Hierarchy For All Packages

Package Hierarchies:

• demo,
• org.biojava.nbio.aaproperties,
• org.biojava.nbio.aaproperties.profeat,
• org.biojava.nbio.aaproperties.profeat.convertor,
• org.biojava.nbio.aaproperties.xml,
• org.biojava.nbio.alignment,
• org.biojava.nbio.alignment.io,
• org.biojava.nbio.alignment.routines,
• org.biojava.nbio.alignment.template,
• org.biojava.nbio.core.alignment,
• org.biojava.nbio.core.alignment.matrices,
• org.biojava.nbio.core.alignment.template,
• org.biojava.nbio.core.exceptions,
• org.biojava.nbio.core.search.io,
• org.biojava.nbio.core.search.io.blast,
• org.biojava.nbio.core.sequence,
• org.biojava.nbio.core.sequence.compound,
• org.biojava.nbio.core.sequence.edits,
• org.biojava.nbio.core.sequence.features,
• org.biojava.nbio.core.sequence.io,
• org.biojava.nbio.core.sequence.io.template,
• org.biojava.nbio.core.sequence.io.util,
• org.biojava.nbio.core.sequence.loader,
• org.biojava.nbio.core.sequence.location,
• org.biojava.nbio.core.sequence.location.template,
• org.biojava.nbio.core.sequence.storage,
• org.biojava.nbio.core.sequence.template,
• org.biojava.nbio.core.sequence.transcription,
• org.biojava.nbio.core.sequence.views,
• org.biojava.nbio.core.util,
• org.biojava.nbio.data.sequence,
• org.biojava.nbio.genome,
• org.biojava.nbio.genome.homology,
• org.biojava.nbio.genome.parsers.cytoband,
• org.biojava.nbio.genome.parsers.geneid,
• org.biojava.nbio.genome.parsers.genename,
• org.biojava.nbio.genome.parsers.gff,
• org.biojava.nbio.genome.parsers.twobit,
• org.biojava.nbio.genome.query,
• org.biojava.nbio.genome.uniprot,
• org.biojava.nbio.genome.util,
• org.biojava.nbio.ontology,
• org.biojava.nbio.ontology.io,
• org.biojava.nbio.ontology.obo,
• org.biojava.nbio.ontology.utils,
• org.biojava.nbio.phosphosite,
• org.biojava.nbio.phylo,
• org.biojava.nbio.protmod,
• org.biojava.nbio.protmod.io,
• org.biojava.nbio.protmod.structure,
• org.biojava.nbio.ronn,
• org.biojava.nbio.sequencing.io.fastq,
• org.biojava.nbio.structure,
• org.biojava.nbio.structure.align,
• org.biojava.nbio.structure.align.ce,
• org.biojava.nbio.structure.align.client,
• org.biojava.nbio.structure.align.events,
• org.biojava.nbio.structure.align.fatcat,
• org.biojava.nbio.structure.align.fatcat.calc,
• org.biojava.nbio.structure.align.gui,
• org.biojava.nbio.structure.align.gui.aligpanel,
• org.biojava.nbio.structure.align.gui.autosuggest,
• org.biojava.nbio.structure.align.gui.jmol,
• org.biojava.nbio.structure.align.helper,
• org.biojava.nbio.structure.align.model,
• org.biojava.nbio.structure.align.multiple,
• org.biojava.nbio.structure.align.multiple.mc,
• org.biojava.nbio.structure.align.multiple.util,
• org.biojava.nbio.structure.align.pairwise,
• org.biojava.nbio.structure.align.seq,
• org.biojava.nbio.structure.align.util,
• org.biojava.nbio.structure.align.webstart,
• org.biojava.nbio.structure.align.xml,
• org.biojava.nbio.structure.asa,
• org.biojava.nbio.structure.cath,
• org.biojava.nbio.structure.contact,
• org.biojava.nbio.structure.domain,
• org.biojava.nbio.structure.domain.pdp,
• org.biojava.nbio.structure.ecod,
• org.biojava.nbio.structure.gui,
• org.biojava.nbio.structure.gui.events,
• org.biojava.nbio.structure.gui.util,
• org.biojava.nbio.structure.gui.util.color,
• org.biojava.nbio.structure.io,
• org.biojava.nbio.structure.io.mmcif,
• org.biojava.nbio.structure.io.mmcif.chem,
• org.biojava.nbio.structure.io.mmcif.model,
• org.biojava.nbio.structure.io.sifts,
• org.biojava.nbio.structure.io.util,
• org.biojava.nbio.structure.jama,
• org.biojava.nbio.structure.math,
• org.biojava.nbio.structure.quaternary,
• org.biojava.nbio.structure.quaternary.io,
• org.biojava.nbio.structure.rcsb,
• org.biojava.nbio.structure.scop,
• org.biojava.nbio.structure.scop.server,
• org.biojava.nbio.structure.secstruc,
• org.biojava.nbio.structure.symmetry.analysis,
• org.biojava.nbio.structure.symmetry.core,
• org.biojava.nbio.structure.symmetry.geometry,
• org.biojava.nbio.structure.symmetry.gui,
• org.biojava.nbio.structure.symmetry.internal,
• org.biojava.nbio.structure.symmetry.jmolScript,
• org.biojava.nbio.structure.symmetry.misc,
• org.biojava.nbio.structure.symmetry.utils,
• org.biojava.nbio.structure.validation,
• org.biojava.nbio.structure.xtal,
• org.biojava.nbio.structure.xtal.io,
• org.biojava.nbio.survival.cox,
• org.biojava.nbio.survival.cox.comparators,
• org.biojava.nbio.survival.cox.matrix,
• org.biojava.nbio.survival.cox.stats,
• org.biojava.nbio.survival.data,
• org.biojava.nbio.survival.kaplanmeier.figure,
• org.biojava.nbio.survival.kaplanmeier.metadata,
• org.biojava.nbio.ws.alignment,
• org.biojava.nbio.ws.alignment.qblast,
• org.biojava.nbio.ws.hmmer

Class Hierarchy

• java.lang.Object
  • org.biojava.nbio.core.alignment.matrices.AAindexFactory
  • org.biojava.nbio.core.alignment.matrices.AAIndexFileParser
  • org.biojava.nbio.structure.align.gui.AboutDialog
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • org.biojava.nbio.structure.align.gui.ChooseDirAction
  • org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol (implements java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener)
    • org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
    • org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
  • org.biojava.nbio.ontology.utils.AbstractAnnotation (implements org.biojava.nbio.ontology.utils.Annotation, java.io.Serializable)
    • org.biojava.nbio.ontology.utils.SmallAnnotation
  • org.biojava.nbio.structure.io.mmcif.model.AbstractBean
    • org.biojava.nbio.structure.io.mmcif.model.AtomSite
    • org.biojava.nbio.structure.io.mmcif.model.Cell
    • org.biojava.nbio.structure.io.mmcif.model.DatabasePDBremark
    • org.biojava.nbio.structure.io.mmcif.model.EntityPolySeq
    • org.biojava.nbio.structure.io.mmcif.model.Exptl
    • org.biojava.nbio.structure.io.mmcif.model.PdbxPolySeqScheme
    • org.biojava.nbio.structure.io.mmcif.model.StructAsym
    • org.biojava.nbio.structure.io.mmcif.model.StructConn
    • org.biojava.nbio.structure.io.mmcif.model.StructNcsOper
    • org.biojava.nbio.structure.io.mmcif.model.StructRef
    • org.biojava.nbio.structure.io.mmcif.model.StructRefSeq
    • org.biojava.nbio.structure.io.mmcif.model.StructSiteGen
    • org.biojava.nbio.structure.io.mmcif.model.Symmetry
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • org.biojava.nbio.genome.parsers.gff.FeatureList
  • org.biojava.nbio.core.sequence.template.AbstractCompound (implements org.biojava.nbio.core.sequence.template.Compound)
    • org.biojava.nbio.core.sequence.compound.AminoAcidCompound (implements java.io.Serializable)
    • org.biojava.nbio.core.sequence.compound.CodonCompound
    • org.biojava.nbio.core.sequence.compound.NucleotideCompound (implements org.biojava.nbio.core.sequence.template.ComplementCompound)
  • org.biojava.nbio.core.sequence.template.AbstractCompoundSet<C> (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>)
    • org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet<C>
      • org.biojava.nbio.core.sequence.compound.DNACompoundSet
        • org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet
        • org.biojava.nbio.core.sequence.compound.AmbiguityDNARNAHybridCompoundSet
      • org.biojava.nbio.core.sequence.compound.RNACompoundSet
        • org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet
  • org.biojava.nbio.core.sequence.template.AbstractCompoundTranslator<F,T> (implements org.biojava.nbio.core.sequence.template.CompoundTranslator<F,T>)
    • org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator
    • org.biojava.nbio.core.sequence.transcription.RNAToAminoAcidTranslator
  • org.biojava.nbio.core.sequence.features.AbstractFeature<S,C> (implements org.biojava.nbio.core.sequence.features.FeatureInterface<S,C>)
    • org.biojava.nbio.core.sequence.features.QualityFeature<S,C>
    • org.biojava.nbio.core.sequence.features.QuantityFeature<S,C>
    • org.biojava.nbio.core.sequence.features.TextFeature<S,C>
  • org.biojava.nbio.core.sequence.location.template.AbstractLocation (implements org.biojava.nbio.core.sequence.location.template.Location, java.io.Serializable)
    • org.biojava.nbio.core.sequence.location.InsdcLocations.BondLocation
    • org.biojava.nbio.core.sequence.location.InsdcLocations.OneOfLocation
    • org.biojava.nbio.core.sequence.location.SimpleLocation
      • org.biojava.nbio.core.sequence.location.InsdcLocations.GroupLocation
      • org.biojava.nbio.core.sequence.location.InsdcLocations.OrderLocation
      • org.biojava.nbio.core.sequence.location.SequenceLocation<S,C>
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • org.biojava.nbio.structure.align.util.AlignmentTools.IdentityMap<K>
    • org.biojava.nbio.ontology.utils.SmallMap (implements java.io.Serializable)
    • org.biojava.nbio.core.util.SoftHashMap<K,V>
    • org.biojava.nbio.ontology.utils.WeakValueHashMap
  • org.biojava.nbio.alignment.template.AbstractScorer (implements org.biojava.nbio.alignment.template.Scorer)
    • org.biojava.nbio.alignment.template.AbstractMatrixAligner<S,C> (implements org.biojava.nbio.alignment.template.MatrixAligner<S,C>)
      • org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C>)
        • org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner<S,C>
          • org.biojava.nbio.alignment.routines.GuanUberbacher<S,C>
          • org.biojava.nbio.alignment.NeedlemanWunsch<S,C>
        • org.biojava.nbio.alignment.SmithWaterman<S,C>
      • org.biojava.nbio.alignment.template.AbstractProfileProfileAligner<S,C> (implements org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C>)
        • org.biojava.nbio.alignment.SimpleProfileProfileAligner<S,C>
    • org.biojava.nbio.alignment.FractionalIdentityScorer<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
      • org.biojava.nbio.alignment.FractionalIdentityInProfileScorer<S,C> (implements org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>)
    • org.biojava.nbio.alignment.FractionalSimilarityScorer<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
      • org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer<S,C> (implements org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>)
    • org.biojava.nbio.alignment.StandardRescoreRefiner<S,C> (implements org.biojava.nbio.alignment.template.RescoreRefiner<S,C>)
    • org.biojava.nbio.alignment.SubstitutionMatrixScorer<S,C> (implements org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
  • org.biojava.nbio.structure.align.multiple.AbstractScoresCache (implements org.biojava.nbio.structure.align.multiple.ScoresCache)
    • org.biojava.nbio.structure.align.multiple.BlockImpl (implements org.biojava.nbio.structure.align.multiple.Block, java.lang.Cloneable, java.io.Serializable)
    • org.biojava.nbio.structure.align.multiple.BlockSetImpl (implements org.biojava.nbio.structure.align.multiple.BlockSet, java.lang.Cloneable, java.io.Serializable)
    • org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble, java.io.Serializable)
    • org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.align.multiple.MultipleAlignment, java.io.Serializable)
  • org.biojava.nbio.core.sequence.template.AbstractSequence<C> (implements org.biojava.nbio.core.sequence.template.Sequence<C>)
    • org.biojava.nbio.core.sequence.BasicSequence<C>
    • org.biojava.nbio.core.sequence.DNASequence
      • org.biojava.nbio.core.sequence.CDSSequence
      • org.biojava.nbio.core.sequence.ChromosomeSequence
      • org.biojava.nbio.core.sequence.ExonSequence
      • org.biojava.nbio.core.sequence.GeneSequence
      • org.biojava.nbio.core.sequence.IntronSequence
      • org.biojava.nbio.core.sequence.StartCodonSequence
      • org.biojava.nbio.core.sequence.StopCodonSequence
      • org.biojava.nbio.core.sequence.TranscriptSequence
    • org.biojava.nbio.core.sequence.ProteinSequence
    • org.biojava.nbio.core.sequence.RNASequence
  • org.biojava.nbio.structure.align.AbstractStructureAlignment (implements org.biojava.nbio.structure.align.StructureAlignment)
    • org.biojava.nbio.structure.align.ce.CeMain (implements org.biojava.nbio.structure.align.StructureAlignment)
      • org.biojava.nbio.structure.align.ce.CeCPMain
      • org.biojava.nbio.structure.align.ce.CeSideChainMain (implements org.biojava.nbio.structure.align.StructureAlignment)
      • org.biojava.nbio.structure.align.ce.OptimalCECPMain
    • org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner (implements org.biojava.nbio.structure.align.StructureAlignment)
  • org.biojava.nbio.ontology.AbstractTerm (implements org.biojava.nbio.ontology.Term)
    • org.biojava.nbio.ontology.RemoteTerm.Impl (implements org.biojava.nbio.ontology.RemoteTerm, java.io.Serializable)
    • org.biojava.nbio.ontology.Term.Impl (implements java.io.Serializable, org.biojava.nbio.ontology.Term)
      • org.biojava.nbio.ontology.Variable.Impl (implements org.biojava.nbio.ontology.Variable)
  • org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor (implements org.biojava.nbio.structure.align.ce.UserArgumentProcessor)
    • org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor
      • org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor
      • org.biojava.nbio.structure.align.ce.CeSideChainUserArgumentProcessor
    • org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor
    • org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor
  • org.biojava.nbio.core.sequence.AccessionID
  • org.biojava.nbio.structure.align.model.AFP (implements java.io.Serializable)
  • org.biojava.nbio.structure.align.util.AFPAlignmentDisplay
  • org.biojava.nbio.structure.align.fatcat.calc.AFPCalculator
  • org.biojava.nbio.structure.align.model.AFPChain (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
  • org.biojava.nbio.structure.align.fatcat.calc.AFPChainer
  • org.biojava.nbio.structure.align.xml.AFPChainFlipper
  • org.biojava.nbio.structure.align.util.AFPChainScorer
  • org.biojava.nbio.structure.align.model.AfpChainWriter
  • org.biojava.nbio.structure.align.xml.AFPChainXMLConverter
  • org.biojava.nbio.structure.align.xml.AFPChainXMLParser
  • demo.AFPFromFasta
  • org.biojava.nbio.structure.align.fatcat.calc.AFPOptimizer
  • org.biojava.nbio.structure.align.fatcat.calc.AFPPostProcessor
  • org.biojava.nbio.structure.align.AFPTwister
  • org.biojava.nbio.survival.cox.stats.AgScore
  • org.biojava.nbio.structure.gui.util.AlignedPosition
  • org.biojava.nbio.alignment.routines.AlignerHelper
  • org.biojava.nbio.alignment.routines.AlignerHelper.Anchor
  • org.biojava.nbio.alignment.routines.AlignerHelper.Anchor.QueryIndexComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.alignment.routines.AlignerHelper.Cut
  • org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
  • org.biojava.nbio.structure.align.gui.AlignmentCalc (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
  • org.biojava.nbio.structure.gui.util.AlignmentCalc (implements java.lang.Runnable)
  • org.biojava.nbio.structure.align.gui.AlignmentCalcDB (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
  • demo.AlignmentGuiDemo
  • org.biojava.nbio.structure.align.pairwise.AlignmentProgressListener
  • org.biojava.nbio.structure.align.pairwise.AlignmentResult (implements java.io.Serializable)
  • org.biojava.nbio.alignment.Alignments
  • org.biojava.nbio.structure.align.util.AlignmentTools
  • org.biojava.nbio.structure.align.pairwise.AligNPE
  • org.biojava.nbio.structure.align.helper.AlignTools
  • org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.biojava.nbio.structure.align.webstart.AligUIManager
  • org.biojava.nbio.structure.io.mmcif.AllChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider, java.lang.Runnable)
  • org.biojava.nbio.structure.align.pairwise.AltAligComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.structure.align.pairwise.AlternativeAlignment (implements java.io.Serializable)
  • org.biojava.nbio.aaproperties.xml.AminoAcidComposition
  • org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable
  • org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>, java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.internal.AngleOrderDetectorPlus (implements org.biojava.nbio.structure.symmetry.internal.OrderDetector)
  • org.biojava.nbio.structure.validation.AngleOutlier
  • org.biojava.nbio.genome.App
  • org.biojava.nbio.ontology.App
  • org.biojava.nbio.core.sequence.storage.ArrayListSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.SequenceReader<C>)
    • org.biojava.nbio.core.sequence.loader.ArrayListProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.structure.asa.AsaCalculator
  • org.biojava.nbio.structure.domain.AssignmentXMLSerializer
  • org.biojava.nbio.structure.scop.Astral
  • org.biojava.nbio.structure.align.util.AtomCache
  • org.biojava.nbio.structure.contact.AtomContact (implements java.io.Serializable)
  • org.biojava.nbio.structure.contact.AtomContactSet (implements java.lang.Iterable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.contact.AtomIdentifier (implements java.io.Serializable)
  • org.biojava.nbio.structure.AtomImpl (implements org.biojava.nbio.structure.Atom, org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.nbio.structure.align.gui.jmol.AtomInfo
  • org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
  • org.biojava.nbio.structure.AtomIterator (implements java.util.Iterator<E>)
  • org.biojava.nbio.structure.AtomPositionMap
  • org.biojava.nbio.structure.io.mmcif.model.AuditAuthor
  • org.biojava.nbio.structure.Author (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.core.AxisAligner
    • org.biojava.nbio.structure.symmetry.core.HelixAxisAligner
    • org.biojava.nbio.structure.symmetry.core.RotationAxisAligner
  • org.biojava.nbio.structure.secstruc.BetaBridge
  • org.biojava.nbio.structure.BioAssemblyIdentifier (implements org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.quaternary.BioAssemblyInfo (implements java.io.Serializable)
  • org.biojava.nbio.structure.quaternary.BioAssemblyTools
  • demo.BioJavaAADemo
  • org.biojava.nbio.structure.gui.BiojavaJmol
  • org.biojava.nbio.structure.align.BioJavaStructureAlignment (implements org.biojava.nbio.structure.align.StructureAlignment)
  • org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder
  • org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.nbio.structure.quaternary.io.BioUnitDataProviderFactory
  • org.biojava.nbio.core.sequence.storage.BitSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
    • org.biojava.nbio.core.sequence.storage.FourBitSequenceReader<C>
    • org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader<C>
  • org.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>
    • org.biojava.nbio.core.sequence.storage.FourBitSequenceReader.FourBitArrayWorker<C>
    • org.biojava.nbio.core.sequence.storage.TwoBitSequenceReader.TwoBitArrayWorker<C>
  • org.biojava.nbio.structure.symmetry.utils.BlastClustReader (implements java.io.Serializable)
  • org.biojava.nbio.core.search.io.blast.BlastHitBuilder
  • org.biojava.nbio.genome.homology.BlastHomologyHits
  • org.biojava.nbio.core.search.io.blast.BlastHspBuilder
  • org.biojava.nbio.ws.alignment.qblast.BlastJob
  • org.biojava.nbio.core.search.io.blast.BlastResultBuilder
  • org.biojava.nbio.core.search.io.blast.BlastTabularParser (implements org.biojava.nbio.core.search.io.ResultFactory)
  • org.biojava.nbio.core.search.io.blast.BlastXMLParser (implements org.biojava.nbio.core.search.io.ResultFactory)
  • org.biojava.nbio.genome.query.BlastXMLQuery
  • org.biojava.nbio.structure.BondImpl (implements org.biojava.nbio.structure.Bond, java.io.Serializable)
  • org.biojava.nbio.structure.io.BondMaker
  • org.biojava.nbio.structure.validation.BondOutlier
  • org.biojava.nbio.structure.contact.BoundingBox (implements java.io.Serializable)
  • org.biojava.nbio.structure.align.webstart.BrowserOpener
  • org.biojava.nbio.structure.symmetry.core.C2RotationSolver (implements org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver)
  • org.biojava.nbio.structure.align.util.CacheFactory
  • org.biojava.nbio.structure.io.CAConverter
  • org.biojava.nbio.structure.Calc
  • org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry
  • org.biojava.nbio.alignment.template.CallablePairwiseSequenceAligner<S,C> (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.alignment.template.CallablePairwiseSequenceScorer<S,C> (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.alignment.template.CallableProfileProfileAligner<S,C> (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.structure.align.CallableStructureAlignment (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.structure.quaternary.CartesianProduct<T>
  • org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>)
  • org.biojava.nbio.core.sequence.transcription.CaseInsensitiveCompound (implements org.biojava.nbio.core.sequence.template.Compound)
  • org.biojava.nbio.structure.cath.CathDomain (implements java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.cath.CathFactory
  • org.biojava.nbio.structure.cath.CathFragment (implements java.io.Serializable)
  • org.biojava.nbio.structure.cath.CathInstallation (implements org.biojava.nbio.structure.cath.CathDatabase)
  • org.biojava.nbio.structure.cath.CathNode (implements java.io.Serializable)
  • org.biojava.nbio.structure.cath.CathSegment (implements java.io.Serializable)
  • org.biojava.nbio.core.sequence.CDSComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.structure.align.ce.CECalculator
  • org.biojava.nbio.structure.align.ce.CeCalculatorEnhanced
  • org.biojava.nbio.structure.align.ce.CeCPMain.CPRange
  • org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus (implements java.lang.Comparable<T>)
  • org.biojava.nbio.structure.align.ce.CeParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
    • org.biojava.nbio.structure.align.ce.CECPParameters
    • org.biojava.nbio.structure.symmetry.internal.CESymmParameters
    • org.biojava.nbio.structure.align.ce.OptimalCECPParameters
