All Classes and Interfaces
Class
Description
Base class for SIF Miners.
Checks if the PhysicalEntity controls anything.
This is a very specialized constraint that checks if two PhysicalEntity of the same
EntityReference have differential features, such that we can predict an activity change based on
gain or loss of these features.
Adjacency matrix representation of a graph.
Used for getting logical AND of a set of constraints.
A blacklist is used for not using ubiquitous small molecules in patterns.
This class generates a blacklist for the given model.
This class generates a blacklist for the given model.
This class generates a blacklist for the given model.
Miner for the catalysis-precedes pattern.
Miner for the chemical-affects-protein pattern.
Miner for the chemical-affects-protein pattern.
This class is used for finding a standard name for a small molecule.
Tries to get Gene Symbols or UniProt IDs for genes
and - display names for small molecules;
This id-fetcher is mainly to use with the BioPAX pathway data
from Pathway Commons (PC2) db (normalized and enriched with xrefs).
Some predefined constraints.
Tries to get preferred type IDs of an entity reference.
A constraint to check if a set of variables satisfy the requirements.
This is a base class for a Constraint.
Used for using several constraints as a chain.
Miner for the consumption-controlled-by pattern.
Yet another miner for the controls-degradation pattern.
Miner for the transcriptional regulation pattern.
Miner for the transcriptional regulation pattern, modeled using Conversion.
Checks if a controller of this Control is also a participant of the controlled interactions.
Miner for the controls-phosphorylation pattern.
Miner for the controls-production-of pattern.
Miner for the controls-state-change-detailed pattern.
Miner for the controls-state-change pattern.
Miner for the controls-transport pattern.
Miner for the controls-transport-of-chemical pattern.
This constraint is used to collect related EntityReference of the controllers of a Control.
Given Conversion and its one of the participants (at the left or right), traverses to either
the participants at the other side or the same side.
This enum tells if the user want to traverse towards other side of the conversion or stay at
the same side.
Miner for the controls-state-change pattern.
Miner for the controls-state-change pattern.
Miner for the controls-state-change pattern.
Miner for the controls-state-change pattern.
Miner for the degradation pattern.
Used for customizing the columns in the SIF text output.
This class goes over the state change pattern results and writes down the gained and lost
modifications through these directed relations.
This is the user interface with GUI for selecting a model, a pattern miner, and an output file.
THis class is used for comparing modification features of two PhysicalEntity objects of same
EntityReference.
Miner for the directed relations between proteins.
Checks if the parameter constraint cannot generate any candidate.
Checks identity of two elements.
This class is used for writing the binary interactions to a text output stream in the
so called Pathway Commons EXTENDED_BINARY_SIF format.
Checks if an element has or has not a specific value for a field, or the field value of another
element.
Checks if generated elements has or has not a specific value for a field, or the field value of
another set of generated elements.
Checks if the element has a valid ID.
This class provides a mapping between HGNC IDs and Symbols.
Checks if the element has the desired ID.
Miner for the degradation pattern.
Miner for the "interacts-with" relation.
This constraint is used to collect related EntityReference of the participant physical entities.
Many times we want to link PhysicalEntities (PE) while traversing a relation.
Two type of linking between PhysicalEntity.
This is a mapping from a constraint to the elements in a match.
A pattern match is an array of biopax elements that satisfies the list of mapped constraints in a
pattern.
A miner provides a pattern to mine, and knows how to use the result set to prepare the text
output.
Adapter class for a miner.
This class checks if there exists a desired type of modification change among two PhysicalEntity.
Logical OR of several PathConstraints.
Miner for the "neighbor-of" relation.
This is a non-generative constraint that checks if the small molecule is ubiquitous in any
context.
Negation of a constraint.
Logical OR of several constraints.
This class is used for defining a custom column in the te
Type of the output column.
Gets input or output participants of a Conversion.
Gets the related Conversion where the PhysicalEntity is input or output, whichever is desired.
PathConstraint encapsulates PathAccessor of Paxtools.
A pattern is a list of mapped constraints.
This class contains several pattern samples.
This constraint checks if two chains of linked physical entities are intersecting or not.
This class takes two PhysicalEntity objects linked with generic or complex member relationships,
and prepares an array of PEs that link those.
Values for activity.
This interface is to use for tracking progress of a process.
Miner for the "reacts-with" relation.
After traversing a PhysicalEntity and the Conversion it participates, this constraint takes us to
the Control.
Miner for the related genes (participant or controller) of interactions.
Distinguishes between input and output.
Searcher for searching a given pattern in a model.
When a constraint excludes the origin element, but it is needed to be among them, use this
constraint.
Enum for representing supported SIF edge types.
This interface tells that the miner supports SIF output.
Searches a model and generates SIF network using the pattern matches.
An interface for converting a SIF interaction to text.
Simple gets the URI (of an entity reference);
Checks the size of the generated elements of the wrapped constraint.
Type of the (in)equality.
Checks if a variable is a specific type or its subclass.
Miner for getting ubiquitous small molecules in a model.
Miner for the "used-for-production-of" relation.
Used for getting logical XOR of a set of constraints.