Interface | Description |
---|---|
IDFetcher | |
Miner |
A miner provides a pattern to mine, and knows how to use the result set to prepare the text
output.
|
SIFMiner |
This interface tells that the miner supports SIF output.
|
SIFToText |
An interface for converting a SIF interaction to text.
|
SIFType |
Class | Description |
---|---|
AbstractSIFMiner |
Base class for SIF Miners.
|
BlacklistGenerator |
This class generates a blacklist for the given model.
|
CatalysisPrecedesMiner |
Miner for the catalysis-precedes pattern.
|
ChemicalAffectsThroughBindingMiner |
Miner for the chemical-affects-protein pattern.
|
ChemicalAffectsThroughControlMiner |
Miner for the chemical-affects-protein pattern.
|
CommonIDFetcher |
Tries to get gene symbols or uniprot IDs for genes and display names for small molecules.
|
ConsumptionControlledByMiner |
Miner for the consumption-controlled-by pattern.
|
ControlsDegradationIndirectMiner |
Yet another miner for the controls-degradation pattern.
|
ControlsExpressionMiner |
Miner for the transcriptional regulation pattern.
|
ControlsExpressionWithConvMiner |
Miner for the transcriptional regulation pattern, modeled using Conversion.
|
ControlsPhosphorylationMiner |
Miner for the controls-phosphorylation pattern.
|
ControlsProductionOfMiner |
Miner for the controls-production-of pattern.
|
ControlsStateChangeDetailedMiner |
Miner for the controls-state-change-detailed pattern.
|
ControlsStateChangeOfMiner |
Miner for the controls-state-change pattern.
|
ControlsTransportMiner |
Miner for the controls-transport pattern.
|
ControlsTransportOfChemicalMiner |
Miner for the controls-transport-of-chemical pattern.
|
CSCOBothControllerAndParticipantMiner |
Miner for the controls-state-change pattern.
|
CSCOButIsParticipantMiner |
Miner for the controls-state-change pattern.
|
CSCOThroughBindingSmallMoleculeMiner |
Miner for the controls-state-change pattern.
|
CSCOThroughControllingSmallMoleculeMiner |
Miner for the controls-state-change pattern.
|
CSCOThroughDegradationMiner |
Miner for the degradation pattern.
|
CustomFormat |
Used for customizing the columns in the SIF text output.
|
Dialog |
This is the user interface with GUI for selecting a model, a pattern miner, and an output file.
|
DirectedRelationMiner |
Miner for the directed relations between proteins.
|
InComplexWithMiner |
Miner for the degradation pattern.
|
InteractsWithMiner |
Miner for the "interacts-with" relation.
|
MinerAdapter |
Adapter class for a miner.
|
NeighborOfMiner |
Miner for the "neighbor-of" relation.
|
OldFormatWriter |
This class is used for writing the binary interactions to a text output stream in the old
EXTENDED_BINARY_SIF format.
|
OutputColumn |
This class is used for defining a custom column in the te
|
ReactsWithMiner |
Miner for the "reacts-with" relation.
|
RelatedGenesOfInteractionsMiner |
Miner for the related genes (participant or controller) of interactions.
|
SIFInteraction | |
SIFSearcher |
Searches a model and generates SIF network using the pattern matches.
|
UbiquitousIDMiner |
Miner for getting ubiquitous small molecules in a model.
|
UsedToProduceMiner |
Miner for the "used-for-production-of" relation.
|
Enum | Description |
---|---|
OutputColumn.Type |
Type of the output column.
|
SIFEnum |
Enum for representing supported SIF edge types.
|
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