  • org.biojava.nbio.structure.symmetry.internal.CeSymm
  • org.biojava.nbio.structure.symmetry.internal.CeSymmIterative
  • org.biojava.nbio.structure.symmetry.internal.CeSymmResult
  • org.biojava.nbio.structure.symmetry.core.ChainClusterer
  • org.biojava.nbio.structure.ChainImpl (implements org.biojava.nbio.structure.Chain, java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.misc.ChainSignature (implements java.lang.Comparable<T>)
  • org.biojava.nbio.structure.io.ChargeAdder
  • org.biojava.nbio.structure.io.mmcif.model.ChemComp (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.ChemCompAtom (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.ChemCompBond (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.ChemCompConsumer (implements org.biojava.nbio.structure.io.mmcif.MMcifConsumer)
  • org.biojava.nbio.structure.io.mmcif.model.ChemCompDescriptor (implements java.io.Serializable)
  • demo.ChemCompDistribution
  • org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory
  • org.biojava.nbio.structure.io.mmcif.chem.ChemCompTools
  • org.biojava.nbio.structure.io.mmcif.ChemicalComponentDictionary
  • org.biojava.nbio.survival.cox.stats.ChiSq
  • org.biojava.nbio.survival.cox.stats.Cholesky2
  • org.biojava.nbio.structure.jama.CholeskyDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.survival.cox.stats.Chsolve2
  • org.biojava.nbio.structure.validation.Clash
  • org.biojava.nbio.core.sequence.io.util.ClasspathResource
  • org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
  • org.biojava.nbio.structure.align.util.CliTools
  • org.biojava.nbio.structure.align.ClusterAltAligs
  • org.biojava.nbio.structure.domain.pdp.ClusterDomains
  • org.biojava.nbio.structure.symmetry.core.ClusterMerger
  • org.biojava.nbio.structure.symmetry.core.ClusterProteinChains
  • org.biojava.nbio.structure.align.util.CollectionTools
  • org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
  • java.awt.color.ColorSpace (implements java.io.Serializable)
    • org.biojava.nbio.structure.gui.util.color.HSVColorSpace
  • org.biojava.nbio.structure.gui.util.color.ColorUtils
  • org.biojava.nbio.structure.symmetry.utils.CombinationGenerator
  • org.biojava.nbio.aaproperties.CommandPrompt
  • org.biojava.nbio.survival.data.CompactCharSequence (implements java.lang.CharSequence, java.io.Serializable)
  • org.biojava.nbio.phylo.Comparison
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
          • org.biojava.nbio.structure.align.gui.DBSearchGUI
          • org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
          • org.biojava.nbio.structure.gui.util.color.GradientPanel
          • org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener (implements java.awt.event.ActionListener, org.biojava.nbio.structure.align.events.AlignmentProgressListener)
          • org.biojava.nbio.structure.gui.JMatrixPanel
          • org.biojava.nbio.structure.align.gui.JPrintPanel (implements java.awt.event.ActionListener, java.awt.print.Printable)
            • org.biojava.nbio.structure.align.gui.AlignmentTextPanel
            • org.biojava.nbio.structure.align.gui.aligpanel.AligPanel (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
            • org.biojava.nbio.structure.align.gui.jmol.JmolPanel (implements java.awt.event.ActionListener)
            • org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
          • org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
          • org.biojava.nbio.structure.align.gui.MemoryMonitor
          • org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface (implements java.lang.Runnable)
          • org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
          • org.biojava.nbio.structure.gui.util.PDBDirPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.util.PDBServerPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.util.PDBUploadPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.ScaleableMatrixPanel (implements java.awt.event.ActionListener, javax.swing.event.ChangeListener)
            • org.biojava.nbio.structure.align.gui.DotPlotPanel
          • org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer (implements javax.swing.ListCellRenderer<E>)
          • org.biojava.nbio.structure.gui.util.ScopSelectPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.util.SelectMultiplePanel
          • org.biojava.nbio.structure.align.gui.SelectPDBPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.SequenceDisplay (implements javax.swing.event.ChangeListener)
          • org.biojava.nbio.structure.gui.util.SequenceScalePanel
        • javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • javax.swing.JTextField (implements javax.swing.SwingConstants)
            • org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
            • org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
            • org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.biojava.nbio.structure.align.gui.AlignmentGui
            • org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
            • org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
            • org.biojava.nbio.structure.align.gui.ParameterGUI
            • org.biojava.nbio.structure.symmetry.gui.SymmetryGui
  • org.biojava.nbio.protmod.Component
  • org.biojava.nbio.protmod.io.ComponentXMLConverter
  • org.biojava.nbio.structure.Compound (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.CompoundFinder
  • org.biojava.nbio.core.util.ConcurrencyTools
  • org.biojava.nbio.aaproperties.Constraints
  • org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform (implements org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper)
    • org.biojava.nbio.structure.gui.util.color.LogColorMapper
    • org.biojava.nbio.structure.gui.util.color.SqrtColorMapper
  • org.biojava.nbio.aaproperties.profeat.convertor.Convertor
    • org.biojava.nbio.aaproperties.profeat.convertor.Convert2Charge
    • org.biojava.nbio.aaproperties.profeat.convertor.Convert2Hydrophobicity
    • org.biojava.nbio.aaproperties.profeat.convertor.Convert2NormalizedVanDerWaalsVolume
    • org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarity
    • org.biojava.nbio.aaproperties.profeat.convertor.Convert2Polarizability
    • org.biojava.nbio.aaproperties.profeat.convertor.Convert2SecondaryStructure
    • org.biojava.nbio.aaproperties.profeat.convertor.Convert2SolventAccessibility
  • demo.CookBook
  • demo.CookbookMSA
  • org.biojava.nbio.structure.gui.util.CoordManager
  • org.biojava.nbio.structure.align.multiple.util.CoreSuperimposer (implements org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer)
  • org.biojava.nbio.structure.align.client.CountProgressListener (implements org.biojava.nbio.structure.align.events.AlignmentProgressListener)
  • org.biojava.nbio.survival.cox.CoxCC
  • org.biojava.nbio.survival.cox.CoxCoefficient
  • org.biojava.nbio.survival.cox.CoxHelper
  • org.biojava.nbio.survival.cox.CoxInfo
  • org.biojava.nbio.survival.cox.CoxMart
  • org.biojava.nbio.survival.cox.CoxR
  • org.biojava.nbio.survival.cox.CoxScore
  • org.biojava.nbio.survival.cox.CoxVariables
  • org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator (implements org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface)
  • org.biojava.nbio.core.util.CRC64Checksum (implements java.util.zip.Checksum)
  • org.biojava.nbio.structure.xtal.CrystalBuilder
  • org.biojava.nbio.structure.xtal.CrystalCell (implements java.io.Serializable)
  • org.biojava.nbio.structure.xtal.CrystalTransform (implements java.io.Serializable)
  • org.biojava.nbio.structure.domain.pdp.Cut
  • org.biojava.nbio.structure.domain.pdp.CutDomain
  • org.biojava.nbio.structure.domain.pdp.CutSites
  • org.biojava.nbio.structure.domain.pdp.CutValues
  • org.biojava.nbio.genome.parsers.cytoband.Cytoband (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.genome.parsers.cytoband.CytobandParser
  • org.biojava.nbio.structure.io.mmcif.model.DatabasePDBrev
  • org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord (implements java.io.Serializable)
  • org.biojava.nbio.phosphosite.Dataset
  • org.biojava.nbio.structure.DBRef (implements org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.nbio.structure.align.gui.DBResultTable (implements java.awt.event.ActionListener)
  • org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProvider (implements org.biojava.nbio.core.alignment.matrices.AAIndexProvider)
  • org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider (implements org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider)
  • org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
  • org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper (implements org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper)
  • org.biojava.nbio.ontology.DefaultOps (implements org.biojava.nbio.ontology.OntologyOps, java.io.Serializable)
  • demo.DemoAlignmentFromFasta
  • demo.DemoAlignProteins
  • demo.DemoAsa
  • demo.DemoAtomCache
  • demo.DemoBerkeleyScop
  • demo.DemoCATH
  • demo.DemoCE
  • demo.DemoCeSymm
  • demo.DemoChangeChemCompProvider
  • demo.DemoCommandLineStartup
  • demo.DemoContacts
  • demo.DemoCrystalInterfaces
  • demo.DemoDistanceTree
  • demo.DemoDomainsplit
  • demo.DemoFATCAT
  • demo.DemoLoadSecStruc
  • demo.DemoLoadStructure
  • demo.DemoLoadSubstMax
  • demo.DemoMMCIFReader
  • demo.DemoMultipleMC
  • demo.DemoNWALignment
  • demo.DemoOrientBioAssembly
  • demo.DemoRotationAxis
  • demo.DemoSCOP
  • demo.DemoSecStrucCalc
  • demo.DemoShowBiolAssembly
  • demo.DemoShowCATHDomain
  • demo.DemoShowLargeAssembly
  • demo.DemoShowValidationResults
  • demo.DemoSixFrameTranslation
  • demo.DemoStructureFromFasta
  • demo.DemoSW3DAligner
  • org.biojava.nbio.structure.align.gui.DisplayAFP
  • org.biojava.nbio.structure.symmetry.geometry.DistanceBox<T>
  • org.biojava.nbio.phylo.DistanceMatrixCalculator
  • org.biojava.nbio.phylo.DistanceTreeEvaluator
  • org.biojava.nbio.core.sequence.io.DNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava.nbio.structure.domain.pdp.Domain (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.domain.DomainProviderFactory
  • org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider)
  • org.biojava.nbio.structure.secstruc.DSSPParser
  • org.biojava.nbio.structure.ecod.EcodDomain (implements java.lang.Cloneable, java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.ecod.EcodFactory
  • org.biojava.nbio.structure.ecod.EcodInstallation (implements org.biojava.nbio.structure.ecod.EcodDatabase)
  • org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser
  • org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit<C> (implements org.biojava.nbio.core.sequence.edits.Edit<C>)
    • org.biojava.nbio.core.sequence.edits.Edit.Delete<C>
    • org.biojava.nbio.core.sequence.edits.Edit.Insert<C>
    • org.biojava.nbio.core.sequence.edits.Edit.Substitute<C>
  • org.biojava.nbio.structure.jama.EigenvalueDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.aaproperties.xml.Element
  • org.biojava.nbio.aaproperties.xml.ElementTable
  • org.biojava.nbio.structure.io.mmcif.model.Entity
  • org.biojava.nbio.structure.io.mmcif.model.EntitySrcGen
  • org.biojava.nbio.structure.io.mmcif.model.EntitySrcNat
  • org.biojava.nbio.structure.io.mmcif.model.EntitySrcSyn
  • org.biojava.nbio.structure.validation.Entry
  • org.biojava.nbio.core.util.Equals
  • org.biojava.nbio.core.sequence.ExonComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.structure.align.FarmJob (implements java.lang.Runnable)
  • org.biojava.nbio.structure.align.client.FarmJobParameters
  • org.biojava.nbio.structure.align.client.FarmJobRunnable (implements java.lang.Runnable)
  • org.biojava.nbio.structure.io.FastaAFPChainConverter
  • org.biojava.nbio.core.sequence.io.FastaGeneWriter
  • org.biojava.nbio.core.sequence.io.FastaReader<S,C>
  • org.biojava.nbio.core.sequence.io.FastaReaderHelper
  • org.biojava.nbio.data.sequence.FastaSequence (implements java.lang.Comparable<T>)
  • org.biojava.nbio.core.sequence.io.FastaSequenceParser (implements org.biojava.nbio.core.sequence.io.template.SequenceParserInterface)
  • org.biojava.nbio.structure.io.FastaStructureParser
  • org.biojava.nbio.core.sequence.io.FastaWriter<S,C>
  • org.biojava.nbio.core.sequence.io.FastaWriterHelper
  • org.biojava.nbio.sequencing.io.fastq.Fastq
  • org.biojava.nbio.sequencing.io.fastq.FastqBuilder
  • org.biojava.nbio.sequencing.io.fastq.FastqTools
  • org.biojava.nbio.structure.align.fatcat.FatCat
    • org.biojava.nbio.structure.align.fatcat.FatCatFlexible (implements org.biojava.nbio.structure.align.StructureAlignment)
    • org.biojava.nbio.structure.align.fatcat.FatCatRigid (implements org.biojava.nbio.structure.align.StructureAlignment)
  • org.biojava.nbio.structure.align.fatcat.calc.FatCatAligner
  • org.biojava.nbio.structure.align.fatcat.calc.FatCatParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
  • org.biojava.nbio.structure.align.fatcat.calc.FCAlignHelper
  • org.biojava.nbio.genome.parsers.gff.Feature (implements org.biojava.nbio.genome.parsers.gff.FeatureI)
  • org.biojava.nbio.genome.parsers.gff.FeatureHelper
  • org.biojava.nbio.structure.io.FileConvert
  • org.biojava.nbio.structure.io.util.FileDownloadUtils
  • org.biojava.nbio.structure.io.FileParsingParameters (implements java.io.Serializable)
  • org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava.nbio.core.util.FlatFileCache
  • org.biojava.nbio.phylo.ForesterWrapper
  • org.biojava.nbio.structure.align.pairwise.FragmentJoiner
  • org.biojava.nbio.structure.align.pairwise.FragmentPair
  • org.biojava.nbio.structure.align.helper.GapArray
  • org.biojava.nbio.genome.parsers.gff.GCStats
  • org.biojava.nbio.core.sequence.io.GenbankReader<S,C>
  • org.biojava.nbio.core.sequence.io.GenbankReaderHelper
  • org.biojava.nbio.core.sequence.io.GenbankSequenceParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceParserInterface)
  • org.biojava.nbio.core.sequence.io.GenbankWriter<S,C>
  • org.biojava.nbio.core.sequence.io.GenbankWriterHelper
  • org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
  • org.biojava.nbio.genome.GeneFeatureHelper
  • org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
  • org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
  • org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
  • org.biojava.nbio.genome.parsers.genename.GeneName (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.genome.parsers.genename.GeneNamesParser
  • org.biojava.nbio.core.sequence.io.GenericFastaHeaderFormat<S,C> (implements org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface<S,C>)
  • org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>)
  • org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>)
  • org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat<S,C>
    • org.biojava.nbio.core.sequence.io.GenericGenbankHeaderFormat<S,C> (implements org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface<S,C>)
  • org.biojava.nbio.structure.domain.pdp.GetDistanceMatrix
  • org.biojava.nbio.structure.rcsb.GetRepresentatives
  • org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
  • org.biojava.nbio.genome.parsers.gff.GFF3Reader
  • org.biojava.nbio.genome.parsers.gff.GFF3Writer
  • org.biojava.nbio.ontology.io.GOParser
  • org.biojava.nbio.structure.align.pairwise.Gotoh
  • org.biojava.nbio.structure.gui.util.color.GradientMapper (implements org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper, java.util.Map<K,V>)
  • org.biojava.nbio.structure.symmetry.internal.GraphComponentOrderDetector (implements org.biojava.nbio.structure.symmetry.internal.OrderDetector)
  • org.biojava.nbio.structure.symmetry.internal.GraphComponentRefiner (implements org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner)
  • org.biojava.nbio.structure.contact.Grid
  • org.biojava.nbio.structure.contact.GridCell
  • org.biojava.nbio.structure.asa.GroupAsa (implements java.io.Serializable)
  • org.biojava.nbio.structure.contact.GroupContact (implements java.io.Serializable)
  • org.biojava.nbio.structure.contact.GroupContactSet (implements java.lang.Iterable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.GroupIterator (implements java.util.Iterator<E>)
  • org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
  • org.biojava.nbio.structure.io.GroupToSDF
  • org.biojava.nbio.alignment.GuideTree<S,C> (implements java.lang.Iterable<T>)
  • org.biojava.nbio.alignment.GuideTree.Node (implements org.biojava.nbio.alignment.template.GuideTreeNode<S,C>)
  • org.biojava.nbio.structure.align.gui.GUIFarmJobRunnable (implements java.lang.Runnable)
  • org.biojava.nbio.structure.align.ce.GuiWrapper
  • org.biojava.nbio.core.util.Hashcoder
  • org.biojava.nbio.structure.align.xml.HasResultXMLConverter
  • org.biojava.nbio.structure.secstruc.HBond
  • org.biojava.nbio.survival.data.HeaderInfo
  • org.biojava.nbio.structure.symmetry.core.HelicalRepeatUnit
  • org.biojava.nbio.structure.symmetry.core.Helix
  • org.biojava.nbio.structure.symmetry.core.HelixExtender
  • org.biojava.nbio.structure.symmetry.core.HelixLayers
  • org.biojava.nbio.structure.symmetry.core.HelixSolver
  • org.biojava.nbio.structure.align.gui.HelpDialog
  • org.biojava.nbio.structure.HetatomImpl (implements org.biojava.nbio.structure.Group, java.io.Serializable)
    • org.biojava.nbio.structure.AminoAcidImpl (implements org.biojava.nbio.structure.AminoAcid, java.io.Serializable)
    • org.biojava.nbio.structure.NucleotideImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.Group, java.io.Serializable)
  • org.biojava.nbio.core.search.io.Hit (implements java.lang.Iterable<T>)
  • demo.HmmerDemo
  • org.biojava.nbio.ws.hmmer.HmmerDomain (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.ws.hmmer.HmmerResult (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.core.search.io.Hsp<S,C>
  • org.biojava.nbio.structure.align.util.HTTPConnectionTools
  • org.biojava.nbio.structure.symmetry.geometry.IcosahedralSampler
  • org.biojava.nbio.structure.symmetry.geometry.Icosahedron (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • org.biojava.nbio.structure.Identifier
  • org.biojava.nbio.structure.align.helper.IdxComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReader
  • org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriter
  • org.biojava.nbio.structure.align.helper.IndexPair (implements java.io.Serializable)
    • org.biojava.nbio.structure.align.helper.AligMatEl
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • org.biojava.nbio.core.util.UncompressInputStream
    • org.biojava.nbio.genome.parsers.twobit.TwoBitParser
  • org.biojava.nbio.core.util.InputStreamProvider
  • org.biojava.nbio.core.sequence.location.InsdcLocations
  • org.biojava.nbio.core.sequence.location.InsdcParser<S,C>
  • org.biojava.nbio.ontology.IntegerOntology (implements org.biojava.nbio.ontology.Ontology)
  • org.biojava.nbio.ontology.IntegerOntology.IntTerm (implements org.biojava.nbio.ontology.Term)
  • org.biojava.nbio.core.sequence.io.util.IOUtils
  • org.biojava.nbio.aaproperties.xml.Isotope
  • org.biojava.nbio.core.sequence.io.IUPACParser
  • org.biojava.nbio.core.sequence.io.IUPACParser.IUPACTable (implements org.biojava.nbio.core.sequence.transcription.Table)
  • org.biojava.nbio.structure.align.client.JFatCatClient
  • org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener)
  • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
    • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
    • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
  • org.biojava.nbio.structure.align.gui.jmol.JmolTools
  • org.biojava.nbio.structure.gui.JmolViewerImpl (implements org.biojava.nbio.structure.gui.StructureViewer)
  • org.biojava.nbio.structure.align.webstart.JNLPProxy
  • org.biojava.nbio.core.sequence.storage.JoiningSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.structure.align.helper.JointFragments
  • org.biojava.nbio.structure.JournalArticle (implements java.io.Serializable)
  • org.biojava.nbio.ronn.Jronn
  • org.biojava.nbio.ronn.Jronn.Range
  • java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
    • org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
    • org.biojava.nbio.structure.gui.RasmolCommandListener (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
  • org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
  • org.biojava.nbio.structure.secstruc.Ladder
  • org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator (implements org.biojava.nbio.structure.gui.util.color.ColorInterpolator)
  • org.biojava.nbio.structure.scop.server.ListStringWrapper (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.LocalPDBDirectory (implements org.biojava.nbio.structure.io.StructureIOFile)
    • org.biojava.nbio.structure.io.MMCIFFileReader
    • org.biojava.nbio.structure.io.PDBFileReader
  • org.biojava.nbio.structure.domain.LocalProteinDomainParser
  • org.biojava.nbio.genome.parsers.gff.Location (implements java.lang.Iterable<T>)
  • org.biojava.nbio.core.sequence.location.template.Location.Tools
  • org.biojava.nbio.core.sequence.location.LocationHelper
  • org.biojava.nbio.genome.parsers.gff.LocIterator (implements java.util.Iterator<E>)
  • org.biojava.nbio.structure.jama.LUDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
  • org.biojava.nbio.structure.jama.Maths
  • org.biojava.nbio.structure.jama.Matrix (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.nbio.survival.cox.matrix.Matrix
  • org.biojava.nbio.survival.cox.comparators.MeanModelComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.survival.kaplanmeier.metadata.MeanQuantizer (implements org.biojava.nbio.survival.kaplanmeier.metadata.DiscreteQuantizerInterface)
  • org.biojava.nbio.structure.align.gui.MenuCreator
  • org.biojava.nbio.structure.gui.util.MenuCreator
  • org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.core.exceptions.Messages
  • org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
