All Classes and Interfaces
Class
Description
Base class for implementing various filter sets.
This is the base class for all property editors.
This is an all-in-one Traverser/Visitor combination
to use when deep recursive visiting is required.
This is a decorator set for capturing a set member that is equal to the given parameter.
Interface for demarcating excise-able boundaries of the object graph.
Definition: Imposes ordering on a step in a biochemical pathway.
A conversion interaction in which one or more entities (substrates) undergo
ovalent changes to become one or more other entities (products).
Definition: A conversion interaction in which one or more entities (substrates) undergo covalent
changes to become one or more other entities (products).
This class represents a general BioPAXElement, regardless of Level.
Abstract factory class for instantiating BioPAX classes.
This exception is thrown if a problem occurs during an input/output operation related to BioPAX Handlers.
This interface defines IO related operations that can be performed on
BioPAX models.
Enumeration type for BioPAX levels.
A thread-safe set of BioPAX objects that also prevents adding several elements
having the same URI.
The biological source of an entity (e.g.
Definition: The biological source of an entity (e.g.
This interface is responsible for setting the class
and initialize and load factor for all sets and maps
used in all model objects for performance purposes.
A control interaction in which a physical entity (a catalyst) increases the
rate of a conversion interaction by lowering its activation energy.
Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion
interaction by lowering its activation energy.
This enum represents the direction of a catalysis under all physiological conditions if there is one.
Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
Definition: A reference to the Cell Type Ontology (CL).
Describes a small molecule structure.
Definition: The chemical structure of a small molecule.
A FilterSet that filters based on the class.
Specifically "Clones" the BioPAX elements set
(traverses to obtain dependent elements),
puts them to the new model using the visitor and traverser framework;
ignores elements that are not in the source list (compare to
Fetcher).This is a class for manipulating a BioPAX model via undoable commands
This class is used for getting a valid subgraph from a set of BioPAX elements.
A physical entity whose structure is comprised of other physical entities
bound to each other non-covalently, at least one of which is a macromolecule
(e.g.
Definition: A physical entity whose structure is comprised of other physical entities bound to each other
non-covalently, at least one of which is a macromolecule (e.g.
A conversion interaction in which a set of physical entities, at least one
being a macromolecule (e.g.
Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
A composite iterator that iterates over multiple iterators.
Confidence that the containing instance actually occurs or exists in vivo,
usually a statistical measure.
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity,
i.e.
Definition: This class represents a term from an external controlled vocabulary (CV).
This is a role interface for pathway elements that can control processes, namely
Pathway and PhysicalEntity.User: root Date: Aug 1, 2006 Time: 5:37:34 PM_DOT
Defines the nature of the control relationship between the controller and the controlled entities.
Definition: An interaction in which molecules of one or more
PhysicalEntity pools are physically
transformed and become a member of one or more other PhysicalEntity pools.This enum is used for specifying the direction of a Conversion.
Encapsulation of scores of conversions, and related information
Definition: An entity feature that represent the covalently bound state of a physical entity.
Created by igor on 13/08/15.
XREF Should be only unification and publication xrefs
Definition: A conversion in which a pool of macromolecules are degraded into their elementary
units.
Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants
(sums of species), delta-G'o.
Catalysis direction controlled vocabulary
Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic
acid.
A DNA reference is a grouping of several DNA entities that are common in
sequence and genomic position.
Definition: A region on a DNA molecule.
Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and
genomic position.
This class contains methods that eases to use editors for
specific or a set of property.
This is the base adapter for all editor maps.
This class represents a discrete biological unit used when describing
pathways.
This class represents a discrete biological unit used when describing
pathways.
Description: A characteristic of a physical entity that can change while the entity still retains its biological
identity.
Definition: An entity reference is a grouping of several physical entities across different
contexts and molecular states, that share common physical properties and often named and treated
as a single entity with multiple states by biologists.
Definiiton: A reference to a term from an entity reference group ontology.
Provides an ENUM class compatible editor by extending the
PropertyEditor.Utility class for equivalence based comparison of a set of BioPAXElements.
Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
Definition: A reference to the PSI Molecular Interaction ontology
experimental method types, including "interaction detection method", "participant identification method",
"feature detection method".
Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of
experimental design.
