| Package | Description |
|---|---|
| org.colomoto.biolqm.io |
Input/Output for Logical Model.
|
| org.colomoto.biolqm.io.bnet |
The format used by boolnet and pyboolnet
|
| org.colomoto.biolqm.io.booleannet |
The format used by booleannet and related tools in Reka Albert's group
|
| org.colomoto.biolqm.io.boolsim |
The format used by boolsim/GenYsis.
|
| org.colomoto.biolqm.io.cnet |
The format used by boolnet and pyboolnet
|
| org.colomoto.biolqm.io.functions |
logical functions.
|
| org.colomoto.biolqm.io.ginml |
GINML support.
|
| org.colomoto.biolqm.io.gna |
GNA (non-xml) support.
|
| org.colomoto.biolqm.io.implicanttables |
Implicant table format.
|
| org.colomoto.biolqm.io.maboss |
The format used by MaBoSS - https://maboss.curie.fr/
|
| org.colomoto.biolqm.io.mnet |
A custom text format for multi-valued networks
|
| org.colomoto.biolqm.io.petrinet |
Petri net support.
|
| org.colomoto.biolqm.io.pint |
The format used by Pint - http://loicpauleve.name/pint
|
| org.colomoto.biolqm.io.sbml |
SBML qual support.
|
| org.colomoto.biolqm.io.truthtable |
TruthTable file reader.
|
| org.colomoto.biolqm.modifier.booleanize |
Construct Boolean versions of Multi-valued models
|
| org.colomoto.biolqm.modifier.buffer |
Expand a model using "buffer components".
|
| org.colomoto.biolqm.modifier.perturbation |
Perturbation of logical models: local modifications of its logical functions.
|
| org.colomoto.biolqm.modifier.reduction |
model modification: remove components from the core.
|
| org.colomoto.biolqm.modifier.reverse |
model modification: creates a new model capable of generating the reverse dynamics.
|
| org.colomoto.biolqm.modifier.sanitize |
Cleanups and sanity-checks, preserving the same model
|
| org.colomoto.biolqm.modifier.submodel | |
| org.colomoto.biolqm.modifier.subspace | |
| org.colomoto.biolqm.tool |
Tool definition, used to run actions from the command-line interface.
|
| org.colomoto.biolqm.tool.attractor |
Identification of the stable states of a logical model.
|
| org.colomoto.biolqm.tool.fixpoints |
Identification of the stable states of a logical model.
|
| org.colomoto.biolqm.tool.simulation.deterministic |
Implementation of updating schemes: update the state of a model (i.e.
|
| org.colomoto.biolqm.tool.simulation.random |
Implementation of updating schemes: update the state of a model (i.e.
|
| org.colomoto.biolqm.tool.trapspaces |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractFormat
Simple helper to fill in the boring parts of format declaration classes.
|
| Modifier and Type | Class and Description |
|---|---|
class |
BNetFormat |
| Modifier and Type | Class and Description |
|---|---|
class |
BooleanNetFormat |
| Modifier and Type | Class and Description |
|---|---|
class |
BoolSimFormat |
| Modifier and Type | Class and Description |
|---|---|
class |
CNetFormat |
| Modifier and Type | Class and Description |
|---|---|
class |
BooleanFunctionFormat |
| Modifier and Type | Class and Description |
|---|---|
class |
GINMLFormat
Format description for GINML files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
GNAFormat
Format description for GNA (non-xml) files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ImplicantTableFormat |
| Modifier and Type | Class and Description |
|---|---|
class |
MaBoSSFormat |
| Modifier and Type | Class and Description |
|---|---|
class |
MNetFormat |
| Modifier and Type | Class and Description |
|---|---|
class |
APNNFormat
PNML is an xml-based format for Petri net models.
|
class |
INAFormat
PNML is an xml-based format for Petri net models.
|
class |
PetriNetFormat
Base format for the PN formats
|
class |
PNMLFormat
PNML is an xml-based format for Petri net models.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PintFormat |
| Modifier and Type | Class and Description |
|---|---|
class |
SBMLFormat
Format description for SBML files, using the qual extension.
|
| Modifier and Type | Class and Description |
|---|---|
class |
TruthTableFormat
Format description for TruthTable (.tt) files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
BooleanizeService
A service for model booleanization.
|
| Modifier and Type | Class and Description |
|---|---|
class |
BufferingService
A service to add buffer components.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PerturbationService
Service to apply perturbations to Logical Models.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ReductionService
Orchestrator for model reduction tools
|
| Modifier and Type | Class and Description |
|---|---|
class |
ReverseService
Wrap the reverser code into the ModelModifier interface.
|
| Modifier and Type | Class and Description |
|---|---|
class |
SanitizeService
A service for model cleanups and sanity checks.
|
| Modifier and Type | Class and Description |
|---|---|
class |
SubmodelService |
| Modifier and Type | Class and Description |
|---|---|
class |
SubSpaceService
Modifier Service for subspace restriction
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractToolService<R,T extends ToolTask<R>>
Base class for the boring parts of tool declaration classes.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AttractorService
Identification of synchronous attractors using a SAT solver,
as proposed by E.
|
| Modifier and Type | Class and Description |
|---|---|
class |
FixpointService |
| Modifier and Type | Class and Description |
|---|---|
class |
TraceService |
| Modifier and Type | Class and Description |
|---|---|
class |
RandomWalkService |
| Modifier and Type | Class and Description |
|---|---|
class |
TrapSpaceService |
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