  • org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider (implements org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider)
  • org.biojava.nbio.structure.io.mmcif.MMCIFFileTools
  • org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider (implements org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider)
  • org.biojava.nbio.structure.validation.ModelledSubgroup
  • org.biojava.nbio.ronn.ModelLoader
  • org.biojava.nbio.ronn.ModelLoader.Model
  • org.biojava.nbio.ronn.ModelLoader.Threshold
  • org.biojava.nbio.protmod.ModificationConditionImpl (implements org.biojava.nbio.protmod.ModificationCondition)
  • org.biojava.nbio.protmod.ModificationLinkage
  • org.biojava.nbio.aaproperties.xml.ModifiedAminoAcidCompoundSet (implements org.biojava.nbio.core.sequence.template.CompoundSet<C>)
  • org.biojava.nbio.protmod.structure.ModifiedCompoundImpl (implements java.lang.Comparable<T>, org.biojava.nbio.protmod.structure.ModifiedCompound, java.io.Serializable)
  • org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter
  • org.biojava.nbio.structure.validation.MogAngleOutlier
  • org.biojava.nbio.structure.validation.MogBondOutlier
  • org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia
  • org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
  • org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
  • org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentDisplay
  • org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
  • org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer
  • org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools
  • org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter
  • org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLConverter
  • org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser
  • org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain (implements org.biojava.nbio.structure.align.MultipleStructureAligner)
  • org.biojava.nbio.structure.align.multiple.mc.MultipleMcOptimizer (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
  • org.biojava.nbio.core.sequence.MultipleSequenceAlignment<S,C> (implements org.biojava.nbio.core.sequence.template.LightweightProfile<S,C>)
  • org.biojava.nbio.structure.align.MultiThreadedDBSearch
  • org.biojava.nbio.structure.Mutator
  • org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.MyDistMaxListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.MyExportListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener (implements org.jmol.api.JmolStatusListener)
  • org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.MySaveFileListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.aaproperties.xml.MyValidationEventHandler (implements javax.xml.bind.ValidationEventHandler)
  • org.biojava.nbio.aaproperties.xml.Name2Count
  • org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties (implements org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties)
  • org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties (implements org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties)
  • org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService (implements org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService)
  • demo.NCBIQBlastServiceDemo
  • org.biojava.nbio.structure.validation.ObjectFactory
  • org.biojava.nbio.ontology.obo.OboFileHandler (implements org.biojava.nbio.ontology.obo.OboFileEventListener)
  • org.biojava.nbio.ontology.obo.OboFileParser
  • org.biojava.nbio.ontology.obo.OboFileParser.SOPair
  • org.biojava.nbio.ontology.io.OboParser
  • org.biojava.nbio.structure.symmetry.geometry.Octahedron (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • org.biojava.nbio.ontology.Ontology.Impl (implements org.biojava.nbio.ontology.Ontology, java.io.Serializable)
  • org.biojava.nbio.ontology.OntologyTerm.Impl (implements org.biojava.nbio.ontology.OntologyTerm, java.io.Serializable)
  • org.biojava.nbio.ontology.OntoTools
  • org.biojava.nbio.structure.quaternary.OperatorResolver
  • org.biojava.nbio.structure.quaternary.OrderedPair<T>
  • org.biojava.nbio.ronn.ORonn (implements java.util.concurrent.Callable<V>)
  • org.biojava.nbio.ronn.ORonnModel
  • org.biojava.nbio.genome.query.OutputHitsGFF
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • org.biojava.nbio.ronn.NullOutputStream
  • org.biojava.nbio.structure.contact.Pair<T> (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.core.PairwiseAlignment
  • demo.ParseFastaFileDemo
  • demo.ParseGO
  • org.biojava.nbio.structure.PassthroughIdentifier (implements org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.io.PDBBioAssemblyParser
  • org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider (implements org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider)
  • org.biojava.nbio.structure.PDBCrystallographicInfo (implements java.io.Serializable)
  • org.biojava.nbio.structure.domain.PDBDomainProvider (implements org.biojava.nbio.structure.domain.DomainProvider)
  • org.biojava.nbio.structure.io.PDBFileParser
  • org.biojava.nbio.structure.PDBHeader (implements org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.nbio.structure.rcsb.PdbIdLists
  • org.biojava.nbio.structure.align.client.PdbPair (implements java.lang.Comparable<T>)
  • org.biojava.nbio.structure.align.xml.PdbPairsMessage
  • org.biojava.nbio.structure.align.xml.PdbPairXMLConverter
  • org.biojava.nbio.structure.PDBStatus
  • org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils
  • org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord
  • org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompDescriptor
  • org.biojava.nbio.structure.io.mmcif.model.PdbxChemCompIdentifier
  • org.biojava.nbio.structure.io.mmcif.model.PdbxEntityNonPoly
  • org.biojava.nbio.structure.io.mmcif.model.PdbxNonPolyScheme
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGenXMLContainer
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyXMLContainer
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperListXMLContainer
  • org.biojava.nbio.structure.domain.pdp.PDPDistanceMatrix
  • org.biojava.nbio.structure.domain.PDPDomain (implements org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.domain.pdp.PDPParameters
  • org.biojava.nbio.aaproperties.PeptideProperties
  • org.biojava.nbio.aaproperties.PeptidePropertiesImpl (implements org.biojava.nbio.aaproperties.IPeptideProperties)
  • org.biojava.nbio.structure.symmetry.utils.PermutationGenerator
  • org.biojava.nbio.structure.symmetry.core.PermutationGroup
  • org.biojava.nbio.structure.align.webstart.PersistentConfig
  • org.biojava.nbio.core.sequence.io.PlainFastaHeaderParser<S,C> (implements org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>)
  • org.biojava.nbio.structure.align.xml.PositionInQueueXMLConverter
  • demo.PredictDisorder
  • org.biojava.nbio.core.util.PrettyXMLWriter (implements org.biojava.nbio.core.util.XMLWriter)
  • org.biojava.nbio.structure.symmetry.geometry.Prism (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • org.biojava.nbio.aaproperties.profeat.ProfeatProperties
  • org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl (implements org.biojava.nbio.aaproperties.profeat.IProfeatProperties)
  • org.biojava.nbio.structure.validation.Program
  • org.biojava.nbio.structure.validation.Programs
  • org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor
  • org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature
  • org.biojava.nbio.protmod.structure.ProteinModificationIdentifier
  • org.biojava.nbio.protmod.ProteinModificationImpl (implements java.lang.Comparable<T>, org.biojava.nbio.protmod.ProteinModification)
  • org.biojava.nbio.protmod.ProteinModificationImpl.Builder
  • org.biojava.nbio.protmod.ProteinModificationRegistry
  • org.biojava.nbio.protmod.io.ProteinModificationXmlReader
  • org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer
  • org.biojava.nbio.core.sequence.io.ProteinSequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
    • org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator
  • org.biojava.nbio.structure.jama.QRDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.core.sequence.features.Qualifier
    • org.biojava.nbio.core.sequence.features.DBReferenceInfo
      • org.biojava.nbio.core.sequence.features.FeatureDbReferenceInfo<S,C> (implements org.biojava.nbio.core.sequence.features.FeatureInterface<S,C>)
  • org.biojava.nbio.structure.symmetry.core.QuatSuperpositionScorer
  • org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
  • org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults
  • org.biojava.nbio.structure.symmetry.core.QuatSymmetryScores
  • org.biojava.nbio.structure.rcsb.RCSBDescription
  • org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory
  • org.biojava.nbio.structure.rcsb.RCSBLigand
  • org.biojava.nbio.structure.rcsb.RCSBLigands
  • org.biojava.nbio.structure.rcsb.RCSBLigandsFactory
  • org.biojava.nbio.structure.rcsb.RCSBMacromolecule
  • org.biojava.nbio.structure.rcsb.RCSBPolymer
  • org.biojava.nbio.structure.rcsb.RCSBTaxonomy
  • org.biojava.nbio.structure.rcsb.RCSBUpdates
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead
  • org.biojava.nbio.structure.rcsb.ReadUtils
  • org.biojava.nbio.structure.symmetry.geometry.RectangularPrism (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider)
  • java.lang.ref.Reference<T>
    • java.lang.ref.WeakReference<T>
      • org.biojava.nbio.ontology.utils.KeyedWeakReference
  • org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer (implements org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer)
  • org.biojava.nbio.structure.io.mmcif.model.Refine
  • org.biojava.nbio.structure.quaternary.io.RemoteBioUnitDataProvider (implements org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider)
  • org.biojava.nbio.ws.hmmer.RemoteHmmerScan (implements org.biojava.nbio.ws.hmmer.HmmerScan)
  • org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider (implements org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider)
  • org.biojava.nbio.structure.scop.RemoteScopInstallation (implements org.biojava.nbio.structure.scop.ScopDatabase)
  • org.biojava.nbio.structure.align.xml.RepresentativeXMLConverter
  • org.biojava.nbio.survival.cox.ResidualsCoxph
  • org.biojava.nbio.structure.symmetry.internal.ResidueGroup
  • org.biojava.nbio.structure.ResidueNumber (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.ResidueRange
    • org.biojava.nbio.structure.ResidueRangeAndLength
      • org.biojava.nbio.structure.AugmentedResidueRange
  • org.biojava.nbio.structure.align.util.ResourceManager
  • org.biojava.nbio.core.search.io.Result (implements java.lang.Iterable<T>)
    • org.biojava.nbio.core.search.io.blast.BlastResult
  • org.biojava.nbio.survival.cox.RiskInfo
  • org.biojava.nbio.core.sequence.io.RNASequenceCreator (implements org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>)
  • org.biojava.nbio.ronn.RonnConstraint
  • org.biojava.nbio.structure.symmetry.core.Rotation
  • org.biojava.nbio.structure.align.util.RotationAxis
  • org.biojava.nbio.structure.symmetry.core.RotationGroup
  • org.biojava.nbio.structure.symmetry.core.RotationSolver (implements org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver)
  • javax.swing.RowSorter<M>
    • javax.swing.DefaultRowSorter<M,I>
      • javax.swing.table.TableRowSorter<M>
        • org.biojava.nbio.structure.align.gui.MyTableRowSorter
  • org.biojava.nbio.structure.io.SandboxStyleStructureProvider (implements org.biojava.nbio.structure.io.StructureProvider)
  • org.biojava.nbio.sequencing.io.fastq.SangerFastqReader
  • org.biojava.nbio.sequencing.io.fastq.SangerFastqWriter
  • org.biojava.nbio.core.alignment.matrices.ScaledSubstitutionMatrix (implements org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C>)
  • org.biojava.nbio.structure.symmetry.analysis.ScanSymmetry (implements java.lang.Runnable)
  • javax.xml.bind.SchemaOutputResolver
    • org.biojava.nbio.aaproperties.xml.SchemaGenerator
  • org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider (implements org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider)
  • org.biojava.nbio.structure.scop.ScopDescription (implements java.lang.Cloneable, java.io.Serializable)
  • org.biojava.nbio.structure.scop.server.ScopDescriptions (implements java.io.Serializable)
  • org.biojava.nbio.structure.scop.ScopDomain (implements java.lang.Cloneable, java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.scop.server.ScopDomains (implements java.io.Serializable)
  • org.biojava.nbio.structure.scop.ScopFactory
  • org.biojava.nbio.structure.scop.ScopInstallation (implements org.biojava.nbio.structure.scop.LocalScopDatabase)
    • org.biojava.nbio.structure.scop.BerkeleyScopInstallation
  • org.biojava.nbio.structure.gui.util.ScopInstallationInstance
  • org.biojava.nbio.structure.scop.ScopMirror
  • org.biojava.nbio.structure.scop.ScopNode (implements java.io.Serializable)
  • org.biojava.nbio.structure.scop.server.ScopNodes (implements java.io.Serializable)
  • org.biojava.nbio.core.search.io.SearchIO (implements java.lang.Iterable<T>)
  • org.biojava.nbio.structure.secstruc.SecStrucCalc
  • org.biojava.nbio.structure.secstruc.SecStrucElement
  • org.biojava.nbio.structure.secstruc.SecStrucInfo
    • org.biojava.nbio.structure.secstruc.SecStrucState
  • org.biojava.nbio.structure.secstruc.SecStrucTools
  • org.biojava.nbio.structure.domain.pdp.Segment (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.domain.pdp.SegmentComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.structure.gui.SelectionImpl (implements org.biojava.nbio.structure.gui.Selection)
  • org.biojava.nbio.structure.SeqMisMatchImpl (implements org.biojava.nbio.structure.SeqMisMatch, java.io.Serializable)
  • org.biojava.nbio.structure.io.SeqRes2AtomAligner
  • org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster (implements java.lang.Cloneable)
  • org.biojava.nbio.core.sequence.storage.SequenceAsStringHelper<C>
  • org.biojava.nbio.core.sequence.SequenceComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.core.sequence.loader.SequenceFileProxyLoader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.structure.symmetry.internal.SequenceFunctionOrderDetector (implements org.biojava.nbio.structure.symmetry.internal.OrderDetector)
  • org.biojava.nbio.structure.symmetry.internal.SequenceFunctionRefiner (implements org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner)
  • org.biojava.nbio.core.sequence.template.SequenceMixin
  • org.biojava.nbio.core.sequence.template.SequenceMixin.SequenceIterator<C> (implements java.util.Iterator<E>)
  • org.biojava.nbio.structure.gui.util.SequenceMouseListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.biojava.nbio.core.sequence.SequenceOptimizationHints
  • org.biojava.nbio.core.sequence.template.SequenceProxyView<C> (implements org.biojava.nbio.core.sequence.template.SequenceView<C>)
    • org.biojava.nbio.core.sequence.views.ComplementSequenceView<C>
    • org.biojava.nbio.core.sequence.views.ReversedSequenceView<C>
    • org.biojava.nbio.core.sequence.views.RnaSequenceView (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.core.util.SequenceTools
  • org.biojava.nbio.data.sequence.SequenceUtil
  • org.biojava.nbio.structure.domain.SerializableCache<K,V>
    • org.biojava.nbio.structure.scop.CachedRemoteScopInstallation (implements org.biojava.nbio.structure.scop.ScopDatabase)
    • org.biojava.nbio.structure.domain.RemoteDomainProvider (implements org.biojava.nbio.structure.domain.DomainProvider)
    • org.biojava.nbio.structure.domain.RemotePDPProvider (implements org.biojava.nbio.structure.domain.PDPProvider)
  • org.biojava.nbio.structure.domain.pdp.ShortSegmentRemover
  • org.biojava.nbio.structure.align.gui.ShowPDBIDListener (implements java.awt.event.ActionListener)
  • demo.ShowStructureInJmol
  • org.biojava.nbio.structure.io.sifts.SiftsChainEntry
  • org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
  • org.biojava.nbio.structure.io.sifts.SiftsEntity (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.sifts.SiftsMappingProvider
  • org.biojava.nbio.structure.io.sifts.SiftsResidue (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.sifts.SiftsSegment (implements java.io.Serializable)
  • org.biojava.nbio.structure.io.sifts.SiftsXMLParser
  • org.biojava.nbio.structure.align.fatcat.calc.SigEva
  • org.biojava.nbio.core.alignment.SimpleAlignedSequence<S,C> (implements org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>, java.io.Serializable)
  • org.biojava.nbio.alignment.SimpleGapPenalty (implements org.biojava.nbio.alignment.template.GapPenalty, java.io.Serializable)
  • org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer (implements org.biojava.nbio.structure.io.mmcif.MMcifConsumer)
  • org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser (implements org.biojava.nbio.structure.io.mmcif.MMcifParser)
  • org.biojava.nbio.core.sequence.location.SimplePoint (implements org.biojava.nbio.core.sequence.location.template.Point, java.io.Serializable)
    • org.biojava.nbio.core.sequence.location.FuzzyPoint
  • org.biojava.nbio.core.alignment.SimpleProfile<S,C> (implements org.biojava.nbio.core.alignment.template.Profile<S,C>, java.io.Serializable)
    • org.biojava.nbio.core.alignment.SimpleProfilePair<S,C> (implements org.biojava.nbio.core.alignment.template.ProfilePair<S,C>)
    • org.biojava.nbio.core.alignment.SimpleSequencePair<S,C> (implements org.biojava.nbio.core.alignment.template.SequencePair<S,C>)
  • org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix<C> (implements java.io.Serializable, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C>)
  • org.biojava.nbio.core.sequence.storage.SingleCompoundSequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.core.util.SingleLinkageClusterer
  • org.biojava.nbio.structure.jama.SingularValueDecomposition (implements java.io.Serializable)
  • org.biojava.nbio.structure.Site (implements java.lang.Comparable<T>, org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.nbio.phosphosite.Site
  • org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters (implements org.biojava.nbio.structure.align.ce.ConfigStrucAligParams)
  • org.biojava.nbio.sequencing.io.fastq.SolexaFastqReader
  • org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriter
  • org.biojava.nbio.structure.xtal.SpaceGroup (implements java.io.Serializable)
  • org.biojava.nbio.structure.xtal.io.SpaceGroupMapElements
  • org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot
  • org.biojava.nbio.structure.math.SparseSquareMatrix (implements java.io.Serializable)
  • org.biojava.nbio.structure.math.SparseVector (implements java.io.Serializable)
  • org.biojava.nbio.structure.symmetry.geometry.SphereSampler
  • org.biojava.nbio.genome.util.SplitFasta
  • org.biojava.nbio.structure.io.SSBondImpl (implements java.lang.Cloneable, org.biojava.nbio.structure.PDBRecord, java.io.Serializable)
  • org.biojava.nbio.structure.StandardAminoAcid
  • org.biojava.nbio.structure.align.ce.StartupParameters
    • org.biojava.nbio.structure.align.ce.CeUserArgumentProcessor.CeStartupParams
      • org.biojava.nbio.structure.align.ce.CeCPUserArgumentProcessor.CeCPStartupParams
    • org.biojava.nbio.structure.align.fatcat.FatCatUserArgumentProcessor.FatCatStartupParams
    • org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams
  • org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder (implements java.io.Serializable)
  • org.biojava.nbio.survival.cox.matrix.StdArrayIO
  • org.biojava.nbio.alignment.io.StockholmFileAnnotation
  • org.biojava.nbio.alignment.io.StockholmFileAnnotation.StockholmFileAnnotationReference
  • org.biojava.nbio.alignment.io.StockholmFileParser
  • org.biojava.nbio.alignment.io.StockholmStructure
  • org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference
  • org.biojava.nbio.survival.cox.StrataInfo
  • org.biojava.nbio.structure.align.pairwise.StrCompAlignment (implements org.biojava.nbio.structure.align.pairwise.Alignable)
  • org.biojava.nbio.core.util.StringManipulationHelper
  • org.biojava.nbio.core.sequence.loader.StringProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
    • org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface, org.biojava.nbio.core.sequence.features.FeatureRetriever, org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface)
  • org.biojava.nbio.structure.align.StrucAligParameters
  • org.biojava.nbio.structure.io.mmcif.model.Struct
  • org.biojava.nbio.structure.io.mmcif.model.StructKeywords
  • org.biojava.nbio.structure.io.mmcif.model.StructRefSeqDif
  • org.biojava.nbio.structure.io.mmcif.model.StructSite
  • org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
  • org.biojava.nbio.structure.align.StructureAlignmentFactory
  • org.biojava.nbio.structure.align.fatcat.calc.StructureAlignmentOptimizer
  • org.biojava.nbio.protmod.structure.StructureAtom
  • org.biojava.nbio.protmod.structure.StructureAtomLinkage
  • org.biojava.nbio.protmod.io.StructureAtomXMLConverter
  • org.biojava.nbio.protmod.structure.StructureGroup (implements java.lang.Comparable<T>)
  • org.biojava.nbio.protmod.io.StructureGroupXMLConverter
  • org.biojava.nbio.structure.StructureImpl (implements java.io.Serializable, org.biojava.nbio.structure.Structure)
  • org.biojava.nbio.structure.contact.StructureInterface (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.contact.StructureInterfaceCluster (implements java.io.Serializable)
  • org.biojava.nbio.structure.contact.StructureInterfaceList (implements java.lang.Iterable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.StructureIO
  • org.biojava.nbio.structure.align.client.StructureName (implements java.lang.Comparable<T>, java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.align.StructurePairAligner
  • org.biojava.nbio.structure.io.StructureSequenceMatcher
  • org.biojava.nbio.structure.StructureTools
  • org.biojava.nbio.protmod.structure.StructureUtil
  • org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper (implements java.io.Serializable)
  • org.biojava.nbio.structure.SubstructureIdentifier (implements java.io.Serializable, org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.symmetry.core.SubunitGraph
  • org.biojava.nbio.structure.symmetry.core.Subunits
  • org.biojava.nbio.structure.symmetry.geometry.SuperPosition
  • org.biojava.nbio.structure.symmetry.geometry.SuperPositionQCP
  • org.biojava.nbio.survival.cox.SurvFitInfo
  • org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
  • org.biojava.nbio.survival.cox.SurvivalInfo (implements java.lang.Comparable<T>)
  • org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.survival.cox.SurvivalInfoHelper
  • org.biojava.nbio.survival.cox.SurvivalInfoIndex (implements java.lang.Comparable<T>)
  • org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator (implements java.util.Comparator<T>)
  • org.biojava.nbio.structure.SVDSuperimposer
  • javax.swing.SwingWorker<T,V> (implements java.util.concurrent.RunnableFuture<V>)
    • org.biojava.nbio.structure.align.gui.StructureLoaderThread
  • org.biojava.nbio.structure.math.SymbolTable<Key,Value> (implements java.lang.Iterable<T>, java.io.Serializable)
  • org.biojava.nbio.structure.validation.SymmClash
  • org.biojava.nbio.structure.symmetry.internal.SymmetryAxes
  • org.biojava.nbio.structure.symmetry.gui.SymmetryCalc (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
  • org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
  • org.biojava.nbio.structure.symmetry.gui.SymmetryListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.symmetry.utils.SymmetryTools
  • org.biojava.nbio.structure.symmetry.internal.SymmOptimizer
  • org.biojava.nbio.structure.xtal.SymoplibParser
  • org.biojava.nbio.structure.align.util.SynchronizedOutFile
  • org.biojava.nbio.ontology.Synonym (implements java.lang.Comparable<T>)
  • org.biojava.nbio.structure.symmetry.core.SystematicSolver (implements org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver)
  • org.biojava.nbio.structure.align.gui.SystemInfo
  • org.biojava.nbio.ontology.io.TabDelimParser
  • org.biojava.nbio.core.sequence.transcription.Table.CaseInsensitiveTriplet
  • org.biojava.nbio.core.sequence.transcription.Table.Codon (implements org.biojava.nbio.core.sequence.template.Compound)
  • org.biojava.nbio.core.sequence.TaxonomyID
  • demo.TestDNANeedlemanWunsch
  • org.biojava.nbio.structure.symmetry.geometry.Tetrahedron (implements org.biojava.nbio.structure.symmetry.geometry.Polyhedron)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Error
      • java.lang.AssertionError
        • org.biojava.nbio.ontology.utils.AssertionFailure
    • java.lang.Exception
      • org.biojava.nbio.core.exceptions.CompoundNotFoundException
      • org.biojava.nbio.structure.align.util.ConfigurationException
      • org.biojava.nbio.structure.align.client.JobKillException
      • org.biojava.nbio.ontology.OntologyException
        • org.biojava.nbio.ontology.AlreadyExistsException
        • org.biojava.nbio.ontology.InvalidTermException
      • org.biojava.nbio.structure.io.PDBParseException
      • org.biojava.nbio.structure.symmetry.internal.RefinerFailedException
      • java.lang.RuntimeException
        • org.biojava.nbio.core.exceptions.ParserException
        • org.biojava.nbio.structure.scop.ScopIOException
        • org.biojava.nbio.core.exceptions.TranslationException
      • org.biojava.nbio.structure.StructureException
  • org.biojava.nbio.ronn.Timer
  • org.biojava.nbio.core.sequence.transcription.TranscriptionEngine
  • org.biojava.nbio.core.sequence.transcription.TranscriptionEngine.Builder
  • org.biojava.nbio.phylo.TreeConstructor
  • org.biojava.nbio.structure.xtal.io.TreeMapSpaceGroupWrapper (implements java.io.Serializable)
  • org.biojava.nbio.structure.scop.server.TreeSetStringWrapper (implements java.io.Serializable)
  • org.biojava.nbio.ontology.Triple.Impl (implements java.io.Serializable, org.biojava.nbio.ontology.Triple)
  • org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader<C> (implements org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface, org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface, org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>)
  • org.biojava.nbio.genome.uniprot.UniprotToFasta
  • org.biojava.nbio.structure.symmetry.core.UniqueSequenceList (implements java.lang.Cloneable)
  • org.biojava.nbio.structure.xtal.UnitCellBoundingBox
  • org.biojava.nbio.structure.URLIdentifier (implements org.biojava.nbio.structure.StructureIdentifier)
  • org.biojava.nbio.structure.align.util.UserConfiguration
  • org.biojava.nbio.aaproperties.Utils
  • org.biojava.nbio.survival.cox.WaldTest
  • org.biojava.nbio.survival.cox.WaldTestInfo
  • demo.WebStartClientDemo
  • org.biojava.nbio.structure.align.webstart.WebStartDBSearch
  • org.biojava.nbio.structure.align.webstart.WebStartDBSearchResults
  • org.biojava.nbio.structure.align.webstart.WebStartMain
  • org.biojava.nbio.core.sequence.views.WindowedSequence<C> (implements java.lang.Iterable<T>)
  • org.biojava.nbio.survival.data.WorkSheet
  • org.biojava.nbio.structure.validation.WwPDBValidationInformation (implements java.io.Serializable)
  • javax.xml.bind.annotation.adapters.XmlAdapter<ValueType,BoundType>
    • org.biojava.nbio.structure.xtal.io.TransfAlgebraicAdapter
  • org.biojava.nbio.core.util.XMLHelper
  • org.biojava.nbio.structure.scop.server.XMLUtil
  • org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider (implements org.biojava.nbio.structure.io.mmcif.ChemCompProvider)

Interface Hierarchy

• org.biojava.nbio.core.alignment.matrices.AAIndexProvider
• org.biojava.nbio.core.sequence.template.Accessioned
  • org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.location.template.Location)
  • org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>
    • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava.nbio.core.sequence.location.template.Location (also extends java.lang.Iterable<T>)
    • org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.template.Accessioned)
  • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
  • org.biojava.nbio.core.sequence.template.Sequence<C> (also extends java.lang.Iterable<T>)
    • org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>
      • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
    • org.biojava.nbio.core.sequence.template.SequenceReader<C>
      • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
    • org.biojava.nbio.core.sequence.template.SequenceView<C>
  • org.biojava.nbio.core.sequence.template.SequenceReader<C>
    • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
  • org.biojava.nbio.core.sequence.template.SequenceView<C>
• org.biojava.nbio.structure.align.pairwise.Alignable
• org.biojava.nbio.structure.gui.events.AlignmentPositionListener
• org.biojava.nbio.structure.align.events.AlignmentProgressListener
• org.biojava.nbio.ontology.utils.Annotatable
  • org.biojava.nbio.ontology.OntologyTerm
  • org.biojava.nbio.ontology.RemoteTerm
  • org.biojava.nbio.ontology.Term
    • org.biojava.nbio.ontology.OntologyTerm
    • org.biojava.nbio.ontology.RemoteTerm
    • org.biojava.nbio.ontology.Triple
    • org.biojava.nbio.ontology.Variable
  • org.biojava.nbio.ontology.Triple
  • org.biojava.nbio.ontology.Variable
• org.biojava.nbio.ontology.utils.Annotation
• org.biojava.nbio.structure.AtomPositionMap.GroupMatcher
• org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
• org.biojava.nbio.structure.quaternary.io.BioUnitDataProvider
• org.biojava.nbio.structure.Bond
• org.biojava.nbio.structure.cath.CathDatabase
• org.biojava.nbio.survival.kaplanmeier.figure.CensorStatusSelect
• org.biojava.nbio.structure.Chain
• org.biojava.nbio.survival.data.ChangeValue
• org.biojava.nbio.structure.io.mmcif.ChemCompProvider
• java.lang.Cloneable
  • org.biojava.nbio.structure.Atom (also extends org.biojava.nbio.structure.PDBRecord)
  • org.biojava.nbio.structure.Structure
• org.biojava.nbio.structure.gui.util.color.ColorInterpolator
• java.lang.Comparable<T>
  • org.biojava.nbio.core.sequence.location.template.Point
• java.util.Comparator<T>
  • org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
• org.biojava.nbio.core.sequence.template.Compound
  • org.biojava.nbio.core.sequence.template.ComplementCompound
• org.biojava.nbio.core.sequence.template.CompoundSet<C>
• org.biojava.nbio.core.sequence.template.CompoundTranslator<F,T>
• org.biojava.nbio.structure.align.ce.ConfigStrucAligParams
• org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper
• org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface
• org.biojava.nbio.survival.kaplanmeier.metadata.DiscreteQuantizerInterface
• org.biojava.nbio.structure.domain.DomainProvider
• org.biojava.nbio.structure.ecod.EcodDatabase
• org.biojava.nbio.core.sequence.edits.Edit<C>
• org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface<S,C>
• org.biojava.nbio.sequencing.io.fastq.FastqReader
• org.biojava.nbio.sequencing.io.fastq.FastqWriter
• org.biojava.nbio.genome.parsers.gff.FeatureI
• org.biojava.nbio.core.sequence.features.FeatureInterface<S,C>
• org.biojava.nbio.core.sequence.features.FeatureRetriever
• org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface
• org.biojava.nbio.alignment.template.GapPenalty
• org.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface<S,C>
• org.biojava.nbio.structure.Group
  • org.biojava.nbio.structure.AminoAcid
• org.biojava.nbio.alignment.template.HierarchicalClusterer<S,C>
• org.biojava.nbio.ws.hmmer.HmmerScan
• org.biojava.nbio.core.sequence.io.util.IOUtils.ReaderProcessor
• org.biojava.nbio.aaproperties.IPeptideProperties
• org.biojava.nbio.aaproperties.profeat.IProfeatProperties
• java.lang.Iterable<T>
  • org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.template.Accessioned, org.biojava.nbio.core.sequence.location.template.Location)
  • org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>
    • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava.nbio.core.sequence.location.template.Location (also extends org.biojava.nbio.core.sequence.template.Accessioned)
    • org.biojava.nbio.core.sequence.location.template.AccesionedLocation (also extends org.biojava.nbio.core.sequence.template.Accessioned)
  • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
  • org.biojava.nbio.core.alignment.template.MutableProfile<S,C>
    • org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.ProfilePair<S,C>)
    • org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.SequencePair<S,C>)
  • org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>, org.biojava.nbio.core.alignment.template.ProfilePair<S,C>)
  • org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>, org.biojava.nbio.core.alignment.template.SequencePair<S,C>)
  • org.biojava.nbio.core.alignment.template.Profile<S,C>
    • org.biojava.nbio.core.alignment.template.MutableProfile<S,C>
      • org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.ProfilePair<S,C>)
      • org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.SequencePair<S,C>)
    • org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>, org.biojava.nbio.core.alignment.template.ProfilePair<S,C>)
    • org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>, org.biojava.nbio.core.alignment.template.SequencePair<S,C>)
    • org.biojava.nbio.core.alignment.template.ProfilePair<S,C>
      • org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>)
    • org.biojava.nbio.core.alignment.template.ProfileView<S,C>
    • org.biojava.nbio.core.alignment.template.SequencePair<S,C>
      • org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>)
  • org.biojava.nbio.core.alignment.template.ProfilePair<S,C>
    • org.biojava.nbio.core.alignment.template.MutableProfilePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>)
  • org.biojava.nbio.core.alignment.template.ProfileView<S,C>
  • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
  • org.biojava.nbio.core.sequence.template.Sequence<C> (also extends org.biojava.nbio.core.sequence.template.Accessioned)
    • org.biojava.nbio.core.alignment.template.AlignedSequence<S,C>
      • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava.nbio.core.alignment.template.MutableAlignedSequence<S,C>
    • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
    • org.biojava.nbio.core.sequence.template.SequenceReader<C>
      • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
    • org.biojava.nbio.core.sequence.template.SequenceView<C>
  • org.biojava.nbio.core.alignment.template.SequencePair<S,C>
    • org.biojava.nbio.core.alignment.template.MutableSequencePair<S,C> (also extends org.biojava.nbio.core.alignment.template.MutableProfile<S,C>)
  • org.biojava.nbio.core.sequence.template.SequenceReader<C>
    • org.biojava.nbio.core.sequence.template.ProxySequenceReader<C>
  • org.biojava.nbio.core.sequence.template.SequenceView<C>
• org.biojava.nbio.core.sequence.template.LightweightProfile<S,C>
• org.biojava.nbio.structure.align.ce.MatrixListener
• org.biojava.nbio.structure.io.mmcif.MMcifConsumer
• org.biojava.nbio.structure.io.mmcif.MMcifParser
• org.biojava.nbio.protmod.ModificationCondition
• org.biojava.nbio.protmod.structure.ModifiedCompound
• org.biojava.nbio.structure.align.MultipleStructureAligner
• org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer
• org.biojava.nbio.ontology.obo.OboFileEventListener
• org.biojava.nbio.ontology.Ontology
• org.biojava.nbio.ontology.OntologyFactory
• org.biojava.nbio.ontology.OntologyOps
• org.biojava.nbio.structure.symmetry.internal.OrderDetector
• org.biojava.nbio.sequencing.io.fastq.ParseListener
• org.biojava.nbio.structure.PDBRecord
  • org.biojava.nbio.structure.Atom (also extends java.lang.Cloneable)
• org.biojava.nbio.structure.domain.PDPProvider
• org.biojava.nbio.core.sequence.location.template.Point.Resolver<T>
• org.biojava.nbio.structure.symmetry.geometry.Polyhedron
• org.biojava.nbio.protmod.ProteinModification
• org.biojava.nbio.structure.symmetry.core.QuatSymmetrySolver
• org.biojava.nbio.structure.quaternary.io.RawBioUnitDataProvider
• org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService
• org.biojava.nbio.core.search.io.ResultFactory
• java.lang.Runnable
  • org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
• org.biojava.nbio.structure.scop.ScopDatabase
  • org.biojava.nbio.structure.scop.LocalScopDatabase
• org.biojava.nbio.alignment.template.Scorer
  • org.biojava.nbio.alignment.template.Aligner<S,C>
    • org.biojava.nbio.alignment.template.MatrixAligner<S,C>
    • org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
    • org.biojava.nbio.alignment.template.PartitionRefiner<S,C> (also extends org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
    • org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
    • org.biojava.nbio.alignment.template.RescoreRefiner<S,C>
  • org.biojava.nbio.alignment.template.MatrixAligner<S,C>
  • org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>
  • org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>, org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>)
  • org.biojava.nbio.alignment.template.PairwiseSequenceScorer<S,C>
    • org.biojava.nbio.alignment.template.PairInProfileScorer<S,C>
    • org.biojava.nbio.alignment.template.PairwiseSequenceAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>)
  • org.biojava.nbio.alignment.template.PartitionRefiner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>, org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
  • org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>, org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>)
  • org.biojava.nbio.alignment.template.ProfileProfileScorer<S,C>
    • org.biojava.nbio.alignment.template.PartitionRefiner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>)
    • org.biojava.nbio.alignment.template.ProfileProfileAligner<S,C> (also extends org.biojava.nbio.alignment.template.Aligner<S,C>)
  • org.biojava.nbio.alignment.template.RescoreRefiner<S,C>
• org.biojava.nbio.structure.align.multiple.ScoresCache
  • org.biojava.nbio.structure.align.multiple.Block
  • org.biojava.nbio.structure.align.multiple.BlockSet
  • org.biojava.nbio.structure.align.multiple.MultipleAlignment
  • org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble
• org.biojava.nbio.structure.gui.Selection
• org.biojava.nbio.structure.SeqMisMatch
• org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<C>
• org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<S,C>
• org.biojava.nbio.core.sequence.io.template.SequenceParserInterface
• java.io.Serializable
  • org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
  • org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
• org.biojava.nbio.sequencing.io.fastq.StreamListener
• org.biojava.nbio.structure.align.StructureAlignment
• org.biojava.nbio.structure.StructureIdentifier
• org.biojava.nbio.structure.gui.util.StructurePairSelector
• org.biojava.nbio.structure.io.StructureProvider
  • org.biojava.nbio.structure.io.StructureIOFile
• org.biojava.nbio.structure.gui.StructureViewer
• org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C>
• org.biojava.nbio.structure.symmetry.internal.SymmetryRefiner
• org.biojava.nbio.core.sequence.transcription.Table
• javax.swing.tree.TreeNode
  • org.biojava.nbio.alignment.template.GuideTreeNode<S,C>
• org.biojava.nbio.structure.align.ce.UserArgumentProcessor
• org.biojava.nbio.core.util.XMLWriter

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.biojava.nbio.core.alignment.template.Profile.StringFormat
    • org.biojava.nbio.core.alignment.template.AlignedSequence.Step
    • org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceUsage
    • org.biojava.nbio.core.sequence.SequenceOptimizationHints.SequenceCollection
    • org.biojava.nbio.core.sequence.DNASequence.DNAType
    • org.biojava.nbio.core.sequence.Strand
    • org.biojava.nbio.core.sequence.DataSource
    • org.biojava.nbio.core.sequence.template.LightweightProfile.StringFormat
    • org.biojava.nbio.core.sequence.template.AbstractSequence.AnnotationType
    • org.biojava.nbio.core.sequence.transcription.Frame
    • org.biojava.nbio.phylo.TreeType
    • org.biojava.nbio.phylo.TreeConstructorType
    • org.biojava.nbio.alignment.Alignments.PairInProfileScorerType
    • org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType
    • org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType
    • org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType
    • org.biojava.nbio.alignment.Alignments.RefinerType
    • org.biojava.nbio.alignment.routines.AlignerHelper.Last
    • org.biojava.nbio.alignment.template.GapPenalty.Type
    • org.biojava.nbio.structure.BondType
    • org.biojava.nbio.structure.StructureIO.StructureFiletype
    • org.biojava.nbio.structure.HetatomImpl.PerformanceBehavior
    • org.biojava.nbio.structure.ExperimentalTechnique
    • org.biojava.nbio.structure.GroupType
    • org.biojava.nbio.structure.ElementType (implements java.io.Serializable)
    • org.biojava.nbio.structure.Element (implements java.io.Serializable)
    • org.biojava.nbio.structure.PDBStatus.Status
    • org.biojava.nbio.structure.align.ce.CECPParameters.DuplicationHint
    • org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy
    • org.biojava.nbio.structure.align.client.StructureName.Source
    • org.biojava.nbio.structure.cath.CathCategory
    • org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior
    • org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior
    • org.biojava.nbio.structure.io.mmcif.chem.PolymerType (implements java.io.Serializable)
    • org.biojava.nbio.structure.io.mmcif.chem.ResidueType (implements java.io.Serializable)
    • org.biojava.nbio.structure.scop.Astral.AstralSet
    • org.biojava.nbio.structure.scop.ScopCategory (implements java.io.Serializable)
    • org.biojava.nbio.structure.secstruc.SecStrucType
    • org.biojava.nbio.structure.secstruc.BridgeType
    • org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia.SymmetryClass
    • org.biojava.nbio.structure.symmetry.internal.CESymmParameters.OrderDetectorMethod
    • org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod
    • org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType
    • org.biojava.nbio.structure.xtal.TransformType
    • org.biojava.nbio.structure.xtal.BravaisLattice
    • org.biojava.nbio.structure.gui.RenderStyle
    • org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
    • org.biojava.nbio.sequencing.io.fastq.FastqVariant
    • org.biojava.nbio.genome.parsers.cytoband.StainType (implements java.io.Serializable)
    • org.biojava.nbio.protmod.ModificationOccurrenceType
    • org.biojava.nbio.protmod.ModificationCategory
    • org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
    • org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
    • org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
    • org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
    • org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
    • org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
    • org.biojava.nbio.ronn.RonnConstraint.Threshold
    • org.biojava.nbio.aaproperties.PeptideProperties.SingleLetterAACode
    • org.biojava.nbio.aaproperties.CommandPrompt.PropertyName
    • org.biojava.nbio.aaproperties.profeat.IProfeatProperties.ATTRIBUTE
    • org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING
    • org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION
    • org.biojava.nbio.aaproperties.profeat.IProfeatProperties.DISTRIBUTION
    • org.biojava.nbio.survival.cox.ResidualsCoxph.Type
    • org.biojava.nbio.survival.cox.CoxMethod
    • org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
    • org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
    • org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
    • org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower