Name | Description | Type | Package | Framework |
AAindexFactory | Factory class to get Providers for substitution matrices the are provided by the AAINDEX database. | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
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AAIndexFileParser | | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
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AAIndexProvider | | Interface | org.biojava.nbio.core.alignment.matrices | BioJava |
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AboutDialog | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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AbstractAlignmentJmol | An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
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AbstractAnnotation | A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map. | Class | org.biojava.nbio.ontology.utils | BioJava |
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AbstractBean | a generic class that implements the toString method for a beanAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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AbstractCompound | | Class | org.biojava.nbio.core.sequence.template | BioJava |
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AbstractCompoundSet | | Class | org.biojava.nbio.core.sequence.template | BioJava |
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AbstractCompoundTranslator | | Class | org.biojava.nbio.core.sequence.template | BioJava |
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AbstractFeature | A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user | Class | org.biojava.nbio.core.sequence.features | BioJava |
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AbstractLocation | Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand | Class | org.biojava.nbio.core.sequence.location.template | BioJava |
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AbstractMatrixAligner | | Class | org.biojava.nbio.alignment.template | BioJava |
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AbstractNucleotideCompoundSet | | Class | org.biojava.nbio.core.sequence.template | BioJava |
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AbstractPairwiseSequenceAligner | | Class | org.biojava.nbio.alignment.template | BioJava |
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AbstractProfileProfileAligner | | Class | org.biojava.nbio.alignment.template | BioJava |
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AbstractScorer | | Class | org.biojava.nbio.alignment.template | BioJava |
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AbstractScoresCache | Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
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AbstractSequence | The base class for DNA, RNA and Protein sequences. | Class | org.biojava.nbio.core.sequence.template | BioJava |
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AbstractStructureAlignment | | Class | org.biojava.nbio.structure.align | BioJava |
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AbstractTerm | Abstract implementation of term This provides basic change-forwarding functionality from | Class | org.biojava.nbio.ontology | BioJava |
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AbstractUserArgumentProcessor | Base class for a new structure alignment CLI. | Class | org.biojava.nbio.structure.align.ce | BioJava |
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AccesionedLocation | A location which is bound to an AccessionID. | Interface | org.biojava.nbio.core.sequence.location.template | BioJava |
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Accessioned | | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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AccessionID | Used in Sequences as the unique indentifier. | Class | org.biojava.nbio.core.sequence | BioJava |
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AFP | A class to represent a FATCAT AFPAuthor:Andreas PrlicSee Also:Serialized Form | Class | org.biojava.nbio.structure.align.model | BioJava |
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AFPAlignmentDisplay | | Class | org.biojava.nbio.structure.align.util | BioJava |
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AFPCalculator | a class that performs calculations on AFPCHainsAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
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AFPChain | A bean to contain the core of a structure alignment. | Class | org.biojava.nbio.structure.align.model | BioJava |
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AFPChainCoordManager | | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
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AFPChainer | a class to chain AFPs to an alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
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AFPChainFlipper | | Class | org.biojava.nbio.structure.align.xml | BioJava |
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AFPChainScorer | | Class | org.biojava.nbio.structure.align.util | BioJava |
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AfpChainWriter | A class to convert the data in an AfpChain object to various String outputs. | Class | org.biojava.nbio.structure.align.model | BioJava |
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AFPChainXMLConverter | | Class | org.biojava.nbio.structure.align.xml | BioJava |
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AFPChainXMLParser | | Class | org.biojava.nbio.structure.align.xml | BioJava |
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AFPFromFasta | Demo displaying a structural alignment from a FASTA file using FastaAFPChainConverter. | Class | demo | BioJava |
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AFPOptimizer | | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
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AFPPostProcessor | does post processing after alignment chainginAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
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AFPTwister | | Class | org.biojava.nbio.structure.align | BioJava |
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AgScore | | Class | org.biojava.nbio.survival.cox.stats | BioJava |
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AligMatEl | | Class | org.biojava.nbio.structure.align.helper | BioJava |
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Alignable | | Interface | org.biojava.nbio.structure.align.pairwise | BioJava |
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AlignedPosition | | Class | org.biojava.nbio.structure.gui.util | BioJava |
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AlignedSequence | Defines a data structure for a Sequence within an alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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Aligner | Defines an algorithm which computes an alignment Profile from a list of Sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
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AlignerHelper | Static utility to construct alignment routines from a common library of methods. | Class | org.biojava.nbio.alignment.routines | BioJava |
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AlignmentCalc | A class that obtains two structures via DAS and aligns them This is done in a separate thread. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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AlignmentCalc | A class that obtains two structures via DAS and aligns them This is done in a separate thread. | Class | org.biojava.nbio.structure.gui.util | BioJava |
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AlignmentCalcDB | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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AlignmentCalculationRunnable | | Interface | org.biojava.nbio.structure.align.gui | BioJava |
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AlignmentGui | A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, | Class | org.biojava.nbio.structure.align.gui | BioJava |
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AlignmentGuiDemo | Get an instance of the two alignment GUIs. | Class | demo | BioJava |
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AlignmentPositionListener | | Interface | org.biojava.nbio.structure.gui.events | BioJava |
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AlignmentProgressListener | | Interface | org.biojava.nbio.structure.align.events | BioJava |
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AlignmentProgressListener | | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
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AlignmentResult | A class to track the alignment results in a flat fileAuthor:andreasSee Also:Serialized Form | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
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Alignments | Static utility to easily run alignment routines. | Class | org.biojava.nbio.alignment | BioJava |
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AlignmentTextPanel | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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AlignmentTools | Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities. | Class | org.biojava.nbio.structure.align.util | BioJava |
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AligNPE | | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
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AlignTools | | Class | org.biojava.nbio.structure.align.helper | BioJava |
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AligPanel | A JPanel that can display an AFPChain in a nice way and interact with Jmol. | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
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AligPanelMouseMotionListener | | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
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AligUIManager | | Class | org.biojava.nbio.structure.align.webstart | BioJava |
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AllChemCompProvider | A ChemComp provider that downloads and caches the components. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
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AlreadyExistsException | Thrown to indicate that a term or triple can't be added to an ontology because it is already present. | Class | org.biojava.nbio.ontology | BioJava |
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AltAligComparator | a comparator to sort AlternativeAlignments based on their number of equivalent residuesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
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AlternativeAlignment | Alternative alignments arise from different seed alignments or seed FPairs. | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
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AlternativeAlignmentFrame | a frame showing the alternative alignments, which are the result of a structure superimpositionSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
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AmbiguityDNACompoundSet | | Class | org.biojava.nbio.core.sequence.compound | BioJava |
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AmbiguityDNARNAHybridCompoundSet | Ambiguity set for hybrid DNA/RNA sequences. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
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AmbiguityRNACompoundSet | | Class | org.biojava.nbio.core.sequence.compound | BioJava |
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AminoAcid | A Group that represents an AminoAcid. | Interface | org.biojava.nbio.structure | BioJava |
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AminoAcidComposition | | Class | org.biojava.nbio.aaproperties.xml | BioJava |
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AminoAcidCompositionTable | | Class | org.biojava.nbio.aaproperties.xml | BioJava |
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AminoAcidCompound | Used to describe an Amino Acid. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
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AminoAcidCompoundSet | Set of proteinogenic amino acids. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
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AminoAcidImpl | AminoAcid inherits most from Hetatom. | Class | org.biojava.nbio.structure | BioJava |
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AnchoredPairwiseSequenceAligner | This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced | Class | org.biojava.nbio.alignment.routines | BioJava |
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AngleOrderDetectorPlus | Guesses an order of rotational symmetry from the angle. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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AngleOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
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Annotatable | Indicates that an object has an associated annotation. | Interface | org.biojava.nbio.ontology.utils | BioJava |
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Annotation | Arbitrary annotation associated with one or more objects. | Interface | org.biojava.nbio.ontology.utils | BioJava |
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App | | Class | org.biojava.nbio.genome | BioJava |
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App | | Class | org.biojava.nbio.ontology | BioJava |
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ArrayListProxySequenceReader | | Class | org.biojava.nbio.core.sequence.loader | BioJava |
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ArrayListSequenceReader | | Class | org.biojava.nbio.core.sequence.storage | BioJava |
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AsaCalculator | Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley. | Class | org.biojava.nbio.structure.asa | BioJava |
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AssertionFailure | An unchecked exception representing an Assertion failure. | Class | org.biojava.nbio.ontology.utils | BioJava |
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AssignmentXMLSerializer | | Class | org.biojava.nbio.structure.domain | BioJava |
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Astral | Provides programmatic access to ASTRAL representative sets. | Class | org.biojava.nbio.structure.scop | BioJava |
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Atom | A simple interface for an Atom. | Interface | org.biojava.nbio.structure | BioJava |
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AtomCache | A utility class that provides easy access to Structure objects. | Class | org.biojava.nbio.structure.align.util | BioJava |
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AtomContact | A pair of atoms that are in contactAuthor:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
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AtomContactSet | A set of atom-atom contacts to hold the results of intra and inter-chain contact calculationsAuthor:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
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AtomIdentifier | | Class | org.biojava.nbio.structure.contact | BioJava |
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AtomImpl | currently the coordinates of an atom are represented by a double[3] array. | Class | org.biojava.nbio.structure | BioJava |
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AtomInfo | This class uniquely describes an atomAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
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AtomInfoParser | | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
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AtomIterator | an iterator over all atoms of a structure / group. | Class | org.biojava.nbio.structure | BioJava |
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AtomPositionMap | A map from ResidueNumbers to ATOM record positions in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
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AtomSite | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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AuditAuthor | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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AugmentedResidueRange | Created by douglas on 1/23/15. | Class | org.biojava.nbio.structure | BioJava |
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Author | Describes author attributes for author information in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
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AutoSuggestProvider | | Interface | org.biojava.nbio.structure.align.gui.autosuggest | BioJava |
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AxisAligner | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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BasicSequence | Bare bones version of the Sequence object to be used sparingly. | Class | org.biojava.nbio.core.sequence | BioJava |
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BerkeleyScopInstallation | The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop. | Class | org.biojava.nbio.structure.scop | BioJava |
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BetaBridge | Container that represents a beta Bridge between two residues. | Class | org.biojava.nbio.structure.secstruc | BioJava |
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BioAssemblyIdentifier | | Class | org.biojava.nbio.structure | BioJava |
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BioAssemblyInfo | Representation of a Biological Assembly annotation as provided by the PDB. | Class | org.biojava.nbio.structure.quaternary | BioJava |
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BioAssemblyTools | | Class | org.biojava.nbio.structure.quaternary | BioJava |
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BioJavaAADemo | Created by andreas on 8/9/14. | Class | demo | BioJava |
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BiojavaJmol | A class that provides a simple GUI for JmolSince:1. | Class | org.biojava.nbio.structure.gui | BioJava |
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BioJavaStructureAlignment | Wrapper for the BioJava Structure Alignment ImplementationAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align | BioJava |
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BiologicalAssemblyBuilder | Reconstructs the quaternary structure of a protein from an asymmetric unitAuthor:Peter Rose, Andreas Prlic | Class | org.biojava.nbio.structure.quaternary | BioJava |
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BiologicalAssemblyTransformation | The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file. | Class | org.biojava.nbio.structure.quaternary | BioJava |
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BioUnitDataProvider | Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein. | Interface | org.biojava.nbio.structure.quaternary.io | BioJava |
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BioUnitDataProviderFactory | Factory to create BioUnitDataProvider instances. | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
