajavadoc
AbstractUserArgumentProcessorBase class for a new structure alignment CLI.Classorg.biojava.nbio.structure.align.ceBioJavajavadoc
AccesionedLocationA location which is bound to an AccessionID.Interfaceorg.biojava.nbio.core.sequence.location.templateBioJavajavadoc
AccessionedInterfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc

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AccessionIDUsed in Sequences as the unique indentifier.Classorg.biojava.nbio.core.sequenceBioJavajavadoc
AFPA class to represent a FATCAT AFPAuthor:Andreas PrlicSee Also:Serialized FormClassorg.biojava.nbio.structure.align.modelBioJavajavadoc
AFPAlignmentDisplayClassorg.biojava.nbio.structure.align.utilBioJavajavadoc
AFPCalculatora class that performs calculations on AFPCHainsAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.fatcat.calcBioJavajavadoc
AFPChainA bean to contain the core of a structure alignment.Classorg.biojava.nbio.structure.align.modelBioJavajavadoc
AFPChainCoordManagerClassorg.biojava.nbio.structure.align.gui.aligpanelBioJavajavadoc
AFPChainera class to chain AFPs to an alignmentAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.fatcat.calcBioJavajavadoc
AFPChainFlipperClassorg.biojava.nbio.structure.align.xmlBioJavajavadoc
AFPChainScorerClassorg.biojava.nbio.structure.align.utilBioJavajavadoc
AfpChainWriterA class to convert the data in an AfpChain object to various String outputs.Classorg.biojava.nbio.structure.align.modelBioJavajavadoc
AFPChainXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJavajavadoc
AFPChainXMLParserClassorg.biojava.nbio.structure.align.xmlBioJavajavadoc
AFPFromFastaDemo displaying a structural alignment from a FASTA file using FastaAFPChainConverter.ClassdemoBioJavajavadoc
AFPOptimizerClassorg.biojava.nbio.structure.align.fatcat.calcBioJavajavadoc
AFPPostProcessordoes post processing after alignment chainginAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.fatcat.calcBioJavajavadoc
AFPTwisterClassorg.biojava.nbio.structure.alignBioJavajavadoc
AgScoreClassorg.biojava.nbio.survival.cox.statsBioJavajavadoc
AligMatElClassorg.biojava.nbio.structure.align.helperBioJavajavadoc
AlignableInterfaceorg.biojava.nbio.structure.align.pairwiseBioJavajavadoc
AlignedPositionClassorg.biojava.nbio.structure.gui.utilBioJavajavadoc
AlignedSequenceDefines a data structure for a Sequence within an alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJavajavadoc
AlignerDefines an algorithm which computes an alignment Profile from a list of Sequences.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
AlignerHelperStatic utility to construct alignment routines from a common library of methods.Classorg.biojava.nbio.alignment.routinesBioJavajavadoc
AlignmentCalcA class that obtains two structures via DAS and aligns them This is done in a separate thread.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
AlignmentCalcA class that obtains two structures via DAS and aligns them This is done in a separate thread.Classorg.biojava.nbio.structure.gui.utilBioJavajavadoc

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AlignmentCalcDBClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
AlignmentCalculationRunnableInterfaceorg.biojava.nbio.structure.align.guiBioJavajavadoc
AlignmentGuiA JFrame that allows to trigger a pairwise structure alignment, either from files in a directory,Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
AlignmentGuiDemoGet an instance of the two alignment GUIs.ClassdemoBioJavajavadoc
AlignmentPositionListenerInterfaceorg.biojava.nbio.structure.gui.eventsBioJavajavadoc
AlignmentProgressListenerInterfaceorg.biojava.nbio.structure.align.eventsBioJavajavadoc
AlignmentProgressListenerClassorg.biojava.nbio.structure.align.pairwiseBioJavajavadoc
AlignmentResultA class to track the alignment results in a flat fileAuthor:andreasSee Also:Serialized FormClassorg.biojava.nbio.structure.align.pairwiseBioJavajavadoc
AlignmentsStatic utility to easily run alignment routines.Classorg.biojava.nbio.alignmentBioJavajavadoc
AlignmentTextPanelClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
AlignmentToolsMethods for analyzing and manipulating AFPChains and for other pairwise alignment utilities.Classorg.biojava.nbio.structure.align.utilBioJavajavadoc
AligNPEClassorg.biojava.nbio.structure.align.pairwiseBioJavajavadoc
AlignToolsClassorg.biojava.nbio.structure.align.helperBioJavajavadoc
AligPanelA JPanel that can display an AFPChain in a nice way and interact with Jmol.Classorg.biojava.nbio.structure.align.gui.aligpanelBioJavajavadoc
AligPanelMouseMotionListenerClassorg.biojava.nbio.structure.align.gui.aligpanelBioJavajavadoc
AligUIManagerClassorg.biojava.nbio.structure.align.webstartBioJavajavadoc
AllChemCompProviderA ChemComp provider that downloads and caches the components.Classorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
AlreadyExistsExceptionThrown to indicate that a term or triple can't be added to an ontology because it is already present.Classorg.biojava.nbio.ontologyBioJavajavadoc
AltAligComparatora comparator to sort AlternativeAlignments based on their number of equivalent residuesAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.pairwiseBioJavajavadoc
AlternativeAlignment Alternative alignments arise from different seed alignments or seed FPairs.Classorg.biojava.nbio.structure.align.pairwiseBioJavajavadoc
AlternativeAlignmentFramea frame showing the alternative alignments, which are the result of a structure superimpositionSince:1.Classorg.biojava.nbio.structure.gui.utilBioJavajavadoc
AmbiguityDNACompoundSetClassorg.biojava.nbio.core.sequence.compoundBioJavajavadoc
AmbiguityDNARNAHybridCompoundSetAmbiguity set for hybrid DNA/RNA sequences.Classorg.biojava.nbio.core.sequence.compoundBioJavajavadoc
AmbiguityRNACompoundSetClassorg.biojava.nbio.core.sequence.compoundBioJavajavadoc
AminoAcid A Group that represents an AminoAcid.Interfaceorg.biojava.nbio.structureBioJavajavadoc

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AminoAcidCompositionClassorg.biojava.nbio.aaproperties.xmlBioJavajavadoc
AminoAcidCompositionTableClassorg.biojava.nbio.aaproperties.xmlBioJavajavadoc
AminoAcidCompoundUsed to describe an Amino Acid.Classorg.biojava.nbio.core.sequence.compoundBioJavajavadoc
AminoAcidCompoundSetSet of proteinogenic amino acids.Classorg.biojava.nbio.core.sequence.compoundBioJavajavadoc
AminoAcidImplAminoAcid inherits most from Hetatom.Classorg.biojava.nbio.structureBioJavajavadoc
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.routinesBioJavajavadoc
AngleOrderDetectorPlusGuesses an order of rotational symmetry from the angle.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
AngleOutlierJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
AnnotatableIndicates that an object has an associated annotation.Interfaceorg.biojava.nbio.ontology.utilsBioJavajavadoc
Annotation Arbitrary annotation associated with one or more objects.Interfaceorg.biojava.nbio.ontology.utilsBioJavajavadoc
AppClassorg.biojava.nbio.genomeBioJavajavadoc
AppClassorg.biojava.nbio.ontologyBioJavajavadoc
ArrayListProxySequenceReaderClassorg.biojava.nbio.core.sequence.loaderBioJavajavadoc
ArrayListSequenceReaderClassorg.biojava.nbio.core.sequence.storageBioJavajavadoc
AsaCalculatorClass to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley.Classorg.biojava.nbio.structure.asaBioJavajavadoc
AssertionFailureAn unchecked exception representing an Assertion failure.Classorg.biojava.nbio.ontology.utilsBioJavajavadoc
AssignmentXMLSerializerClassorg.biojava.nbio.structure.domainBioJavajavadoc
AstralProvides programmatic access to ASTRAL representative sets.Classorg.biojava.nbio.structure.scopBioJavajavadoc
AtomA simple interface for an Atom.Interfaceorg.biojava.nbio.structureBioJavajavadoc
AtomCacheA utility class that provides easy access to Structure objects.Classorg.biojava.nbio.structure.align.utilBioJavajavadoc
AtomContactA pair of atoms that are in contactAuthor:duarte_jSee Also:Serialized FormClassorg.biojava.nbio.structure.contactBioJavajavadoc
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.contactBioJavajavadoc
AtomIdentifierClassorg.biojava.nbio.structure.contactBioJavajavadoc
AtomImpl currently the coordinates of an atom are represented by a double[3] array.Classorg.biojava.nbio.structureBioJavajavadoc
AtomInfoThis class uniquely describes an atomAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.gui.jmolBioJavajavadoc

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AtomInfoParserClassorg.biojava.nbio.structure.align.gui.jmolBioJavajavadoc
AtomIteratoran iterator over all atoms of a structure / group.Classorg.biojava.nbio.structureBioJavajavadoc
AtomPositionMapA map from ResidueNumbers to ATOM record positions in a PDB file.Classorg.biojava.nbio.structureBioJavajavadoc
AtomSiteClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
AuditAuthorClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
AugmentedResidueRangeCreated by douglas on 1/23/15.Classorg.biojava.nbio.structureBioJavajavadoc
AuthorDescribes author attributes for author information in a PDB file.Classorg.biojava.nbio.structureBioJavajavadoc
AutoSuggestProviderInterfaceorg.biojava.nbio.structure.align.gui.autosuggestBioJavajavadoc
AxisAlignerClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
BasicSequenceBare bones version of the Sequence object to be used sparingly.Classorg.biojava.nbio.core.sequenceBioJavajavadoc
BerkeleyScopInstallation The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.Classorg.biojava.nbio.structure.scopBioJavajavadoc
BetaBridgeContainer that represents a beta Bridge between two residues.Classorg.biojava.nbio.structure.secstrucBioJavajavadoc
BioAssemblyIdentifierClassorg.biojava.nbio.structureBioJavajavadoc
BioAssemblyInfoRepresentation of a Biological Assembly annotation as provided by the PDB.Classorg.biojava.nbio.structure.quaternaryBioJavajavadoc
BioAssemblyToolsClassorg.biojava.nbio.structure.quaternaryBioJavajavadoc
BioJavaAADemoCreated by andreas on 8/9/14.ClassdemoBioJavajavadoc
BiojavaJmolA class that provides a simple GUI for JmolSince:1.Classorg.biojava.nbio.structure.guiBioJavajavadoc
BioJavaStructureAlignmentWrapper for the BioJava Structure Alignment ImplementationAuthor:Andreas PrlicClassorg.biojava.nbio.structure.alignBioJavajavadoc
BiologicalAssemblyBuilderReconstructs the quaternary structure of a protein from an asymmetric unitAuthor:Peter Rose, Andreas PrlicClassorg.biojava.nbio.structure.quaternaryBioJavajavadoc
BiologicalAssemblyTransformationThe transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file.Classorg.biojava.nbio.structure.quaternaryBioJavajavadoc
BioUnitDataProviderProvides access to the data that is needed in order to rebuild the correct biological assembly of a protein.Interfaceorg.biojava.nbio.structure.quaternary.ioBioJavajavadoc
BioUnitDataProviderFactoryFactory to create BioUnitDataProvider instances.Classorg.biojava.nbio.structure.quaternary.ioBioJavajavadoc
BitSequenceReaderAn implementation of the popular bit encodings.Classorg.biojava.nbio.core.sequence.storageBioJavajavadoc
BlastAlignmentParameterEnumenum BlastAlignmentParameterEnumAlignment request parameters accepted by QBlast service.Classorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
BlastClustReaderClassorg.biojava.nbio.structure.symmetry.utilsBioJavajavadoc

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BlastHitBuilderDesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.io.blastBioJavajavadoc
BlastHomologyHitsClassorg.biojava.nbio.genome.homologyBioJavajavadoc
BlastHspBuilderDesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.io.blastBioJavajavadoc
BlastJobInformation about QBlast search jobAuthor:Gediminas RimsaClassorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
BlastMatrixEnumenum BlastMatrixEnumEnum representing matrices supported by QBlastClassorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
BlastOutputAlignmentFormatEnumenum BlastOutputAlignmentFormatEnumEnum representing available output alignment types.Classorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
BlastOutputFormatEnumenum BlastOutputFormatEnumEnum representing available output formats.Classorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
BlastOutputParameterEnumenum BlastOutputParameterEnumOutput parameters accepted by QBlast service.Classorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
BlastProgramEnumenum BlastProgramEnumEnum representing available blast programs.Classorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
BlastResultThis class models a Blast/Blast plus result.Classorg.biojava.nbio.core.search.io.blastBioJavajavadoc
BlastResultBuilderDesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.io.blastBioJavajavadoc
BlastTabularParserDesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.io.blastBioJavajavadoc
BlastXMLParserRe-designed by Paolo Pavan on the footprint of: org.Classorg.biojava.nbio.core.search.io.blastBioJavajavadoc
BlastXMLQueryClassorg.biojava.nbio.genome.queryBioJavajavadoc
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.multipleBioJavajavadoc
BlockImplGeneral implementation of a Block that supports any type of sequential alignment with gaps.Classorg.biojava.nbio.structure.align.multipleBioJavajavadoc
BlockSetA BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment.Interfaceorg.biojava.nbio.structure.align.multipleBioJavajavadoc
BlockSetImplA general implementation of a BlockSet to store a flexible part of a multiple alignment.Classorg.biojava.nbio.structure.align.multipleBioJavajavadoc
BondA simple bond -- it stores information about two atoms as well as information about its bond order.Interfaceorg.biojava.nbio.structureBioJavajavadoc
BondImplA simple bond -- it stores information about two atoms as well as information about its bond order.Classorg.biojava.nbio.structureBioJavajavadoc
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.ioBioJavajavadoc
BondOutlierJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
BondTypeWork in progress - NOT final!Author:Jules Jacobsen Classorg.biojava.nbio.structureBioJavajavadoc
BoundingBoxA bounding box for short cutting some geometrical calculations.Classorg.biojava.nbio.structure.contactBioJavajavadoc
BravaisLatticeAn enum to represent the 7 Bravais latticesEnum Constant SummaryClassorg.biojava.nbio.structure.xtalBioJavajavadoc

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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.secstrucBioJavajavadoc
BrowserOpenerClassorg.biojava.nbio.structure.align.webstartBioJavajavadoc
BufferedReaderBytesReadNeed to keep track of actual bytes read and take advantage of buffered reader performance.Classorg.biojava.nbio.core.sequence.ioBioJavajavadoc
C2RotationSolverClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
CachedRemoteScopInstallationAn extension of the RemoteScopInstallation that caches some of the data locally.Classorg.biojava.nbio.structure.scopBioJavajavadoc
CacheFactoryprovides a SoftHashMap singleton.Classorg.biojava.nbio.structure.align.utilBioJavajavadoc
CAConverterConverts full atom representations to Calpha only ones.Classorg.biojava.nbio.structure.ioBioJavajavadoc
CalcUtility operations on Atoms, AminoAcids, etc.Classorg.biojava.nbio.structureBioJavajavadoc
CalcBioAssemblySymmetryClassorg.biojava.nbio.structure.symmetry.analysisBioJavajavadoc
CallablePairwiseSequenceAlignerClassorg.biojava.nbio.alignment.templateBioJavajavadoc
CallablePairwiseSequenceScorerClassorg.biojava.nbio.alignment.templateBioJavajavadoc
CallableProfileProfileAlignerClassorg.biojava.nbio.alignment.templateBioJavajavadoc
CallableStructureAlignmentClassorg.biojava.nbio.structure.alignBioJavajavadoc
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.quaternaryBioJavajavadoc
CaseFreeAminoAcidCompoundSetSet of proteinogenic amino acids.Classorg.biojava.nbio.aaproperties.xmlBioJavajavadoc
CaseInsensitiveCompoundAttempts to wrap compounds so it is possible to view them in a case insensitive mannerClassorg.biojava.nbio.core.sequence.transcriptionBioJavajavadoc
CasePreservingProteinSequenceCreatorA sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.Classorg.biojava.nbio.core.sequence.ioBioJavajavadoc
CathCategoryThe categories found within CATH.Classorg.biojava.nbio.structure.cathBioJavajavadoc
CathDatabaseGeneral API for interacting with CATH.Interfaceorg.biojava.nbio.structure.cathBioJavajavadoc
CathDomainA class which represents a single CATH domain.Classorg.biojava.nbio.structure.cathBioJavajavadoc
CathFactoryControls global CathDatabases being used.Classorg.biojava.nbio.structure.cathBioJavajavadoc
CathFragmentClassorg.biojava.nbio.structure.cathBioJavajavadoc
CathInstallationClassorg.biojava.nbio.structure.cathBioJavajavadoc
CathNodeRepresents a node in the CATH hierarchy.Classorg.biojava.nbio.structure.cathBioJavajavadoc
CathSegmentClassorg.biojava.nbio.structure.cathBioJavajavadoc

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CDSComparatorClassorg.biojava.nbio.core.sequenceBioJavajavadoc
CDSSequenceRepresents a exon or coding sequence in a gene.Classorg.biojava.nbio.core.sequenceBioJavajavadoc
CECalculatorThis is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.Classorg.biojava.nbio.structure.align.ceBioJavajavadoc
CeCalculatorEnhancedThis is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.Classorg.biojava.nbio.structure.align.ceBioJavajavadoc
CeCPMainA wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.Classorg.biojava.nbio.structure.align.ceBioJavajavadoc
CECPParametersProvides parameters to CeCPMainAuthor:Spencer BlivenClassorg.biojava.nbio.structure.align.ceBioJavajavadoc
CeCPUserArgumentProcessorClassorg.biojava.nbio.structure.align.ceBioJavajavadoc
CellClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
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.ceBioJavajavadoc
CensorStatusClassorg.biojava.nbio.survival.kaplanmeier.figureBioJavajavadoc
CensorStatusSelectInterfaceorg.biojava.nbio.survival.kaplanmeier.figureBioJavajavadoc
CeParametersContains the parameters that can be sent to CEAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.ceBioJavajavadoc
CeSideChainMainClassorg.biojava.nbio.structure.align.ceBioJavajavadoc
CeSideChainUserArgumentProcessorClassorg.biojava.nbio.structure.align.ceBioJavajavadoc
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.internalBioJavajavadoc
CeSymmIterativeIterative version of CeSymm that aims at identifying all symmetry axis (internal or quaternary) of a particular structure.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
CESymmParametersProvides parameters to CeSymm.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
CeSymmResultThis Class stores all the relevant information of an internal symmetry result obtained with CeSymm.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
CeUserArgumentProcessorprocess the arguments from command lineAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.ceBioJavajavadoc
Chain Defines the interface for a Chain.Interfaceorg.biojava.nbio.structureBioJavajavadoc
ChainClustererClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
ChainImplA Chain in a PDB file.Classorg.biojava.nbio.structureBioJavajavadoc
ChainSignatureClassorg.biojava.nbio.structure.symmetry.miscBioJavajavadoc
ChangeValueInterfaceorg.biojava.nbio.survival.dataBioJavajavadoc
ChargeAdderClassorg.biojava.nbio.structure.ioBioJavajavadoc

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ChemCompA definition for a Chemical Component, as maintained by the wwPDB.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
ChemCompAtomstores these fields: _chem_comp_atom.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
ChemCompBondClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
ChemCompConsumerClassorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
ChemCompDescriptorContainer object for _pdbx_chem_comp_descriptorSince:3.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
ChemCompDistributionClassdemoBioJavajavadoc
ChemCompGroupFactoryClassorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
ChemCompProviderInterface that is implemented by all classes that can provide ChemComp definitions.Interfaceorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
ChemCompToolsSome tools for working with chemical compounds.Classorg.biojava.nbio.structure.io.mmcif.chemBioJavajavadoc
ChemicalComponentDictionaryA representation of the Chemical Component Dictionary.Classorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
ChiSqClassorg.biojava.nbio.survival.cox.statsBioJavajavadoc
Cholesky2Classorg.biojava.nbio.survival.cox.statsBioJavajavadoc
CholeskyDecompositionCholesky Decomposition.Classorg.biojava.nbio.structure.jamaBioJavajavadoc
ChooseDirActionAsk the user to provide a directory containting PDB files.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
ChromosomeSequenceA ChromosomeSequence is a DNASequence but keeps track of geneSequencesAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJavajavadoc
Chsolve2Classorg.biojava.nbio.survival.cox.statsBioJavajavadoc
ClashJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
ClasspathResourceThis object represents a classpath resource on the local system.Classorg.biojava.nbio.core.sequence.io.utilBioJavajavadoc
ClinicalMetaDataOutcomeClassorg.biojava.nbio.survival.kaplanmeier.metadataBioJavajavadoc
CliToolsUtilities for autoconfiguring javabeans based on command line arguments.Classorg.biojava.nbio.structure.align.utilBioJavajavadoc
ClusterAltAligsA class that clusters alternative alignments according to theirSince:1.Classorg.biojava.nbio.structure.alignBioJavajavadoc
ClusterDomainsClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
ClusterMergerMerges clusters based on their sequence identity.Classorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
ClusterProteinChainsClusters the chains of one or two structures by sequence.Classorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
CodonCompoundClassorg.biojava.nbio.core.sequence.compoundBioJavajavadoc

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CollectionToolsUtilities for working with collections.Classorg.biojava.nbio.structure.align.utilBioJavajavadoc
ColorConverterClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
ColorInterpolatorInterfaceorg.biojava.nbio.structure.gui.util.colorBioJavajavadoc
ColorUtilsClassorg.biojava.nbio.structure.gui.util.colorBioJavajavadoc
CombinationGeneratorClassorg.biojava.nbio.structure.symmetry.utilsBioJavajavadoc
CommandPromptClassorg.biojava.nbio.aapropertiesBioJavajavadoc
CompactCharSequencehttp://www.Classorg.biojava.nbio.survival.dataBioJavajavadoc
ComparisonThis class provides static methods for the calculation of the percentage of identity between two aligned sequences.Classorg.biojava.nbio.phyloBioJavajavadoc
ComplementCompoundInterfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc
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.viewsBioJavajavadoc
Componentcontains information about a certain Component.Classorg.biojava.nbio.protmodBioJavajavadoc
ComponentXMLConverterClassorg.biojava.nbio.protmod.ioBioJavajavadoc
CompoundInterfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc
CompoundAn object to contain the info from the PDB header for a Molecule.Classorg.biojava.nbio.structureBioJavajavadoc
CompoundFinderHeuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure.Classorg.biojava.nbio.structure.ioBioJavajavadoc
CompoundNotFoundExceptionClassorg.biojava.nbio.core.exceptionsBioJavajavadoc
CompoundSetInterfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc
CompoundTranslatorInterfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc
ConcurrencyToolsStatic utility to easily share a thread pool for concurrent/parallel/lazy execution.Classorg.biojava.nbio.core.utilBioJavajavadoc
ConfigPDBInstallPanelClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
ConfigStrucAligParamsInterfaceorg.biojava.nbio.structure.align.ceBioJavajavadoc
ConfigurationExceptionClassorg.biojava.nbio.structure.align.utilBioJavajavadoc
ConfigXMLHandlerClassorg.biojava.nbio.structure.align.webstartBioJavajavadoc
ConstraintsThis class is used to support the implementation of properties stated in IPeptideProperties.Classorg.biojava.nbio.aapropertiesBioJavajavadoc
ContinuousColorMapperProvides a mapping between real numbers and Colors.Interfaceorg.biojava.nbio.structure.gui.util.colorBioJavajavadoc

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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.colorBioJavajavadoc
Convert2ChargeClassorg.biojava.nbio.aaproperties.profeat.convertorBioJavajavadoc
Convert2HydrophobicityClassorg.biojava.nbio.aaproperties.profeat.convertorBioJavajavadoc
Convert2NormalizedVanDerWaalsVolumeClassorg.biojava.nbio.aaproperties.profeat.convertorBioJavajavadoc
Convert2PolarityClassorg.biojava.nbio.aaproperties.profeat.convertorBioJavajavadoc
Convert2PolarizabilityClassorg.biojava.nbio.aaproperties.profeat.convertorBioJavajavadoc
Convert2SecondaryStructureClassorg.biojava.nbio.aaproperties.profeat.convertorBioJavajavadoc
Convert2SolventAccessibilityClassorg.biojava.nbio.aaproperties.profeat.convertorBioJavajavadoc
ConvertorClassorg.biojava.nbio.aaproperties.profeat.convertorBioJavajavadoc
CookBookClassdemoBioJavajavadoc
CookbookMSAClassdemoBioJavajavadoc
CoordManagera class that manages the conversion of sequence coordinate system to JPanel drawing coordinatesClassorg.biojava.nbio.structure.gui.utilBioJavajavadoc
CoreSuperimposerSuperimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure.Classorg.biojava.nbio.structure.align.multiple.utilBioJavajavadoc
CountProgressListenerClassorg.biojava.nbio.structure.align.clientBioJavajavadoc
CoxCCClassorg.biojava.nbio.survival.coxBioJavajavadoc
CoxCoefficientClassorg.biojava.nbio.survival.coxBioJavajavadoc
CoxComparatorInterfaceInterfaceorg.biojava.nbio.survival.cox.comparatorsBioJavajavadoc
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.coxBioJavajavadoc
CoxInfoHolds the results of a cox analysis where calling dump(), toString() will give an output similar to RAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJavajavadoc
CoxMartClassorg.biojava.nbio.survival.coxBioJavajavadoc
CoxMethodClassorg.biojava.nbio.survival.coxBioJavajavadoc
CoxRThis is a port of the R survival code used for doing Cox Regression.Classorg.biojava.nbio.survival.coxBioJavajavadoc
CoxScoreClassorg.biojava.nbio.survival.coxBioJavajavadoc
CoxVariablesClassorg.biojava.nbio.survival.coxBioJavajavadoc
CoxVariablesOverallModelFitComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJavajavadoc

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CoxVariablesVariableComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJavajavadoc
CRC64ChecksumUtility class that calculates a CRC64 checksum on a stream of bytes.Classorg.biojava.nbio.core.utilBioJavajavadoc
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.xtalBioJavajavadoc
CrystalCellA crystal cell's parameters.Classorg.biojava.nbio.structure.xtalBioJavajavadoc
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.xtalBioJavajavadoc
CutClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
CutDomainClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
CutSitesClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
CutValuesClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
CytobandClassorg.biojava.nbio.genome.parsers.cytobandBioJavajavadoc
CytobandParserParses the cytoband (karyotype) file from UCSC.Classorg.biojava.nbio.genome.parsers.cytobandBioJavajavadoc
DatabasePDBremarkClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
DatabasePDBrevClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
DatabasePdbrevRecordClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
DatabaseReferenceInterfaceIf a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s)Interfaceorg.biojava.nbio.core.sequence.featuresBioJavajavadoc
DatasetClassorg.biojava.nbio.phosphositeBioJavajavadoc
DataSource GenBank giClassorg.biojava.nbio.core.sequenceBioJavajavadoc
DBRefA class to represent database cross references.Classorg.biojava.nbio.structureBioJavajavadoc
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.featuresBioJavajavadoc
DBResultTableClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
DBSearchGUIClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
DefaultAAIndexProviderThe default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directoryAuthor:Andreas PrlicClassorg.biojava.nbio.core.alignment.matricesBioJavajavadoc
DefaultAutoSuggestProviderClassorg.biojava.nbio.structure.align.gui.autosuggestBioJavajavadoc
DefaultMatrixMapperColor Mapper which mimics the default coloring of JMatrixPanel pixels.Classorg.biojava.nbio.structure.gui.util.colorBioJavajavadoc
DefaultOpsDefault implementation of OntologyOps.Classorg.biojava.nbio.ontologyBioJavajavadoc

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DemoAlignmentFromFastaDemo of how to use the FastaStructureParser class to read protein structures from a FASTA file.ClassdemoBioJavajavadoc
DemoAlignProteinsClassdemoBioJavajavadoc
DemoAsaClassdemoBioJavajavadoc
DemoAtomCacheExample of how to load PDB files using the AtomCache class.ClassdemoBioJavajavadoc
DemoBerkeleyScopA demo for how to use the Berkeley version of SCOP instead of the default UK-SCOPSince:3.ClassdemoBioJavajavadoc
DemoCATHAn example for how to access CATH data.ClassdemoBioJavajavadoc
DemoCEExample of how to run a structure alignment using the CE algorithm.ClassdemoBioJavajavadoc
DemoCeSymmQuick demo of how to call CE-Symm programmatically.ClassdemoBioJavajavadoc
DemoChangeChemCompProviderThis demo shows how to use an alternative ChemCompProvider.ClassdemoBioJavajavadoc
DemoCommandLineStartupClassdemoBioJavajavadoc
DemoContactsClassdemoBioJavajavadoc
DemoCrystalInterfacesClassdemoBioJavajavadoc
DemoDistanceTreeThis demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA).ClassdemoBioJavajavadoc
DemoDomainsplitClassdemoBioJavajavadoc
DemoFATCATClassdemoBioJavajavadoc
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 theClassdemoBioJavajavadoc
DemoLoadStructureExample for how to load protein structures (from PDB files).ClassdemoBioJavajavadoc
DemoLoadSubstMaxClassdemoBioJavajavadoc
DemoMMCIFReaderAn example of how to read MMcif filesAuthor:Andreas PrlicClassdemoBioJavajavadoc
DemoMultipleMCDemo for running the MultipleMC Algorithm on a protein family.ClassdemoBioJavajavadoc
DemoNWALignmentClassdemoBioJavajavadoc
DemoOrientBioAssemblyCreated by ap3 on 02/04/2015.ClassdemoBioJavajavadoc
DemoRotationAxisA demo for how to use RotationAxis to display the rotation for an alignment.ClassdemoBioJavajavadoc
DemoSCOPA class demonstrating the use of the SCOP parsing toolsAuthor:Andreas PrlicClassdemoBioJavajavadoc
DemoSecStrucCalcDemonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations andClassdemoBioJavajavadoc

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DemoShowBiolAssemblyClassdemoBioJavajavadoc
DemoShowCATHDomainClassdemoBioJavajavadoc
DemoShowLargeAssemblyClassdemoBioJavajavadoc
DemoShowValidationResultsClassdemoBioJavajavadoc
DemoSixFrameTranslationCreated by andreas on 8/10/15.ClassdemoBioJavajavadoc
DemoStructureFromFastaDemo of how to use the FastaStructureParser class to read protein structures from a FASTA file.ClassdemoBioJavajavadoc
DemoSW3DAlignerClassdemoBioJavajavadoc
DiscreteQuantizerInterfaceInterfaceorg.biojava.nbio.survival.kaplanmeier.metadataBioJavajavadoc
DisplayAFPA utility class for visualistion of structure alignmentsAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
DistanceBoxClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
DistanceMatrixCalculatorThe DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).Classorg.biojava.nbio.phyloBioJavajavadoc
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.phyloBioJavajavadoc
DNACompoundSetClassorg.biojava.nbio.core.sequence.compoundBioJavajavadoc
DNASequenceThis is class should model the attributes associated with a DNA sequenceAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJavajavadoc
DNASequenceCreatorA helper class that allows different ways to read a string and create a DNA sequence.Classorg.biojava.nbio.core.sequence.ioBioJavajavadoc
DNAToRNATranslatorPerforms the first stage of transcription by going from DNA to RNA.Classorg.biojava.nbio.core.sequence.transcriptionBioJavajavadoc
DomainClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
DomainProviderInterfaceorg.biojava.nbio.structure.domainBioJavajavadoc
DomainProviderFactoryClassorg.biojava.nbio.structure.domainBioJavajavadoc
DotPlotPanelDisplays the dot plot trace for an alignment.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
DownloadChemCompProviderThis provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site.Classorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
DSSPParserClass to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure.Classorg.biojava.nbio.structure.secstrucBioJavajavadoc
EcodDatabaseGeneral API for interacting with CATH.Interfaceorg.biojava.nbio.structure.ecodBioJavajavadoc
EcodDomainClassorg.biojava.nbio.structure.ecodBioJavajavadoc
EcodFactoryControls global CathDatabases being used.Classorg.biojava.nbio.structure.ecodBioJavajavadoc

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EcodInstallationProvides access to the Evolutionary Classification of Protein Domains (ECOD).Classorg.biojava.nbio.structure.ecodBioJavajavadoc
EditInterface for carrying out edit operations on a Sequence.Interfaceorg.biojava.nbio.core.sequence.editsBioJavajavadoc
EigenvalueDecompositionEigenvalues and eigenvectors of a real matrix.Classorg.biojava.nbio.structure.jamaBioJavajavadoc
ElementClassorg.biojava.nbio.aaproperties.xmlBioJavajavadoc
ElementElement is an enumeration of the elements of the periodic table.Classorg.biojava.nbio.structureBioJavajavadoc
ElementTableClassorg.biojava.nbio.aaproperties.xmlBioJavajavadoc
ElementTypeElementType is an enumeration of the types of elements found in the periodic table.Classorg.biojava.nbio.structureBioJavajavadoc
EntityA simple class to represent Entity records in mmCif filesAuthor:Andreas PrlicClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
EntityPolySeqContainer for _entity_poly_seq recordsField Name mmCIF Data ItemClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
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.modelBioJavajavadoc
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.modelBioJavajavadoc
EntitySrcSynPDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
EntryJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
EqualsA set of helper methods which return true if the two parameters are equal to each other.Classorg.biojava.nbio.core.utilBioJavajavadoc
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.sequenceBioJavajavadoc
ExonSequenceA gene contains a collection of Exon sequencesAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJavajavadoc
ExperimentalTechniqueenum ExperimentalTechniqueAn enum to represent the experimental technique of a PDB structureClassorg.biojava.nbio.structureBioJavajavadoc
ExpressionFigureClassorg.biojava.nbio.survival.kaplanmeier.figureBioJavajavadoc
ExptlClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
FarmJobA job as it can be run on the farm.Classorg.biojava.nbio.structure.alignBioJavajavadoc
FarmJobParametersClassorg.biojava.nbio.structure.align.clientBioJavajavadoc
FarmJobRunnableContains the single thread for a job that can run multiple alignments.Classorg.biojava.nbio.structure.align.clientBioJavajavadoc
FastaAFPChainConverterA collection of static utilities to convert between AFPChains and FastaSequences.Classorg.biojava.nbio.structure.ioBioJavajavadoc
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.ioBioJavajavadoc
FastaHeaderFormatInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJavajavadoc

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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.ioBioJavajavadoc
FastaReaderHelperClassorg.biojava.nbio.core.sequence.ioBioJavajavadoc
FastaSequenceA FASTA formatted sequence.Classorg.biojava.nbio.data.sequenceBioJavajavadoc
FastaSequenceParserUsed to parse a stream of a fasta file to get the sequenceAuthor:Scooter Willis Classorg.biojava.nbio.core.sequence.ioBioJavajavadoc
FastaStructureParserReads a protein sequence from a fasta file and attempts to match it to a 3D structure.Classorg.biojava.nbio.structure.ioBioJavajavadoc
FastaWriterThe FastaWriter writes a collection of sequences to an outputStream.Classorg.biojava.nbio.core.sequence.ioBioJavajavadoc
FastaWriterHelperThe class that should be used to write out fasta file of a sequence collectionAuthor:Scooter Willis Classorg.biojava.nbio.core.sequence.ioBioJavajavadoc
FastqFASTQ formatted sequence.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
FastqBuilderFluent builder API for creating FASTQ formatted sequences.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
FastqReaderReader for FASTQ formatted sequences.Interfaceorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
FastqToolsUtility methods for FASTQ formatted sequences.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
FastqVariantFASTQ sequence format variant.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
FastqWriterWriter for FASTQ formatted sequences.Interfaceorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
FatCatClassorg.biojava.nbio.structure.align.fatcatBioJavajavadoc
FatCatAlignerA class that does calculations on an AFPChainAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.fatcat.calcBioJavajavadoc
FatCatFlexibleClassorg.biojava.nbio.structure.align.fatcatBioJavajavadoc
FatCatParametersClassorg.biojava.nbio.structure.align.fatcat.calcBioJavajavadoc
FatCatRigidClassorg.biojava.nbio.structure.align.fatcatBioJavajavadoc
FatCatUserArgumentProcessorClassorg.biojava.nbio.structure.align.fatcatBioJavajavadoc
FCAlignHelperClassorg.biojava.nbio.structure.align.fatcat.calcBioJavajavadoc
FeatureA Feature corresponds to a single row in a GFF file.Classorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
FeatureDbReferenceInfoIt is DBReferenceInfo which implements FeatureInterface.Classorg.biojava.nbio.core.sequence.featuresBioJavajavadoc
FeatureHelperClassorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
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.gffBioJavajavadoc
FeatureInterfaceInterface class to handle describing arbitrary features.Interfaceorg.biojava.nbio.core.sequence.featuresBioJavajavadoc

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FeatureListA list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.Classorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
FeatureRetrieverIf a SequenceProxyReader implements this interface then that external source has a list featuresInterfaceorg.biojava.nbio.core.sequence.featuresBioJavajavadoc
FeaturesKeyWordInterfaceModels the keywords that are annotated for a protein sequence at Uniprot.Interfaceorg.biojava.nbio.core.sequence.featuresBioJavajavadoc
FileConvertMethods to convert a structure object into different file formats.Classorg.biojava.nbio.structure.ioBioJavajavadoc
FileDownloadUtilsClassorg.biojava.nbio.structure.io.utilBioJavajavadoc
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.ioBioJavajavadoc
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.ioBioJavajavadoc
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.ioBioJavajavadoc
FlatFileCacheProvides a cache for storing multiple small files in memory.Classorg.biojava.nbio.core.utilBioJavajavadoc
ForesterWrapperThis class contains wrapper methods for communication between BioJava and forester (e.Classorg.biojava.nbio.phyloBioJavajavadoc
FourBitSequenceReaderFour bit encoding of the bit formats.Classorg.biojava.nbio.core.sequence.storageBioJavajavadoc
FractionalIdentityInProfileScorer Profile.Classorg.biojava.nbio.alignmentBioJavajavadoc
FractionalIdentityScorer alignment columns which have identical Compounds.Classorg.biojava.nbio.alignmentBioJavajavadoc
FractionalSimilarityInProfileScorer Profile.Classorg.biojava.nbio.alignmentBioJavajavadoc
FractionalSimilarityScorer alignment columns which have similar Compounds.Classorg.biojava.nbio.alignmentBioJavajavadoc
FragmentJoinerJoins the initial Fragments together to larger FragmentsSince:1.Classorg.biojava.nbio.structure.align.pairwiseBioJavajavadoc
FragmentPaira pair of fragments of two protein structuresSince:1.Classorg.biojava.nbio.structure.align.pairwiseBioJavajavadoc
FrameIndicates a way of translating a sequence.Classorg.biojava.nbio.core.sequence.transcriptionBioJavajavadoc
FuzzyPointClassorg.biojava.nbio.core.sequence.locationBioJavajavadoc
GapArrayClassorg.biojava.nbio.structure.align.helperBioJavajavadoc
GapPenaltyDefines a data structure for the gap penalties used during a sequence alignment routine.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
GCStatsClassorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
GenbankHeaderFormatInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJavajavadoc
GenbankProxySequenceReaderClassorg.biojava.nbio.core.sequence.loaderBioJavajavadoc
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.ioBioJavajavadoc

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GenbankReaderHelperClassorg.biojava.nbio.core.sequence.ioBioJavajavadoc
GenbankSequenceParserClassorg.biojava.nbio.core.sequence.ioBioJavajavadoc
GenbankWriterClassorg.biojava.nbio.core.sequence.ioBioJavajavadoc
GenbankWriterHelperClassorg.biojava.nbio.core.sequence.ioBioJavajavadoc
GeneChromosomePositionClassorg.biojava.nbio.genome.parsers.genenameBioJavajavadoc
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.genenameBioJavajavadoc
GeneFeatureHelperClassorg.biojava.nbio.genomeBioJavajavadoc
GeneIDGFF2Readerhttp://www.Classorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
GeneIDXMLReaderClassorg.biojava.nbio.genome.parsers.geneidBioJavajavadoc
GeneMarkGTFReaderhttp://www.Classorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
GeneNameA simple bean that contains gene name information as available from www.Classorg.biojava.nbio.genome.parsers.genenameBioJavajavadoc
GeneNamesParserParses a file from the www.Classorg.biojava.nbio.genome.parsers.genenameBioJavajavadoc
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.ioBioJavajavadoc
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.ioBioJavajavadoc
GenericGenbankHeaderFormatClassorg.biojava.nbio.core.sequence.ioBioJavajavadoc
GenericGenbankHeaderParserClassorg.biojava.nbio.core.sequence.ioBioJavajavadoc
GenericInsdcHeaderFormatClassorg.biojava.nbio.core.sequence.ioBioJavajavadoc
GeneSequenceClassorg.biojava.nbio.core.sequenceBioJavajavadoc
GetDistanceMatrixClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
GetRepresentativesTODO Move this to Representatives.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
GFF3FromUniprotBlastHitsClassorg.biojava.nbio.genome.homologyBioJavajavadoc
GFF3Readerhttp://www.Classorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
GFF3WriterClassorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
GOParserSimple parser for the Gene Ontology (GO) flatfile format.Classorg.biojava.nbio.ontology.ioBioJavajavadoc
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.pairwiseBioJavajavadoc

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GradientMapperMaps a set of real values onto a gradient.Classorg.biojava.nbio.structure.gui.util.colorBioJavajavadoc
GradientPanelClassorg.biojava.nbio.structure.gui.util.colorBioJavajavadoc
GraphComponentOrderDetectorThe GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
GraphComponentRefinerThe GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
GridA grid to be used for calculating atom contacts through geometric hashing algorithm.Classorg.biojava.nbio.structure.contactBioJavajavadoc
GridCellA grid cell to be used in contact calculation via geometric hashing algorithm.Classorg.biojava.nbio.structure.contactBioJavajavadoc
GroupThis is the data structure for a single Group of atoms.Interfaceorg.biojava.nbio.structureBioJavajavadoc
GroupAsaA class to store the results of ASA calculations, it can hold ASA values per atom present in GroupClassorg.biojava.nbio.structure.asaBioJavajavadoc
GroupContactA pair of residues that are in contactAuthor:duarte_jSee Also:Serialized FormClassorg.biojava.nbio.structure.contactBioJavajavadoc
GroupContactSetA set of residue-residue contacts.Classorg.biojava.nbio.structure.contactBioJavajavadoc
GroupIteratorAn iterator over all groups of a structure.Classorg.biojava.nbio.structureBioJavajavadoc
GroupResultsClassorg.biojava.nbio.survival.kaplanmeier.figureBioJavajavadoc
GroupToSDFClassorg.biojava.nbio.structure.ioBioJavajavadoc
GroupTypeThis contains basic categories for Group types.Classorg.biojava.nbio.structureBioJavajavadoc
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.routinesBioJavajavadoc
GUIAlignmentProgressListenera GUI that allows to watch progress as multiple alignments are being processed.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
GuideTree GuideTree.Classorg.biojava.nbio.alignmentBioJavajavadoc
GuideTreeNodeDefines a data structure for the node in a guide tree used during progressive multiple sequence alignment.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
GUIFarmJobRunnableClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
GuiWrapperA class to wrap some of the strucutre.Classorg.biojava.nbio.structure.align.ceBioJavajavadoc
HashcoderContains helper methods for generating a HashCode without having to resort to the commons lang hashcode builders.Classorg.biojava.nbio.core.utilBioJavajavadoc
HasResultXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJavajavadoc
HBondContainer that represents a hidrogen bond.Classorg.biojava.nbio.structure.secstrucBioJavajavadoc
HeaderInfoClassorg.biojava.nbio.survival.dataBioJavajavadoc
HelicalRepeatUnitClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc

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HelixClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
HelixAxisAlignerClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
HelixExtenderClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
HelixLayersClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
HelixSolverClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
HelpDialogClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
HetatomImplGeneric Implementation of a Group interface.Classorg.biojava.nbio.structureBioJavajavadoc
HierarchicalClustererDefines a clustering algorithm that converts a distance matrix into a tree.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
HitThis class models a search Hit.Classorg.biojava.nbio.core.search.ioBioJavajavadoc
HmmerDemoThe cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 serviceSince:3.ClassdemoBioJavajavadoc
HmmerDomainProvides the details of a domain hitSince:3.Classorg.biojava.nbio.ws.hmmerBioJavajavadoc
HmmerResultThe results of a Hmmer search for a single sequenceSince:3.Classorg.biojava.nbio.ws.hmmerBioJavajavadoc
HmmerScanInterface for performing Hmmscans on sequences.Interfaceorg.biojava.nbio.ws.hmmerBioJavajavadoc
HspThis class models a search Hsp.Classorg.biojava.nbio.core.search.ioBioJavajavadoc
HSVColorSpaceClassorg.biojava.nbio.structure.gui.util.colorBioJavajavadoc
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.utilBioJavajavadoc
IcosahedralSamplerClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
IcosahedronClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
IdentifierA collection of utilities to create StructureIdentifiers.Classorg.biojava.nbio.structureBioJavajavadoc
IdxComparatorClassorg.biojava.nbio.structure.align.helperBioJavajavadoc
IlluminaFastqReaderReader for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
IlluminaFastqWriterWriter for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
IndexPairClassorg.biojava.nbio.structure.align.helperBioJavajavadoc
InputStreamProviderA class that provides an InputStream from a File.Classorg.biojava.nbio.core.utilBioJavajavadoc
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.locationBioJavajavadoc

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InsdcParserParser for working with INSDC style locations.Classorg.biojava.nbio.core.sequence.locationBioJavajavadoc
IntegerOntologyClassorg.biojava.nbio.ontologyBioJavajavadoc
IntronSequenceClassorg.biojava.nbio.core.sequenceBioJavajavadoc
InvalidTermExceptionThrown to indicate that an ontology term is not acceptable or appropriate in a given contextClassorg.biojava.nbio.ontologyBioJavajavadoc
IOUtilsClassorg.biojava.nbio.core.sequence.io.utilBioJavajavadoc
IPeptidePropertiesAn interface to generate some basic physico-chemical properties of protein sequences.Interfaceorg.biojava.nbio.aapropertiesBioJavajavadoc
IProfeatPropertiesInterfaceorg.biojava.nbio.aaproperties.profeatBioJavajavadoc
IsotopeClassorg.biojava.nbio.aaproperties.xmlBioJavajavadoc
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.ioBioJavajavadoc
JAutoSuggestA JTextField that can make suggestions for auto-complete.Classorg.biojava.nbio.structure.align.gui.autosuggestBioJavajavadoc
JFatCatClientClassorg.biojava.nbio.structure.align.clientBioJavajavadoc
JMatrixPanela JPanel that can display a difference of distance matrix and paths that have been taken for the alignmentClassorg.biojava.nbio.structure.guiBioJavajavadoc
JmolAlignedPositionListenerClassorg.biojava.nbio.structure.gui.eventsBioJavajavadoc
JmolPanelClassorg.biojava.nbio.structure.align.gui.jmolBioJavajavadoc
JmolSymmetryScriptGeneratorClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
JmolSymmetryScriptGeneratorC1Classorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
JmolSymmetryScriptGeneratorCnClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
JmolSymmetryScriptGeneratorDnClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
JmolSymmetryScriptGeneratorHClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
JmolSymmetryScriptGeneratorIClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
JmolSymmetryScriptGeneratorOClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
JmolSymmetryScriptGeneratorPointGroupClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
JmolSymmetryScriptGeneratorTClassorg.biojava.nbio.structure.symmetry.jmolScriptBioJavajavadoc
JmolToolsClassorg.biojava.nbio.structure.align.gui.jmolBioJavajavadoc
JmolViewerImplClassorg.biojava.nbio.structure.guiBioJavajavadoc

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JNLPProxyClassorg.biojava.nbio.structure.align.webstartBioJavajavadoc
JobKillExceptionClassorg.biojava.nbio.structure.align.clientBioJavajavadoc
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.storageBioJavajavadoc
JointFragmentsA utility class that defines which set of atoms are considered to be on equivalent positions.Classorg.biojava.nbio.structure.align.helperBioJavajavadoc
JournalArticleClassorg.biojava.nbio.structureBioJavajavadoc
JPrintPanelClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
JronnThis class gives public API to RONN functions.Classorg.biojava.nbio.ronnBioJavajavadoc
KaplanMeierFigureClassorg.biojava.nbio.survival.kaplanmeier.figureBioJavajavadoc
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.utilsBioJavajavadoc
KMFigureInfoClassorg.biojava.nbio.survival.kaplanmeier.figureBioJavajavadoc
LadderA Ladder is a set of one or more consecutive bridges of identical type.Classorg.biojava.nbio.structure.secstrucBioJavajavadoc
LightweightProfileDefines a minimal data structure for reading and writing a sequence alignment.Interfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc
LinearColorInterpolatorClassorg.biojava.nbio.structure.gui.util.colorBioJavajavadoc
ListStringWrapperClassorg.biojava.nbio.structure.scop.serverBioJavajavadoc
LocalPDBDirectorySuperclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and MMCIFFileReader.Classorg.biojava.nbio.structure.ioBioJavajavadoc
LocalProteinDomainParserProtein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.Classorg.biojava.nbio.structure.domainBioJavajavadoc
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.scopBioJavajavadoc
LocationSets of integers used to represent the location of features on sequence.Interfaceorg.biojava.nbio.core.sequence.location.templateBioJavajavadoc
LocationA location on a sequence.Classorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
LocationHelperHelper methods for use with the Location classes.Classorg.biojava.nbio.core.sequence.locationBioJavajavadoc
LocIteratorMove a sliding window over a Location.Classorg.biojava.nbio.genome.parsers.gffBioJavajavadoc
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.colorBioJavajavadoc
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.jamaBioJavajavadoc
MapToStringTransformerTransforms Map to String.Classorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
MathsClassorg.biojava.nbio.structure.jamaBioJavajavadoc

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MatrixJama = Java Matrix class.Classorg.biojava.nbio.structure.jamaBioJavajavadoc
Matrix*********************************************************************** Compilation: javac Matrix.Classorg.biojava.nbio.survival.cox.matrixBioJavajavadoc
MatrixAlignerDefines an Aligner which builds a score matrix during computation.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
MatrixListenerInterfaceorg.biojava.nbio.structure.align.ceBioJavajavadoc
MeanModelComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJavajavadoc
MeanQuantizerClassorg.biojava.nbio.survival.kaplanmeier.metadataBioJavajavadoc
MemoryMonitorTracks Memory allocated & used, displayed in graph form.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
MenuCreatorCreate the menus for structure alignment GUI windows (JFrames).Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
MenuCreatorCreate the menu for BiojavaJmolSince:1.Classorg.biojava.nbio.structure.gui.utilBioJavajavadoc
MessagesClassorg.biojava.nbio.core.exceptionsBioJavajavadoc
MetaDataInfoClassorg.biojava.nbio.survival.kaplanmeier.metadataBioJavajavadoc
MmCifBiolAssemblyProviderClassorg.biojava.nbio.structure.quaternary.ioBioJavajavadoc
MMcifConsumerAn interface for the events triggered by a MMcifParser.Interfaceorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
MMCIFFileReaderHow to parse an mmCif file:public static void main(String[] args) throws Exception {Classorg.biojava.nbio.structure.ioBioJavajavadoc
MMCIFFileToolsSome tools for mmCIF file writing.Classorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
MMcifParserInterface that needs to be implemented by an MMcifParserSince:1.Interfaceorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
MmCifPDBBiolAssemblyProviderA provider for information about biological units for PDB files that is based on reading local MMcif files.Classorg.biojava.nbio.structure.quaternary.ioBioJavajavadoc
ModelledSubgroupJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
ModelLoaderClass that loads data from the model files into ModelLoader.Classorg.biojava.nbio.ronnBioJavajavadoc
ModificationCategoryenum ModificationCategorydefine modification categories.Classorg.biojava.nbio.protmodBioJavajavadoc
ModificationConditionConditions of a protein modification, e.Interfaceorg.biojava.nbio.protmodBioJavajavadoc
ModificationConditionImplClassorg.biojava.nbio.protmodBioJavajavadoc
ModificationLinkageClassorg.biojava.nbio.protmodBioJavajavadoc
ModificationOccurrenceTypeenum ModificationOccurrenceTypeSince:3.Classorg.biojava.nbio.protmodBioJavajavadoc
ModifiedAminoAcidCompoundSetClassorg.biojava.nbio.aaproperties.xmlBioJavajavadoc

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ModifiedCompoundRoot interface for all modifications in structure.Interfaceorg.biojava.nbio.protmod.structureBioJavajavadoc
ModifiedCompoundImplClassorg.biojava.nbio.protmod.structureBioJavajavadoc
ModifiedCompoundXMLConverterClassorg.biojava.nbio.protmod.ioBioJavajavadoc
MogAngleOutlierJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
MogBondOutlierJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
MomentsOfInertiaClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
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.multipleBioJavajavadoc
MultipleAlignmentCalcA class that obtains structures via DAS and aligns them.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
MultipleAlignmentCoordManagerGeneralization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.Classorg.biojava.nbio.structure.align.gui.aligpanelBioJavajavadoc
MultipleAlignmentDisplayUtility functions to generalize the visualization of MultipleAlignments in molecular viewers.Classorg.biojava.nbio.structure.align.multiple.utilBioJavajavadoc
MultipleAlignmentEnsembleA MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm,Interfaceorg.biojava.nbio.structure.align.multipleBioJavajavadoc
MultipleAlignmentEnsembleImplA general implementation of a MultipleAlignmentEnsemble.Classorg.biojava.nbio.structure.align.multipleBioJavajavadoc
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.guiBioJavajavadoc
MultipleAlignmentImplA general implementation of a MultipleAlignment.Classorg.biojava.nbio.structure.align.multipleBioJavajavadoc
MultipleAlignmentJmolA class that provides a 3D visualization Frame in Jmol for MultipleAlignments.Classorg.biojava.nbio.structure.align.gui.jmolBioJavajavadoc
MultipleAlignmentJmolDisplayUtility Class that provides helper methods for the visualization of MultipleAlignments.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
MultipleAlignmentScorerUtility class for calculating common scores of MultipleAlignments.Classorg.biojava.nbio.structure.align.multiple.utilBioJavajavadoc
MultipleAlignmentToolsUtility functions for working with MultipleAlignment.Classorg.biojava.nbio.structure.align.multiple.utilBioJavajavadoc
MultipleAlignmentWriterThis class contains functions for the conversion of MultipleAlignment to various String outputs.Classorg.biojava.nbio.structure.align.multiple.utilBioJavajavadoc
MultipleAlignmentXMLConverterHelper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format.Classorg.biojava.nbio.structure.align.xmlBioJavajavadoc
MultipleAlignmentXMLParserParse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered.Classorg.biojava.nbio.structure.align.xmlBioJavajavadoc
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.aligpanelBioJavajavadoc
MultipleAligPanelMouseMotionListenerMouse Motion Listener for the MultipleAligPanel, which provides methods to obtain positions of the mouseClassorg.biojava.nbio.structure.align.gui.aligpanelBioJavajavadoc
MultipleMcMainMain class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm,Classorg.biojava.nbio.structure.align.multiple.mcBioJavajavadoc
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.mcBioJavajavadoc

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MultipleMcParametersContains the parameters to be sent to the MC optimization.Classorg.biojava.nbio.structure.align.multiple.mcBioJavajavadoc
MultipleSequenceAlignment structure in the alignment module provides additional functionality.Classorg.biojava.nbio.core.sequenceBioJavajavadoc
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.aligpanelBioJavajavadoc
MultipleStructureAlignerInterface for the Multiple Structure Alignment Algorithms.Interfaceorg.biojava.nbio.structure.alignBioJavajavadoc
MultipleSuperimposerInterface for Multiple Alignment superposition algorithms.Interfaceorg.biojava.nbio.structure.align.multiple.utilBioJavajavadoc
MultiThreadedDBSearchPerforms a multi threaded database search for an input protein structureAuthor:Andreas PrlicClassorg.biojava.nbio.structure.alignBioJavajavadoc
MutableAlignedSequenceDefines a mutable (editable) data structure for an AlignedSequence.Interfaceorg.biojava.nbio.core.alignment.templateBioJavajavadoc
MutableProfileDefines a mutable (editable) data structure for a Profile.Interfaceorg.biojava.nbio.core.alignment.templateBioJavajavadoc
MutableProfilePairDefines a mutable (editable) data structure for a ProfilePair.Interfaceorg.biojava.nbio.core.alignment.templateBioJavajavadoc
MutableSequencePairDefines a mutable (editable) data structure for the results of pairwise sequence alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJavajavadoc
MutatorA class that can change one amino acid to another.Classorg.biojava.nbio.structureBioJavajavadoc
MyAlignmentLoadListenerLoads an alignment in an XML format and displays its content in a new Jmol panel.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
MyDistMaxListenerShows the interatomic Distance Matrices of all the Structures aligned in different Frames.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
MyExportListenerClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
MyJmolStatusListenerClassorg.biojava.nbio.structure.align.gui.jmolBioJavajavadoc
MyOpenPdbFileListenerClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
MySaveFileListenerSave an alignment to a specified File by the user.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
MyTableRowSorterClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
MyValidationEventHandlerClassorg.biojava.nbio.aaproperties.xmlBioJavajavadoc
Name2CountClassorg.biojava.nbio.aaproperties.xmlBioJavajavadoc
NCBIQBlastAlignmentPropertiesThis class wraps a QBlast search request parameter Map by adding several convenient parameter addition methods.Classorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
NCBIQBlastOutputPropertiesThis class wraps a QBlast output parameter Map by adding several convenient parameter addition methods.Classorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
NCBIQBlastServiceProvides a simple way of submitting BLAST request to the QBlast service at NCBI.Classorg.biojava.nbio.ws.alignment.qblastBioJavajavadoc
NCBIQBlastServiceDemoA simple demo showing NCBIQBlastService usageAuthor:Gediminas RimsaClassdemoBioJavajavadoc
NeedlemanWunschNeedleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).Classorg.biojava.nbio.alignmentBioJavajavadoc

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NucleotideCompoundClassorg.biojava.nbio.core.sequence.compoundBioJavajavadoc
NucleotideImplA nucleotide group is almost the same as a Hetatm group.Classorg.biojava.nbio.structureBioJavajavadoc
NullOutputStreamThe stream that void its inputSince:3.Classorg.biojava.nbio.ronnBioJavajavadoc
NumbersAtRiskPanelClassorg.biojava.nbio.survival.kaplanmeier.figureBioJavajavadoc
ObjectFactoryThis object contains factory methods for each Java content interface and Java element interfaceClassorg.biojava.nbio.structure.validationBioJavajavadoc
OboFileEventListeneran interface for events that occur during parsing of .Interfaceorg.biojava.nbio.ontology.oboBioJavajavadoc
OboFileHandlerA file handler for .Classorg.biojava.nbio.ontology.oboBioJavajavadoc
OboFileParserA class to parse the content of an OBO file.Classorg.biojava.nbio.ontology.oboBioJavajavadoc
OboParser OboParser parser = new OboParser(); InputStream inStream = this.Classorg.biojava.nbio.ontology.ioBioJavajavadoc
OctahedronClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
Ontology This is just a set of Term objects, and a set of Triple objects describing relationships between these terms.Interfaceorg.biojava.nbio.ontologyBioJavajavadoc
OntologyExceptionThrown to indicate an error in an Ontology objectSince:1.Classorg.biojava.nbio.ontologyBioJavajavadoc
OntologyFactoryA factory for Ontology instances.Interfaceorg.biojava.nbio.ontologyBioJavajavadoc
OntologyOpsThis is an interface for optimizing ontology operators.Interfaceorg.biojava.nbio.ontologyBioJavajavadoc
OntologyTermA term in an ontology which identifies another ontology.Interfaceorg.biojava.nbio.ontologyBioJavajavadoc
OntoToolsTools for manipulating ontologies.Classorg.biojava.nbio.ontologyBioJavajavadoc
OperatorResolverClassorg.biojava.nbio.structure.quaternaryBioJavajavadoc
OptimalCECPMainA wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations.Classorg.biojava.nbio.structure.align.ceBioJavajavadoc
OptimalCECPParametersContains the parameters that can be sent to CEAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.ceBioJavajavadoc
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.internalBioJavajavadoc
OrderedPairAn ordered pair represents a component of a cartesian product.Classorg.biojava.nbio.structure.quaternaryBioJavajavadoc
ORonnFully re-factored and enhanced version of RONN.Classorg.biojava.nbio.ronnBioJavajavadoc
ORonnModelFully re-factored version of RONN model.Classorg.biojava.nbio.ronnBioJavajavadoc
OutputHitsGFFClassorg.biojava.nbio.genome.queryBioJavajavadoc
PairA Pair of objects.Classorg.biojava.nbio.structure.contactBioJavajavadoc

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PairInProfileScorerDefines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
PairwiseAlignmentClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
PairwiseSequenceAlignerDefines an Aligner for a pair of Sequences.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
PairwiseSequenceScorerDefines an algorithm which computes a score for a pair of sequences.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
ParameterGUIUI for ConfigStrucAligParams, for the AlignmentGUI.Classorg.biojava.nbio.structure.align.guiBioJavajavadoc
ParseFastaFileDemoCreated by andreas on 6/17/15.ClassdemoBioJavajavadoc
ParseGOClassdemoBioJavajavadoc
ParseListenerLow-level event based parser callback.Interfaceorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
ParserExceptionGeneral abstraction of different parsing errorsAuthor:Scooter Willis See Also:Serialized FormClassorg.biojava.nbio.core.exceptionsBioJavajavadoc
PartitionRefinerDefines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
PassthroughIdentifierA stub StructureIdentifier, representing the full structure in all cases.Classorg.biojava.nbio.structureBioJavajavadoc
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.ioBioJavajavadoc
PDBBioUnitDataProviderA BioUnitDataProvider that extracts the necessary info from PDB filesAuthor:Andreas PrlicClassorg.biojava.nbio.structure.quaternary.ioBioJavajavadoc
PDBCrystallographicInfoA class to hold crystallographic information about a PDB structure.Classorg.biojava.nbio.structureBioJavajavadoc
PDBDirPanelA class to define where a structure for the alignment is coming fromSince:1.Classorg.biojava.nbio.structure.gui.utilBioJavajavadoc
PDBDomainProviderClass to fetch domains through the RCSB's REST API.Classorg.biojava.nbio.structure.domainBioJavajavadoc
PDBFileParserThis class implements the actual PDB file parsing.Classorg.biojava.nbio.structure.ioBioJavajavadoc
PDBFileReader The wrapper class for parsing a PDB file.Classorg.biojava.nbio.structure.ioBioJavajavadoc
PDBHeaderA class that contains PDB Header information.Classorg.biojava.nbio.structureBioJavajavadoc
PdbIdListsUtility classes for retrieving lists of PDB IDs.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
PdbPairA pair for structure alignmentAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.clientBioJavajavadoc
PdbPairsMessageClassorg.biojava.nbio.structure.align.xmlBioJavajavadoc
PdbPairXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJavajavadoc
PDBParseExceptionAn exception during the parsing of a PDB file.Classorg.biojava.nbio.structure.ioBioJavajavadoc
PDBRecordAn interface implemented by all classes that represent PDB recordsSince:1.Interfaceorg.biojava.nbio.structureBioJavajavadoc

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PDBServerPanelA class to define where a structure for the alignment is coming fromSince:1.Classorg.biojava.nbio.structure.gui.utilBioJavajavadoc
PDBStatusMethods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure.Classorg.biojava.nbio.structureBioJavajavadoc
PDBTemporaryStorageUtilsInternal use only.Classorg.biojava.nbio.structure.io.utilBioJavajavadoc
PDBUploadPanelA JPanel to upload 2 custom PDB files.Classorg.biojava.nbio.structure.gui.utilBioJavajavadoc
PdbxChemCompDescriptorClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxChemCompIdentifier_pdbx_chem_comp_identifier.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxEntityNonPolyA bean for the Pdbx_entity_nonpoly category.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxNonPolySchemeA bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxPolySeqSchemeA bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxStructAssemblyClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxStructAssemblyGenClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxStructAssemblyGenXMLContainerClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxStructAssemblyXMLContainerClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxStructOperListClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PdbxStructOperListXMLContainerClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
PDPDistanceMatrixClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
PDPDomainClassorg.biojava.nbio.structure.domainBioJavajavadoc
PDPParametersClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
PDPProviderDecomposes a structure into representative PDP domains.Interfaceorg.biojava.nbio.structure.domainBioJavajavadoc
PeptidePropertiesThis is an adaptor class which enable the ease of generating protein properties.Classorg.biojava.nbio.aapropertiesBioJavajavadoc
PeptidePropertiesImplThis class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.Classorg.biojava.nbio.aapropertiesBioJavajavadoc
PermutationGeneratorClassorg.biojava.nbio.structure.symmetry.utilsBioJavajavadoc
PermutationGroupClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
PersistentConfiga class to store the config using the Java Web StartAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.webstartBioJavajavadoc
PlainFastaHeaderParserThe plain fasta header takes everything in the header as a single entity.Classorg.biojava.nbio.core.sequence.ioBioJavajavadoc

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PointInterfaceorg.biojava.nbio.core.sequence.location.templateBioJavajavadoc
PolyhedronInterfaceorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
PolymerTypeEnumerates the classification of polymers.Classorg.biojava.nbio.structure.io.mmcif.chemBioJavajavadoc
PositionInQueueXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJavajavadoc
PredictDisorderClassdemoBioJavajavadoc
PrettyXMLWriterClassorg.biojava.nbio.core.utilBioJavajavadoc
PrismClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
ProfeatPropertiesThis is an adaptor class which enable the ease of generating profeat properties.Classorg.biojava.nbio.aaproperties.profeatBioJavajavadoc
ProfeatPropertiesImplClassorg.biojava.nbio.aaproperties.profeatBioJavajavadoc
ProfileDefines a data structure for the results of sequence alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJavajavadoc
ProfilePairDefines a data structure for the results of the alignment of a pair of Profiles.Interfaceorg.biojava.nbio.core.alignment.templateBioJavajavadoc
ProfileProfileAlignerDefines an Aligner for a pair of Profiles.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
ProfileProfileScorerDefines an algorithm which computes a score for a pairing of alignment profiles.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
ProfileViewDefines a data structure for a view of sequence alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJavajavadoc
ProgramJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
ProgramsJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
ProteinChainExtractorExtracts information about all the chains in a structure, including chain Ids, sequences, and atoms.Classorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
ProteinComplexSignatureClassorg.biojava.nbio.structure.symmetry.miscBioJavajavadoc
ProteinModificationThis interface defines information about a specific proteinSince:3.Interfaceorg.biojava.nbio.protmodBioJavajavadoc
ProteinModificationIdentifierIdentify attachment modification in a 3-D structure.Classorg.biojava.nbio.protmod.structureBioJavajavadoc
ProteinModificationImplThis class contains information about a specific proteinSince:3.Classorg.biojava.nbio.protmodBioJavajavadoc
ProteinModificationRegistryThis class serves as a instance registry by maintaining a pool of ProteinModification instances.Classorg.biojava.nbio.protmodBioJavajavadoc
ProteinModificationXmlReaderClassorg.biojava.nbio.protmod.ioBioJavajavadoc
ProteinSequenceThe representation of a ProteinSequenceAuthor:Scooter Willis, Paolo PavanClassorg.biojava.nbio.core.sequenceBioJavajavadoc
ProteinSequenceClustererRepresents a set of non-identical protein sequences.Classorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc

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ProteinSequenceCreatorUsed to create a ProteinSequence from a String to allow for details about the location of the sequence etc.Classorg.biojava.nbio.core.sequence.ioBioJavajavadoc
ProxySequenceReaderInterfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc
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.jamaBioJavajavadoc
QualifierClassorg.biojava.nbio.core.sequence.featuresBioJavajavadoc
QualityFeatureDNA Sequences produced by modern sequencers usually have quality informaion attached to them.Classorg.biojava.nbio.core.sequence.featuresBioJavajavadoc
QuantityFeatureIt is common to have a numerical value or values associated with a feature.Classorg.biojava.nbio.core.sequence.featuresBioJavajavadoc
QuatSuperpositionScorerClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
QuatSymmetryDetectorDetects global and local quaternary protein structure symmetry in a structure.Classorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
QuatSymmetryParametersClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
QuatSymmetryResultsHolds the results of quaternary symmetry perception.Classorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
QuatSymmetryScoresClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
QuatSymmetrySolverInterfaceorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
RasmolCommandListenera utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.gui.jmolBioJavajavadoc
RasmolCommandListenera utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas PrlicClassorg.biojava.nbio.structure.guiBioJavajavadoc
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.ioBioJavajavadoc
RCSBDescriptionCorresponds to the wrapper element in an RCSB describeMol XML file.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
RCSBDescriptionFactoryFetches information from RCSB's RESTful Web Service Interface.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
RCSBLigandCorresponds to a ligand in a ligandInfo XML file.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
RCSBLigandsCorresponds to the wrapper element "ligandInfo" in an RCSB ligandInfo XML file.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
RCSBLigandsFactoryFetches information from RCSB's RESTful Web Service Interface.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
RCSBMacromoleculeCorresponds to a macromolecule in an RCSB describeMol XML file.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
RCSBPolymerCorresponds to a polymer in a describeMol XML file.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
RCSBTaxonomyCorresponds to a taxonomy in a describeMol XML file.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc
RCSBUpdatesClassorg.biojava.nbio.structure.rcsbBioJavajavadoc
ReadUtilsPackage-level static utilities for parsing XML.Classorg.biojava.nbio.structure.rcsbBioJavajavadoc

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RectangularPrismClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
ReducedChemCompProviderUnlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions.Classorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
ReferenceSuperimposerSuperimposes each structure in a MultipleAlignment onto a reference Performs a global superposition of the MultipleAlignment in caseClassorg.biojava.nbio.structure.align.multiple.utilBioJavajavadoc
RefineClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
RefinerFailedExceptionRefinement of the self-alignment failed.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
RemoteBioUnitDataProviderClassorg.biojava.nbio.structure.quaternary.ioBioJavajavadoc
RemoteDomainProviderA DomainProvider that uses a mixture of SCOP and PDP domains.Classorg.biojava.nbio.structure.domainBioJavajavadoc
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.hmmerBioJavajavadoc
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.alignmentBioJavajavadoc
RemotePairwiseAlignmentPropertiesRemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties.Interfaceorg.biojava.nbio.ws.alignmentBioJavajavadoc
RemotePairwiseAlignmentServiceThis interface specifies minimal information needed to execute a pairwise alignment on a remote service.Interfaceorg.biojava.nbio.ws.alignmentBioJavajavadoc
RemotePDPProviderA class that provided PDP assignments that are loaded from a remote web serverAuthor:Andreas PrlicClassorg.biojava.nbio.structure.domainBioJavajavadoc
RemoteRawBioUnitDataProviderA BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDBAuthor:Andreas PrlicClassorg.biojava.nbio.structure.quaternary.ioBioJavajavadoc
RemoteScopInstallationA class that fetches information about SCOP from a remote data-source.Classorg.biojava.nbio.structure.scopBioJavajavadoc
RemoteTermA term in another ontology.Interfaceorg.biojava.nbio.ontologyBioJavajavadoc
RenderStyleClassorg.biojava.nbio.structure.guiBioJavajavadoc
RepresentativeXMLConverterClassorg.biojava.nbio.structure.align.xmlBioJavajavadoc
RescoreRefinerInterfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
ResidualsCoxphClassorg.biojava.nbio.survival.coxBioJavajavadoc
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.internalBioJavajavadoc
ResidueNumberEverything that is needed to uniquely describe a residue positionAuthor:Andreas PrlicSee Also:Serialized FormClassorg.biojava.nbio.structureBioJavajavadoc
ResidueRangeA chain, a start residue, and an end residue.Classorg.biojava.nbio.structureBioJavajavadoc
ResidueRangeAndLengthA chain, a start residue, and an end residue.Classorg.biojava.nbio.structureBioJavajavadoc
ResidueTypeEnumerates the possible classifications of residues.Classorg.biojava.nbio.structure.io.mmcif.chemBioJavajavadoc
ResourceManagerA class that manages the Strings that are defined in the spice.Classorg.biojava.nbio.structure.align.utilBioJavajavadoc

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ResultThis class models a search result.Classorg.biojava.nbio.core.search.ioBioJavajavadoc
ResultFactoryDesigned by Paolo Pavan.Interfaceorg.biojava.nbio.core.search.ioBioJavajavadoc
ReversedSequenceViewFor a given sequence this class will return the base at the reversed position i.Classorg.biojava.nbio.core.sequence.viewsBioJavajavadoc
RiskInfoClassorg.biojava.nbio.survival.coxBioJavajavadoc
RNACompoundSetClassorg.biojava.nbio.core.sequence.compoundBioJavajavadoc
RNASequenceRNASequence where RNACompoundSet are the allowed valuesAuthor:Scooter Willis Classorg.biojava.nbio.core.sequenceBioJavajavadoc
RNASequenceCreatorUsed to create a RNA sequenceAuthor:Scooter Willis Classorg.biojava.nbio.core.sequence.ioBioJavajavadoc
RnaSequenceViewClassorg.biojava.nbio.core.sequence.viewsBioJavajavadoc
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.transcriptionBioJavajavadoc
RonnConstraintA collection of various constrain values used by RONNSince:3.Classorg.biojava.nbio.ronnBioJavajavadoc
RotationClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
RotationAxisCalculates the rotation axis for an alignment A superposition of two structures is generally represented as a rotationClassorg.biojava.nbio.structure.align.utilBioJavajavadoc
RotationAxisAlignerClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
RotationGroupClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
RotationSolverClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
SandboxStyleStructureProviderThe "Sandbox" style of organizing files is to have a directory structure like below, i.Classorg.biojava.nbio.structure.ioBioJavajavadoc
SangerFastqReaderReader for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
SangerFastqWriterWriter for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
ScaleableMatrixPanelA JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm.Classorg.biojava.nbio.structure.guiBioJavajavadoc
ScaledSubstitutionMatrixThe biojava-alignment module represents substitution matrices with short values.Classorg.biojava.nbio.core.alignment.matricesBioJavajavadoc
ScanSymmetryClassorg.biojava.nbio.structure.symmetry.analysisBioJavajavadoc
SchemaGeneratorClassorg.biojava.nbio.aaproperties.xmlBioJavajavadoc
SCOPAutoSuggestProviderClassorg.biojava.nbio.structure.align.gui.autosuggestBioJavajavadoc
ScopCategoryThe various categories provided by SCOP.Classorg.biojava.nbio.structure.scopBioJavajavadoc
ScopDatabaseGeneral API how to interact with SCOPSince:3.Interfaceorg.biojava.nbio.structure.scopBioJavajavadoc

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ScopDescription dir.Classorg.biojava.nbio.structure.scopBioJavajavadoc
ScopDescriptionsClassorg.biojava.nbio.structure.scop.serverBioJavajavadoc
ScopDomainContainer for the information for a domain.Classorg.biojava.nbio.structure.scopBioJavajavadoc
ScopDomainsClassorg.biojava.nbio.structure.scop.serverBioJavajavadoc
ScopFactoryControls the global ScopDatabase being used.Classorg.biojava.nbio.structure.scopBioJavajavadoc
ScopInstallationThis class provides access to the SCOP protein structure classification.Classorg.biojava.nbio.structure.scopBioJavajavadoc
ScopInstallationInstanceClassorg.biojava.nbio.structure.gui.utilBioJavajavadoc
ScopIOExceptionIndicates that an I/O error occurred with SCOP lazy initialization.Classorg.biojava.nbio.structure.scopBioJavajavadoc
ScopMirrorHelper class to store paths to the four SCOP files The string "%s" is replaced with the version number.Classorg.biojava.nbio.structure.scopBioJavajavadoc
ScopNodeClassorg.biojava.nbio.structure.scopBioJavajavadoc
ScopNodesClassorg.biojava.nbio.structure.scop.serverBioJavajavadoc
ScopSelectPanelClassorg.biojava.nbio.structure.gui.utilBioJavajavadoc
ScorerDefines an algorithm which computes a score.Interfaceorg.biojava.nbio.alignment.templateBioJavajavadoc
ScoresCacheInterface for classes which implement a temporary cache for various numeric scores, e.Interfaceorg.biojava.nbio.structure.align.multipleBioJavajavadoc
SearchIODesigned by Paolo Pavan.Classorg.biojava.nbio.core.search.ioBioJavajavadoc
SecStrucCalcCalculate and assign the secondary structure (SS) to the Groups of a Structure object.Classorg.biojava.nbio.structure.secstrucBioJavajavadoc
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.secstrucBioJavajavadoc
SecStrucInfoContainer for the secondary structure information of a single residue.Classorg.biojava.nbio.structure.secstrucBioJavajavadoc
SecStrucStateThis class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm.Classorg.biojava.nbio.structure.secstrucBioJavajavadoc
SecStrucToolsThis class contains methods for obtaining and converting secondary structure information from BioJava Structures.Classorg.biojava.nbio.structure.secstrucBioJavajavadoc
SecStrucTypeThis enum contains all of the secondary structure types found in the DSSP output.Classorg.biojava.nbio.structure.secstrucBioJavajavadoc
SegmentClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
SegmentComparatorClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
SelectionInterfaceorg.biojava.nbio.structure.guiBioJavajavadoc
SelectionImplClassorg.biojava.nbio.structure.guiBioJavajavadoc

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SelectMultiplePanelA Text Panel that allows the user to specify multiple structure identifiers, space separated.Classorg.biojava.nbio.structure.gui.utilBioJavajavadoc
SelectPDBPanelA Panel that allows user to specify PDB & chain ID, as well as sub-rangesAuthor:AndreasSee Also:Serialized FormClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
SeqMisMatchCreated by andreas on 9/11/15.Interfaceorg.biojava.nbio.structureBioJavajavadoc
SeqMisMatchImplCreated by andreas on 9/11/15.Classorg.biojava.nbio.structureBioJavajavadoc
SeqRes2AtomAlignerAligns the SEQRES residues to the ATOM residues.Classorg.biojava.nbio.structure.ioBioJavajavadoc
SequenceMain interface for defining a collection of Compounds and accessing them using biological indexesInterfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc
SequenceAlignmentClusterClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
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.storageBioJavajavadoc
SequenceComparatorUsed to sort sequencesAuthor:Scooter Willis Classorg.biojava.nbio.core.sequenceBioJavajavadoc
SequenceCreatorInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJavajavadoc
SequenceDisplayA sequence display that can show the results of a protein structure alignment.Classorg.biojava.nbio.structure.guiBioJavajavadoc
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.loaderBioJavajavadoc
SequenceFunctionOrderDetectorCalls Spencer's method for determining order.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
SequenceFunctionRefinerCreates a refined alignment with the CE-Symm alternative self-alignment.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
SequenceHeaderParserInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJavajavadoc
SequenceLocationA location in a sequence that keeps a reference to its parent sequenceAuthor:Scooter Willis , Paolo PavanSee Also:Serialized FormClassorg.biojava.nbio.core.sequence.locationBioJavajavadoc
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.templateBioJavajavadoc
SequenceMouseListenera mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriateClassorg.biojava.nbio.structure.gui.utilBioJavajavadoc
SequenceOptimizationHintsA static class that provides optimization hints for memory or performance handling of sequence data.Classorg.biojava.nbio.core.sequenceBioJavajavadoc
SequencePairDefines a data structure for the results of pairwise sequence alignment.Interfaceorg.biojava.nbio.core.alignment.templateBioJavajavadoc
SequenceParserInterfaceInterfaceorg.biojava.nbio.core.sequence.io.templateBioJavajavadoc
SequenceProxyViewClassorg.biojava.nbio.core.sequence.templateBioJavajavadoc
SequenceReaderInterfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc
SequenceScalePanelA class that draws a Sequence as a rectangle, a scale display over it.Classorg.biojava.nbio.structure.gui.utilBioJavajavadoc
SequenceToolsClassorg.biojava.nbio.core.utilBioJavajavadoc

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SequenceUtilUtility class for operations on sequencesSince:3.Classorg.biojava.nbio.data.sequenceBioJavajavadoc
SequenceViewInterfaceorg.biojava.nbio.core.sequence.templateBioJavajavadoc
SerializableCacheA class that provides all that is necessary to create a Serializable CacheSince:3.Classorg.biojava.nbio.structure.domainBioJavajavadoc
ShortSegmentRemoverClassorg.biojava.nbio.structure.domain.pdpBioJavajavadoc
ShowPDBIDListenerClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
ShowStructureInJmolDemo how to load and display a structure in JmolAuthor:Andreas PrlicClassdemoBioJavajavadoc
SiftsChainEntryAn entry in the chain-level SIFTS mapping between UniProt and the PDB.Classorg.biojava.nbio.structure.io.siftsBioJavajavadoc
SiftsChainToUniprotMappingA mapping between UniProt entries and PDB chains.Classorg.biojava.nbio.structure.io.siftsBioJavajavadoc
SiftsEntityClassorg.biojava.nbio.structure.io.siftsBioJavajavadoc
SiftsMappingProviderClassorg.biojava.nbio.structure.io.siftsBioJavajavadoc
SiftsResidueClassorg.biojava.nbio.structure.io.siftsBioJavajavadoc
SiftsSegmentClassorg.biojava.nbio.structure.io.siftsBioJavajavadoc
SiftsXMLParserClassorg.biojava.nbio.structure.io.siftsBioJavajavadoc
SigEvaClassorg.biojava.nbio.structure.align.fatcat.calcBioJavajavadoc
SimpleAlignedSequenceClassorg.biojava.nbio.core.alignmentBioJavajavadoc
SimpleGapPenaltyClassorg.biojava.nbio.alignmentBioJavajavadoc
SimpleLocationVery basic implementation of the Location interface which defines a series of simple constructors.Classorg.biojava.nbio.core.sequence.locationBioJavajavadoc
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.mmcifBioJavajavadoc
SimpleMMcifParserA simple mmCif file parserString file = "path/to/mmcif/file";Classorg.biojava.nbio.structure.io.mmcifBioJavajavadoc
SimplePointBasic implementation of the Point interface.Classorg.biojava.nbio.core.sequence.locationBioJavajavadoc
SimpleProfileClassorg.biojava.nbio.core.alignmentBioJavajavadoc
SimpleProfilePairClassorg.biojava.nbio.core.alignmentBioJavajavadoc
SimpleProfileProfileAligner NeedlemanWunsch pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score.Classorg.biojava.nbio.alignmentBioJavajavadoc
SimpleSequencePairClassorg.biojava.nbio.core.alignmentBioJavajavadoc
SimpleSubstitutionMatrix Compound in a sequence for another.Classorg.biojava.nbio.core.alignment.matricesBioJavajavadoc

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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.storageBioJavajavadoc
SingleLinkageClustererAn implementation of a single linkage clusterer See http://en.Classorg.biojava.nbio.core.utilBioJavajavadoc
SingularValueDecompositionSingular Value Decomposition.Classorg.biojava.nbio.structure.jamaBioJavajavadoc
SiteCreated by ap3 on 31/10/2014.Classorg.biojava.nbio.phosphositeBioJavajavadoc
SiteHolds the data of sites presented in PDB files.Classorg.biojava.nbio.structureBioJavajavadoc
SmallAnnotationAnnotation that is optimized for memory usage.Classorg.biojava.nbio.ontology.utilsBioJavajavadoc
SmallMapLightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.Classorg.biojava.nbio.ontology.utilsBioJavajavadoc
SmithWatermanSmith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).Classorg.biojava.nbio.alignmentBioJavajavadoc
SmithWaterman3Dalignerprovides a 3D superimposition based on the sequence alignmentAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.seqBioJavajavadoc
SmithWaterman3DParametersClassorg.biojava.nbio.structure.align.seqBioJavajavadoc
SmithWatermanUserArgumentProcessorClassorg.biojava.nbio.structure.align.seqBioJavajavadoc
SoftHashMapA in memory cache using soft references.Classorg.biojava.nbio.core.utilBioJavajavadoc
SolexaFastqReaderReader for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
SolexaFastqWriterWriter for FastqVariant.Classorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
SpaceGroupA crystallographic space group.Classorg.biojava.nbio.structure.xtalBioJavajavadoc
SpaceGroupMapElementsClassorg.biojava.nbio.structure.xtal.ioBioJavajavadoc
SpaceGroupMapRootClassorg.biojava.nbio.structure.xtal.ioBioJavajavadoc
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.mathBioJavajavadoc
SparseVectorA sparse vector, implemented using a symbol table.Classorg.biojava.nbio.structure.mathBioJavajavadoc
SphereSamplerClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
SplitFastaUtility to write each Fasta entry to a unique fileAuthor:Scooter Willis Classorg.biojava.nbio.genome.utilBioJavajavadoc
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.colorBioJavajavadoc
SSBondImplA simple bean to store disulfide bridge information, the SSBOND records in the PDB files.Classorg.biojava.nbio.structure.ioBioJavajavadoc
StainTypeClassorg.biojava.nbio.genome.parsers.cytobandBioJavajavadoc
StandardAminoAcidA class that provides a set of standard amino acids.Classorg.biojava.nbio.structureBioJavajavadoc

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StandardRescoreRefinerClassorg.biojava.nbio.alignmentBioJavajavadoc
StartCodonSequenceUsed to map the start codon feature on a geneAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJavajavadoc
StartupParametersa simple bean that contains the parameters that can get set at startupAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.ceBioJavajavadoc
StaticMemberPlaceHolderClassorg.biojava.nbio.ontology.utilsBioJavajavadoc
StatusDisplayClassorg.biojava.nbio.structure.align.gui.aligpanelBioJavajavadoc
StdArrayIOStandard array IO.Classorg.biojava.nbio.survival.cox.matrixBioJavajavadoc
StockholmFileAnnotationStores all the content parsed from the #=GF linesSince:3.Classorg.biojava.nbio.alignment.ioBioJavajavadoc
StockholmFileParserStockholm file parser.Classorg.biojava.nbio.alignment.ioBioJavajavadoc
StockholmStructureStores all the content of a Stockholm file.Classorg.biojava.nbio.alignment.ioBioJavajavadoc
StopCodonSequenceUsed to map the stop codon sequence on a geneAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJavajavadoc
StrandProvides a way of representing the strand of a sequence, locationEnum Constant SummaryClassorg.biojava.nbio.core.sequenceBioJavajavadoc
StrataInfoInformation needed to represent a survival curveAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJavajavadoc
StrCompAlignmentClassorg.biojava.nbio.structure.align.pairwiseBioJavajavadoc
StreamListenerEvent based parser callback.Interfaceorg.biojava.nbio.sequencing.io.fastqBioJavajavadoc
StringManipulationHelperA utility class for common String manipulation tasks.Classorg.biojava.nbio.core.utilBioJavajavadoc
StringProxySequenceReaderAn example of a ProxySequenceReader that is created from a String.Classorg.biojava.nbio.core.sequence.loaderBioJavajavadoc
StrucAligParametersA class that contains all the parameters of the structure alignment algorithm.Classorg.biojava.nbio.structure.alignBioJavajavadoc
Structa bean to contain the data of the _struct linesAuthor:Andreas PrlicClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
StructAsymContains the data for _struct_asymSince:1.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
StructConnClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
StructKeywordsClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
StructNcsOperClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
StructRefA class to containt the _struct_ref field dataAuthor:Andreas PrlicClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
StructRefSeqClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
StructRefSeqDifClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc

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StructSiteCreated by Matt on 11/1/2015.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
StructSiteGenCreated by Matt on 10/31/2015.Classorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
StructureInterface for a structure object.Interfaceorg.biojava.nbio.structureBioJavajavadoc
StructureAlignmentInterfaceorg.biojava.nbio.structure.alignBioJavajavadoc
StructureAlignmentDisplayClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
StructureAlignmentFactoryClassorg.biojava.nbio.structure.alignBioJavajavadoc
StructureAlignmentJmolA class that provides a simple GUI for JmolSince:1.Classorg.biojava.nbio.structure.align.gui.jmolBioJavajavadoc
StructureAlignmentOptimizerClassorg.biojava.nbio.structure.align.fatcat.calcBioJavajavadoc
StructureAtomEverything that is needed to uniquely describe a atom.Classorg.biojava.nbio.protmod.structureBioJavajavadoc
StructureAtomLinkageClassorg.biojava.nbio.protmod.structureBioJavajavadoc
StructureAtomXMLConverterClassorg.biojava.nbio.protmod.ioBioJavajavadoc
StructureExceptionAn exception during the parsing of a PDB file.Classorg.biojava.nbio.structureBioJavajavadoc
StructureGroupInformation of a group (residue or ligand) involved in a modification.Classorg.biojava.nbio.protmod.structureBioJavajavadoc
StructureGroupXMLConverterClassorg.biojava.nbio.protmod.ioBioJavajavadoc
StructureIdentifierAn identifier that uniquely identifies a whole Structure or arbitrary substructure.Interfaceorg.biojava.nbio.structureBioJavajavadoc
StructureImpl provides the data contained in a PDB file.Classorg.biojava.nbio.structureBioJavajavadoc
StructureInterfaceAn interface between 2 molecules (2 sets of atoms).Classorg.biojava.nbio.structure.contactBioJavajavadoc
StructureInterfaceClusterClassorg.biojava.nbio.structure.contactBioJavajavadoc
StructureInterfaceListA list of interfaces between 2 molecules (2 sets of atoms)Author:duarte_jSee Also:Serialized FormClassorg.biojava.nbio.structure.contactBioJavajavadoc
StructureIOA class that provides static access methods for easy lookup of protein structure related componentsSince:3.Classorg.biojava.nbio.structureBioJavajavadoc
StructureIOFileStructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.Interfaceorg.biojava.nbio.structure.ioBioJavajavadoc
StructureLoaderThreadClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
StructureNameA utility class that makes working with names of structures, domains and ranges easier.Classorg.biojava.nbio.structure.align.clientBioJavajavadoc
StructurePairAlignerPerform a pairwise protein structure superimposition.Classorg.biojava.nbio.structure.alignBioJavajavadoc
StructurePairSelectorTo be implemented by JPanels that are part of the GUI to trigger structure aligmnents.Interfaceorg.biojava.nbio.structure.gui.utilBioJavajavadoc

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StructureProviderA class that can provide a protein structure object from somewhere.Interfaceorg.biojava.nbio.structure.ioBioJavajavadoc
StructureSequenceMatcherA utility class with methods for matching ProteinSequences withAuthor:Spencer BlivenClassorg.biojava.nbio.structure.ioBioJavajavadoc
StructureToolsA class that provides some tool methods.Classorg.biojava.nbio.structureBioJavajavadoc
StructureUtilClassorg.biojava.nbio.protmod.structureBioJavajavadoc
StructureViewerInterfaceorg.biojava.nbio.structure.guiBioJavajavadoc
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.templateBioJavajavadoc
SubstitutionMatrixHelperStatic utility to access substitution matrices that come bundled with BioJava.Classorg.biojava.nbio.core.alignment.matricesBioJavajavadoc
SubstitutionMatrixScorerScores using a substitution matrix.Classorg.biojava.nbio.alignmentBioJavajavadoc
SubstructureIdentifierThis is the canonical way to identify a part of a structure.Classorg.biojava.nbio.structureBioJavajavadoc
SubunitGraphClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
SubunitsA bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment.Classorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
SuperPositionClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
SuperPositionQCPClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
SurvFitInfoContains info for graphing km figuresAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJavajavadoc
SurvFitKMPorted from survfitKM.Classorg.biojava.nbio.survival.kaplanmeier.figureBioJavajavadoc
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.coxBioJavajavadoc
SurvivalInfoComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJavajavadoc
SurvivalInfoHelperUsed to work with SurvivalInfoAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJavajavadoc
SurvivalInfoIndexNot used and probably should be deletedAuthor:Scooter Willis Classorg.biojava.nbio.survival.coxBioJavajavadoc
SurvivalInfoValueComparatorClassorg.biojava.nbio.survival.cox.comparatorsBioJavajavadoc
SVDSuperimposerA class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class.Classorg.biojava.nbio.structureBioJavajavadoc
SymbolTableSorted symbol table implementation using a java.Classorg.biojava.nbio.structure.mathBioJavajavadoc
SymmClashJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
SymmetryClassorg.biojava.nbio.structure.io.mmcif.modelBioJavajavadoc
SymmetryAxesData Structure that stores all the symmetry axis that describe the symmetry of a structure.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc

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SymmetryCalcCalculates a symmetry analysis and displays the results.Classorg.biojava.nbio.structure.symmetry.guiBioJavajavadoc
SymmetryDisplayClass that provides visualizations methods for symmetry alignments.Classorg.biojava.nbio.structure.symmetry.guiBioJavajavadoc
SymmetryGuiA JFrame that allows to trigger a symmetry analysis, either from files in a directory or after manual uploadClassorg.biojava.nbio.structure.symmetry.guiBioJavajavadoc
SymmetryListenerAction Listener for the symmetry menu.Classorg.biojava.nbio.structure.symmetry.guiBioJavajavadoc
SymmetryRefinerInterface for all symmetry refinement implementations.Interfaceorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
SymmetryToolsUtility methods for the internal symmetry identification and manipulation.Classorg.biojava.nbio.structure.symmetry.utilsBioJavajavadoc
SymmOptimizerOptimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment.Classorg.biojava.nbio.structure.symmetry.internalBioJavajavadoc
SymoplibParserA class containing static methods to parse the symop.Classorg.biojava.nbio.structure.xtalBioJavajavadoc
SynchronizedOutFileClassorg.biojava.nbio.structure.align.utilBioJavajavadoc
SynonymClassorg.biojava.nbio.ontologyBioJavajavadoc
SystematicSolverClassorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
SystemInfoClassorg.biojava.nbio.structure.align.guiBioJavajavadoc
TabDelimParserParse tab-delimited ontology files into Ontology objects.Classorg.biojava.nbio.ontology.ioBioJavajavadoc
TableProvides a way of separating us from the specific IUPACParser.Interfaceorg.biojava.nbio.core.sequence.transcriptionBioJavajavadoc
TaxonomyIDA sequence can be associated with a species or Taxonomy IDAuthor:Scooter WillisClassorg.biojava.nbio.core.sequenceBioJavajavadoc
TermA term in an ontology.Interfaceorg.biojava.nbio.ontologyBioJavajavadoc
TestDNANeedlemanWunschClassdemoBioJavajavadoc
TetrahedronClassorg.biojava.nbio.structure.symmetry.geometryBioJavajavadoc
TextFeatureA implmentation of AbstractFeatureAuthor:Scooter Willis Classorg.biojava.nbio.core.sequence.featuresBioJavajavadoc
TimerA simple timer, calculates the time interval between two events.Classorg.biojava.nbio.ronnBioJavajavadoc
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.transcriptionBioJavajavadoc
TranscriptSequenceThis is the sequence if you want to go from a gene sequence to a protein sequence.Classorg.biojava.nbio.core.sequenceBioJavajavadoc
TransfAlgebraicAdapterClassorg.biojava.nbio.structure.xtal.ioBioJavajavadoc
TransformTypeClassorg.biojava.nbio.structure.xtalBioJavajavadoc
TranslationExceptionThrown from AbstractCompundTranslatorAuthor:Andy YatesSee Also:Serialized FormClassorg.biojava.nbio.core.exceptionsBioJavajavadoc

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TreeConstructorThe TreeConstructor uses the forester library to build different types of phylogenetic trees.Classorg.biojava.nbio.phyloBioJavajavadoc
TreeConstructorTypeenum TreeConstructorTypeThe TreeConstructorType specifies the aligorithm used to construct the treeClassorg.biojava.nbio.phyloBioJavajavadoc
TreeMapSpaceGroupWrapperClassorg.biojava.nbio.structure.xtal.ioBioJavajavadoc
TreeSetStringWrapperClassorg.biojava.nbio.structure.scop.serverBioJavajavadoc
TreeTypeThe TreeType specifies the optimization criteria used to generate the tree.Classorg.biojava.nbio.phyloBioJavajavadoc
TripleA triple in an ontology.Interfaceorg.biojava.nbio.ontologyBioJavajavadoc
TwoBitParserdownloaded from http://storage.Classorg.biojava.nbio.genome.parsers.twobitBioJavajavadoc
TwoBitSequenceReader 0 - T1 - C2 - A3 - G We also do not support case sensitive encodings therefore if you pass aClassorg.biojava.nbio.core.sequence.storageBioJavajavadoc
UncompressInputStreamThis class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).Classorg.biojava.nbio.core.utilBioJavajavadoc
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.loaderBioJavajavadoc
UniprotToFastaClassorg.biojava.nbio.genome.uniprotBioJavajavadoc
UniqueSequenceListBean for a single sequence.Classorg.biojava.nbio.structure.symmetry.coreBioJavajavadoc
UnitCellBoundingBoxClassorg.biojava.nbio.structure.xtalBioJavajavadoc
URLIdentifierRepresents a structure loaded from a URL (including a file URL) A few custom query parameters are supported:Classorg.biojava.nbio.structureBioJavajavadoc
UserArgumentProcessorInterfaceorg.biojava.nbio.structure.align.ceBioJavajavadoc
UserConfigurationA container to persist config to the file systemAuthor:Andreas PrlicClassorg.biojava.nbio.structure.align.utilBioJavajavadoc
UtilsThis is a utility class that contains utility methods which will facilitates the coding of other methodsSince:3.Classorg.biojava.nbio.aapropertiesBioJavajavadoc
VariableInterfaceorg.biojava.nbio.ontologyBioJavajavadoc
WaldTestClassorg.biojava.nbio.survival.coxBioJavajavadoc
WaldTestInfoClassorg.biojava.nbio.survival.coxBioJavajavadoc
WeakValueHashMapMap implementation which keeps weak references to values.Classorg.biojava.nbio.ontology.utilsBioJavajavadoc
WebStartClientDemoClassdemoBioJavajavadoc
WebStartDBSearchA Web Start wrapper for a FarmJobRunnable.Classorg.biojava.nbio.structure.align.webstartBioJavajavadoc
WebStartDBSearchResultsClassorg.biojava.nbio.structure.align.webstartBioJavajavadoc
WebStartMainClassorg.biojava.nbio.structure.align.webstartBioJavajavadoc

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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.viewsBioJavajavadoc
WorkSheetNeed to handle very large spreadsheets of expression data so keep memoryAuthor:Scooter Willis Classorg.biojava.nbio.survival.dataBioJavajavadoc
WwPDBValidationInformationJava class for anonymous complex type.Classorg.biojava.nbio.structure.validationBioJavajavadoc
XMLHelperClassorg.biojava.nbio.core.utilBioJavajavadoc
XMLUtilUtility classes for the XML serialization and de-serialization of SCOP.Classorg.biojava.nbio.structure.scop.serverBioJavajavadoc
XMLWriterSimple interface for building XML documents.Interfaceorg.biojava.nbio.core.utilBioJavajavadoc
ZipChemCompProviderThis chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction.Classorg.biojava.nbio.structure.io.mmcifBioJavajavadoc

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