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BN++ Class List
Here are the classes, structs, unions and interfaces with brief descriptions:| BNPP::AATRNA | Aminoacyl tRNA |
| BNPP::Activator | An Activator is a positive Regulator that controls an event |
| BNPP::ActivatorTF | ActivatorTF: Molecule capable of activating the transcription of a gene by activating the transcription factor |
| BNPP::Active | Possible StateProperty |
| BNPP::Artificial | Artificial is one kind of Source for a biochemical object |
| BNPP::MIF::attributeType | AttributeType class representation |
| BNPP::MIF::availabilityType | AvailabilityType class representation |
| BNPP::Exception::Base | Exception base class |
| BNPP::MIF::baseLocationType | BaseLocationType class representation |
| BNPP::BentTo | Used to describe if one part of a Thing is bent to another part of the same Thing |
| BNPP::MIF::bibrefType | BibrefType class representation |
| BNPP::BindingSite | Binding site: Locality on a protein's surface that attracts another molecule of whatever type and leads to a docking of the two |
| BNPP::BINDReader | Importer class for bind xml format |
| BNPP::BINDReaderHandlers | Handler class for the bind xml format |
| BNPP::BioBaseDBAdapter | Database Adapter for Biobase databases |
| BNPP::MIF::bioSourceType | BioSourceType class representation |
| BNPP::BNPPReader | Class for converting kernel objects into the internal MIF 1.0 structure |
| BNPP::BNPPWriter | Class for writing the MIF Objects into BN++ Kernal object |
| BNPP::Bound | Used to describe that Participants are bound to each other |
| BNPP::Exception::BufferOverflow | Buffer overflow exception |
| BNPP::CAPMapper | Mapper for the CAP database |
| BNPP::Catalyst | A substance which increases the rate of a reaction without itself being consumed and without altering the equilibrium of the reaction |
| BNPP::CDNA | We have three definitions of cDNAs derived from two diferent sources |
| BNPP::CDNAClone | CDNA clone is a duplex DNA, representing an mRNA, carried in a cloning vector |
| BNPP::CDNALibrary | A collection of all of the mRNA molecules present in a cell or organism, all turned into cDNA molecules with the enzyme reverse transcriptase, then inserted into vectors (other DNA molecules which can continue to replicate after addition of foreign DNA) |
| BNPP::CellCycleState | Possible State |
| BNPP::Centromere | The region in eukaryote chromosomes where daughter chromatids are joined together |
| BNPP::ChromatinStructure | ChromatinStructure is a possible NAStateProperty |
| BNPP::ChromosomalLocation | ChromosomalLocation is a meta information and contains chromosomallocations of things |
| BNPP::Chromosome | The DNA of eukaryotes is subdivided into chromosomes, presumably for convenience of handling, each of which has a long length of DNA associated with various proteins |
| BNPP::Cofactor | Inorganic complement of an enzyme reaction, usually a metal ion |
| BNPP::Coiling | Coiling describes the coiling of a dna moecule |
| BNPP::Collection | Collection is used to group Participants by assigning their database source |
| BNPP::CompositeDataSourceKey | CompositeDataSourceKey is used if a datasource has two keys |
| BNPP::Compound | Compound describes all biochemical compounds belonging not to Protein or NucleicAcid classes |
| BNPP::Concentration | Concentration of a GenericCompound |
| BNPP::Condition | Condition represents conditions for several biochemical processes like events or pathways |
| BNPP::MIF::confidenceType | ConfidenceType class representation |
| BNPP::ConformationalChange | Conformational change is the alteration in the shape - usually the tertiary structure of a protein - as a result of alteration in the environment (pH, temperature, ionic strength) or the binding of a ligand (to a receptor) or binding of substrate (to an enzyme) |
| BNPP::ConnectedComponent | Connected Component Algorithm |
| BNPP::ConsensusSequence | Of a series of related DNA, RNA or protein sequences, the sequence that reflects the most common choice of base or amino acid at each position |
| BNPP::ConservedRegion | ConservedRegion represents conserved sub parts in sequences |
| BNPP::ConservedRegionPosition | ConservedRegionPosition describes the position of a conserved sequence defined by the class ConservedRegion in a concrete sequence |
| BNPP::ContainerSerializer | Container Serializer |
| BNPP::ControlEvent | Describes events like activation or inhibition of other participants or of regulative events on transcription level |
| BNPP::ControlSource | ControlSource is the source of any kind of control event, eg |
| BNPP::ControlTarget | ControlTarget is the target for any kind of control event, eg |
| BNPP::MIF::cvType | CvType class representation |
| BNPP::CytosineMethylation | CytosineMethylation is given as a percentage |
| BNPP::DataSet | A DataSet is a class which sum up a set of Things |
| BNPP::DataSource | DataSource is a meta information and describes where the associated Virtual Things were taken from |
| BNPP::DataSourceKey | DataSourceKey is a meta information and contains an "id" - data_source_key - for an object taken from a database |
| BNPP::DataValue | Class to hold a string or numeric value (integer, double, float, short integer, long integer) |
| BNPP::DataValue::EmptyDataValue | Exception in case of access to an empty DataValue object To prevent Exception use memberfunction isEmpty() |
| BNPP::DataValue::InvalidConversion | Inner Classes for Exception handling Excpetion in case of invalid conversion, i.e |
| BNPP::DBAdapter | DBAdapter is the superclass for all database adapters |
| BNPP::DBAlgorithms | This class intends to be the parser for the data gained by Amersham DNA chips |
| BNPP::MIF::dbReferenceType | DbReferenceType class representation |
| BNPP::Definition | Definition is a meta information and contains definitions of things |
| BNPP::Description | Description is a meta information |
| BNPP::DevelopmentState | Possible State |
| BNPP::Disease | The class Disease is a meta information and describes diseases |
| BNPP::Exception::DivisionByZero | Division by zero error |
| BNPP::DNA | The genetic material of all cells and many viruses |
| BNPP::DNAChipMapper | Mapper for Amersham DNA chip data |
| BNPP::DNAChipParser | Parser for Amersham DNA chip data |
| BNPP::DNAChipParser::Dataset | Data structure representing one dataset |
| BNPP::DNAChipParser::Headerinformation | Data structure storing the header information |
| BNPP::DNAChipReader | Reader for Amersham DNA chip data |
| BNPP::DNAConsensusSequence | Dna consensus sequence reflects the most common choice of base or amino acid at each position |
| BNPP::Domain | Domains are used to describe a part of a molecule or structure that shares common physicochemical features, eg |
| BNPP::DomainClass | DomainClass is a classification of domains |
| BNPP::DownRegulation | DownRegulation - negative regulation of a participant on the transcriptional level |
| BNPP::EdgePredicate | Edge predicate |
| BNPP::Educt | Educt is one kind of Substrate |
| BNPP::Effect | Effect arosen after a biochemical event or pathway |
| BNPP::Exception::ElementNotFound< T > | Element could not be found |
| BNPP::Enhancer | Enhancer: A DNA control element frequently found 5' to the start site of a gene, which when bound by a specific transcription factor, enhances the levels of expression of the gene, but is not sufficient alone to cause expression |
| BNPP::MIF::entry | Entry class representation |
| BNPP::MIF::entrySet | EntrySet class representation |
| BNPP::Enzyme | A biological catalyst, most often a protein although ribozymes are RNA molecules |
| BNPP::EnzymeClass | EnzymeClass is a classification for Enzymes |
| BNPP::STRFUNCT::eqstr | This struct defines an equality predicate for strings |
| BNPP::EST | We have three definitions of ESTs derived from three diferent sources |
| BNPP::Event | The class Event is the basis class of all biochemical events like reactions, regulatory events, interactions etc |
| BNPP::EventEquation | Characterizes the equation of an event |
| BNPP::EventType | EventType is a classification of events |
| BNPP::EventTypeCollection | EventTypeCollection collects several classifications of biochemical events |
| BNPP::Exon | Exon: The sequences of the RNA primary transcript (or the DNA that encodes them) that exit the nucleus as part of a messenger RNA molecule |
| BNPP::Experiment | Experiment is a MetaInformation |
| BNPP::ExperimentalCondition | Describes experimental conditions of an event or path |
| BNPP::ExperimentalFunction | Experimental role is a parent class for all roles specifying molecules and other participants within a event observed in an experiment |
| BNPP::MIF::experimentType | ExperimentType class representation |
| BNPP::Expression | The full use of the information in a gene via transcription and translation leading to production of a protein and hence the appearance of the phenotype determined by that gene (contains sub events Transcription, Splicing, Translation ) |
| BNPP::ExpressionExperiment | An ExpressionExperiment describe a number of Things observed during an expression experiment, like DNA chip experiments |
| BNPP::ExpressionProduct | Role for the event Expression played by a molecule have been expressed and coded by a gene or RNA (ExpressionScheme) |
| BNPP::ExpressionScheme | Role for the event Expression played by a gene or RNA coding the expressed molecule (ExpressionProduct) |
| BNPP::MIF::featureType | FeatureType class representation |
| BNPP::FeedbackLoop | Possible RegulatoryPathway |
| BNPP::Exception::FileMisformatted | File is misformatted |
| BNPP::Exception::FileNotFound | File not found |
| BNPP::Filter | The Filter class represents a filter in a Query |
| BNPP::FilteredGraph | BN++ Filtered Graph |
| BNPP::FilteredGraph::FilteredGraphConstEdgeIterator | Rudimentary const_index_iterator for FilteredGraph |
| BNPP::FilteredGraph::FilteredGraphConstIndexIterator | Rudimentary const_index_iterator for FilteredGraph |
| BNPP::FilteredGraph::FilteredGraphConstVertexIterator | Rudimentary const_vertex_iterator for FilteredGraph |
| BNPP::FilteredGraph::FilteredGraphEdgeIterator | Rudimentary edge_iterator for FilteredGraph |
| BNPP::FilteredGraph::FilteredGraphIndexIterator | Rudimentary index_iterator for FilteredGraph |
| BNPP::FilteredGraph::FilteredGraphVertexIterator | Rudimentary vertex_iterator for FilteredGraph |
| BNPP::Formula | Formula contains the formula of a participant |
| BNPP::FoundationsForNucDistrMatrix | Represents foundations for nucleotide distribution matrices for the binding sites of transcription factors |
| META::FrameForm | In der FrameForm werden die erzeugten BNPP-Objekte abgelegt |
| BNPP::FunctionalDescription | The class FunctionalDescription is a kind or description and describes functions of things |
| BNPP::GarbageCollector | Creates kernel objects and collect all these objects |
| BNPP::Gene | Gene is originally defined as the physical unit of heredity but the meaning has changed with increasing knowledge; it is probably best defined as the unit of inheritance that occupies a specific locus on a chromosome, the existence of which can be confirmed by the occurrence of different allelic forms |
| BNPP::GeneProductPolymorphism | Polymorphisms in polypeptide sequences |
| BNPP::GeneProductSequence | GeneProductSequence represents sequence information of gene products |
| BNPP::GenericCompound | GenericCompound is the base class for all biochemical compounds |
| BNPP::GeneticLocus | GeneticLocus is the position of a gene on a chromosome, plasmid or on an other nucleic acid molecule |
| BNPP::GeneVariant | Different forms or variants of a gene found at the same place, or locus, on a chromosome |
| BNPP::Genome | Genome represents the total set of genes carried by an individual or cell |
| BNPP::GlobalContainer | Global container |
| BNPP::Graph | BN++ Graph |
| BNPP::Graph::GraphConstEdgeIterator | Rudimentary const_index_iterator for Graph |
| BNPP::Graph::GraphConstIndexIterator | Rudimentary const_index_iterator for Graph |
| BNPP::Graph::GraphConstVertexIterator | Rudimentary const_vertex_iterator for Graph |
| BNPP::Graph::GraphEdgeIterator | Rudimentary edge_iterator for Graph |
| BNPP::Graph::GraphIndexIterator | Rudimentary index_iterator for Graph |
| BNPP::Graph::GraphVertexIterator | Rudimentary vertex_iterator for Graph |
| BNPP::GRNA | GRNA (= Guide RNA): Small RNA molecules (60-80 nucleotides) that are found in the editosome |
| BNPP::Histology | Histology of an Thing |
| BNPP::HistoneModification | HistoneModification, given in percentage per modification type |
| BNPP::HNRNA | Heterogenous nuclear RNA (= hnRNA): Originally identified as a class of RNA, found in the nucleus but not the nucleolus, which is rapidly labelled and with a very wide range of sizes, 2-40 kilobases |
| BNPP::Homologues | Homologue - Homologues proteins have evolved from a common ancestor, and their evolutionary relationship is evident from similarities in sequence, structure and/or function |
| BNPP::Hybridization | The Class Hybridization describes hybridization processes observed on micro array chips |
| BNPP::IDGenerator | Generator of OID |
| idType | Soap structures |
| BNPP::Exception::IllegalPosition | Invalid Position |
| BNPP::Exception::IllegalSelfOperation | Illegal self operation |
| BNPP::Exception::IllegalTreeOperation | Illegal tree operation |
| BNPP::ImmunRegulation | Describes the immun_regulation process |
| BNPP::Exception::IncompatibleIterators | Incompatible iterator |
| BNPP::Exception::IndexOverflow | Index overflow |
| BNPP::Exception::IndexUnderflow | Index underflow |
| BNPP::Individual | Individual is a 'single instance' of an organism group |
| BNPP::Inducer | Inducers are molecules that cause an increase in a protein activity when added to cells |
| BNPP::Inhibitor | An Inhibitor is a negative Regulator that controls an event |
| BNPP::InhibitorTF | InhibitorTF: Molecule capable of preventing the transcription of a gene by blocking the transcription factor |
| BNPP::Interaction | Interactions are for example Reactions, Protein-Protein-Interactions or Protein-Molecule-Interactions |
| BNPP::MIF::interactionElementType | InteractionElementType class representation |
| BNPP::InteractionPathway | Collection of interactions |
| BNPP::InterProParser | SwissParser reads the InterPro files |
| BNPP::InterProParserHandler | Handler class for the InterPro xml format |
| BNPP::Intron | (= intervening sequence) A non-coding sequence of DNA within a gene (cf |
| BNPP::Exception::InvalidFormat | Invalid format |
| BNPP::Exception::InvalidIterator | Invalid iterator |
| BNPP::Exception::InvalidRange | Invalid range |
| BNPP::Exception::InvalidSize | Invalid Size |
| BNPP::Isoform | Isoform: A protein having the same function and similar (or identical sequence), but the product of a different gene and (usually) tissue-specific |
| BNPP::Isolator | An Isolator blocks an Enhancer |
| BNPP::KeggChromosome | KeggChromosome represents in the KEGG data base contained information about chromosomes |
| BNPP::KeggCompound | KeggCompound represents all compound objects contained in the KEGG data base |
| BNPP::KeggDBAdapter | KeggDBAdapter is an importer class for kegg flat files |
| BNPP::KeggEnzyme | KeggEnzyme represents all enzyme classes contained in the KEGG data base |
| BNPP::KeggGene | KeggGene represents all gene objects contained in KEGG data base |
| BNPP::KeggGenome | KeggGenome represents all in the KEGG data base contained genomes |
| BNPP::KeggGlycan | KeggGlycan represents a kind of compounds - glycans |
| BNPP::KeggMapTitle | Class KeggMapTitle represents titles of all contained standard maps or pathways in the KEGG data base |
| BNPP::KeggMetaPathway | KeggMetaPathway represents meta pathways of KEGG data base, that are not organism specific and serve only as a scheme for the orientation to describe, which reactions may be involved in a pathway (e.g |
| BNPP::KeggOrganism | KeggOrganism represents organism specific information in KEGG data base |
| BNPP::KeggPathway | Organism specific pathways, containing the gene lists which code the enzymes given in the meta pathway's enzyme list |
| BNPP::KeggPlasmid | KeggPlasmid represents plasmid objects in the KEGG database |
| BNPP::KeggReaction | KeggReaction represents all in KEGG data base contained reaction objects |
| BNPP::KeggReference | KeggReference represents publications mentioned in the KEGG data base |
| BNPP::KeggTaxonomy | KeggTaxonomy represents taxonomies of organisms contained in the KEGG data base |
| BNPP::Location | Location describes the location of several things |
| BNPP::MIF::LocationContainer | LocationContainer class representation |
| BNPP::LocationStateProperty | StateProperty for Locations |
| BNPP::LocationType | Eg, CellType, OrganType, |
| BNPP::MainEduct | MainEduct is one kind of Educt |
| BNPP::MainProduct | MainProduct is one kind of Product |
| BNPP::Exception::MatrixHasWrongDimension | Matrix Dimension Error |
| BNPP::MetabolicPathway | Collection of metaboic events - reactions |
| META::MetaFrame | MetaKlasse für Frames (Daten, wie auch Klassen-Frames) |
| BNPP::MetaInformation | MetaInformation is the base class for all additional information for a thing, for example publications, db links, etc |
| META::MetaList | MetaKlasse für die Klasse 'FrameList' |
| META::MetaSlot | MetaKlasse für SlotFrames (sowohl Link- als auch Value-Slots) |
| BNPP::Method | The class Method is a meta information and describes biochemical methods or techniques used to derive the information about the concerning Thing associated to the respective method object via the association inharited from the class MetaInformation |
| BNPP::MIF::MIF | Abstract MIF class |
| BNPP::MIFReader | Class for reading the MIF 1.0 xml format |
| BNPP::MIFReaderHandler | Handler class for the MIF 1.0 xml format |
| BNPP::MIFWriter | Class for writing the MIF 1.0 xml format |
| BNPP::MinimumSpanningTree | Minimum Spanning Tree Algorithm |
| BNPP::MiRNA | MiRNA (= microRNA): These are tiny (~22 nts) RNA molecules that appear to regulate the expression of messenger RNA (mRNA) molecules |
| BNPP::Modification | Describes the modification process |
| BNPP::ModifiedForm | Modifiedform is the source of any kind of control event, eg |
| BNPP::MRNA | Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains |
| BNPP::Mutation | Describes the mutation process |
| BNPP::NAConsensusSequence | Nucleic acid consensus sequence reflects the most common choice of base or amino acid at each position |
| BNPP::Name | Name contains a name string for a Thing |
| BNPP::MIF::namesType | NamesType class representation |
| BNPP::NAPolymorphism | NAPolymorphism represents polymorphisms in nucleic acid sequences (see the definition of polymorphism) |
| BNPP::NASecondaryStructure | NASecondaryStructure describes the secondary structure of nucleic acid |
| BNPP::NAStateProperty | NAStateProperty: A cavity or space within a tube or sac |
| BNPP::NegativeControlEvent | Negative control (inhibition) of an participant (event) |
| BNPP::Exception::NotImplemented | Not implemented exception |
| BNPP::NucDistributionMatrix | Represents nucleotide distribution matrices for the binding sites of transcription factors |
| BNPP::NucleicAcid | More abstract class for nucleic acids describing more general information of nucleic acid objects |
| BNPP::NucleicAcidSequence | NucleicAcidSequence represents sequence information of nucleic acids |
| BNPP::Exception::NullPointer | Null pointer argument is invalid |
| BNPP::ObjectManager | ObjectManager: Keeps tracj if all BNPP objects, offering add and remove methods |
| BNPP::Open | Possible StateProperty |
| BNPP::MIF::openCvType | OpenCvType class representation |
| BNPP::Operator | The site on DNA to which a specific repressor protein binds and prevents the initiation of transcription at the adjacent promoter |
| BNPP::Operon | Operon represents groups of bacterial genes with a common promotor, that are controlled as a unit and produce mRNA as a single piece, polycistronic messenger |
| BNPP::ORF | ORF (open reading frame) is a possible reading frame of DNA which is capable of being translated into protein, ie |
| BNPP::Organ | Organ is a unit consisting of various cells and tissues with different structure and fulfilling specific functions |
| BNPP::Organism | Organism is a meta information and describes objects being in relationship with this organism |
| BNPP::ORI | ORI ( = origin of replication) Regions of DNA that are necessary for its replication to begin, such as pBR322 ori , required for plasmid replication |
| BNPP::Orthologues | Orthologue - Orthologs are equivalent genes in different species that evolved from a common ancestor by speciation |
| BNPP::Exception::OutOfGrid | Out of grid error |
| BNPP::Exception::OutOfMemory | Out of memory |
| BNPP::Exception::OutOfRange | Out of range |
| BNPP::Paralogues | Paralogue - Homologous sequences (that is, sequences that share a common evolutionary ancestor) that diverged by gene duplication (within one organism) |
| BNPP::Param | This class provides a means to associate string names to int/double/sting values |
| BNPP::ParamXMLHandler | SAX Handler for the Param class |
| BNPP::Exception::ParseError | Parse Error |
| BNPP::PartialSQLSerializer | Partial SQL Serializer |
| BNPP::Participant | Participant describes objects taking part in biochemical events |
| BNPP::ParticipantClassification | ParticipantClassification allows the classification of a Participant |
| BNPP::PartOf | Used to represent 'part of' relations between Things |
| BNPP::Pathway | Pathway is the base class for all biochemical pathways |
| BNPP::PeripherallyAssociated | Used to describe that Participants are near by each other |
| BNPP::PersistentObject | Persistent object |
| BNPP::PhysicalTrigger | PhysicalTrigger represents objects acting as physical triggers in biochemical events |
| BNPP::PhysicalTriggerType | PhysicalTriggerType is a classification of physical triggers |
| BNPP::PhysiologicalProperty | PhysiologicalProperty is a LocationStateProperty |
| BNPP::Plasmid | Plasmid is a small, independently-replicating, piece of cytoplasmic DNA that can be transferred from one organism to another |
| BNPP::Polymerase | A biological catalyst, most often a protein although ribozymes are RNA molecules |
| BNPP::Polymorphism | There are two definitions of Polymorphism |
| BNPP::PositiveControlEvent | Positive control (activation) of an participant (event) |
| BNPP::PositiveEdgeWeightPredicate | Positive edge predicate |
| BNPP::PreciseTime | Time class |
| BNPP::PrimaryTranscript | PrimaryTranscript (= pre-RNA) is the product of eukaryotic transcription before post-transcriptional modifications take place |
| BNPP::Product | Product is one kind of Substrate |
| BNPP::Promoter | A region of DNA to which RNA polymerase binds before initiating the transcription of DNA into RNA |
| BNPP::PromoterClass | PromoterClass is a classification for promoters |
| BNPP::Protein | Protein is any of a group of complex organic compounds, consisting essentially of combinations of amino acids in peptide linkages, that contain carbon, hydrogen, oxygen, nitrogen, and usually sulfur |
| BNPP::ProteinClassification | ProteinClassification can, eg, be ProteinFamily or EnzymeClass |
| BNPP::ProteinClassificationCollection | ProteinClassificationCollection collects several classifications of proteins |
| BNPP::ProteinComplex | Complex of different proteins |
| BNPP::ProteinConsensusSequence | Protein consensus sequence reflects the most common choice of base or amino acid at each position |
| BNPP::ProteinFamily | ProteinFamily is a classification for Proteins as used in 'Gene Ontology' or 'SwissProt' |
| BNPP::MIF::proteinInteractorType | ProteinInteractorType class representation |
| BNPP::MIF::proteinParticipantType | ProteinParticipantType class representation |
| BNPP::ProteinPolymorphism | ProteinPolymorphism represents polymorphisms in protein sequences (see the definition of polymorphism) |
| BNPP::ProteinSequence | ProteinSequence represents sequence information of proteins |
| BNPP::Publication | Publication: Publication is a DataSource and a MetaInformation |
| BNPP::Query | The Query class represents a query to the BNPP-database |
| BNPP::Reaction | Describes biochemical reactions, containing essential roles Educt and Product |
| BNPP::Rearrangement | Describes the rearrangement process |
| BNPP::RefSeqDBAdapter | RefSeqDBAdapter is derived from DBAdapter |
| BNPP::RegulativeEvent | RegulativeEvent is a control event on transcription level with positive or negative effect on the SignalReceptor (ControlTarget in control event) |
| BNPP::Regulator | A Regulator controls an event |
| BNPP::RegulatoryElement | A RegulatoryElement regulates an event |
| BNPP::RegulatoryPathway | Collection of regulatory events |
| BNPP::Reliability | Reliability is one kind of MetaInformation and gives a reability estimation for a thing |
| BNPP::Repressor | Repressor: Eg repressor protein, a protein that binds to an operator of a gene preventing the transcription of the gene |
| BNPP::ReverseGraph | BN++ Reverse Graph |
| BNPP::ReverseGraph::ReverseGraphConstEdgeIterator | Rudimentary const_index_iterator for ReverseGraph |
| BNPP::ReverseGraph::ReverseGraphConstIndexIterator | Rudimentary const_index_iterator for ReverseGraph |
| BNPP::ReverseGraph::ReverseGraphConstVertexIterator | Rudimentary const_vertex_iterator for ReverseGraph |
| BNPP::ReverseGraph::ReverseGraphEdgeIterator | Rudimentary edge_iterator for ReverseGraph |
| BNPP::ReverseGraph::ReverseGraphIndexIterator | Rudimentary index_iterator for ReverseGraph |
| BNPP::ReverseGraph::ReverseGraphVertexIterator | Rudimentary vertex_iterator for ReverseGraph |
| BNPP::RNA | This molecular species has an informational role, a structural role and an enzymic role and is thus used in a more versatile way than either DNA or proteins |
| BNPP::RNAConsensusSequence | Rna consensus sequence reflects the most common choice of base or amino acid at each position |
| BNPP::Role | Role describes the 'functional role' played by a Participant in a biochemical Event |
| BNPP::RRNA | RRNA (ribosomal RNA) is one of the structural components of the ribosome |
| BNPP::SAR | Scaffold/matrix attached regions (S/MARs) represent a relatively novel addition to the class of cis-acting DNA sequences in the eukaryotic genome |
| BNPP::SCRNA | ScRNA: Small cytoplasmic RNA; any one of several small cytoplasmic RNA molecules present in the cytoplasm and (sometimes) nucleus of a eukaryote |
| BNPP::Sequence | Sequence represents sequence information of proteins and nucleic acids and consensus sequences |
| BNPP::SequenceUnit | SequenceUnit represents a part of a sequence, eg intron, exon, terminator |
| BNPP::Serializer | Serializer |
| Service | Soap Service Definition |
| BNPP::ShortestPath | Shortest Path Algorithm |
| BNPP::SideEduct | SideEduct is one kind of Educt |
| BNPP::SideProduct | SideProduct is one kind of Product |
| BNPP::SignalEffector | A SignalEffector induces a signal |
| BNPP::SignalPeptide | SignalPeptide: A peptide present on proteins that are destined either to be secreted or to be membrane components |
| BNPP::SignalReceptor | A SignalReceptor is the recipient of a signal |
| BNPP::SignalTransductionPathway | Possible RegulatoryPathway |
| BNPP::SignificantPathwayPoint | The class SignificantPathwayPoint describes specific points of a pathway like start point or target point |
| BNPP::Silencer | A Silencer blocks the transcription |
| BNPP::SimpleDBWriter | Simple Database Writer |
| BNPP::SimpleKeggMapper | SimpleKeggMaper writes the kernel classes containing the KEGG database into the BN++ database |
| BNPP::Exception::SizeUnderflow | Size underflow |
| BNPP::SNoRNA | SnoRNA (small nucleolar RNA): Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus |
| BNPP::SNP | SNPs (Single Nucleotide Polymorphisms) are common DNA sequence variations among individuals |
| BNPP::SNRNA | SnRNA - small nuclear RNA is involved in the machinery that processes RNA's as they travel between the nucleus and the cytoplasm |
| SOAP_ENV__Header | Dummy structures to make soap communication working outside of the namespace |
| BNPP::Source | Source is a meta information and defines where a certain object comes from |
| BNPP::SourceDatabase | SourceDatabase is one kind of DataSource |
| BNPP::MIF::sourceType | SourceType class representation |
| BNPP::SpecificationEventCondition | SpecificationEventCondition specifies a condition of an event |
| BNPP::SpecificationPathwayCondition | SpecificationPathwayCondition specifies a condition of an pathway |
| BNPP::SpecificationProcessCondition | SpecificationProcessCondition is a virtual class for specification or description of processes with a certain condition |
| BNPP::SpecificationRoleState | SpecificationRoleState specifies the state of the role in an event |
| BNPP::Splicing | Describes the splicing process by which introns are removed from hnRNA to produce mature messenger RNA that contains only exons |
| BNPP::SQLSerializer | SQL Serializer |
| BNPP::StartPoint | The class StartPoint describes start points of a pathway |
| BNPP::StartPointParticipant | The class StartPointParticipant describes start points of a pathway specified by a participant object |
| BNPP::StartPointRole | The class StartPointRole describes start points of a pathway specified by a role object |
| BNPP::State | Describes states of a participant in an biochemical event |
| BNPP::StateProperty | Properties of a State |
| BNPP::StopWatch | StopWatch Class |
| BNPP::StrandBreak | Describes the strand_break process |
| BNPP::String | String Class |
| BNPP::StringIDGenerator | Generator of OID |
| BNPP::SubSequencePosition | SubSequencePosition describes the position of a sub sequence in their 'parent' sequence |
| BNPP::Substrate | Substrate is one kind of Role |
| BNPP::SwissParser | SwissParser reads the SwissProt files |
| BNPP::SwissParserHandler | Handler class for the SwissProt xml format |
| BNPP::SystematicGroup | Class SystematicGroup represents Linnaean taxonomic system |
| BNPP::Tag | Tag is a sub class of the class ExperimentalFunction |
| BNPP::TargetPoint | The class TargetPoint describes target points of a pathway |
| BNPP::TargetPointParticipant | The class TargetPointParticipant describes target points of a pathway specified by a participant object |
| BNPP::TargetPointRole | The class TargetPointRole describes target points of a pathway specified by a role object |
| BNPP::Telomere | A Telomere is the end of a chromosome |
| BNPP::TemplateForModification | Modifiedform is the source of any kind of control event, eg |
| BNPP::TemporaryDependency | Temporary dependency |
| BNPP::Terminator | Terminator: DNA sequence at the end of a transcription unit that causes RNA polymerase to stop transcription |
| BNPP::Thing | Thing is the base class for all other BNPP classes |
| BNPP::TimeStamp | Time stamp concept |
| BNPP::Transcription | Transcription event describes the synthesis of RNA by RNA polymerases using a DNA template |
| BNPP::TranscriptionActivity | TranscriptionActivity for an allel |
| BNPP::TranscriptionFactor | Protein required for recognition by RNA polymerases of specific stimulatory sequences in eukaryotic genes |
| BNPP::TranscriptionFactorClass | TranscriptionFactorClass is a classification for TranscriptionFactors as, eg, used in TransPath |
| BNPP::TranscriptionUnit | A region of DNA that is transcribed to produce a single primary RNA transcript, ie |
| BNPP::TransfacDBAdapter | Database Adapter for the TransFac database |
| BNPP::Translation | The Class Translation describes a tranlation process that occurs at the ribosome whereby the information in mRNA is used to specify the sequence of amino acids in a polypeptide chain |
| BNPP::Translocation | Translocation means transport of a compound or participant from one location to an other (target) location |
| BNPP::TranspathDBAdapter | Database Adapter for the TransPath database |
| BNPP::TRNA | TRNA (= transfer RNA; s-RNA; 4S RNA): The low molecular weight RNAs that specifically bind amino acids by amino-acylation to form aminoacyl tRNA, and that possess a special nucleotide triplet, the anticodon, sometimes containing the base inosine |
| BNPP::Exception::UnableToCreateFile | Unable to create file |
| BNPP::UpRegulation | UpRegulation - positive regulation of a participant on the transcription level |
| BNPP::UserData | UserData is one kind of DataSource |
| BNPP::VertexPredicate | Vertex predicate |
| BNPP::VertexProperty | Vertex property |
| BNPP::XMLHandler | Common SAX Handler |
| BNPP::XMLSerializer | XML Serializer |
| BNPP::MIF::xrefType | XrefType class representation |