Definition: A term that describes the form of the physical entity in the context of the experiment.
This class is used to fetch an element (traverse it to obtain
its dependent elements) and to add this element into a model
using the visitor and traverse functions.
Generic interface for defining filter decorators.
This class is a decorating property accessor that filters the seed arguments, only accepts if they are assignable to
filter class.
This class is a decorating property accessor that filters values with a given class.
Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or
degradation event.
Definition: A continuant that encodes information that can be inherited through replication.
Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
Tries to get preferred type IDs of an entity reference.
This exception is thrown typically when BioPAX domain or cardinality restrictions are violated.
This class is intended to merge and to integrate BioPAX Level2 models
not necessarily from the same resource - if models allow such a
thing.
Definition: A biological relationship between two or more entities.
marker interface for entities and PEPs
A reference to the PSI Molecular Interaction ontology (MI) interaction type.
The apparent equilibrium constant, K', and associated values.
Base BioPAX Level3 element.
Created by IntelliJ IDEA.
A Level 3 specific element.
Upgrades BioPAX L1 and L2 to Level 3.
Utility class to merge multiple biopax models into one.
This factory returns decorated objects for testing.
A model acts as a container for BioPAX elements.
A generic filter interface for Models.
This is the default implementation of the
Model.Several useful algorithms and examples, e.g., to extract root or child
BioPAX L3 elements, remove dangling, replace elements
or URIs, fix/infer property values, etc.
Definition: A covalently modified feature on a sequence, relevant to an interaction,
such as a post-translational modification.
get controlled should be catalysis
Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
Definition: An interaction in which at least one participant is a physical entity, e.g.
Interface for all classes that can have names in BioPAX.
Tagger interface for DNA and RNA
Role interface for NucleicAcidReferences, namely DNA and RNA.
Provides an editor for all object value types, e.g.
User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
This class is a composite property accessor that allows users to chain multiple
property accessors to define paths in the BioPAX object graph.
Interface for pathway steps and processes
This represents a set of pathway events.
This represents a set of pathway events.
Provides a primitive (int, float, double) class compatible editor by extending the
PropertyEditor.Tagging interface for entities that needs evidence and can be targeted by a
control : Pathway and Interaction
Tagging interface for entities that can participate in a pathway
and can be targeted by a control : Pathway and Interaction
Allows generic access to the properties or a path of properties from a bean.
Adapter class for all property accessors.
A generic interface for bidirectional property filter
Description: A protein reference is a grouping of several protein entities that are encoded by the same
genetic sequence.
Definition: The direct source of a pathway data or score.
Vocabulary for defining relationship Xref types.
Definition: An xref that defines a reference to an entity in an external resource that
does not have the same biological identity as the referring entity.
This class contains methods for handling reused PEPs - a historically common problem in BioPAX L2 exports.
Definition: A region on a RNA molecule.
A RNA region reference
Definition: A score associated with a publication reference describing how the score was
determined, the name of the method and a comment briefly describing the method.
User: root Date: Aug 7, 2006 Time: 4:51:19 PM_DOT
Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
Tagger interface for protein, dna and rna entities
Definition: A location on a nucleotide or amino acid sequence.
Definition: A term that describes the covalent modifications to an amino
acid or nucleic acid chain.
Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO)
Homepage at http://www.sequenceontology.org.
This class performs set operations based on equivalence.
"Clones" a BioPAX element - using direct properties and dependent children only.
Provides a simple editor map for a level with a given factory.
Simple BioPAX reader/writer.
A "simple" BioPAX merger, a utility class to merge
'source' BioPAX models or a set of elements into the target model,
using (URI) identity only.
Tagger interface for non-complex physical entities
Catalysis direction controlled vocabulary
Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
Provides an String class compatible editor by extending the
PropertyEditor.TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM
Definition: A reference to the BRENDA
This class is a transitive decorator for PropertyAccessors.
This is a utility class for traversing over the dependent objects of a biopax element, based on
property editors
A bi-directional BioPAX properties traverser.
Definition: A unification xref defines a reference to an entity in an external resource that has the same
biological identity as the referring entity.
In OWL a single property can have multiple domains.
Basic visitor interface for classes using Traverser.
This class helps with managing the bidirectional xref links.