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BitSequenceReader | An implementation of the popular bit encodings. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
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BlastAlignmentParameterEnum | enum BlastAlignmentParameterEnumAlignment request parameters accepted by QBlast service. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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BlastClustReader | | Class | org.biojava.nbio.structure.symmetry.utils | BioJava |
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BlastHitBuilder | Designed by Paolo Pavan. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
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BlastHomologyHits | | Class | org.biojava.nbio.genome.homology | BioJava |
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BlastHspBuilder | Designed by Paolo Pavan. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
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BlastJob | Information about QBlast search jobAuthor:Gediminas Rimsa | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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BlastMatrixEnum | enum BlastMatrixEnumEnum representing matrices supported by QBlast | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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BlastOutputAlignmentFormatEnum | enum BlastOutputAlignmentFormatEnumEnum representing available output alignment types. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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BlastOutputFormatEnum | enum BlastOutputFormatEnumEnum representing available output formats. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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BlastOutputParameterEnum | enum BlastOutputParameterEnumOutput parameters accepted by QBlast service. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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BlastProgramEnum | enum BlastProgramEnumEnum representing available blast programs. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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BlastResult | This class models a Blast/Blast plus result. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
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BlastResultBuilder | Designed by Paolo Pavan. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
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BlastTabularParser | Designed by Paolo Pavan. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
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BlastXMLParser | Re-designed by Paolo Pavan on the footprint of: org. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
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BlastXMLQuery | | Class | org.biojava.nbio.genome.query | BioJava |
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Block | A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
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BlockImpl | General implementation of a Block that supports any type of sequential alignment with gaps. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
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BlockSet | A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment. | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
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BlockSetImpl | A general implementation of a BlockSet to store a flexible part of a multiple alignment. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
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Bond | A simple bond -- it stores information about two atoms as well as information about its bond order. | Interface | org.biojava.nbio.structure | BioJava |
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BondImpl | A simple bond -- it stores information about two atoms as well as information about its bond order. | Class | org.biojava.nbio.structure | BioJava |
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BondMaker | Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary | Class | org.biojava.nbio.structure.io | BioJava |
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BondOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
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BondType | Work in progress - NOT final!Author:Jules Jacobsen | Class | org.biojava.nbio.structure | BioJava |
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BoundingBox | A bounding box for short cutting some geometrical calculations. | Class | org.biojava.nbio.structure.contact | BioJava |
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BravaisLattice | An enum to represent the 7 Bravais latticesEnum Constant Summary | Class | org.biojava.nbio.structure.xtal | BioJava |
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BridgeType | A bridge is formed by two non-overlapping stretches of three residues each (i-1,i,i+1) and (j-1,j,j+1), where i | Class | org.biojava.nbio.structure.secstruc | BioJava |
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BrowserOpener | | Class | org.biojava.nbio.structure.align.webstart | BioJava |
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BufferedReaderBytesRead | Need to keep track of actual bytes read and take advantage of buffered reader performance. | Class | org.biojava.nbio.core.sequence.io | BioJava |
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C2RotationSolver | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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CachedRemoteScopInstallation | An extension of the RemoteScopInstallation that caches some of the data locally. | Class | org.biojava.nbio.structure.scop | BioJava |
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CacheFactory | provides a SoftHashMap singleton. | Class | org.biojava.nbio.structure.align.util | BioJava |
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CAConverter | Converts full atom representations to Calpha only ones. | Class | org.biojava.nbio.structure.io | BioJava |
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Calc | Utility operations on Atoms, AminoAcids, etc. | Class | org.biojava.nbio.structure | BioJava |
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CalcBioAssemblySymmetry | | Class | org.biojava.nbio.structure.symmetry.analysis | BioJava |
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CallablePairwiseSequenceAligner | | Class | org.biojava.nbio.alignment.template | BioJava |
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CallablePairwiseSequenceScorer | | Class | org.biojava.nbio.alignment.template | BioJava |
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CallableProfileProfileAligner | | Class | org.biojava.nbio.alignment.template | BioJava |
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CallableStructureAlignment | | Class | org.biojava.nbio.structure.align | BioJava |
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CartesianProduct | A cartesian product between two lists A and B is the set of all ordered pairs of the elements of both sets. | Class | org.biojava.nbio.structure.quaternary | BioJava |
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CaseFreeAminoAcidCompoundSet | Set of proteinogenic amino acids. | Class | org.biojava.nbio.aaproperties.xml | BioJava |
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CaseInsensitiveCompound | Attempts to wrap compounds so it is possible to view them in a case insensitive manner | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
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CasePreservingProteinSequenceCreator | A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence. | Class | org.biojava.nbio.core.sequence.io | BioJava |
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CathCategory | The categories found within CATH. | Class | org.biojava.nbio.structure.cath | BioJava |
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CathDatabase | General API for interacting with CATH. | Interface | org.biojava.nbio.structure.cath | BioJava |
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CathDomain | A class which represents a single CATH domain. | Class | org.biojava.nbio.structure.cath | BioJava |
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CathFactory | Controls global CathDatabases being used. | Class | org.biojava.nbio.structure.cath | BioJava |
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CathFragment | | Class | org.biojava.nbio.structure.cath | BioJava |
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CathInstallation | | Class | org.biojava.nbio.structure.cath | BioJava |
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CathNode | Represents a node in the CATH hierarchy. | Class | org.biojava.nbio.structure.cath | BioJava |
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CathSegment | | Class | org.biojava.nbio.structure.cath | BioJava |
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CDSComparator | | Class | org.biojava.nbio.core.sequence | BioJava |
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CDSSequence | Represents a exon or coding sequence in a gene. | Class | org.biojava.nbio.core.sequence | BioJava |
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CECalculator | This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2. | Class | org.biojava.nbio.structure.align.ce | BioJava |
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CeCalculatorEnhanced | This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2. | Class | org.biojava.nbio.structure.align.ce | BioJava |
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CeCPMain | A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations. | Class | org.biojava.nbio.structure.align.ce | BioJava |
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CECPParameters | Provides parameters to CeCPMainAuthor:Spencer Bliven | Class | org.biojava.nbio.structure.align.ce | BioJava |
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CeCPUserArgumentProcessor | | Class | org.biojava.nbio.structure.align.ce | BioJava |
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Cell | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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CeMain | The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I. | Class | org.biojava.nbio.structure.align.ce | BioJava |
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CensorStatus | | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava |
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CensorStatusSelect | | Interface | org.biojava.nbio.survival.kaplanmeier.figure | BioJava |
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CeParameters | Contains the parameters that can be sent to CEAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
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CeSideChainMain | | Class | org.biojava.nbio.structure.align.ce | BioJava |
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CeSideChainUserArgumentProcessor | | Class | org.biojava.nbio.structure.align.ce | BioJava |
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CeSymm | Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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CeSymmIterative | Iterative version of CeSymm that aims at identifying all symmetry axis (internal or quaternary) of a particular structure. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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CESymmParameters | Provides parameters to CeSymm. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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CeSymmResult | This Class stores all the relevant information of an internal symmetry result obtained with CeSymm. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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CeUserArgumentProcessor | process the arguments from command lineAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
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Chain | Defines the interface for a Chain. | Interface | org.biojava.nbio.structure | BioJava |
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ChainClusterer | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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ChainImpl | A Chain in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
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ChainSignature | | Class | org.biojava.nbio.structure.symmetry.misc | BioJava |
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ChangeValue | | Interface | org.biojava.nbio.survival.data | BioJava |
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ChargeAdder | | Class | org.biojava.nbio.structure.io | BioJava |
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ChemComp | A definition for a Chemical Component, as maintained by the wwPDB. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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ChemCompAtom | stores these fields: _chem_comp_atom. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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ChemCompBond | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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ChemCompConsumer | | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
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ChemCompDescriptor | Container object for _pdbx_chem_comp_descriptorSince:3. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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ChemCompDistribution | | Class | demo | BioJava |
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ChemCompGroupFactory | | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
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ChemCompProvider | Interface that is implemented by all classes that can provide ChemComp definitions. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
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ChemCompTools | Some tools for working with chemical compounds. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
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ChemicalComponentDictionary | A representation of the Chemical Component Dictionary. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
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ChiSq | | Class | org.biojava.nbio.survival.cox.stats | BioJava |
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Cholesky2 | | Class | org.biojava.nbio.survival.cox.stats | BioJava |
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CholeskyDecomposition | Cholesky Decomposition. | Class | org.biojava.nbio.structure.jama | BioJava |
|
ChooseDirAction | Ask the user to provide a directory containting PDB files. | Class | org.biojava.nbio.structure.align.gui | BioJava |
|
ChromosomeSequence | A ChromosomeSequence is a DNASequence but keeps track of geneSequencesAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
|
Chsolve2 | | Class | org.biojava.nbio.survival.cox.stats | BioJava |
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Clash | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
|
ClasspathResource | This object represents a classpath resource on the local system. | Class | org.biojava.nbio.core.sequence.io.util | BioJava |
|
ClinicalMetaDataOutcome | | Class | org.biojava.nbio.survival.kaplanmeier.metadata | BioJava |
|
CliTools | Utilities for autoconfiguring javabeans based on command line arguments. | Class | org.biojava.nbio.structure.align.util | BioJava |
|
ClusterAltAligs | A class that clusters alternative alignments according to theirSince:1. | Class | org.biojava.nbio.structure.align | BioJava |
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ClusterDomains | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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ClusterMerger | Merges clusters based on their sequence identity. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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ClusterProteinChains | Clusters the chains of one or two structures by sequence. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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CodonCompound | | Class | org.biojava.nbio.core.sequence.compound | BioJava |
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CollectionTools | Utilities for working with collections. | Class | org.biojava.nbio.structure.align.util | BioJava |
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ColorConverter | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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ColorInterpolator | | Interface | org.biojava.nbio.structure.gui.util.color | BioJava |
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ColorUtils | | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
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CombinationGenerator | | Class | org.biojava.nbio.structure.symmetry.utils | BioJava |
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CommandPrompt | | Class | org.biojava.nbio.aaproperties | BioJava |
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CompactCharSequence | http://www. | Class | org.biojava.nbio.survival.data | BioJava |
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Comparison | This class provides static methods for the calculation of the percentage of identity between two aligned sequences. | Class | org.biojava.nbio.phylo | BioJava |
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ComplementCompound | | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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ComplementSequenceView | For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying | Class | org.biojava.nbio.core.sequence.views | BioJava |
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Component | contains information about a certain Component. | Class | org.biojava.nbio.protmod | BioJava |
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ComponentXMLConverter | | Class | org.biojava.nbio.protmod.io | BioJava |
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Compound | | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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Compound | An object to contain the info from the PDB header for a Molecule. | Class | org.biojava.nbio.structure | BioJava |
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CompoundFinder | Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure. | Class | org.biojava.nbio.structure.io | BioJava |
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CompoundNotFoundException | | Class | org.biojava.nbio.core.exceptions | BioJava |
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CompoundSet | | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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CompoundTranslator | | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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ConcurrencyTools | Static utility to easily share a thread pool for concurrent/parallel/lazy execution. | Class | org.biojava.nbio.core.util | BioJava |
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ConfigPDBInstallPanel | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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ConfigStrucAligParams | | Interface | org.biojava.nbio.structure.align.ce | BioJava |
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ConfigurationException | | Class | org.biojava.nbio.structure.align.util | BioJava |
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ConfigXMLHandler | | Class | org.biojava.nbio.structure.align.webstart | BioJava |
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Constraints | This class is used to support the implementation of properties stated in IPeptideProperties. | Class | org.biojava.nbio.aaproperties | BioJava |
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ContinuousColorMapper | Provides a mapping between real numbers and Colors. | Interface | org.biojava.nbio.structure.gui.util.color | BioJava |
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ContinuousColorMapperTransform | Maps colors by performing a transform of the input data and then passing the transformed value to a ContinuousColorMapper for rendering. | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
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Convert2Charge | | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava |
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Convert2Hydrophobicity | | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava |
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Convert2NormalizedVanDerWaalsVolume | | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava |
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Convert2Polarity | | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava |
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Convert2Polarizability | | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava |
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Convert2SecondaryStructure | | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava |
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Convert2SolventAccessibility | | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava |
|
Convertor | | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava |
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CookBook | | Class | demo | BioJava |
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CookbookMSA | | Class | demo | BioJava |
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CoordManager | a class that manages the conversion of sequence coordinate system to JPanel drawing coordinates | Class | org.biojava.nbio.structure.gui.util | BioJava |
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CoreSuperimposer | Superimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
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CountProgressListener | | Class | org.biojava.nbio.structure.align.client | BioJava |
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CoxCC | | Class | org.biojava.nbio.survival.cox | BioJava |
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CoxCoefficient | | Class | org.biojava.nbio.survival.cox | BioJava |
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CoxComparatorInterface | | Interface | org.biojava.nbio.survival.cox.comparators | BioJava |
|
CoxHelper | The CoxHelper class is provided to start with a tab delimited file in a similar process in R and return the results as a CoxInfo class. | Class | org.biojava.nbio.survival.cox | BioJava |
|
CoxInfo | Holds the results of a cox analysis where calling dump(), toString() will give an output similar to RAuthor:Scooter Willis | Class | org.biojava.nbio.survival.cox | BioJava |
|
CoxMart | | Class | org.biojava.nbio.survival.cox | BioJava |
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CoxMethod | | Class | org.biojava.nbio.survival.cox | BioJava |
|
CoxR | This is a port of the R survival code used for doing Cox Regression. | Class | org.biojava.nbio.survival.cox | BioJava |
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CoxScore | | Class | org.biojava.nbio.survival.cox | BioJava |
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CoxVariables | | Class | org.biojava.nbio.survival.cox | BioJava |
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CoxVariablesOverallModelFitComparator | | Class | org.biojava.nbio.survival.cox.comparators | BioJava |
|
CoxVariablesVariableComparator | | Class | org.biojava.nbio.survival.cox.comparators | BioJava |
|
CRC64Checksum | Utility class that calculates a CRC64 checksum on a stream of bytes. | Class | org.biojava.nbio.core.util | BioJava |
|
CrystalBuilder | A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators | Class | org.biojava.nbio.structure.xtal | BioJava |
|
CrystalCell | A crystal cell's parameters. | Class | org.biojava.nbio.structure.xtal | BioJava |
|
CrystalTransform | Representation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m) | Class | org.biojava.nbio.structure.xtal | BioJava |
|
Cut | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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CutDomain | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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CutSites | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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CutValues | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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Cytoband | | Class | org.biojava.nbio.genome.parsers.cytoband | BioJava |
|
CytobandParser | Parses the cytoband (karyotype) file from UCSC. | Class | org.biojava.nbio.genome.parsers.cytoband | BioJava |
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DatabasePDBremark | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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DatabasePDBrev | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
|
DatabasePdbrevRecord | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
|
DatabaseReferenceInterface | If a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s) | Interface | org.biojava.nbio.core.sequence.features | BioJava |
|
Dataset | | Class | org.biojava.nbio.phosphosite | BioJava |
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DataSource | GenBank gi | Class | org.biojava.nbio.core.sequence | BioJava |
|
DBRef | A class to represent database cross references. | Class | org.biojava.nbio.structure | BioJava |
|
DBReferenceInfo | If you have a uniprot ID then it is possible to get a collection of other id(s) that the protein is known by. | Class | org.biojava.nbio.core.sequence.features | BioJava |
|
DBResultTable | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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DBSearchGUI | | Class | org.biojava.nbio.structure.align.gui | BioJava |
|
DefaultAAIndexProvider | The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directoryAuthor:Andreas Prlic | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
|
DefaultAutoSuggestProvider | | Class | org.biojava.nbio.structure.align.gui.autosuggest | BioJava |
|
DefaultMatrixMapper | Color Mapper which mimics the default coloring of JMatrixPanel pixels. | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
|
DefaultOps | Default implementation of OntologyOps. | Class | org.biojava.nbio.ontology | BioJava |
|
DemoAlignmentFromFasta | Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file. | Class | demo | BioJava |
|
DemoAlignProteins | | Class | demo | BioJava |
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DemoAsa | | Class | demo | BioJava |
|
DemoAtomCache | Example of how to load PDB files using the AtomCache class. | Class | demo | BioJava |
|
DemoBerkeleyScop | A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOPSince:3. | Class | demo | BioJava |
|
DemoCATH | An example for how to access CATH data. | Class | demo | BioJava |
|
DemoCE | Example of how to run a structure alignment using the CE algorithm. | Class | demo | BioJava |
|
DemoCeSymm | Quick demo of how to call CE-Symm programmatically. | Class | demo | BioJava |
|
DemoChangeChemCompProvider | This demo shows how to use an alternative ChemCompProvider. | Class | demo | BioJava |
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DemoCommandLineStartup | | Class | demo | BioJava |
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DemoContacts | | Class | demo | BioJava |
|
DemoCrystalInterfaces | | Class | demo | BioJava |
|
DemoDistanceTree | This demo contains the CookBook example to create a phylogenetic tree from a multiple sequence alignment (MSA). | Class | demo | BioJava |
|
DemoDomainsplit | | Class | demo | BioJava |
|
DemoFATCAT | | Class | demo | BioJava |
|
DemoLoadSecStruc | Demonstration of how to load a Structure with the SS information, either from the PDB file annotation (Author's assignment) or from the DSSP file in the | Class | demo | BioJava |
|
DemoLoadStructure | Example for how to load protein structures (from PDB files). | Class | demo | BioJava |
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DemoLoadSubstMax | | Class | demo | BioJava |
|
DemoMMCIFReader | An example of how to read MMcif filesAuthor:Andreas Prlic | Class | demo | BioJava |
|
DemoMultipleMC | Demo for running the MultipleMC Algorithm on a protein family. | Class | demo | BioJava |
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DemoNWALignment | | Class | demo | BioJava |
|
DemoOrientBioAssembly | Created by ap3 on 02/04/2015. | Class | demo | BioJava |
|
DemoRotationAxis | A demo for how to use RotationAxis to display the rotation for an alignment. | Class | demo | BioJava |
|
DemoSCOP | A class demonstrating the use of the SCOP parsing toolsAuthor:Andreas Prlic | Class | demo | BioJava |
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DemoSecStrucCalc | Demonstration on how to use the Secondary Structure Prediction (DSSP) implementation in BioJava and obtain different SS representations and | Class | demo | BioJava |
|
DemoShowBiolAssembly | | Class | demo | BioJava |
|
DemoShowCATHDomain | | Class | demo | BioJava |
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DemoShowLargeAssembly | | Class | demo | BioJava |
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DemoShowValidationResults | | Class | demo | BioJava |
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DemoSixFrameTranslation | Created by andreas on 8/10/15. | Class | demo | BioJava |
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DemoStructureFromFasta | Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file. | Class | demo | BioJava |
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DemoSW3DAligner | | Class | demo | BioJava |
|
DiscreteQuantizerInterface | | Interface | org.biojava.nbio.survival.kaplanmeier.metadata | BioJava |
|
DisplayAFP | A utility class for visualistion of structure alignmentsAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.gui | BioJava |
|
DistanceBox | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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DistanceMatrixCalculator | The DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD). | Class | org.biojava.nbio.phylo | BioJava |
|
DistanceTreeEvaluator | Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix. | Class | org.biojava.nbio.phylo | BioJava |
|
DNACompoundSet | | Class | org.biojava.nbio.core.sequence.compound | BioJava |
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DNASequence | This is class should model the attributes associated with a DNA sequenceAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
|
DNASequenceCreator | A helper class that allows different ways to read a string and create a DNA sequence. | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
DNAToRNATranslator | Performs the first stage of transcription by going from DNA to RNA. | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
|
Domain | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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DomainProvider | | Interface | org.biojava.nbio.structure.domain | BioJava |
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DomainProviderFactory | | Class | org.biojava.nbio.structure.domain | BioJava |
|
DotPlotPanel | Displays the dot plot trace for an alignment. | Class | org.biojava.nbio.structure.align.gui | BioJava |
|
DownloadChemCompProvider | This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
|
DSSPParser | Class to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure. | Class | org.biojava.nbio.structure.secstruc | BioJava |
|
EcodDatabase | General API for interacting with CATH. | Interface | org.biojava.nbio.structure.ecod | BioJava |
|
EcodDomain | | Class | org.biojava.nbio.structure.ecod | BioJava |
|
EcodFactory | Controls global CathDatabases being used. | Class | org.biojava.nbio.structure.ecod | BioJava |
|
EcodInstallation | Provides access to the Evolutionary Classification of Protein Domains (ECOD). | Class | org.biojava.nbio.structure.ecod | BioJava |
|
Edit | Interface for carrying out edit operations on a Sequence. | Interface | org.biojava.nbio.core.sequence.edits | BioJava |
|
EigenvalueDecomposition | Eigenvalues and eigenvectors of a real matrix. | Class | org.biojava.nbio.structure.jama | BioJava |
|
Element | | Class | org.biojava.nbio.aaproperties.xml | BioJava |
|
Element | Element is an enumeration of the elements of the periodic table. | Class | org.biojava.nbio.structure | BioJava |
|
ElementTable | | Class | org.biojava.nbio.aaproperties.xml | BioJava |
|
ElementType | ElementType is an enumeration of the types of elements found in the periodic table. | Class | org.biojava.nbio.structure | BioJava |
|
Entity | A simple class to represent Entity records in mmCif filesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
|
EntityPolySeq | Container for _entity_poly_seq recordsField Name mmCIF Data Item | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
|
EntitySrcGen | Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
|
EntitySrcNat | Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
|
EntitySrcSyn | PDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
|
Entry | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
|
Equals | A set of helper methods which return true if the two parameters are equal to each other. | Class | org.biojava.nbio.core.util | BioJava |
|
ExonComparator | Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction. | Class | org.biojava.nbio.core.sequence | BioJava |
|
ExonSequence | A gene contains a collection of Exon sequencesAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
|
ExperimentalTechnique | enum ExperimentalTechniqueAn enum to represent the experimental technique of a PDB structure | Class | org.biojava.nbio.structure | BioJava |
|
ExpressionFigure | | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava |
|
Exptl | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
|
FarmJob | A job as it can be run on the farm. | Class | org.biojava.nbio.structure.align | BioJava |
|
FarmJobParameters | | Class | org.biojava.nbio.structure.align.client | BioJava |
|
FarmJobRunnable | Contains the single thread for a job that can run multiple alignments. | Class | org.biojava.nbio.structure.align.client | BioJava |
|
FastaAFPChainConverter | A collection of static utilities to convert between AFPChains and FastaSequences. | Class | org.biojava.nbio.structure.io | BioJava |
|
FastaGeneWriter | A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version. | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
FastaHeaderFormatInterface | | Interface | org.biojava.nbio.core.sequence.io.template | BioJava |
|
FastaReader | Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
FastaReaderHelper | | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
FastaSequence | A FASTA formatted sequence. | Class | org.biojava.nbio.data.sequence | BioJava |
|
FastaSequenceParser | Used to parse a stream of a fasta file to get the sequenceAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
FastaStructureParser | Reads a protein sequence from a fasta file and attempts to match it to a 3D structure. | Class | org.biojava.nbio.structure.io | BioJava |
|
FastaWriter | The FastaWriter writes a collection of sequences to an outputStream. | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
FastaWriterHelper | The class that should be used to write out fasta file of a sequence collectionAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
Fastq | FASTQ formatted sequence. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
|
FastqBuilder | Fluent builder API for creating FASTQ formatted sequences. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
|
FastqReader | Reader for FASTQ formatted sequences. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |
|
FastqTools | Utility methods for FASTQ formatted sequences. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
|
FastqVariant | FASTQ sequence format variant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
|
FastqWriter | Writer for FASTQ formatted sequences. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |
|
FatCat | | Class | org.biojava.nbio.structure.align.fatcat | BioJava |
|
FatCatAligner | A class that does calculations on an AFPChainAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
|
FatCatFlexible | | Class | org.biojava.nbio.structure.align.fatcat | BioJava |
|
FatCatParameters | | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
|
FatCatRigid | | Class | org.biojava.nbio.structure.align.fatcat | BioJava |
|
FatCatUserArgumentProcessor | | Class | org.biojava.nbio.structure.align.fatcat | BioJava |
|
FCAlignHelper | | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
|
Feature | A Feature corresponds to a single row in a GFF file. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
|
FeatureDbReferenceInfo | It is DBReferenceInfo which implements FeatureInterface. | Class | org.biojava.nbio.core.sequence.features | BioJava |
|
FeatureHelper | | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
|
FeatureI | A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs. | Interface | org.biojava.nbio.genome.parsers.gff | BioJava |
|
FeatureInterface | Interface class to handle describing arbitrary features. | Interface | org.biojava.nbio.core.sequence.features | BioJava |
|
FeatureList | A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
|
FeatureRetriever | If a SequenceProxyReader implements this interface then that external source has a list features | Interface | org.biojava.nbio.core.sequence.features | BioJava |
|
FeaturesKeyWordInterface | Models the keywords that are annotated for a protein sequence at Uniprot. | Interface | org.biojava.nbio.core.sequence.features | BioJava |
|
FileConvert | Methods to convert a structure object into different file formats. | Class | org.biojava.nbio.structure.io | BioJava |
|
FileDownloadUtils | | Class | org.biojava.nbio.structure.io.util | BioJava |
|
FileParsingParameters | A class that configures parameters that can be sent to the PDB file parsers setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed. | Class | org.biojava.nbio.structure.io | BioJava |
|
FileProxyDNASequenceCreator | This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily. | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
FileProxyProteinSequenceCreator | This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily. | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
FlatFileCache | Provides a cache for storing multiple small files in memory. | Class | org.biojava.nbio.core.util | BioJava |
|
ForesterWrapper | This class contains wrapper methods for communication between BioJava and forester (e. | Class | org.biojava.nbio.phylo | BioJava |
|
FourBitSequenceReader | Four bit encoding of the bit formats. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
|
FractionalIdentityInProfileScorer | Profile. | Class | org.biojava.nbio.alignment | BioJava |
|
FractionalIdentityScorer | alignment columns which have identical Compounds. | Class | org.biojava.nbio.alignment | BioJava |
|
FractionalSimilarityInProfileScorer | Profile. | Class | org.biojava.nbio.alignment | BioJava |
|
FractionalSimilarityScorer | alignment columns which have similar Compounds. | Class | org.biojava.nbio.alignment | BioJava |
|
FragmentJoiner | Joins the initial Fragments together to larger FragmentsSince:1. | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
|
FragmentPair | a pair of fragments of two protein structuresSince:1. | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
|
Frame | Indicates a way of translating a sequence. | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
|
FuzzyPoint | | Class | org.biojava.nbio.core.sequence.location | BioJava |
|
GapArray | | Class | org.biojava.nbio.structure.align.helper | BioJava |
|
GapPenalty | Defines a data structure for the gap penalties used during a sequence alignment routine. | Interface | org.biojava.nbio.alignment.template | BioJava |
|
GCStats | | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
|
GenbankHeaderFormatInterface | | Interface | org.biojava.nbio.core.sequence.io.template | BioJava |
|
GenbankProxySequenceReader | | Class | org.biojava.nbio.core.sequence.loader | BioJava |
|
GenbankReader | Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
GenbankReaderHelper | | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
GenbankSequenceParser | | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
GenbankWriter | | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
GenbankWriterHelper | | Class | org.biojava.nbio.core.sequence.io | BioJava |
|
GeneChromosomePosition | | Class | org.biojava.nbio.genome.parsers.genename | BioJava |
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GeneChromosomePositionParser | A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positionsAuthor:Andreas Prlic | Class | org.biojava.nbio.genome.parsers.genename | BioJava |
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GeneFeatureHelper | | Class | org.biojava.nbio.genome | BioJava |
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GeneIDGFF2Reader | http://www. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
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GeneIDXMLReader | | Class | org.biojava.nbio.genome.parsers.geneid | BioJava |
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GeneMarkGTFReader | http://www. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
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GeneName | A simple bean that contains gene name information as available from www. | Class | org.biojava.nbio.genome.parsers.genename | BioJava |
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GeneNamesParser | Parses a file from the www. | Class | org.biojava.nbio.genome.parsers.genename | BioJava |
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GenericFastaHeaderFormat | We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file. | Class | org.biojava.nbio.core.sequence.io | BioJava |
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GenericFastaHeaderParser | The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier | Class | org.biojava.nbio.core.sequence.io | BioJava |
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GenericGenbankHeaderFormat | | Class | org.biojava.nbio.core.sequence.io | BioJava |
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GenericGenbankHeaderParser | | Class | org.biojava.nbio.core.sequence.io | BioJava |
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GenericInsdcHeaderFormat | | Class | org.biojava.nbio.core.sequence.io | BioJava |
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GeneSequence | | Class | org.biojava.nbio.core.sequence | BioJava |
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GetDistanceMatrix | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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GetRepresentatives | TODO Move this to Representatives. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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GFF3FromUniprotBlastHits | | Class | org.biojava.nbio.genome.homology | BioJava |
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GFF3Reader | http://www. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
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GFF3Writer | | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
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GOParser | Simple parser for the Gene Ontology (GO) flatfile format. | Class | org.biojava.nbio.ontology.io | BioJava |
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Gotoh | a class to perform Gotoh algorithmSince:10:56:53 AMVersion:%I% %G%Author:Andreas Prlic (Java), Peter Lackner (original C code) | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
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GradientMapper | Maps a set of real values onto a gradient. | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
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GradientPanel | | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
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GraphComponentOrderDetector | The GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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GraphComponentRefiner | The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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Grid | A grid to be used for calculating atom contacts through geometric hashing algorithm. | Class | org.biojava.nbio.structure.contact | BioJava |
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GridCell | A grid cell to be used in contact calculation via geometric hashing algorithm. | Class | org.biojava.nbio.structure.contact | BioJava |
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Group | This is the data structure for a single Group of atoms. | Interface | org.biojava.nbio.structure | BioJava |
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GroupAsa | A class to store the results of ASA calculations, it can hold ASA values per atom present in Group | Class | org.biojava.nbio.structure.asa | BioJava |
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GroupContact | A pair of residues that are in contactAuthor:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
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GroupContactSet | A set of residue-residue contacts. | Class | org.biojava.nbio.structure.contact | BioJava |
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GroupIterator | An iterator over all groups of a structure. | Class | org.biojava.nbio.structure | BioJava |
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GroupResults | | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava |
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GroupToSDF | | Class | org.biojava.nbio.structure.io | BioJava |
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GroupType | This contains basic categories for Group types. | Class | org.biojava.nbio.structure | BioJava |
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GuanUberbacher | Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence). | Class | org.biojava.nbio.alignment.routines | BioJava |
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GUIAlignmentProgressListener | a GUI that allows to watch progress as multiple alignments are being processed. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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GuideTree | GuideTree. | Class | org.biojava.nbio.alignment | BioJava |
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GuideTreeNode | Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment. | Interface | org.biojava.nbio.alignment.template | BioJava |
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GUIFarmJobRunnable | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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GuiWrapper | A class to wrap some of the strucutre. | Class | org.biojava.nbio.structure.align.ce | BioJava |
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Hashcoder | Contains helper methods for generating a HashCode without having to resort to the commons lang hashcode builders. | Class | org.biojava.nbio.core.util | BioJava |
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HasResultXMLConverter | | Class | org.biojava.nbio.structure.align.xml | BioJava |
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HBond | Container that represents a hidrogen bond. | Class | org.biojava.nbio.structure.secstruc | BioJava |
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HeaderInfo | | Class | org.biojava.nbio.survival.data | BioJava |
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HelicalRepeatUnit | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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Helix | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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HelixAxisAligner | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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HelixExtender | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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HelixLayers | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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HelixSolver | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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HelpDialog | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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HetatomImpl | Generic Implementation of a Group interface. | Class | org.biojava.nbio.structure | BioJava |
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HierarchicalClusterer | Defines a clustering algorithm that converts a distance matrix into a tree. | Interface | org.biojava.nbio.alignment.template | BioJava |
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Hit | This class models a search Hit. | Class | org.biojava.nbio.core.search.io | BioJava |
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HmmerDemo | The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 serviceSince:3. | Class | demo | BioJava |
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HmmerDomain | Provides the details of a domain hitSince:3. | Class | org.biojava.nbio.ws.hmmer | BioJava |
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HmmerResult | The results of a Hmmer search for a single sequenceSince:3. | Class | org.biojava.nbio.ws.hmmer | BioJava |
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HmmerScan | Interface for performing Hmmscans on sequences. | Interface | org.biojava.nbio.ws.hmmer | BioJava |
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Hsp | This class models a search Hsp. | Class | org.biojava.nbio.core.search.io | BioJava |
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HSVColorSpace | | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
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HTTPConnectionTools | a class that takes care about opening HttpURLConnections and sets the proper timeoutsSince:9:58:25 AMVersion:%I% %G%Author:Andreas Prlic | Class | org.biojava.nbio.structure.align.util | BioJava |
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IcosahedralSampler | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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Icosahedron | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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Identifier | A collection of utilities to create StructureIdentifiers. | Class | org.biojava.nbio.structure | BioJava |
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IdxComparator | | Class | org.biojava.nbio.structure.align.helper | BioJava |
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IlluminaFastqReader | Reader for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
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IlluminaFastqWriter | Writer for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
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IndexPair | | Class | org.biojava.nbio.structure.align.helper | BioJava |
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InputStreamProvider | A class that provides an InputStream from a File. | Class | org.biojava.nbio.core.util | BioJava |
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InsdcLocations | A collection of locations which are used whenever we work with INSDC; some of which could be deprecated (from INSDC's point of view) yet appear | Class | org.biojava.nbio.core.sequence.location | BioJava |
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InsdcParser | Parser for working with INSDC style locations. | Class | org.biojava.nbio.core.sequence.location | BioJava |
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IntegerOntology | | Class | org.biojava.nbio.ontology | BioJava |
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IntronSequence | | Class | org.biojava.nbio.core.sequence | BioJava |
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InvalidTermException | Thrown to indicate that an ontology term is not acceptable or appropriate in a given context | Class | org.biojava.nbio.ontology | BioJava |
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IOUtils | | Class | org.biojava.nbio.core.sequence.io.util | BioJava |
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IPeptideProperties | An interface to generate some basic physico-chemical properties of protein sequences. | Interface | org.biojava.nbio.aaproperties | BioJava |
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IProfeatProperties | | Interface | org.biojava.nbio.aaproperties.profeat | BioJava |
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Isotope | | Class | org.biojava.nbio.aaproperties.xml | BioJava |
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IUPACParser | Available translations 1 - UNIVERSAL2 - VERTEBRATE_MITOCHONDRIAL3 - YEAST_MITOCHONDRIAL4 - MOLD_MITOCHONDRIAL5 - INVERTEBRATE_MITOCHONDRIAL6 - CILIATE_NUCLEAR9 - ECHINODERM_MITOCHONDRIAL10 - EUPLOTID_NUCLEAR11 - BACTERIAL12 - ALTERNATIVE_YEAST_NUCLEAR13 - ASCIDIAN_MITOCHONDRIAL14 - FLATWORM_MITOCHONDRIAL15 - BLEPHARISMA_MACRONUCLEAR16 - 2CHLOROPHYCEAN_MITOCHONDRIAL21 - TREMATODE_MITOCHONDRIAL23 - SCENEDESMUS_MITOCHONDRIAL | Class | org.biojava.nbio.core.sequence.io | BioJava |
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JAutoSuggest | A JTextField that can make suggestions for auto-complete. | Class | org.biojava.nbio.structure.align.gui.autosuggest | BioJava |
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JFatCatClient | | Class | org.biojava.nbio.structure.align.client | BioJava |
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JMatrixPanel | a JPanel that can display a difference of distance matrix and paths that have been taken for the alignment | Class | org.biojava.nbio.structure.gui | BioJava |
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JmolAlignedPositionListener | | Class | org.biojava.nbio.structure.gui.events | BioJava |
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JmolPanel | | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
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JmolSymmetryScriptGenerator | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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JmolSymmetryScriptGeneratorC1 | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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JmolSymmetryScriptGeneratorCn | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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JmolSymmetryScriptGeneratorDn | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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JmolSymmetryScriptGeneratorH | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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JmolSymmetryScriptGeneratorI | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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JmolSymmetryScriptGeneratorO | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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JmolSymmetryScriptGeneratorPointGroup | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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JmolSymmetryScriptGeneratorT | | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava |
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JmolTools | | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
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JmolViewerImpl | | Class | org.biojava.nbio.structure.gui | BioJava |
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JNLPProxy | | Class | org.biojava.nbio.structure.align.webstart | BioJava |
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JobKillException | | Class | org.biojava.nbio.structure.align.client | BioJava |
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JoiningSequenceReader | This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
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JointFragments | A utility class that defines which set of atoms are considered to be on equivalent positions. | Class | org.biojava.nbio.structure.align.helper | BioJava |
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JournalArticle | | Class | org.biojava.nbio.structure | BioJava |
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JPrintPanel | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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Jronn | This class gives public API to RONN functions. | Class | org.biojava.nbio.ronn | BioJava |
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KaplanMeierFigure | | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava |
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KeyedWeakReference | Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been | Class | org.biojava.nbio.ontology.utils | BioJava |
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KMFigureInfo | | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava |
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Ladder | A Ladder is a set of one or more consecutive bridges of identical type. | Class | org.biojava.nbio.structure.secstruc | BioJava |
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LightweightProfile | Defines a minimal data structure for reading and writing a sequence alignment. | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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LinearColorInterpolator | | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
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ListStringWrapper | | Class | org.biojava.nbio.structure.scop.server | BioJava |
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LocalPDBDirectory | Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and MMCIFFileReader. | Class | org.biojava.nbio.structure.io | BioJava |
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LocalProteinDomainParser | Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures. | Class | org.biojava.nbio.structure.domain | BioJava |
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LocalScopDatabase | Classes which implement ScopDatabase in a way which allows them to serve queries without accessing the internet should implement this interface instead. | Interface | org.biojava.nbio.structure.scop | BioJava |
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Location | Sets of integers used to represent the location of features on sequence. | Interface | org.biojava.nbio.core.sequence.location.template | BioJava |
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Location | A location on a sequence. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
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LocationHelper | Helper methods for use with the Location classes. | Class | org.biojava.nbio.core.sequence.location | BioJava |
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LocIterator | Move a sliding window over a Location. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
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LogColorMapper | Performs a log10 transform on input before passing the values off to another For instance, to map [10^0, 10^10] to a rainbow gradient, use | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
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LUDecomposition | For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n unit lower triangular matrix L, an n-by-n upper triangular matrix U, | Class | org.biojava.nbio.structure.jama | BioJava |
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MapToStringTransformer | Transforms Map to String. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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Maths | | Class | org.biojava.nbio.structure.jama | BioJava |
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Matrix | Jama = Java Matrix class. | Class | org.biojava.nbio.structure.jama | BioJava |
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Matrix | *********************************************************************** Compilation: javac Matrix. | Class | org.biojava.nbio.survival.cox.matrix | BioJava |
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MatrixAligner | Defines an Aligner which builds a score matrix during computation. | Interface | org.biojava.nbio.alignment.template | BioJava |
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MatrixListener | | Interface | org.biojava.nbio.structure.align.ce | BioJava |
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MeanModelComparator | | Class | org.biojava.nbio.survival.cox.comparators | BioJava |
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MeanQuantizer | | Class | org.biojava.nbio.survival.kaplanmeier.metadata | BioJava |
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MemoryMonitor | Tracks Memory allocated & used, displayed in graph form. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MenuCreator | Create the menus for structure alignment GUI windows (JFrames). | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MenuCreator | Create the menu for BiojavaJmolSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
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Messages | | Class | org.biojava.nbio.core.exceptions | BioJava |
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MetaDataInfo | | Class | org.biojava.nbio.survival.kaplanmeier.metadata | BioJava |
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MmCifBiolAssemblyProvider | | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
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MMcifConsumer | An interface for the events triggered by a MMcifParser. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
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MMCIFFileReader | How to parse an mmCif file:public static void main(String[] args) throws Exception { | Class | org.biojava.nbio.structure.io | BioJava |
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MMCIFFileTools | Some tools for mmCIF file writing. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
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MMcifParser | Interface that needs to be implemented by an MMcifParserSince:1. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
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MmCifPDBBiolAssemblyProvider | A provider for information about biological units for PDB files that is based on reading local MMcif files. | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
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ModelledSubgroup | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
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ModelLoader | Class that loads data from the model files into ModelLoader. | Class | org.biojava.nbio.ronn | BioJava |
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ModificationCategory | enum ModificationCategorydefine modification categories. | Class | org.biojava.nbio.protmod | BioJava |
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ModificationCondition | Conditions of a protein modification, e. | Interface | org.biojava.nbio.protmod | BioJava |
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ModificationConditionImpl | | Class | org.biojava.nbio.protmod | BioJava |
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ModificationLinkage | | Class | org.biojava.nbio.protmod | BioJava |
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ModificationOccurrenceType | enum ModificationOccurrenceTypeSince:3. | Class | org.biojava.nbio.protmod | BioJava |
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ModifiedAminoAcidCompoundSet | | Class | org.biojava.nbio.aaproperties.xml | BioJava |
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ModifiedCompound | Root interface for all modifications in structure. | Interface | org.biojava.nbio.protmod.structure | BioJava |
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ModifiedCompoundImpl | | Class | org.biojava.nbio.protmod.structure | BioJava |
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ModifiedCompoundXMLConverter | | Class | org.biojava.nbio.protmod.io | BioJava |
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MogAngleOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
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MogBondOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
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MomentsOfInertia | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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MultipleAlignment | A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type. | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
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MultipleAlignmentCalc | A class that obtains structures via DAS and aligns them. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MultipleAlignmentCoordManager | Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization. | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
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MultipleAlignmentDisplay | Utility functions to generalize the visualization of MultipleAlignments in molecular viewers. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
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MultipleAlignmentEnsemble | A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
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MultipleAlignmentEnsembleImpl | A general implementation of a MultipleAlignmentEnsemble. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
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MultipleAlignmentGUI | A JFrame that allows to trigger a multiple structure alignment, either from files in a directory or after manual upload. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MultipleAlignmentImpl | A general implementation of a MultipleAlignment. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
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MultipleAlignmentJmol | A class that provides a 3D visualization Frame in Jmol for MultipleAlignments. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
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MultipleAlignmentJmolDisplay | Utility Class that provides helper methods for the visualization of MultipleAlignments. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MultipleAlignmentScorer | Utility class for calculating common scores of MultipleAlignments. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
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MultipleAlignmentTools | Utility functions for working with MultipleAlignment. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
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MultipleAlignmentWriter | This class contains functions for the conversion of MultipleAlignment to various String outputs. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
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MultipleAlignmentXMLConverter | Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format. | Class | org.biojava.nbio.structure.align.xml | BioJava |
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MultipleAlignmentXMLParser | Parse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered. | Class | org.biojava.nbio.structure.align.xml | BioJava |
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MultipleAligPanel | A JPanel that can display the sequence alignment of a MultipleAlignment in a nice way and interact with Jmol by | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
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MultipleAligPanelMouseMotionListener | Mouse Motion Listener for the MultipleAligPanel, which provides methods to obtain positions of the mouse | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
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MultipleMcMain | Main class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm, | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
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MultipleMcOptimizer | This class takes a MultipleAlignment seed previously generated and runs a Monte Carlo optimization in order to improve the overall score and highlight | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
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MultipleMcParameters | Contains the parameters to be sent to the MC optimization. | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
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MultipleSequenceAlignment | structure in the alignment module provides additional functionality. | Class | org.biojava.nbio.core.sequence | BioJava |
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MultipleStatusDisplay | This class provides information of the selected positions in the It has to be linked to a MultipleAligPanel in order to obtain | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
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MultipleStructureAligner | Interface for the Multiple Structure Alignment Algorithms. | Interface | org.biojava.nbio.structure.align | BioJava |
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MultipleSuperimposer | Interface for Multiple Alignment superposition algorithms. | Interface | org.biojava.nbio.structure.align.multiple.util | BioJava |
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MultiThreadedDBSearch | Performs a multi threaded database search for an input protein structureAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align | BioJava |
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MutableAlignedSequence | Defines a mutable (editable) data structure for an AlignedSequence. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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MutableProfile | Defines a mutable (editable) data structure for a Profile. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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MutableProfilePair | Defines a mutable (editable) data structure for a ProfilePair. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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MutableSequencePair | Defines a mutable (editable) data structure for the results of pairwise sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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Mutator | A class that can change one amino acid to another. | Class | org.biojava.nbio.structure | BioJava |
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MyAlignmentLoadListener | Loads an alignment in an XML format and displays its content in a new Jmol panel. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MyDistMaxListener | Shows the interatomic Distance Matrices of all the Structures aligned in different Frames. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MyExportListener | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MyJmolStatusListener | | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
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MyOpenPdbFileListener | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MySaveFileListener | Save an alignment to a specified File by the user. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MyTableRowSorter | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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MyValidationEventHandler | | Class | org.biojava.nbio.aaproperties.xml | BioJava |
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Name2Count | | Class | org.biojava.nbio.aaproperties.xml | BioJava |
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NCBIQBlastAlignmentProperties | This class wraps a QBlast search request parameter Map by adding several convenient parameter addition methods. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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NCBIQBlastOutputProperties | This class wraps a QBlast output parameter Map by adding several convenient parameter addition methods. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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NCBIQBlastService | Provides a simple way of submitting BLAST request to the QBlast service at NCBI. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
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NCBIQBlastServiceDemo | A simple demo showing NCBIQBlastService usageAuthor:Gediminas Rimsa | Class | demo | BioJava |
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NeedlemanWunsch | Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence). | Class | org.biojava.nbio.alignment | BioJava |
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NucleotideCompound | | Class | org.biojava.nbio.core.sequence.compound | BioJava |
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NucleotideImpl | A nucleotide group is almost the same as a Hetatm group. | Class | org.biojava.nbio.structure | BioJava |
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NullOutputStream | The stream that void its inputSince:3. | Class | org.biojava.nbio.ronn | BioJava |
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NumbersAtRiskPanel | | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava |
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ObjectFactory | This object contains factory methods for each Java content interface and Java element interface | Class | org.biojava.nbio.structure.validation | BioJava |
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OboFileEventListener | an interface for events that occur during parsing of . | Interface | org.biojava.nbio.ontology.obo | BioJava |
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OboFileHandler | A file handler for . | Class | org.biojava.nbio.ontology.obo | BioJava |
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OboFileParser | A class to parse the content of an OBO file. | Class | org.biojava.nbio.ontology.obo | BioJava |
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OboParser | OboParser parser = new OboParser(); InputStream inStream = this. | Class | org.biojava.nbio.ontology.io | BioJava |
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Octahedron | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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Ontology | This is just a set of Term objects, and a set of Triple objects describing relationships between these terms. | Interface | org.biojava.nbio.ontology | BioJava |
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OntologyException | Thrown to indicate an error in an Ontology objectSince:1. | Class | org.biojava.nbio.ontology | BioJava |
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OntologyFactory | A factory for Ontology instances. | Interface | org.biojava.nbio.ontology | BioJava |
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OntologyOps | This is an interface for optimizing ontology operators. | Interface | org.biojava.nbio.ontology | BioJava |
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OntologyTerm | A term in an ontology which identifies another ontology. | Interface | org.biojava.nbio.ontology | BioJava |
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OntoTools | Tools for manipulating ontologies. | Class | org.biojava.nbio.ontology | BioJava |
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OperatorResolver | | Class | org.biojava.nbio.structure.quaternary | BioJava |
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OptimalCECPMain | A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations. | Class | org.biojava.nbio.structure.align.ce | BioJava |
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OptimalCECPParameters | Contains the parameters that can be sent to CEAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
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OrderDetector | A method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm. | Interface | org.biojava.nbio.structure.symmetry.internal | BioJava |
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OrderedPair | An ordered pair represents a component of a cartesian product. | Class | org.biojava.nbio.structure.quaternary | BioJava |
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ORonn | Fully re-factored and enhanced version of RONN. | Class | org.biojava.nbio.ronn | BioJava |
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ORonnModel | Fully re-factored version of RONN model. | Class | org.biojava.nbio.ronn | BioJava |
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OutputHitsGFF | | Class | org.biojava.nbio.genome.query | BioJava |
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Pair | A Pair of objects. | Class | org.biojava.nbio.structure.contact | BioJava |
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PairInProfileScorer | Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile. | Interface | org.biojava.nbio.alignment.template | BioJava |
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PairwiseAlignment | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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PairwiseSequenceAligner | Defines an Aligner for a pair of Sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
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PairwiseSequenceScorer | Defines an algorithm which computes a score for a pair of sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
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ParameterGUI | UI for ConfigStrucAligParams, for the AlignmentGUI. | Class | org.biojava.nbio.structure.align.gui | BioJava |
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ParseFastaFileDemo | Created by andreas on 6/17/15. | Class | demo | BioJava |
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ParseGO | | Class | demo | BioJava |
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ParseListener | Low-level event based parser callback. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |
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ParserException | General abstraction of different parsing errorsAuthor:Scooter Willis See Also:Serialized Form | Class | org.biojava.nbio.core.exceptions | BioJava |
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PartitionRefiner | Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning. | Interface | org.biojava.nbio.alignment.template | BioJava |
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PassthroughIdentifier | A stub StructureIdentifier, representing the full structure in all cases. | Class | org.biojava.nbio.structure | BioJava |
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PDBBioAssemblyParser | Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit | Class | org.biojava.nbio.structure.io | BioJava |
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PDBBioUnitDataProvider | A BioUnitDataProvider that extracts the necessary info from PDB filesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
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PDBCrystallographicInfo | A class to hold crystallographic information about a PDB structure. | Class | org.biojava.nbio.structure | BioJava |
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PDBDirPanel | A class to define where a structure for the alignment is coming fromSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
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PDBDomainProvider | Class to fetch domains through the RCSB's REST API. | Class | org.biojava.nbio.structure.domain | BioJava |
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PDBFileParser | This class implements the actual PDB file parsing. | Class | org.biojava.nbio.structure.io | BioJava |
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PDBFileReader | The wrapper class for parsing a PDB file. | Class | org.biojava.nbio.structure.io | BioJava |
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PDBHeader | A class that contains PDB Header information. | Class | org.biojava.nbio.structure | BioJava |
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PdbIdLists | Utility classes for retrieving lists of PDB IDs. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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PdbPair | A pair for structure alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.client | BioJava |
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PdbPairsMessage | | Class | org.biojava.nbio.structure.align.xml | BioJava |
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PdbPairXMLConverter | | Class | org.biojava.nbio.structure.align.xml | BioJava |
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PDBParseException | An exception during the parsing of a PDB file. | Class | org.biojava.nbio.structure.io | BioJava |
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PDBRecord | An interface implemented by all classes that represent PDB recordsSince:1. | Interface | org.biojava.nbio.structure | BioJava |
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PDBServerPanel | A class to define where a structure for the alignment is coming fromSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
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PDBStatus | Methods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure. | Class | org.biojava.nbio.structure | BioJava |
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PDBTemporaryStorageUtils | Internal use only. | Class | org.biojava.nbio.structure.io.util | BioJava |
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PDBUploadPanel | A JPanel to upload 2 custom PDB files. | Class | org.biojava.nbio.structure.gui.util | BioJava |
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PdbxChemCompDescriptor | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxChemCompIdentifier | _pdbx_chem_comp_identifier. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxEntityNonPoly | A bean for the Pdbx_entity_nonpoly category. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxNonPolyScheme | A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxPolySeqScheme | A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxStructAssembly | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxStructAssemblyGen | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxStructAssemblyGenXMLContainer | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxStructAssemblyXMLContainer | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxStructOperList | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PdbxStructOperListXMLContainer | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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PDPDistanceMatrix | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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PDPDomain | | Class | org.biojava.nbio.structure.domain | BioJava |
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PDPParameters | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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PDPProvider | Decomposes a structure into representative PDP domains. | Interface | org.biojava.nbio.structure.domain | BioJava |
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PeptideProperties | This is an adaptor class which enable the ease of generating protein properties. | Class | org.biojava.nbio.aaproperties | BioJava |
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PeptidePropertiesImpl | This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use. | Class | org.biojava.nbio.aaproperties | BioJava |
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PermutationGenerator | | Class | org.biojava.nbio.structure.symmetry.utils | BioJava |
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PermutationGroup | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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PersistentConfig | a class to store the config using the Java Web StartAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.webstart | BioJava |
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PlainFastaHeaderParser | The plain fasta header takes everything in the header as a single entity. | Class | org.biojava.nbio.core.sequence.io | BioJava |
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Point | | Interface | org.biojava.nbio.core.sequence.location.template | BioJava |
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Polyhedron | | Interface | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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PolymerType | Enumerates the classification of polymers. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
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PositionInQueueXMLConverter | | Class | org.biojava.nbio.structure.align.xml | BioJava |
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PredictDisorder | | Class | demo | BioJava |
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PrettyXMLWriter | | Class | org.biojava.nbio.core.util | BioJava |
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Prism | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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ProfeatProperties | This is an adaptor class which enable the ease of generating profeat properties. | Class | org.biojava.nbio.aaproperties.profeat | BioJava |
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ProfeatPropertiesImpl | | Class | org.biojava.nbio.aaproperties.profeat | BioJava |
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Profile | Defines a data structure for the results of sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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ProfilePair | Defines a data structure for the results of the alignment of a pair of Profiles. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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ProfileProfileAligner | Defines an Aligner for a pair of Profiles. | Interface | org.biojava.nbio.alignment.template | BioJava |
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ProfileProfileScorer | Defines an algorithm which computes a score for a pairing of alignment profiles. | Interface | org.biojava.nbio.alignment.template | BioJava |
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ProfileView | Defines a data structure for a view of sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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Program | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
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Programs | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
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ProteinChainExtractor | Extracts information about all the chains in a structure, including chain Ids, sequences, and atoms. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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ProteinComplexSignature | | Class | org.biojava.nbio.structure.symmetry.misc | BioJava |
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ProteinModification | This interface defines information about a specific proteinSince:3. | Interface | org.biojava.nbio.protmod | BioJava |
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ProteinModificationIdentifier | Identify attachment modification in a 3-D structure. | Class | org.biojava.nbio.protmod.structure | BioJava |
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ProteinModificationImpl | This class contains information about a specific proteinSince:3. | Class | org.biojava.nbio.protmod | BioJava |
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ProteinModificationRegistry | This class serves as a instance registry by maintaining a pool of ProteinModification instances. | Class | org.biojava.nbio.protmod | BioJava |
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ProteinModificationXmlReader | | Class | org.biojava.nbio.protmod.io | BioJava |
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ProteinSequence | The representation of a ProteinSequenceAuthor:Scooter Willis, Paolo Pavan | Class | org.biojava.nbio.core.sequence | BioJava |
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ProteinSequenceClusterer | Represents a set of non-identical protein sequences. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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ProteinSequenceCreator | Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc. | Class | org.biojava.nbio.core.sequence.io | BioJava |
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ProxySequenceReader | | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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QRDecomposition | For an m-by-n matrix A with m >= n, the QR decomposition is an m-by-n orthogonal matrix Q and an n-by-n upper triangular matrix R so that | Class | org.biojava.nbio.structure.jama | BioJava |
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Qualifier | | Class | org.biojava.nbio.core.sequence.features | BioJava |
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QualityFeature | DNA Sequences produced by modern sequencers usually have quality informaion attached to them. | Class | org.biojava.nbio.core.sequence.features | BioJava |
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QuantityFeature | It is common to have a numerical value or values associated with a feature. | Class | org.biojava.nbio.core.sequence.features | BioJava |
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QuatSuperpositionScorer | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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QuatSymmetryDetector | Detects global and local quaternary protein structure symmetry in a structure. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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QuatSymmetryParameters | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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QuatSymmetryResults | Holds the results of quaternary symmetry perception. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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QuatSymmetryScores | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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QuatSymmetrySolver | | Interface | org.biojava.nbio.structure.symmetry.core | BioJava |
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RasmolCommandListener | a utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
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RasmolCommandListener | a utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.gui | BioJava |
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RawBioUnitDataProvider | Defines the methods that have to be implemented by a class that provides the data that is necessary to recreate the correct biological assembly of a protein. | Interface | org.biojava.nbio.structure.quaternary.io | BioJava |
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RCSBDescription | Corresponds to the wrapper element in an RCSB describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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RCSBDescriptionFactory | Fetches information from RCSB's RESTful Web Service Interface. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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RCSBLigand | Corresponds to a ligand in a ligandInfo XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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RCSBLigands | Corresponds to the wrapper element "ligandInfo" in an RCSB ligandInfo XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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RCSBLigandsFactory | Fetches information from RCSB's RESTful Web Service Interface. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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RCSBMacromolecule | Corresponds to a macromolecule in an RCSB describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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RCSBPolymer | Corresponds to a polymer in a describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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RCSBTaxonomy | Corresponds to a taxonomy in a describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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RCSBUpdates | | Class | org.biojava.nbio.structure.rcsb | BioJava |
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ReadUtils | Package-level static utilities for parsing XML. | Class | org.biojava.nbio.structure.rcsb | BioJava |
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RectangularPrism | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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ReducedChemCompProvider | Unlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
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ReferenceSuperimposer | Superimposes each structure in a MultipleAlignment onto a reference Performs a global superposition of the MultipleAlignment in case | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
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Refine | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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RefinerFailedException | Refinement of the self-alignment failed. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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RemoteBioUnitDataProvider | | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
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RemoteDomainProvider | A DomainProvider that uses a mixture of SCOP and PDP domains. | Class | org.biojava.nbio.structure.domain | BioJava |
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RemoteHmmerScan | Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence. | Class | org.biojava.nbio.ws.hmmer | BioJava |
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RemotePairwiseAlignmentOutputProperties | RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object. | Interface | org.biojava.nbio.ws.alignment | BioJava |
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RemotePairwiseAlignmentProperties | RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties. | Interface | org.biojava.nbio.ws.alignment | BioJava |
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RemotePairwiseAlignmentService | This interface specifies minimal information needed to execute a pairwise alignment on a remote service. | Interface | org.biojava.nbio.ws.alignment | BioJava |
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RemotePDPProvider | A class that provided PDP assignments that are loaded from a remote web serverAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.domain | BioJava |
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RemoteRawBioUnitDataProvider | A BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDBAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
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RemoteScopInstallation | A class that fetches information about SCOP from a remote data-source. | Class | org.biojava.nbio.structure.scop | BioJava |
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RemoteTerm | A term in another ontology. | Interface | org.biojava.nbio.ontology | BioJava |
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RenderStyle | | Class | org.biojava.nbio.structure.gui | BioJava |
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RepresentativeXMLConverter | | Class | org.biojava.nbio.structure.align.xml | BioJava |
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RescoreRefiner | | Interface | org.biojava.nbio.alignment.template | BioJava |
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ResidualsCoxph | | Class | org.biojava.nbio.survival.cox | BioJava |
|
ResidueGroup | A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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ResidueNumber | Everything that is needed to uniquely describe a residue positionAuthor:Andreas PrlicSee Also:Serialized Form | Class | org.biojava.nbio.structure | BioJava |
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ResidueRange | A chain, a start residue, and an end residue. | Class | org.biojava.nbio.structure | BioJava |
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ResidueRangeAndLength | A chain, a start residue, and an end residue. | Class | org.biojava.nbio.structure | BioJava |
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ResidueType | Enumerates the possible classifications of residues. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
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ResourceManager | A class that manages the Strings that are defined in the spice. | Class | org.biojava.nbio.structure.align.util | BioJava |
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Result | This class models a search result. | Class | org.biojava.nbio.core.search.io | BioJava |
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ResultFactory | Designed by Paolo Pavan. | Interface | org.biojava.nbio.core.search.io | BioJava |
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ReversedSequenceView | For a given sequence this class will return the base at the reversed position i. | Class | org.biojava.nbio.core.sequence.views | BioJava |
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RiskInfo | | Class | org.biojava.nbio.survival.cox | BioJava |
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RNACompoundSet | | Class | org.biojava.nbio.core.sequence.compound | BioJava |
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RNASequence | RNASequence where RNACompoundSet are the allowed valuesAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
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RNASequenceCreator | Used to create a RNA sequenceAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.io | BioJava |
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RnaSequenceView | | Class | org.biojava.nbio.core.sequence.views | BioJava |
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RNAToAminoAcidTranslator | Takes a Sequence of NucleotideCompound which should represent an RNA sequence (RNASequence is good for this) and returns a list of | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
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RonnConstraint | A collection of various constrain values used by RONNSince:3. | Class | org.biojava.nbio.ronn | BioJava |
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Rotation | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
|
RotationAxis | Calculates the rotation axis for an alignment A superposition of two structures is generally represented as a rotation | Class | org.biojava.nbio.structure.align.util | BioJava |
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RotationAxisAligner | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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RotationGroup | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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RotationSolver | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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SandboxStyleStructureProvider | The "Sandbox" style of organizing files is to have a directory structure like below, i. | Class | org.biojava.nbio.structure.io | BioJava |
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SangerFastqReader | Reader for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
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SangerFastqWriter | Writer for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
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ScaleableMatrixPanel | A JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm. | Class | org.biojava.nbio.structure.gui | BioJava |
|
ScaledSubstitutionMatrix | The biojava-alignment module represents substitution matrices with short values. | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
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ScanSymmetry | | Class | org.biojava.nbio.structure.symmetry.analysis | BioJava |
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SchemaGenerator | | Class | org.biojava.nbio.aaproperties.xml | BioJava |
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SCOPAutoSuggestProvider | | Class | org.biojava.nbio.structure.align.gui.autosuggest | BioJava |
|
ScopCategory | The various categories provided by SCOP. | Class | org.biojava.nbio.structure.scop | BioJava |
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ScopDatabase | General API how to interact with SCOPSince:3. | Interface | org.biojava.nbio.structure.scop | BioJava |
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ScopDescription | dir. | Class | org.biojava.nbio.structure.scop | BioJava |
|
ScopDescriptions | | Class | org.biojava.nbio.structure.scop.server | BioJava |
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ScopDomain | Container for the information for a domain. | Class | org.biojava.nbio.structure.scop | BioJava |
|
ScopDomains | | Class | org.biojava.nbio.structure.scop.server | BioJava |
|
ScopFactory | Controls the global ScopDatabase being used. | Class | org.biojava.nbio.structure.scop | BioJava |
|
ScopInstallation | This class provides access to the SCOP protein structure classification. | Class | org.biojava.nbio.structure.scop | BioJava |
|
ScopInstallationInstance | | Class | org.biojava.nbio.structure.gui.util | BioJava |
|
ScopIOException | Indicates that an I/O error occurred with SCOP lazy initialization. | Class | org.biojava.nbio.structure.scop | BioJava |
|
ScopMirror | Helper class to store paths to the four SCOP files The string "%s" is replaced with the version number. | Class | org.biojava.nbio.structure.scop | BioJava |
|
ScopNode | | Class | org.biojava.nbio.structure.scop | BioJava |
|
ScopNodes | | Class | org.biojava.nbio.structure.scop.server | BioJava |
|
ScopSelectPanel | | Class | org.biojava.nbio.structure.gui.util | BioJava |
|
Scorer | Defines an algorithm which computes a score. | Interface | org.biojava.nbio.alignment.template | BioJava |
|
ScoresCache | Interface for classes which implement a temporary cache for various numeric scores, e. | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
|
SearchIO | Designed by Paolo Pavan. | Class | org.biojava.nbio.core.search.io | BioJava |
|
SecStrucCalc | Calculate and assign the secondary structure (SS) to the Groups of a Structure object. | Class | org.biojava.nbio.structure.secstruc | BioJava |
|
SecStrucElement | A secondary structure element (SSE) is an object representing a block of sequential residues that share the same secondary structure type. | Class | org.biojava.nbio.structure.secstruc | BioJava |
|
SecStrucInfo | Container for the secondary structure information of a single residue. | Class | org.biojava.nbio.structure.secstruc | BioJava |
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SecStrucState | This class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm. | Class | org.biojava.nbio.structure.secstruc | BioJava |
|
SecStrucTools | This class contains methods for obtaining and converting secondary structure information from BioJava Structures. | Class | org.biojava.nbio.structure.secstruc | BioJava |
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SecStrucType | This enum contains all of the secondary structure types found in the DSSP output. | Class | org.biojava.nbio.structure.secstruc | BioJava |
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Segment | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
|
SegmentComparator | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
|
Selection | | Interface | org.biojava.nbio.structure.gui | BioJava |
|
SelectionImpl | | Class | org.biojava.nbio.structure.gui | BioJava |
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SelectMultiplePanel | A Text Panel that allows the user to specify multiple structure identifiers, space separated. | Class | org.biojava.nbio.structure.gui.util | BioJava |
|
SelectPDBPanel | A Panel that allows user to specify PDB & chain ID, as well as sub-rangesAuthor:AndreasSee Also:Serialized Form | Class | org.biojava.nbio.structure.align.gui | BioJava |
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SeqMisMatch | Created by andreas on 9/11/15. | Interface | org.biojava.nbio.structure | BioJava |
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SeqMisMatchImpl | Created by andreas on 9/11/15. | Class | org.biojava.nbio.structure | BioJava |
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SeqRes2AtomAligner | Aligns the SEQRES residues to the ATOM residues. | Class | org.biojava.nbio.structure.io | BioJava |
|
Sequence | Main interface for defining a collection of Compounds and accessing them using biological indexes | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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SequenceAlignmentCluster | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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SequenceAsStringHelper | This is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
|
SequenceComparator | Used to sort sequencesAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
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SequenceCreatorInterface | | Interface | org.biojava.nbio.core.sequence.io.template | BioJava |
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SequenceDisplay | A sequence display that can show the results of a protein structure alignment. | Class | org.biojava.nbio.structure.gui | BioJava |
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SequenceFileProxyLoader | This class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence. | Class | org.biojava.nbio.core.sequence.loader | BioJava |
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SequenceFunctionOrderDetector | Calls Spencer's method for determining order. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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SequenceFunctionRefiner | Creates a refined alignment with the CE-Symm alternative self-alignment. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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SequenceHeaderParserInterface | | Interface | org.biojava.nbio.core.sequence.io.template | BioJava |
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SequenceLocation | A location in a sequence that keeps a reference to its parent sequenceAuthor:Scooter Willis , Paolo PavanSee Also:Serialized Form | Class | org.biojava.nbio.core.sequence.location | BioJava |
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SequenceMixin | Provides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way. | Class | org.biojava.nbio.core.sequence.template | BioJava |
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SequenceMouseListener | a mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate | Class | org.biojava.nbio.structure.gui.util | BioJava |
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SequenceOptimizationHints | A static class that provides optimization hints for memory or performance handling of sequence data. | Class | org.biojava.nbio.core.sequence | BioJava |
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SequencePair | Defines a data structure for the results of pairwise sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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SequenceParserInterface | | Interface | org.biojava.nbio.core.sequence.io.template | BioJava |
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SequenceProxyView | | Class | org.biojava.nbio.core.sequence.template | BioJava |
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SequenceReader | | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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SequenceScalePanel | A class that draws a Sequence as a rectangle, a scale display over it. | Class | org.biojava.nbio.structure.gui.util | BioJava |
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SequenceTools | | Class | org.biojava.nbio.core.util | BioJava |
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SequenceUtil | Utility class for operations on sequencesSince:3. | Class | org.biojava.nbio.data.sequence | BioJava |
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SequenceView | | Interface | org.biojava.nbio.core.sequence.template | BioJava |
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SerializableCache | A class that provides all that is necessary to create a Serializable CacheSince:3. | Class | org.biojava.nbio.structure.domain | BioJava |
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ShortSegmentRemover | | Class | org.biojava.nbio.structure.domain.pdp | BioJava |
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ShowPDBIDListener | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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ShowStructureInJmol | Demo how to load and display a structure in JmolAuthor:Andreas Prlic | Class | demo | BioJava |
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SiftsChainEntry | An entry in the chain-level SIFTS mapping between UniProt and the PDB. | Class | org.biojava.nbio.structure.io.sifts | BioJava |
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SiftsChainToUniprotMapping | A mapping between UniProt entries and PDB chains. | Class | org.biojava.nbio.structure.io.sifts | BioJava |
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SiftsEntity | | Class | org.biojava.nbio.structure.io.sifts | BioJava |
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SiftsMappingProvider | | Class | org.biojava.nbio.structure.io.sifts | BioJava |
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SiftsResidue | | Class | org.biojava.nbio.structure.io.sifts | BioJava |
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SiftsSegment | | Class | org.biojava.nbio.structure.io.sifts | BioJava |
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SiftsXMLParser | | Class | org.biojava.nbio.structure.io.sifts | BioJava |
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SigEva | | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
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SimpleAlignedSequence | | Class | org.biojava.nbio.core.alignment | BioJava |
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SimpleGapPenalty | | Class | org.biojava.nbio.alignment | BioJava |
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SimpleLocation | Very basic implementation of the Location interface which defines a series of simple constructors. | Class | org.biojava.nbio.core.sequence.location | BioJava |
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SimpleMMcifConsumer | A MMcifConsumer implementation that builds an in-memory representation of the content of a mmcif file as a BioJava Structure object. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
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SimpleMMcifParser | A simple mmCif file parserString file = "path/to/mmcif/file"; | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
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SimplePoint | Basic implementation of the Point interface. | Class | org.biojava.nbio.core.sequence.location | BioJava |
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SimpleProfile | | Class | org.biojava.nbio.core.alignment | BioJava |
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SimpleProfilePair | | Class | org.biojava.nbio.core.alignment | BioJava |
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SimpleProfileProfileAligner | NeedlemanWunsch pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score. | Class | org.biojava.nbio.alignment | BioJava |
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SimpleSequencePair | | Class | org.biojava.nbio.core.alignment | BioJava |
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SimpleSubstitutionMatrix | Compound in a sequence for another. | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
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SingleCompoundSequenceReader | An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String | Class | org.biojava.nbio.core.sequence.storage | BioJava |
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SingleLinkageClusterer | An implementation of a single linkage clusterer See http://en. | Class | org.biojava.nbio.core.util | BioJava |
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SingularValueDecomposition | Singular Value Decomposition. | Class | org.biojava.nbio.structure.jama | BioJava |
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Site | Created by ap3 on 31/10/2014. | Class | org.biojava.nbio.phosphosite | BioJava |
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Site | Holds the data of sites presented in PDB files. | Class | org.biojava.nbio.structure | BioJava |
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SmallAnnotation | Annotation that is optimized for memory usage. | Class | org.biojava.nbio.ontology.utils | BioJava |
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SmallMap | Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability. | Class | org.biojava.nbio.ontology.utils | BioJava |
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SmithWaterman | Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence). | Class | org.biojava.nbio.alignment | BioJava |
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SmithWaterman3Daligner | provides a 3D superimposition based on the sequence alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.seq | BioJava |
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SmithWaterman3DParameters | | Class | org.biojava.nbio.structure.align.seq | BioJava |
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SmithWatermanUserArgumentProcessor | | Class | org.biojava.nbio.structure.align.seq | BioJava |
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SoftHashMap | A in memory cache using soft references. | Class | org.biojava.nbio.core.util | BioJava |
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SolexaFastqReader | Reader for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
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SolexaFastqWriter | Writer for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
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SpaceGroup | A crystallographic space group. | Class | org.biojava.nbio.structure.xtal | BioJava |
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SpaceGroupMapElements | | Class | org.biojava.nbio.structure.xtal.io | BioJava |
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SpaceGroupMapRoot | | Class | org.biojava.nbio.structure.xtal.io | BioJava |
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SparseSquareMatrix | A sparse, square matrix, implementing using two arrays of sparse vectors, one representation for the rows and one for the columns. | Class | org.biojava.nbio.structure.math | BioJava |
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SparseVector | A sparse vector, implemented using a symbol table. | Class | org.biojava.nbio.structure.math | BioJava |
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SphereSampler | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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SplitFasta | Utility to write each Fasta entry to a unique fileAuthor:Scooter Willis | Class | org.biojava.nbio.genome.util | BioJava |
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SqrtColorMapper | Performs a sqrt transform on input before passing the values off to another For instance, to map [0^2, 10^2] to a rainbow gradient, use | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
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SSBondImpl | A simple bean to store disulfide bridge information, the SSBOND records in the PDB files. | Class | org.biojava.nbio.structure.io | BioJava |
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StainType | | Class | org.biojava.nbio.genome.parsers.cytoband | BioJava |
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StandardAminoAcid | A class that provides a set of standard amino acids. | Class | org.biojava.nbio.structure | BioJava |
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StandardRescoreRefiner | | Class | org.biojava.nbio.alignment | BioJava |
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StartCodonSequence | Used to map the start codon feature on a geneAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
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StartupParameters | a simple bean that contains the parameters that can get set at startupAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
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StaticMemberPlaceHolder | | Class | org.biojava.nbio.ontology.utils | BioJava |
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StatusDisplay | | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
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StdArrayIO | Standard array IO. | Class | org.biojava.nbio.survival.cox.matrix | BioJava |
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StockholmFileAnnotation | Stores all the content parsed from the #=GF linesSince:3. | Class | org.biojava.nbio.alignment.io | BioJava |
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StockholmFileParser | Stockholm file parser. | Class | org.biojava.nbio.alignment.io | BioJava |
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StockholmStructure | Stores all the content of a Stockholm file. | Class | org.biojava.nbio.alignment.io | BioJava |
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StopCodonSequence | Used to map the stop codon sequence on a geneAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
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Strand | Provides a way of representing the strand of a sequence, locationEnum Constant Summary | Class | org.biojava.nbio.core.sequence | BioJava |
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StrataInfo | Information needed to represent a survival curveAuthor:Scooter Willis | Class | org.biojava.nbio.survival.cox | BioJava |
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StrCompAlignment | | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
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StreamListener | Event based parser callback. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |
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StringManipulationHelper | A utility class for common String manipulation tasks. | Class | org.biojava.nbio.core.util | BioJava |
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StringProxySequenceReader | An example of a ProxySequenceReader that is created from a String. | Class | org.biojava.nbio.core.sequence.loader | BioJava |
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StrucAligParameters | A class that contains all the parameters of the structure alignment algorithm. | Class | org.biojava.nbio.structure.align | BioJava |
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Struct | a bean to contain the data of the _struct linesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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StructAsym | Contains the data for _struct_asymSince:1. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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StructConn | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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StructKeywords | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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StructNcsOper | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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StructRef | A class to containt the _struct_ref field dataAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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StructRefSeq | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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StructRefSeqDif | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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StructSite | Created by Matt on 11/1/2015. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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StructSiteGen | Created by Matt on 10/31/2015. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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Structure | Interface for a structure object. | Interface | org.biojava.nbio.structure | BioJava |
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StructureAlignment | | Interface | org.biojava.nbio.structure.align | BioJava |
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StructureAlignmentDisplay | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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StructureAlignmentFactory | | Class | org.biojava.nbio.structure.align | BioJava |
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StructureAlignmentJmol | A class that provides a simple GUI for JmolSince:1. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
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StructureAlignmentOptimizer | | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
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StructureAtom | Everything that is needed to uniquely describe a atom. | Class | org.biojava.nbio.protmod.structure | BioJava |
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StructureAtomLinkage | | Class | org.biojava.nbio.protmod.structure | BioJava |
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StructureAtomXMLConverter | | Class | org.biojava.nbio.protmod.io | BioJava |
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StructureException | An exception during the parsing of a PDB file. | Class | org.biojava.nbio.structure | BioJava |
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StructureGroup | Information of a group (residue or ligand) involved in a modification. | Class | org.biojava.nbio.protmod.structure | BioJava |
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StructureGroupXMLConverter | | Class | org.biojava.nbio.protmod.io | BioJava |
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StructureIdentifier | An identifier that uniquely identifies a whole Structure or arbitrary substructure. | Interface | org.biojava.nbio.structure | BioJava |
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StructureImpl | provides the data contained in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
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StructureInterface | An interface between 2 molecules (2 sets of atoms). | Class | org.biojava.nbio.structure.contact | BioJava |
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StructureInterfaceCluster | | Class | org.biojava.nbio.structure.contact | BioJava |
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StructureInterfaceList | A list of interfaces between 2 molecules (2 sets of atoms)Author:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
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StructureIO | A class that provides static access methods for easy lookup of protein structure related componentsSince:3. | Class | org.biojava.nbio.structure | BioJava |
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StructureIOFile | StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem. | Interface | org.biojava.nbio.structure.io | BioJava |
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StructureLoaderThread | | Class | org.biojava.nbio.structure.align.gui | BioJava |
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StructureName | A utility class that makes working with names of structures, domains and ranges easier. | Class | org.biojava.nbio.structure.align.client | BioJava |
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StructurePairAligner | Perform a pairwise protein structure superimposition. | Class | org.biojava.nbio.structure.align | BioJava |
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StructurePairSelector | To be implemented by JPanels that are part of the GUI to trigger structure aligmnents. | Interface | org.biojava.nbio.structure.gui.util | BioJava |
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StructureProvider | A class that can provide a protein structure object from somewhere. | Interface | org.biojava.nbio.structure.io | BioJava |
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StructureSequenceMatcher | A utility class with methods for matching ProteinSequences withAuthor:Spencer Bliven | Class | org.biojava.nbio.structure.io | BioJava |
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StructureTools | A class that provides some tool methods. | Class | org.biojava.nbio.structure | BioJava |
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StructureUtil | | Class | org.biojava.nbio.protmod.structure | BioJava |
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StructureViewer | | Interface | org.biojava.nbio.structure.gui | BioJava |
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SubstitutionMatrix | Defines a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
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SubstitutionMatrixHelper | Static utility to access substitution matrices that come bundled with BioJava. | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
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SubstitutionMatrixScorer | Scores using a substitution matrix. | Class | org.biojava.nbio.alignment | BioJava |
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SubstructureIdentifier | This is the canonical way to identify a part of a structure. | Class | org.biojava.nbio.structure | BioJava |
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SubunitGraph | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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Subunits | A bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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SuperPosition | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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SuperPositionQCP | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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SurvFitInfo | Contains info for graphing km figuresAuthor:Scooter Willis | Class | org.biojava.nbio.survival.cox | BioJava |
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SurvFitKM | Ported from survfitKM. | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava |
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SurvivalInfo | Data class to represent a single sample where time and event/censor status is required Additionally each variable and data associated with that variable. | Class | org.biojava.nbio.survival.cox | BioJava |
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SurvivalInfoComparator | | Class | org.biojava.nbio.survival.cox.comparators | BioJava |
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SurvivalInfoHelper | Used to work with SurvivalInfoAuthor:Scooter Willis | Class | org.biojava.nbio.survival.cox | BioJava |
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SurvivalInfoIndex | Not used and probably should be deletedAuthor:Scooter Willis | Class | org.biojava.nbio.survival.cox | BioJava |
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SurvivalInfoValueComparator | | Class | org.biojava.nbio.survival.cox.comparators | BioJava |
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SVDSuperimposer | A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class. | Class | org.biojava.nbio.structure | BioJava |
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SymbolTable | Sorted symbol table implementation using a java. | Class | org.biojava.nbio.structure.math | BioJava |
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SymmClash | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
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Symmetry | | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
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SymmetryAxes | Data Structure that stores all the symmetry axis that describe the symmetry of a structure. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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SymmetryCalc | Calculates a symmetry analysis and displays the results. | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
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SymmetryDisplay | Class that provides visualizations methods for symmetry alignments. | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
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SymmetryGui | A JFrame that allows to trigger a symmetry analysis, either from files in a directory or after manual upload | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
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SymmetryListener | Action Listener for the symmetry menu. | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
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SymmetryRefiner | Interface for all symmetry refinement implementations. | Interface | org.biojava.nbio.structure.symmetry.internal | BioJava |
|
SymmetryTools | Utility methods for the internal symmetry identification and manipulation. | Class | org.biojava.nbio.structure.symmetry.utils | BioJava |
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SymmOptimizer | Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
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SymoplibParser | A class containing static methods to parse the symop. | Class | org.biojava.nbio.structure.xtal | BioJava |
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SynchronizedOutFile | | Class | org.biojava.nbio.structure.align.util | BioJava |
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Synonym | | Class | org.biojava.nbio.ontology | BioJava |
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SystematicSolver | | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
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SystemInfo | | Class | org.biojava.nbio.structure.align.gui | BioJava |
|
TabDelimParser | Parse tab-delimited ontology files into Ontology objects. | Class | org.biojava.nbio.ontology.io | BioJava |
|
Table | Provides a way of separating us from the specific IUPACParser. | Interface | org.biojava.nbio.core.sequence.transcription | BioJava |
|
TaxonomyID | A sequence can be associated with a species or Taxonomy IDAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
|
Term | A term in an ontology. | Interface | org.biojava.nbio.ontology | BioJava |
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TestDNANeedlemanWunsch | | Class | demo | BioJava |
|
Tetrahedron | | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava |
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TextFeature | A implmentation of AbstractFeatureAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.features | BioJava |
|
Timer | A simple timer, calculates the time interval between two events. | Class | org.biojava.nbio.ronn | BioJava |
|
TranscriptionEngine | Used as a way of encapsulating the data structures required to parse DNA to a In order to build one look at @ TranscriptionEngine. | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
|
TranscriptSequence | This is the sequence if you want to go from a gene sequence to a protein sequence. | Class | org.biojava.nbio.core.sequence | BioJava |
|
TransfAlgebraicAdapter | | Class | org.biojava.nbio.structure.xtal.io | BioJava |
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TransformType | | Class | org.biojava.nbio.structure.xtal | BioJava |
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TranslationException | Thrown from AbstractCompundTranslatorAuthor:Andy YatesSee Also:Serialized Form | Class | org.biojava.nbio.core.exceptions | BioJava |
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TreeConstructor | The TreeConstructor uses the forester library to build different types of phylogenetic trees. | Class | org.biojava.nbio.phylo | BioJava |
|
TreeConstructorType | enum TreeConstructorTypeThe TreeConstructorType specifies the aligorithm used to construct the tree | Class | org.biojava.nbio.phylo | BioJava |
|
TreeMapSpaceGroupWrapper | | Class | org.biojava.nbio.structure.xtal.io | BioJava |
|
TreeSetStringWrapper | | Class | org.biojava.nbio.structure.scop.server | BioJava |
|
TreeType | The TreeType specifies the optimization criteria used to generate the tree. | Class | org.biojava.nbio.phylo | BioJava |
|
Triple | A triple in an ontology. | Interface | org.biojava.nbio.ontology | BioJava |
|
TwoBitParser | downloaded from http://storage. | Class | org.biojava.nbio.genome.parsers.twobit | BioJava |
|
TwoBitSequenceReader | 0 - T1 - C2 - A3 - G We also do not support case sensitive encodings therefore if you pass a | Class | org.biojava.nbio.core.sequence.storage | BioJava |
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UncompressInputStream | This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant). | Class | org.biojava.nbio.core.util | BioJava |
|
UniprotProxySequenceReader | Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot. | Class | org.biojava.nbio.core.sequence.loader | BioJava |
|
UniprotToFasta | | Class | org.biojava.nbio.genome.uniprot | BioJava |
|
UniqueSequenceList | Bean for a single sequence. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
|
UnitCellBoundingBox | | Class | org.biojava.nbio.structure.xtal | BioJava |
|
URLIdentifier | Represents a structure loaded from a URL (including a file URL) A few custom query parameters are supported: | Class | org.biojava.nbio.structure | BioJava |
|
UserArgumentProcessor | | Interface | org.biojava.nbio.structure.align.ce | BioJava |
|
UserConfiguration | A container to persist config to the file systemAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.util | BioJava |
|
Utils | This is a utility class that contains utility methods which will facilitates the coding of other methodsSince:3. | Class | org.biojava.nbio.aaproperties | BioJava |
|
Variable | | Interface | org.biojava.nbio.ontology | BioJava |
|
WaldTest | | Class | org.biojava.nbio.survival.cox | BioJava |
|
WaldTestInfo | | Class | org.biojava.nbio.survival.cox | BioJava |
|
WeakValueHashMap | Map implementation which keeps weak references to values. | Class | org.biojava.nbio.ontology.utils | BioJava |
|
WebStartClientDemo | | Class | demo | BioJava |
|
WebStartDBSearch | A Web Start wrapper for a FarmJobRunnable. | Class | org.biojava.nbio.structure.align.webstart | BioJava |
|
WebStartDBSearchResults | | Class | org.biojava.nbio.structure.align.webstart | BioJava |
|
WebStartMain | | Class | org.biojava.nbio.structure.align.webstart | BioJava |
|
WindowedSequence | A sliding window view of a sequence which does not implement any interfaces like Sequence because they do not fit how this works. | Class | org.biojava.nbio.core.sequence.views | BioJava |
|
WorkSheet | Need to handle very large spreadsheets of expression data so keep memoryAuthor:Scooter Willis | Class | org.biojava.nbio.survival.data | BioJava |
|
WwPDBValidationInformation | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
|
XMLHelper | | Class | org.biojava.nbio.core.util | BioJava |
|
XMLUtil | Utility classes for the XML serialization and de-serialization of SCOP. | Class | org.biojava.nbio.structure.scop.server | BioJava |
|
XMLWriter | Simple interface for building XML documents. | Interface | org.biojava.nbio.core.util | BioJava |
|
ZipChemCompProvider | This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |