Search Java Classes and Packages
# Classes and Interfaces in #BioJava - 1031 results found.
| 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 |
| AAIndexFileParser | Class | org.biojava.nbio.core.alignment.matrices | BioJava | |
| AAIndexProvider | Interface | org.biojava.nbio.core.alignment.matrices | BioJava | |
| AboutDialog | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| 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 |
| 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 |
| AbstractBean | a generic class that implements the toString method for a beanAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| AbstractCompound | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| AbstractCompoundSet | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| AbstractCompoundTranslator | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| 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 |
| 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 |
| AbstractMatrixAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| AbstractNucleotideCompoundSet | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| AbstractPairwiseSequenceAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| AbstractProfileProfileAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| AbstractScorer | Class | org.biojava.nbio.alignment.template | BioJava | |
| 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 |
| AbstractSequence | The base class for DNA, RNA and Protein sequences. | Class | org.biojava.nbio.core.sequence.template | BioJava |
| AbstractStructureAlignment | Class | org.biojava.nbio.structure.align | BioJava | |
| AbstractTerm | Abstract implementation of term This provides basic change-forwarding functionality from | Class | org.biojava.nbio.ontology | BioJava |
| AbstractUserArgumentProcessor | Base class for a new structure alignment CLI. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| AccesionedLocation | A location which is bound to an AccessionID. | Interface | org.biojava.nbio.core.sequence.location.template | BioJava |
| Accessioned | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| AccessionID | Used in Sequences as the unique indentifier. | Class | org.biojava.nbio.core.sequence | BioJava |
| AFP | A class to represent a FATCAT AFPAuthor:Andreas PrlicSee Also:Serialized Form | Class | org.biojava.nbio.structure.align.model | BioJava |
| AFPAlignmentDisplay | Class | org.biojava.nbio.structure.align.util | BioJava | |
| AFPCalculator | a class that performs calculations on AFPCHainsAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| AFPChain | A bean to contain the core of a structure alignment. | Class | org.biojava.nbio.structure.align.model | BioJava |
| AFPChainCoordManager | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava | |
| AFPChainer | a class to chain AFPs to an alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| AFPChainFlipper | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| AFPChainScorer | Class | org.biojava.nbio.structure.align.util | BioJava | |
| AfpChainWriter | A class to convert the data in an AfpChain object to various String outputs. | Class | org.biojava.nbio.structure.align.model | BioJava |
| AFPChainXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| AFPChainXMLParser | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| AFPFromFasta | Demo displaying a structural alignment from a FASTA file using FastaAFPChainConverter. | Class | demo | BioJava |
| AFPOptimizer | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| AFPPostProcessor | does post processing after alignment chainginAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| AFPTwister | Class | org.biojava.nbio.structure.align | BioJava | |
| AgScore | Class | org.biojava.nbio.survival.cox.stats | BioJava | |
| AligMatEl | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| Alignable | Interface | org.biojava.nbio.structure.align.pairwise | BioJava | |
| AlignedPosition | Class | org.biojava.nbio.structure.gui.util | BioJava | |
| AlignedSequence | Defines a data structure for a Sequence within an alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| Aligner | Defines an algorithm which computes an alignment Profile from a list of Sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
| AlignerHelper | Static utility to construct alignment routines from a common library of methods. | Class | org.biojava.nbio.alignment.routines | BioJava |
| 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 |
| 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 |
| AlignmentCalcDB | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| AlignmentCalculationRunnable | Interface | org.biojava.nbio.structure.align.gui | BioJava | |
| 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 |
| AlignmentGuiDemo | Get an instance of the two alignment GUIs. | Class | demo | BioJava |
| AlignmentPositionListener | Interface | org.biojava.nbio.structure.gui.events | BioJava | |
| AlignmentProgressListener | Interface | org.biojava.nbio.structure.align.events | BioJava | |
| AlignmentProgressListener | Class | org.biojava.nbio.structure.align.pairwise | BioJava | |
| AlignmentResult | A class to track the alignment results in a flat fileAuthor:andreasSee Also:Serialized Form | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
| Alignments | Static utility to easily run alignment routines. | Class | org.biojava.nbio.alignment | BioJava |
| AlignmentTextPanel | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| AlignmentTools | Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities. | Class | org.biojava.nbio.structure.align.util | BioJava |
| AligNPE | Class | org.biojava.nbio.structure.align.pairwise | BioJava | |
| AlignTools | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| 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 |
| AligPanelMouseMotionListener | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava | |
| AligUIManager | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| AllChemCompProvider | A ChemComp provider that downloads and caches the components. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| 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 |
| AltAligComparator | a comparator to sort AlternativeAlignments based on their number of equivalent residuesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
| AlternativeAlignment | Alternative alignments arise from different seed alignments or seed FPairs. | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
| AlternativeAlignmentFrame | a frame showing the alternative alignments, which are the result of a structure superimpositionSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| AmbiguityDNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| AmbiguityDNARNAHybridCompoundSet | Ambiguity set for hybrid DNA/RNA sequences. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
| AmbiguityRNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| AminoAcid | A Group that represents an AminoAcid. | Interface | org.biojava.nbio.structure | BioJava |
| AminoAcidComposition | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| AminoAcidCompositionTable | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| AminoAcidCompound | Used to describe an Amino Acid. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
| AminoAcidCompoundSet | Set of proteinogenic amino acids. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
| AminoAcidImpl | AminoAcid inherits most from Hetatom. | Class | org.biojava.nbio.structure | BioJava |
| 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 |
| AngleOrderDetectorPlus | Guesses an order of rotational symmetry from the angle. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| AngleOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| Annotatable | Indicates that an object has an associated annotation. | Interface | org.biojava.nbio.ontology.utils | BioJava |
| Annotation | Arbitrary annotation associated with one or more objects. | Interface | org.biojava.nbio.ontology.utils | BioJava |
| App | Class | org.biojava.nbio.genome | BioJava | |
| App | Class | org.biojava.nbio.ontology | BioJava | |
| ArrayListProxySequenceReader | Class | org.biojava.nbio.core.sequence.loader | BioJava | |
| ArrayListSequenceReader | Class | org.biojava.nbio.core.sequence.storage | BioJava | |
| AsaCalculator | Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley. | Class | org.biojava.nbio.structure.asa | BioJava |
| AssertionFailure | An unchecked exception representing an Assertion failure. | Class | org.biojava.nbio.ontology.utils | BioJava |
| AssignmentXMLSerializer | Class | org.biojava.nbio.structure.domain | BioJava | |
| Astral | Provides programmatic access to ASTRAL representative sets. | Class | org.biojava.nbio.structure.scop | BioJava |
| Atom | A simple interface for an Atom. | Interface | org.biojava.nbio.structure | BioJava |
| AtomCache | A utility class that provides easy access to Structure objects. | Class | org.biojava.nbio.structure.align.util | BioJava |
| AtomContact | A pair of atoms that are in contactAuthor:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
| 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 |
| AtomIdentifier | Class | org.biojava.nbio.structure.contact | BioJava | |
| AtomImpl | currently the coordinates of an atom are represented by a double[3] array. | Class | org.biojava.nbio.structure | BioJava |
| AtomInfo | This class uniquely describes an atomAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| AtomInfoParser | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| AtomIterator | an iterator over all atoms of a structure / group. | Class | org.biojava.nbio.structure | BioJava |
| AtomPositionMap | A map from ResidueNumbers to ATOM record positions in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| AtomSite | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| AuditAuthor | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| AugmentedResidueRange | Created by douglas on 1/23/15. | Class | org.biojava.nbio.structure | BioJava |
| Author | Describes author attributes for author information in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| AutoSuggestProvider | Interface | org.biojava.nbio.structure.align.gui.autosuggest | BioJava | |
| AxisAligner | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| BasicSequence | Bare bones version of the Sequence object to be used sparingly. | Class | org.biojava.nbio.core.sequence | BioJava |
| BerkeleyScopInstallation | The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop. | Class | org.biojava.nbio.structure.scop | BioJava |
| BetaBridge | Container that represents a beta Bridge between two residues. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| BioAssemblyIdentifier | Class | org.biojava.nbio.structure | BioJava | |
| BioAssemblyInfo | Representation of a Biological Assembly annotation as provided by the PDB. | Class | org.biojava.nbio.structure.quaternary | BioJava |
| BioAssemblyTools | Class | org.biojava.nbio.structure.quaternary | BioJava | |
| BioJavaAADemo | Created by andreas on 8/9/14. | Class | demo | BioJava |
| BiojavaJmol | A class that provides a simple GUI for JmolSince:1. | Class | org.biojava.nbio.structure.gui | BioJava |
| BioJavaStructureAlignment | Wrapper for the BioJava Structure Alignment ImplementationAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align | BioJava |
| BiologicalAssemblyBuilder | Reconstructs the quaternary structure of a protein from an asymmetric unitAuthor:Peter Rose, Andreas Prlic | Class | org.biojava.nbio.structure.quaternary | BioJava |
| BiologicalAssemblyTransformation | The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file. | Class | org.biojava.nbio.structure.quaternary | BioJava |
| 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 |
| BioUnitDataProviderFactory | Factory to create BioUnitDataProvider instances. | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
| BitSequenceReader | An implementation of the popular bit encodings. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| BlastAlignmentParameterEnum | enum BlastAlignmentParameterEnumAlignment request parameters accepted by QBlast service. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| BlastClustReader | Class | org.biojava.nbio.structure.symmetry.utils | BioJava | |
| BlastHitBuilder | Designed by Paolo Pavan. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
| BlastHomologyHits | Class | org.biojava.nbio.genome.homology | BioJava | |
| BlastHspBuilder | Designed by Paolo Pavan. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
| BlastJob | Information about QBlast search jobAuthor:Gediminas Rimsa | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| BlastMatrixEnum | enum BlastMatrixEnumEnum representing matrices supported by QBlast | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| BlastOutputAlignmentFormatEnum | enum BlastOutputAlignmentFormatEnumEnum representing available output alignment types. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| BlastOutputFormatEnum | enum BlastOutputFormatEnumEnum representing available output formats. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| BlastOutputParameterEnum | enum BlastOutputParameterEnumOutput parameters accepted by QBlast service. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| BlastProgramEnum | enum BlastProgramEnumEnum representing available blast programs. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| BlastResult | This class models a Blast/Blast plus result. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
| BlastResultBuilder | Designed by Paolo Pavan. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
| BlastTabularParser | Designed by Paolo Pavan. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
| BlastXMLParser | Re-designed by Paolo Pavan on the footprint of: org. | Class | org.biojava.nbio.core.search.io.blast | BioJava |
| BlastXMLQuery | Class | org.biojava.nbio.genome.query | BioJava | |
| 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 |
| BlockImpl | General implementation of a Block that supports any type of sequential alignment with gaps. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| 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 |
| BlockSetImpl | A general implementation of a BlockSet to store a flexible part of a multiple alignment. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| Bond | A simple bond -- it stores information about two atoms as well as information about its bond order. | Interface | org.biojava.nbio.structure | BioJava |
| BondImpl | A simple bond -- it stores information about two atoms as well as information about its bond order. | Class | org.biojava.nbio.structure | BioJava |
| 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 |
| BondOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| BondType | Work in progress - NOT final!Author:Jules Jacobsen | Class | org.biojava.nbio.structure | BioJava |
| BoundingBox | A bounding box for short cutting some geometrical calculations. | Class | org.biojava.nbio.structure.contact | BioJava |
| BravaisLattice | An enum to represent the 7 Bravais latticesEnum Constant Summary | Class | org.biojava.nbio.structure.xtal | BioJava |
| 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 |
| BrowserOpener | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| BufferedReaderBytesRead | Need to keep track of actual bytes read and take advantage of buffered reader performance. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| C2RotationSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| CachedRemoteScopInstallation | An extension of the RemoteScopInstallation that caches some of the data locally. | Class | org.biojava.nbio.structure.scop | BioJava |
| CacheFactory | provides a SoftHashMap singleton. | Class | org.biojava.nbio.structure.align.util | BioJava |
| CAConverter | Converts full atom representations to Calpha only ones. | Class | org.biojava.nbio.structure.io | BioJava |
| Calc | Utility operations on Atoms, AminoAcids, etc. | Class | org.biojava.nbio.structure | BioJava |
| CalcBioAssemblySymmetry | Class | org.biojava.nbio.structure.symmetry.analysis | BioJava | |
| CallablePairwiseSequenceAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| CallablePairwiseSequenceScorer | Class | org.biojava.nbio.alignment.template | BioJava | |
| CallableProfileProfileAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| CallableStructureAlignment | Class | org.biojava.nbio.structure.align | BioJava | |
| 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 |
| CaseFreeAminoAcidCompoundSet | Set of proteinogenic amino acids. | Class | org.biojava.nbio.aaproperties.xml | BioJava |
| 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 |
| 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 |
| CathCategory | The categories found within CATH. | Class | org.biojava.nbio.structure.cath | BioJava |
| CathDatabase | General API for interacting with CATH. | Interface | org.biojava.nbio.structure.cath | BioJava |
| CathDomain | A class which represents a single CATH domain. | Class | org.biojava.nbio.structure.cath | BioJava |
| CathFactory | Controls global CathDatabases being used. | Class | org.biojava.nbio.structure.cath | BioJava |
| CathFragment | Class | org.biojava.nbio.structure.cath | BioJava | |
| CathInstallation | Class | org.biojava.nbio.structure.cath | BioJava | |
| CathNode | Represents a node in the CATH hierarchy. | Class | org.biojava.nbio.structure.cath | BioJava |
| CathSegment | Class | org.biojava.nbio.structure.cath | BioJava | |
| CDSComparator | Class | org.biojava.nbio.core.sequence | BioJava | |
| CDSSequence | Represents a exon or coding sequence in a gene. | Class | org.biojava.nbio.core.sequence | BioJava |
| 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 |
| 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 |
| CeCPMain | A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CECPParameters | Provides parameters to CeCPMainAuthor:Spencer Bliven | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CeCPUserArgumentProcessor | Class | org.biojava.nbio.structure.align.ce | BioJava | |
| Cell | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| 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 |
| CensorStatus | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava | |
| CensorStatusSelect | Interface | org.biojava.nbio.survival.kaplanmeier.figure | BioJava | |
| CeParameters | Contains the parameters that can be sent to CEAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CeSideChainMain | Class | org.biojava.nbio.structure.align.ce | BioJava | |
| CeSideChainUserArgumentProcessor | Class | org.biojava.nbio.structure.align.ce | BioJava | |
| 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 |
| 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 |
| CESymmParameters | Provides parameters to CeSymm. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| CeSymmResult | This Class stores all the relevant information of an internal symmetry result obtained with CeSymm. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| CeUserArgumentProcessor | process the arguments from command lineAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
| Chain | Defines the interface for a Chain. | Interface | org.biojava.nbio.structure | BioJava |
| ChainClusterer | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| ChainImpl | A Chain in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| ChainSignature | Class | org.biojava.nbio.structure.symmetry.misc | BioJava | |
| ChangeValue | Interface | org.biojava.nbio.survival.data | BioJava | |
| ChargeAdder | Class | org.biojava.nbio.structure.io | BioJava | |
| ChemComp | A definition for a Chemical Component, as maintained by the wwPDB. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| ChemCompAtom | stores these fields: _chem_comp_atom. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| ChemCompBond | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| ChemCompConsumer | Class | org.biojava.nbio.structure.io.mmcif | BioJava | |
| ChemCompDescriptor | Container object for _pdbx_chem_comp_descriptorSince:3. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| ChemCompDistribution | Class | demo | BioJava | |
| ChemCompGroupFactory | Class | org.biojava.nbio.structure.io.mmcif | BioJava | |
| ChemCompProvider | Interface that is implemented by all classes that can provide ChemComp definitions. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
| ChemCompTools | Some tools for working with chemical compounds. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
| ChemicalComponentDictionary | A representation of the Chemical Component Dictionary. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| ChiSq | Class | org.biojava.nbio.survival.cox.stats | BioJava | |
| Cholesky2 | Class | org.biojava.nbio.survival.cox.stats | BioJava | |
| 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 | |
| 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 |
| ClusterDomains | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| ClusterMerger | Merges clusters based on their sequence identity. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| ClusterProteinChains | Clusters the chains of one or two structures by sequence. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| CodonCompound | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| CollectionTools | Utilities for working with collections. | Class | org.biojava.nbio.structure.align.util | BioJava |
| ColorConverter | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| ColorInterpolator | Interface | org.biojava.nbio.structure.gui.util.color | BioJava | |
| ColorUtils | Class | org.biojava.nbio.structure.gui.util.color | BioJava | |
| CombinationGenerator | Class | org.biojava.nbio.structure.symmetry.utils | BioJava | |
| CommandPrompt | Class | org.biojava.nbio.aaproperties | BioJava | |
| CompactCharSequence | http://www. | Class | org.biojava.nbio.survival.data | BioJava |
| Comparison | This class provides static methods for the calculation of the percentage of identity between two aligned sequences. | Class | org.biojava.nbio.phylo | BioJava |
| ComplementCompound | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| 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 |
| Component | contains information about a certain Component. | Class | org.biojava.nbio.protmod | BioJava |
| ComponentXMLConverter | Class | org.biojava.nbio.protmod.io | BioJava | |
| Compound | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| Compound | An object to contain the info from the PDB header for a Molecule. | Class | org.biojava.nbio.structure | BioJava |
| CompoundFinder | Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure. | Class | org.biojava.nbio.structure.io | BioJava |
| CompoundNotFoundException | Class | org.biojava.nbio.core.exceptions | BioJava | |
| CompoundSet | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| CompoundTranslator | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| ConcurrencyTools | Static utility to easily share a thread pool for concurrent/parallel/lazy execution. | Class | org.biojava.nbio.core.util | BioJava |
| ConfigPDBInstallPanel | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| ConfigStrucAligParams | Interface | org.biojava.nbio.structure.align.ce | BioJava | |
| ConfigurationException | Class | org.biojava.nbio.structure.align.util | BioJava | |
| ConfigXMLHandler | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| Constraints | This class is used to support the implementation of properties stated in IPeptideProperties. | Class | org.biojava.nbio.aaproperties | BioJava |
| ContinuousColorMapper | Provides a mapping between real numbers and Colors. | Interface | org.biojava.nbio.structure.gui.util.color | BioJava |
| 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 |
| Convert2Charge | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2Hydrophobicity | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2NormalizedVanDerWaalsVolume | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2Polarity | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2Polarizability | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2SecondaryStructure | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2SolventAccessibility | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convertor | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| CookBook | Class | demo | BioJava | |
| CookbookMSA | Class | demo | BioJava | |
| CoordManager | a class that manages the conversion of sequence coordinate system to JPanel drawing coordinates | Class | org.biojava.nbio.structure.gui.util | BioJava |
| 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 |
| CountProgressListener | Class | org.biojava.nbio.structure.align.client | BioJava | |
| CoxCC | Class | org.biojava.nbio.survival.cox | BioJava | |
| CoxCoefficient | Class | org.biojava.nbio.survival.cox | BioJava | |
| 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 | |
| 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 |
| CoxScore | Class | org.biojava.nbio.survival.cox | BioJava | |
| CoxVariables | Class | org.biojava.nbio.survival.cox | BioJava | |
| 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 | |
| CutDomain | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| CutSites | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| CutValues | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| 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 |
| DatabasePDBremark | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| 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 | |
| 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 | |
| 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 | |
| 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 |
| DemoCommandLineStartup | Class | demo | BioJava | |
| 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 |
| 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 |
| 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 |
| 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 | |
| DemoShowLargeAssembly | Class | demo | BioJava | |
| DemoShowValidationResults | Class | demo | BioJava | |
| DemoSixFrameTranslation | Created by andreas on 8/10/15. | Class | demo | BioJava |
| DemoStructureFromFasta | Demo of how to use the FastaStructureParser class to read protein structures from a FASTA file. | Class | demo | BioJava |
| 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 | |
| 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 | |
| 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 | |
| DomainProvider | Interface | org.biojava.nbio.structure.domain | BioJava | |
| 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 | |
| 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 |
| GeneFeatureHelper | Class | org.biojava.nbio.genome | BioJava | |
| GeneIDGFF2Reader | http://www. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
| GeneIDXMLReader | Class | org.biojava.nbio.genome.parsers.geneid | BioJava | |
| GeneMarkGTFReader | http://www. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
| GeneName | A simple bean that contains gene name information as available from www. | Class | org.biojava.nbio.genome.parsers.genename | BioJava |
| GeneNamesParser | Parses a file from the www. | Class | org.biojava.nbio.genome.parsers.genename | BioJava |
| 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 |
| 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 |
| GenericGenbankHeaderFormat | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GenericGenbankHeaderParser | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GenericInsdcHeaderFormat | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GeneSequence | Class | org.biojava.nbio.core.sequence | BioJava | |
| GetDistanceMatrix | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| GetRepresentatives | TODO Move this to Representatives. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| GFF3FromUniprotBlastHits | Class | org.biojava.nbio.genome.homology | BioJava | |
| GFF3Reader | http://www. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
| GFF3Writer | Class | org.biojava.nbio.genome.parsers.gff | BioJava | |
| GOParser | Simple parser for the Gene Ontology (GO) flatfile format. | Class | org.biojava.nbio.ontology.io | BioJava |
| 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 |
| GradientMapper | Maps a set of real values onto a gradient. | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
| GradientPanel | Class | org.biojava.nbio.structure.gui.util.color | BioJava | |
| GraphComponentOrderDetector | The GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| GraphComponentRefiner | The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| Grid | A grid to be used for calculating atom contacts through geometric hashing algorithm. | Class | org.biojava.nbio.structure.contact | BioJava |
| GridCell | A grid cell to be used in contact calculation via geometric hashing algorithm. | Class | org.biojava.nbio.structure.contact | BioJava |
| Group | This is the data structure for a single Group of atoms. | Interface | org.biojava.nbio.structure | BioJava |
| 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 |
| GroupContact | A pair of residues that are in contactAuthor:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
| GroupContactSet | A set of residue-residue contacts. | Class | org.biojava.nbio.structure.contact | BioJava |
| GroupIterator | An iterator over all groups of a structure. | Class | org.biojava.nbio.structure | BioJava |
| GroupResults | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava | |
| GroupToSDF | Class | org.biojava.nbio.structure.io | BioJava | |
| GroupType | This contains basic categories for Group types. | Class | org.biojava.nbio.structure | BioJava |
| 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 |
| GUIAlignmentProgressListener | a GUI that allows to watch progress as multiple alignments are being processed. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| GuideTree | GuideTree. | Class | org.biojava.nbio.alignment | BioJava |
| 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 |
| GUIFarmJobRunnable | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| GuiWrapper | A class to wrap some of the strucutre. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| 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 |
| HasResultXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| HBond | Container that represents a hidrogen bond. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| HeaderInfo | Class | org.biojava.nbio.survival.data | BioJava | |
| HelicalRepeatUnit | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| Helix | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixAxisAligner | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixExtender | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixLayers | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelpDialog | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| HetatomImpl | Generic Implementation of a Group interface. | Class | org.biojava.nbio.structure | BioJava |
| HierarchicalClusterer | Defines a clustering algorithm that converts a distance matrix into a tree. | Interface | org.biojava.nbio.alignment.template | BioJava |
| Hit | This class models a search Hit. | Class | org.biojava.nbio.core.search.io | BioJava |
| HmmerDemo | The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 serviceSince:3. | Class | demo | BioJava |
| HmmerDomain | Provides the details of a domain hitSince:3. | Class | org.biojava.nbio.ws.hmmer | BioJava |
| HmmerResult | The results of a Hmmer search for a single sequenceSince:3. | Class | org.biojava.nbio.ws.hmmer | BioJava |
| HmmerScan | Interface for performing Hmmscans on sequences. | Interface | org.biojava.nbio.ws.hmmer | BioJava |
| Hsp | This class models a search Hsp. | Class | org.biojava.nbio.core.search.io | BioJava |
| HSVColorSpace | Class | org.biojava.nbio.structure.gui.util.color | BioJava | |
| 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 |
| IcosahedralSampler | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| Icosahedron | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| Identifier | A collection of utilities to create StructureIdentifiers. | Class | org.biojava.nbio.structure | BioJava |
| IdxComparator | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| IlluminaFastqReader | Reader for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| IlluminaFastqWriter | Writer for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| IndexPair | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| InputStreamProvider | A class that provides an InputStream from a File. | Class | org.biojava.nbio.core.util | BioJava |
| 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 |
| InsdcParser | Parser for working with INSDC style locations. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| IntegerOntology | Class | org.biojava.nbio.ontology | BioJava | |
| IntronSequence | Class | org.biojava.nbio.core.sequence | BioJava | |
| InvalidTermException | Thrown to indicate that an ontology term is not acceptable or appropriate in a given context | Class | org.biojava.nbio.ontology | BioJava |
| IOUtils | Class | org.biojava.nbio.core.sequence.io.util | BioJava | |
| IPeptideProperties | An interface to generate some basic physico-chemical properties of protein sequences. | Interface | org.biojava.nbio.aaproperties | BioJava |
| IProfeatProperties | Interface | org.biojava.nbio.aaproperties.profeat | BioJava | |
| Isotope | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| 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 |
| JAutoSuggest | A JTextField that can make suggestions for auto-complete. | Class | org.biojava.nbio.structure.align.gui.autosuggest | BioJava |
| JFatCatClient | Class | org.biojava.nbio.structure.align.client | BioJava | |
| 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 |
| JmolAlignedPositionListener | Class | org.biojava.nbio.structure.gui.events | BioJava | |
| JmolPanel | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| JmolSymmetryScriptGenerator | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorC1 | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorCn | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorDn | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorH | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorI | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorO | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorPointGroup | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorT | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolTools | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| JmolViewerImpl | Class | org.biojava.nbio.structure.gui | BioJava | |
| JNLPProxy | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| JobKillException | Class | org.biojava.nbio.structure.align.client | BioJava | |
| 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 |
| 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 |
| JournalArticle | Class | org.biojava.nbio.structure | BioJava | |
| JPrintPanel | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| Jronn | This class gives public API to RONN functions. | Class | org.biojava.nbio.ronn | BioJava |
| KaplanMeierFigure | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava | |
| 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 |
| KMFigureInfo | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava | |
| Ladder | A Ladder is a set of one or more consecutive bridges of identical type. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| LightweightProfile | Defines a minimal data structure for reading and writing a sequence alignment. | Interface | org.biojava.nbio.core.sequence.template | BioJava |
| LinearColorInterpolator | Class | org.biojava.nbio.structure.gui.util.color | BioJava | |
| ListStringWrapper | Class | org.biojava.nbio.structure.scop.server | BioJava | |
| 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 |
| LocalProteinDomainParser | Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures. | Class | org.biojava.nbio.structure.domain | BioJava |
| 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 |
| Location | Sets of integers used to represent the location of features on sequence. | Interface | org.biojava.nbio.core.sequence.location.template | BioJava |
| Location | A location on a sequence. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
| LocationHelper | Helper methods for use with the Location classes. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| LocIterator | Move a sliding window over a Location. | Class | org.biojava.nbio.genome.parsers.gff | BioJava |
| 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 |
| 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 |
| MapToStringTransformer | Transforms Map to String. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| Maths | Class | org.biojava.nbio.structure.jama | BioJava | |
| Matrix | Jama = Java Matrix class. | Class | org.biojava.nbio.structure.jama | BioJava |
| Matrix | *********************************************************************** Compilation: javac Matrix. | Class | org.biojava.nbio.survival.cox.matrix | BioJava |
| MatrixAligner | Defines an Aligner which builds a score matrix during computation. | Interface | org.biojava.nbio.alignment.template | BioJava |
| MatrixListener | Interface | org.biojava.nbio.structure.align.ce | BioJava | |
| MeanModelComparator | Class | org.biojava.nbio.survival.cox.comparators | BioJava | |
| MeanQuantizer | Class | org.biojava.nbio.survival.kaplanmeier.metadata | BioJava | |
| MemoryMonitor | Tracks Memory allocated & used, displayed in graph form. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MenuCreator | Create the menus for structure alignment GUI windows (JFrames). | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MenuCreator | Create the menu for BiojavaJmolSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| Messages | Class | org.biojava.nbio.core.exceptions | BioJava | |
| MetaDataInfo | Class | org.biojava.nbio.survival.kaplanmeier.metadata | BioJava | |
| MmCifBiolAssemblyProvider | Class | org.biojava.nbio.structure.quaternary.io | BioJava | |
| MMcifConsumer | An interface for the events triggered by a MMcifParser. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
| MMCIFFileReader | How to parse an mmCif file:public static void main(String[] args) throws Exception { | Class | org.biojava.nbio.structure.io | BioJava |
| MMCIFFileTools | Some tools for mmCIF file writing. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| MMcifParser | Interface that needs to be implemented by an MMcifParserSince:1. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
| 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 |
| ModelledSubgroup | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| ModelLoader | Class that loads data from the model files into ModelLoader. | Class | org.biojava.nbio.ronn | BioJava |
| ModificationCategory | enum ModificationCategorydefine modification categories. | Class | org.biojava.nbio.protmod | BioJava |
| ModificationCondition | Conditions of a protein modification, e. | Interface | org.biojava.nbio.protmod | BioJava |
| ModificationConditionImpl | Class | org.biojava.nbio.protmod | BioJava | |
| ModificationLinkage | Class | org.biojava.nbio.protmod | BioJava | |
| ModificationOccurrenceType | enum ModificationOccurrenceTypeSince:3. | Class | org.biojava.nbio.protmod | BioJava |
| ModifiedAminoAcidCompoundSet | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| ModifiedCompound | Root interface for all modifications in structure. | Interface | org.biojava.nbio.protmod.structure | BioJava |
| ModifiedCompoundImpl | Class | org.biojava.nbio.protmod.structure | BioJava | |
| ModifiedCompoundXMLConverter | Class | org.biojava.nbio.protmod.io | BioJava | |
| MogAngleOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| MogBondOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| MomentsOfInertia | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| 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 |
| MultipleAlignmentCalc | A class that obtains structures via DAS and aligns them. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| 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 |
| MultipleAlignmentDisplay | Utility functions to generalize the visualization of MultipleAlignments in molecular viewers. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| 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 |
| MultipleAlignmentEnsembleImpl | A general implementation of a MultipleAlignmentEnsemble. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| 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 |
| MultipleAlignmentImpl | A general implementation of a MultipleAlignment. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| MultipleAlignmentJmol | A class that provides a 3D visualization Frame in Jmol for MultipleAlignments. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| MultipleAlignmentJmolDisplay | Utility Class that provides helper methods for the visualization of MultipleAlignments. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MultipleAlignmentScorer | Utility class for calculating common scores of MultipleAlignments. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentTools | Utility functions for working with MultipleAlignment. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentWriter | This class contains functions for the conversion of MultipleAlignment to various String outputs. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentXMLConverter | Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format. | Class | org.biojava.nbio.structure.align.xml | BioJava |
| MultipleAlignmentXMLParser | Parse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered. | Class | org.biojava.nbio.structure.align.xml | BioJava |
| 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 |
| 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 |
| MultipleMcMain | Main class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm, | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
| 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 |
| MultipleMcParameters | Contains the parameters to be sent to the MC optimization. | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
| MultipleSequenceAlignment | structure in the alignment module provides additional functionality. | Class | org.biojava.nbio.core.sequence | BioJava |
| 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 |
| MultipleStructureAligner | Interface for the Multiple Structure Alignment Algorithms. | Interface | org.biojava.nbio.structure.align | BioJava |
| MultipleSuperimposer | Interface for Multiple Alignment superposition algorithms. | Interface | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultiThreadedDBSearch | Performs a multi threaded database search for an input protein structureAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align | BioJava |
| MutableAlignedSequence | Defines a mutable (editable) data structure for an AlignedSequence. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| MutableProfile | Defines a mutable (editable) data structure for a Profile. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| MutableProfilePair | Defines a mutable (editable) data structure for a ProfilePair. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| MutableSequencePair | Defines a mutable (editable) data structure for the results of pairwise sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| Mutator | A class that can change one amino acid to another. | Class | org.biojava.nbio.structure | BioJava |
| 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 |
| MyDistMaxListener | Shows the interatomic Distance Matrices of all the Structures aligned in different Frames. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MyExportListener | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| MyJmolStatusListener | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| MyOpenPdbFileListener | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| MySaveFileListener | Save an alignment to a specified File by the user. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MyTableRowSorter | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| MyValidationEventHandler | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| Name2Count | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| 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 |
| NCBIQBlastOutputProperties | This class wraps a QBlast output parameter Map by adding several convenient parameter addition methods. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| NCBIQBlastService | Provides a simple way of submitting BLAST request to the QBlast service at NCBI. | Class | org.biojava.nbio.ws.alignment.qblast | BioJava |
| NCBIQBlastServiceDemo | A simple demo showing NCBIQBlastService usageAuthor:Gediminas Rimsa | Class | demo | BioJava |
| 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 |
| NucleotideCompound | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| NucleotideImpl | A nucleotide group is almost the same as a Hetatm group. | Class | org.biojava.nbio.structure | BioJava |
| NullOutputStream | The stream that void its inputSince:3. | Class | org.biojava.nbio.ronn | BioJava |
| NumbersAtRiskPanel | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava | |
| ObjectFactory | This object contains factory methods for each Java content interface and Java element interface | Class | org.biojava.nbio.structure.validation | BioJava |
| OboFileEventListener | an interface for events that occur during parsing of . | Interface | org.biojava.nbio.ontology.obo | BioJava |
| OboFileHandler | A file handler for . | Class | org.biojava.nbio.ontology.obo | BioJava |
| OboFileParser | A class to parse the content of an OBO file. | Class | org.biojava.nbio.ontology.obo | BioJava |
| OboParser | OboParser parser = new OboParser(); InputStream inStream = this. | Class | org.biojava.nbio.ontology.io | BioJava |
| Octahedron | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| 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 |
| OntologyException | Thrown to indicate an error in an Ontology objectSince:1. | Class | org.biojava.nbio.ontology | BioJava |
| OntologyFactory | A factory for Ontology instances. | Interface | org.biojava.nbio.ontology | BioJava |
| OntologyOps | This is an interface for optimizing ontology operators. | Interface | org.biojava.nbio.ontology | BioJava |
| OntologyTerm | A term in an ontology which identifies another ontology. | Interface | org.biojava.nbio.ontology | BioJava |
| OntoTools | Tools for manipulating ontologies. | Class | org.biojava.nbio.ontology | BioJava |
| OperatorResolver | Class | org.biojava.nbio.structure.quaternary | BioJava | |
| OptimalCECPMain | A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| OptimalCECPParameters | Contains the parameters that can be sent to CEAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
| 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 |
| OrderedPair | An ordered pair represents a component of a cartesian product. | Class | org.biojava.nbio.structure.quaternary | BioJava |
| ORonn | Fully re-factored and enhanced version of RONN. | Class | org.biojava.nbio.ronn | BioJava |
| ORonnModel | Fully re-factored version of RONN model. | Class | org.biojava.nbio.ronn | BioJava |
| OutputHitsGFF | Class | org.biojava.nbio.genome.query | BioJava | |
| Pair | A Pair of objects. | Class | org.biojava.nbio.structure.contact | BioJava |
| 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 |
| PairwiseAlignment | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| PairwiseSequenceAligner | Defines an Aligner for a pair of Sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
| PairwiseSequenceScorer | Defines an algorithm which computes a score for a pair of sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
| ParameterGUI | UI for ConfigStrucAligParams, for the AlignmentGUI. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| ParseFastaFileDemo | Created by andreas on 6/17/15. | Class | demo | BioJava |
| ParseGO | Class | demo | BioJava | |
| ParseListener | Low-level event based parser callback. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |
| ParserException | General abstraction of different parsing errorsAuthor:Scooter Willis See Also:Serialized Form | Class | org.biojava.nbio.core.exceptions | BioJava |
| PartitionRefiner | Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning. | Interface | org.biojava.nbio.alignment.template | BioJava |
| PassthroughIdentifier | A stub StructureIdentifier, representing the full structure in all cases. | Class | org.biojava.nbio.structure | BioJava |
| 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 |
| PDBBioUnitDataProvider | A BioUnitDataProvider that extracts the necessary info from PDB filesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
| PDBCrystallographicInfo | A class to hold crystallographic information about a PDB structure. | Class | org.biojava.nbio.structure | BioJava |
| PDBDirPanel | A class to define where a structure for the alignment is coming fromSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| PDBDomainProvider | Class to fetch domains through the RCSB's REST API. | Class | org.biojava.nbio.structure.domain | BioJava |
| PDBFileParser | This class implements the actual PDB file parsing. | Class | org.biojava.nbio.structure.io | BioJava |
| PDBFileReader | The wrapper class for parsing a PDB file. | Class | org.biojava.nbio.structure.io | BioJava |
| PDBHeader | A class that contains PDB Header information. | Class | org.biojava.nbio.structure | BioJava |
| PdbIdLists | Utility classes for retrieving lists of PDB IDs. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| PdbPair | A pair for structure alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.client | BioJava |
| PdbPairsMessage | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| PdbPairXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| PDBParseException | An exception during the parsing of a PDB file. | Class | org.biojava.nbio.structure.io | BioJava |
| PDBRecord | An interface implemented by all classes that represent PDB recordsSince:1. | Interface | org.biojava.nbio.structure | BioJava |
| PDBServerPanel | A class to define where a structure for the alignment is coming fromSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| 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 |
| PDBTemporaryStorageUtils | Internal use only. | Class | org.biojava.nbio.structure.io.util | BioJava |
| PDBUploadPanel | A JPanel to upload 2 custom PDB files. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| PdbxChemCompDescriptor | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxChemCompIdentifier | _pdbx_chem_comp_identifier. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| PdbxEntityNonPoly | A bean for the Pdbx_entity_nonpoly category. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| 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 |
| 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 |
| PdbxStructAssembly | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructAssemblyGen | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructAssemblyGenXMLContainer | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructAssemblyXMLContainer | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructOperList | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructOperListXMLContainer | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PDPDistanceMatrix | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| PDPDomain | Class | org.biojava.nbio.structure.domain | BioJava | |
| PDPParameters | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| PDPProvider | Decomposes a structure into representative PDP domains. | Interface | org.biojava.nbio.structure.domain | BioJava |
| PeptideProperties | This is an adaptor class which enable the ease of generating protein properties. | Class | org.biojava.nbio.aaproperties | BioJava |
| 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 |
| PermutationGenerator | Class | org.biojava.nbio.structure.symmetry.utils | BioJava | |
| PermutationGroup | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| PersistentConfig | a class to store the config using the Java Web StartAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.webstart | BioJava |
| PlainFastaHeaderParser | The plain fasta header takes everything in the header as a single entity. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| Point | Interface | org.biojava.nbio.core.sequence.location.template | BioJava | |
| Polyhedron | Interface | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| PolymerType | Enumerates the classification of polymers. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
| PositionInQueueXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| PredictDisorder | Class | demo | BioJava | |
| PrettyXMLWriter | Class | org.biojava.nbio.core.util | BioJava | |
| Prism | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| ProfeatProperties | This is an adaptor class which enable the ease of generating profeat properties. | Class | org.biojava.nbio.aaproperties.profeat | BioJava |
| ProfeatPropertiesImpl | Class | org.biojava.nbio.aaproperties.profeat | BioJava | |
| Profile | Defines a data structure for the results of sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| ProfilePair | Defines a data structure for the results of the alignment of a pair of Profiles. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| ProfileProfileAligner | Defines an Aligner for a pair of Profiles. | Interface | org.biojava.nbio.alignment.template | BioJava |
| ProfileProfileScorer | Defines an algorithm which computes a score for a pairing of alignment profiles. | Interface | org.biojava.nbio.alignment.template | BioJava |
| ProfileView | Defines a data structure for a view of sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| Program | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| Programs | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| ProteinChainExtractor | Extracts information about all the chains in a structure, including chain Ids, sequences, and atoms. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| ProteinComplexSignature | Class | org.biojava.nbio.structure.symmetry.misc | BioJava | |
| ProteinModification | This interface defines information about a specific proteinSince:3. | Interface | org.biojava.nbio.protmod | BioJava |
| ProteinModificationIdentifier | Identify attachment modification in a 3-D structure. | Class | org.biojava.nbio.protmod.structure | BioJava |
| ProteinModificationImpl | This class contains information about a specific proteinSince:3. | Class | org.biojava.nbio.protmod | BioJava |
| ProteinModificationRegistry | This class serves as a instance registry by maintaining a pool of ProteinModification instances. | Class | org.biojava.nbio.protmod | BioJava |
| ProteinModificationXmlReader | Class | org.biojava.nbio.protmod.io | BioJava | |
| ProteinSequence | The representation of a ProteinSequenceAuthor:Scooter Willis, Paolo Pavan | Class | org.biojava.nbio.core.sequence | BioJava |
| ProteinSequenceClusterer | Represents a set of non-identical protein sequences. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| 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 |
| ProxySequenceReader | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| 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 |
| Qualifier | Class | org.biojava.nbio.core.sequence.features | BioJava | |
| QualityFeature | DNA Sequences produced by modern sequencers usually have quality informaion attached to them. | Class | org.biojava.nbio.core.sequence.features | BioJava |
| QuantityFeature | It is common to have a numerical value or values associated with a feature. | Class | org.biojava.nbio.core.sequence.features | BioJava |
| QuatSuperpositionScorer | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| QuatSymmetryDetector | Detects global and local quaternary protein structure symmetry in a structure. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| QuatSymmetryParameters | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| QuatSymmetryResults | Holds the results of quaternary symmetry perception. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| QuatSymmetryScores | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| QuatSymmetrySolver | Interface | org.biojava.nbio.structure.symmetry.core | BioJava | |
| 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 |
| RasmolCommandListener | a utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.gui | BioJava |
| 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 |
| RCSBDescription | Corresponds to the wrapper element in an RCSB describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBDescriptionFactory | Fetches information from RCSB's RESTful Web Service Interface. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBLigand | Corresponds to a ligand in a ligandInfo XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBLigands | Corresponds to the wrapper element "ligandInfo" in an RCSB ligandInfo XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBLigandsFactory | Fetches information from RCSB's RESTful Web Service Interface. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBMacromolecule | Corresponds to a macromolecule in an RCSB describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBPolymer | Corresponds to a polymer in a describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBTaxonomy | Corresponds to a taxonomy in a describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBUpdates | Class | org.biojava.nbio.structure.rcsb | BioJava | |
| ReadUtils | Package-level static utilities for parsing XML. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RectangularPrism | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| ReducedChemCompProvider | Unlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| 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 |
| Refine | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| RefinerFailedException | Refinement of the self-alignment failed. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| RemoteBioUnitDataProvider | Class | org.biojava.nbio.structure.quaternary.io | BioJava | |
| RemoteDomainProvider | A DomainProvider that uses a mixture of SCOP and PDP domains. | Class | org.biojava.nbio.structure.domain | BioJava |
| 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 |
| 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 |
| RemotePairwiseAlignmentProperties | RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties. | Interface | org.biojava.nbio.ws.alignment | BioJava |
| RemotePairwiseAlignmentService | This interface specifies minimal information needed to execute a pairwise alignment on a remote service. | Interface | org.biojava.nbio.ws.alignment | BioJava |
| RemotePDPProvider | A class that provided PDP assignments that are loaded from a remote web serverAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.domain | BioJava |
| 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 |
| RemoteScopInstallation | A class that fetches information about SCOP from a remote data-source. | Class | org.biojava.nbio.structure.scop | BioJava |
| RemoteTerm | A term in another ontology. | Interface | org.biojava.nbio.ontology | BioJava |
| RenderStyle | Class | org.biojava.nbio.structure.gui | BioJava | |
| RepresentativeXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| RescoreRefiner | Interface | org.biojava.nbio.alignment.template | BioJava | |
| 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 |
| ResidueNumber | Everything that is needed to uniquely describe a residue positionAuthor:Andreas PrlicSee Also:Serialized Form | Class | org.biojava.nbio.structure | BioJava |
| ResidueRange | A chain, a start residue, and an end residue. | Class | org.biojava.nbio.structure | BioJava |
| ResidueRangeAndLength | A chain, a start residue, and an end residue. | Class | org.biojava.nbio.structure | BioJava |
| ResidueType | Enumerates the possible classifications of residues. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
| ResourceManager | A class that manages the Strings that are defined in the spice. | Class | org.biojava.nbio.structure.align.util | BioJava |
| Result | This class models a search result. | Class | org.biojava.nbio.core.search.io | BioJava |
| ResultFactory | Designed by Paolo Pavan. | Interface | org.biojava.nbio.core.search.io | BioJava |
| ReversedSequenceView | For a given sequence this class will return the base at the reversed position i. | Class | org.biojava.nbio.core.sequence.views | BioJava |
| RiskInfo | Class | org.biojava.nbio.survival.cox | BioJava | |
| RNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| RNASequence | RNASequence where RNACompoundSet are the allowed valuesAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| RNASequenceCreator | Used to create a RNA sequenceAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.io | BioJava |
| RnaSequenceView | Class | org.biojava.nbio.core.sequence.views | BioJava | |
| 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 |
| RonnConstraint | A collection of various constrain values used by RONNSince:3. | Class | org.biojava.nbio.ronn | BioJava |
| 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 |
| RotationAxisAligner | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| RotationGroup | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| RotationSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| SandboxStyleStructureProvider | The "Sandbox" style of organizing files is to have a directory structure like below, i. | Class | org.biojava.nbio.structure.io | BioJava |
| SangerFastqReader | Reader for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| SangerFastqWriter | Writer for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| 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 |
| ScanSymmetry | Class | org.biojava.nbio.structure.symmetry.analysis | BioJava | |
| SchemaGenerator | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| SCOPAutoSuggestProvider | Class | org.biojava.nbio.structure.align.gui.autosuggest | BioJava | |
| ScopCategory | The various categories provided by SCOP. | Class | org.biojava.nbio.structure.scop | BioJava |
| ScopDatabase | General API how to interact with SCOPSince:3. | Interface | org.biojava.nbio.structure.scop | BioJava |
| ScopDescription | dir. | Class | org.biojava.nbio.structure.scop | BioJava |
| ScopDescriptions | Class | org.biojava.nbio.structure.scop.server | BioJava | |
| 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 |
| 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 |
| SecStrucType | This enum contains all of the secondary structure types found in the DSSP output. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| 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 | |
| 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 |
| SeqMisMatch | Created by andreas on 9/11/15. | Interface | org.biojava.nbio.structure | BioJava |
| SeqMisMatchImpl | Created by andreas on 9/11/15. | Class | org.biojava.nbio.structure | BioJava |
| 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 |
| SequenceAlignmentCluster | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| 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 |
| SequenceCreatorInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| SequenceDisplay | A sequence display that can show the results of a protein structure alignment. | Class | org.biojava.nbio.structure.gui | BioJava |
| 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 |
| SequenceFunctionOrderDetector | Calls Spencer's method for determining order. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| SequenceFunctionRefiner | Creates a refined alignment with the CE-Symm alternative self-alignment. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| SequenceHeaderParserInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| 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 |
| 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 |
| 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 |
| SequenceOptimizationHints | A static class that provides optimization hints for memory or performance handling of sequence data. | Class | org.biojava.nbio.core.sequence | BioJava |
| SequencePair | Defines a data structure for the results of pairwise sequence alignment. | Interface | org.biojava.nbio.core.alignment.template | BioJava |
| SequenceParserInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| SequenceProxyView | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| SequenceReader | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| SequenceScalePanel | A class that draws a Sequence as a rectangle, a scale display over it. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| SequenceTools | Class | org.biojava.nbio.core.util | BioJava | |
| SequenceUtil | Utility class for operations on sequencesSince:3. | Class | org.biojava.nbio.data.sequence | BioJava |
| SequenceView | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| SerializableCache | A class that provides all that is necessary to create a Serializable CacheSince:3. | Class | org.biojava.nbio.structure.domain | BioJava |
| ShortSegmentRemover | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| ShowPDBIDListener | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| ShowStructureInJmol | Demo how to load and display a structure in JmolAuthor:Andreas Prlic | Class | demo | BioJava |
| SiftsChainEntry | An entry in the chain-level SIFTS mapping between UniProt and the PDB. | Class | org.biojava.nbio.structure.io.sifts | BioJava |
| SiftsChainToUniprotMapping | A mapping between UniProt entries and PDB chains. | Class | org.biojava.nbio.structure.io.sifts | BioJava |
| SiftsEntity | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsMappingProvider | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsResidue | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsSegment | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsXMLParser | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SigEva | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| SimpleAlignedSequence | Class | org.biojava.nbio.core.alignment | BioJava | |
| SimpleGapPenalty | Class | org.biojava.nbio.alignment | BioJava | |
| SimpleLocation | Very basic implementation of the Location interface which defines a series of simple constructors. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| 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 |
| SimpleMMcifParser | A simple mmCif file parserString file = "path/to/mmcif/file"; | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| SimplePoint | Basic implementation of the Point interface. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| SimpleProfile | Class | org.biojava.nbio.core.alignment | BioJava | |
| SimpleProfilePair | Class | org.biojava.nbio.core.alignment | BioJava | |
| SimpleProfileProfileAligner | NeedlemanWunsch pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score. | Class | org.biojava.nbio.alignment | BioJava |
| SimpleSequencePair | Class | org.biojava.nbio.core.alignment | BioJava | |
| SimpleSubstitutionMatrix | Compound in a sequence for another. | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
| 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 |
| SingleLinkageClusterer | An implementation of a single linkage clusterer See http://en. | Class | org.biojava.nbio.core.util | BioJava |
| SingularValueDecomposition | Singular Value Decomposition. | Class | org.biojava.nbio.structure.jama | BioJava |
| Site | Created by ap3 on 31/10/2014. | Class | org.biojava.nbio.phosphosite | BioJava |
| Site | Holds the data of sites presented in PDB files. | Class | org.biojava.nbio.structure | BioJava |
| SmallAnnotation | Annotation that is optimized for memory usage. | Class | org.biojava.nbio.ontology.utils | BioJava |
| 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 |
| 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 |
| SmithWaterman3Daligner | provides a 3D superimposition based on the sequence alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.seq | BioJava |
| SmithWaterman3DParameters | Class | org.biojava.nbio.structure.align.seq | BioJava | |
| SmithWatermanUserArgumentProcessor | Class | org.biojava.nbio.structure.align.seq | BioJava | |
| SoftHashMap | A in memory cache using soft references. | Class | org.biojava.nbio.core.util | BioJava |
| SolexaFastqReader | Reader for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| SolexaFastqWriter | Writer for FastqVariant. | Class | org.biojava.nbio.sequencing.io.fastq | BioJava |
| SpaceGroup | A crystallographic space group. | Class | org.biojava.nbio.structure.xtal | BioJava |
| SpaceGroupMapElements | Class | org.biojava.nbio.structure.xtal.io | BioJava | |
| SpaceGroupMapRoot | Class | org.biojava.nbio.structure.xtal.io | BioJava | |
| 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 |
| SparseVector | A sparse vector, implemented using a symbol table. | Class | org.biojava.nbio.structure.math | BioJava |
| SphereSampler | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| SplitFasta | Utility to write each Fasta entry to a unique fileAuthor:Scooter Willis | Class | org.biojava.nbio.genome.util | BioJava |
| 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 |
| SSBondImpl | A simple bean to store disulfide bridge information, the SSBOND records in the PDB files. | Class | org.biojava.nbio.structure.io | BioJava |
| StainType | Class | org.biojava.nbio.genome.parsers.cytoband | BioJava | |
| StandardAminoAcid | A class that provides a set of standard amino acids. | Class | org.biojava.nbio.structure | BioJava |
| StandardRescoreRefiner | Class | org.biojava.nbio.alignment | BioJava | |
| StartCodonSequence | Used to map the start codon feature on a geneAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| StartupParameters | a simple bean that contains the parameters that can get set at startupAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
| StaticMemberPlaceHolder | Class | org.biojava.nbio.ontology.utils | BioJava | |
| StatusDisplay | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava | |
| StdArrayIO | Standard array IO. | Class | org.biojava.nbio.survival.cox.matrix | BioJava |
| StockholmFileAnnotation | Stores all the content parsed from the #=GF linesSince:3. | Class | org.biojava.nbio.alignment.io | BioJava |
| StockholmFileParser | Stockholm file parser. | Class | org.biojava.nbio.alignment.io | BioJava |
| StockholmStructure | Stores all the content of a Stockholm file. | Class | org.biojava.nbio.alignment.io | BioJava |
| StopCodonSequence | Used to map the stop codon sequence on a geneAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| Strand | Provides a way of representing the strand of a sequence, locationEnum Constant Summary | Class | org.biojava.nbio.core.sequence | BioJava |
| StrataInfo | Information needed to represent a survival curveAuthor:Scooter Willis | Class | org.biojava.nbio.survival.cox | BioJava |
| StrCompAlignment | Class | org.biojava.nbio.structure.align.pairwise | BioJava | |
| StreamListener | Event based parser callback. | Interface | org.biojava.nbio.sequencing.io.fastq | BioJava |
| StringManipulationHelper | A utility class for common String manipulation tasks. | Class | org.biojava.nbio.core.util | BioJava |
| StringProxySequenceReader | An example of a ProxySequenceReader that is created from a String. | Class | org.biojava.nbio.core.sequence.loader | BioJava |
| StrucAligParameters | A class that contains all the parameters of the structure alignment algorithm. | Class | org.biojava.nbio.structure.align | BioJava |
| Struct | a bean to contain the data of the _struct linesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructAsym | Contains the data for _struct_asymSince:1. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructConn | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructKeywords | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructNcsOper | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructRef | A class to containt the _struct_ref field dataAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructRefSeq | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructRefSeqDif | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructSite | Created by Matt on 11/1/2015. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructSiteGen | Created by Matt on 10/31/2015. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| Structure | Interface for a structure object. | Interface | org.biojava.nbio.structure | BioJava |
| StructureAlignment | Interface | org.biojava.nbio.structure.align | BioJava | |
| StructureAlignmentDisplay | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| StructureAlignmentFactory | Class | org.biojava.nbio.structure.align | BioJava | |
| StructureAlignmentJmol | A class that provides a simple GUI for JmolSince:1. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| StructureAlignmentOptimizer | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| StructureAtom | Everything that is needed to uniquely describe a atom. | Class | org.biojava.nbio.protmod.structure | BioJava |
| StructureAtomLinkage | Class | org.biojava.nbio.protmod.structure | BioJava | |
| StructureAtomXMLConverter | Class | org.biojava.nbio.protmod.io | BioJava | |
| StructureException | An exception during the parsing of a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| StructureGroup | Information of a group (residue or ligand) involved in a modification. | Class | org.biojava.nbio.protmod.structure | BioJava |
| StructureGroupXMLConverter | Class | org.biojava.nbio.protmod.io | BioJava | |
| StructureIdentifier | An identifier that uniquely identifies a whole Structure or arbitrary substructure. | Interface | org.biojava.nbio.structure | BioJava |
| StructureImpl | provides the data contained in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| StructureInterface | An interface between 2 molecules (2 sets of atoms). | Class | org.biojava.nbio.structure.contact | BioJava |
| StructureInterfaceCluster | Class | org.biojava.nbio.structure.contact | BioJava | |
| 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 |
| StructureIO | A class that provides static access methods for easy lookup of protein structure related componentsSince:3. | Class | org.biojava.nbio.structure | BioJava |
| StructureIOFile | StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem. | Interface | org.biojava.nbio.structure.io | BioJava |
| StructureLoaderThread | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| StructureName | A utility class that makes working with names of structures, domains and ranges easier. | Class | org.biojava.nbio.structure.align.client | BioJava |
| StructurePairAligner | Perform a pairwise protein structure superimposition. | Class | org.biojava.nbio.structure.align | BioJava |
| StructurePairSelector | To be implemented by JPanels that are part of the GUI to trigger structure aligmnents. | Interface | org.biojava.nbio.structure.gui.util | BioJava |
| StructureProvider | A class that can provide a protein structure object from somewhere. | Interface | org.biojava.nbio.structure.io | BioJava |
| StructureSequenceMatcher | A utility class with methods for matching ProteinSequences withAuthor:Spencer Bliven | Class | org.biojava.nbio.structure.io | BioJava |
| StructureTools | A class that provides some tool methods. | Class | org.biojava.nbio.structure | BioJava |
| StructureUtil | Class | org.biojava.nbio.protmod.structure | BioJava | |
| StructureViewer | Interface | org.biojava.nbio.structure.gui | BioJava | |
| 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 |
| SubstitutionMatrixHelper | Static utility to access substitution matrices that come bundled with BioJava. | Class | org.biojava.nbio.core.alignment.matrices | BioJava |
| SubstitutionMatrixScorer | Scores using a substitution matrix. | Class | org.biojava.nbio.alignment | BioJava |
| SubstructureIdentifier | This is the canonical way to identify a part of a structure. | Class | org.biojava.nbio.structure | BioJava |
| SubunitGraph | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| 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 |
| SuperPosition | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| SuperPositionQCP | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| SurvFitInfo | Contains info for graphing km figuresAuthor:Scooter Willis | Class | org.biojava.nbio.survival.cox | BioJava |
| SurvFitKM | Ported from survfitKM. | Class | org.biojava.nbio.survival.kaplanmeier.figure | BioJava |
| 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 |
| SurvivalInfoComparator | Class | org.biojava.nbio.survival.cox.comparators | BioJava | |
| SurvivalInfoHelper | Used to work with SurvivalInfoAuthor:Scooter Willis | Class | org.biojava.nbio.survival.cox | BioJava |
| SurvivalInfoIndex | Not used and probably should be deletedAuthor:Scooter Willis | Class | org.biojava.nbio.survival.cox | BioJava |
| SurvivalInfoValueComparator | Class | org.biojava.nbio.survival.cox.comparators | BioJava | |
| SVDSuperimposer | A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class. | Class | org.biojava.nbio.structure | BioJava |
| SymbolTable | Sorted symbol table implementation using a java. | Class | org.biojava.nbio.structure.math | BioJava |
| SymmClash | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| Symmetry | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| SymmetryAxes | Data Structure that stores all the symmetry axis that describe the symmetry of a structure. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| SymmetryCalc | Calculates a symmetry analysis and displays the results. | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
| SymmetryDisplay | Class that provides visualizations methods for symmetry alignments. | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
| 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 |
| SymmetryListener | Action Listener for the symmetry menu. | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
| 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 |
| SymmOptimizer | Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| SymoplibParser | A class containing static methods to parse the symop. | Class | org.biojava.nbio.structure.xtal | BioJava |
| SynchronizedOutFile | Class | org.biojava.nbio.structure.align.util | BioJava | |
| Synonym | Class | org.biojava.nbio.ontology | BioJava | |
| SystematicSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| 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 |
| TestDNANeedlemanWunsch | Class | demo | BioJava | |
| Tetrahedron | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| 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 | |
| TransformType | Class | org.biojava.nbio.structure.xtal | BioJava | |
| TranslationException | Thrown from AbstractCompundTranslatorAuthor:Andy YatesSee Also:Serialized Form | Class | org.biojava.nbio.core.exceptions | BioJava |
| 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 |
| 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 |