| Package | Description |
|---|---|
| org.colomoto.biolqm |
Core for the bioLQM toolkit:
Main data structures for Logical Models
Service loader and manager
Launcher and Command-Line Interface
Script mode
|
| org.colomoto.biolqm.helper.inferinteraction |
Infer interactions and their signs from a logical model.
|
| org.colomoto.biolqm.io |
Input/Output for Logical Model.
|
| org.colomoto.biolqm.io.antlr |
Parser implementations using the antlr parser generator.
|
| 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 |
Modifications of logical models.
|
| 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.service | |
| 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 |
Some tools to run simulations on logical models.
|
| org.colomoto.biolqm.tool.simulation.deterministic |
Implementation of updating schemes: update the state of a model (i.e.
|
| org.colomoto.biolqm.tool.simulation.grouping | |
| org.colomoto.biolqm.tool.simulation.multiplesuccessor |
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 |
LogicalModelImpl
Implementation of the LogicalModel interface.
|
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
LogicalModel.clone()
Make a copy of this model.
|
LogicalModel |
LogicalModelImpl.clone() |
LogicalModel |
LogicalModel.clone(boolean keepExtra) |
LogicalModel |
LogicalModelImpl.clone(boolean keepExtra) |
LogicalModel |
LogicalModel.getView(List<NodeInfo> neworder)
Get a logical model with the same nodes but a different order for the core components.
|
LogicalModel |
LogicalModelImpl.getView(List<NodeInfo> neworder) |
| Modifier and Type | Method and Description |
|---|---|
static boolean |
LogicalModelComparator.compare(LogicalModel m1,
LogicalModel m2)
Compare two logical models.
|
| Constructor and Description |
|---|
ConnectivityMatrix(LogicalModel model) |
| Constructor and Description |
|---|
InteractionSearcher(LogicalModel model) |
| Modifier and Type | Field and Description |
|---|---|
protected LogicalModel |
BaseExporter.model |
| Modifier and Type | Method and Description |
|---|---|
default LogicalModel |
LogicalModelFormat.load(File source)
Load a file in this format and build a logical model for it.
|
default LogicalModel |
LogicalModelFormat.load(StreamProvider streams)
Load a file in this format and build a logical model for it.
|
default LogicalModel |
LogicalModelFormat.load(String filename)
Load a file in this format and build a logical model for it.
|
| Modifier and Type | Method and Description |
|---|---|
default void |
LogicalModelFormat.export(LogicalModel model,
File destination)
Export a logical model to this format.
|
default void |
LogicalModelFormat.export(LogicalModel model,
StreamProvider streams)
Export a logical model to this format.
|
default void |
LogicalModelFormat.export(LogicalModel model,
String filename)
Export a logical model to this format.
|
default ModelExporter |
LogicalModelFormat.getExporter(LogicalModel model)
Get a new model exporter to this format.
|
| Constructor and Description |
|---|
BaseExporter(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
static LogicalModel |
ExpressionStack.constructModel(org.colomoto.mddlib.logicalfunction.OperandFactory operandFactory,
List<NodeInfo> nodes,
Map<NodeInfo,org.colomoto.mddlib.logicalfunction.FunctionNode> var2function)
Build a LogicalModel from a list of nodes and parsed functions.
|
static LogicalModel |
ExpressionStack.constructMVModel(org.colomoto.mddlib.logicalfunction.OperandFactory operandFactory,
List<NodeInfo> nodes,
Map<NodeInfo,List<Assignment>> var2assign) |
| Modifier and Type | Method and Description |
|---|---|
protected LogicalModel |
BNetImport.performTask() |
| Modifier and Type | Method and Description |
|---|---|
BNetExport |
BNetFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
BNetExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
BooleanNetImport.performTask() |
| Modifier and Type | Method and Description |
|---|---|
BooleanNetExport |
BooleanNetFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
BooleanNetExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
BoolSimImport.performTask() |
| Modifier and Type | Method and Description |
|---|---|
BoolSimExport |
BoolSimFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
BoolSimExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
protected LogicalModel |
CNetImport.performTask() |
| Modifier and Type | Method and Description |
|---|---|
CNetExport |
CNetFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
CNetExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
BooleanFunctionImport.performTask() |
| Modifier and Type | Method and Description |
|---|---|
BooleanFunctionExport |
BooleanFunctionFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
BooleanFunctionExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
org.colomoto.biolqm.io.ginml.GINMLExporter |
GINMLFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
LogicalModel2GINML(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
GNAExport |
GNAFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
GNAExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
protected LogicalModel |
ImplicantTableImport.performTask() |
| Modifier and Type | Method and Description |
|---|---|
ImplicantTableExport |
ImplicantTableFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
ImplicantTableExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
MaBoSSEncoder |
MaBoSSFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
MaBoSSEncoder(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
MNetImport.performTask() |
| Modifier and Type | Method and Description |
|---|---|
MNetExport |
MNetFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
MNetExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
PNEncoderAPNN |
APNNFormat.getExporter(LogicalModel model) |
abstract AbstractPNEncoder |
PetriNetFormat.getExporter(LogicalModel model) |
PNEncoderINA |
INAFormat.getExporter(LogicalModel model) |
PNEncoderPNML |
PNMLFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
AbstractPNEncoder(LogicalModel model) |
PNEncoderAPNN(LogicalModel model) |
PNEncoderINA(LogicalModel model) |
PNEncoderPNML(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
PintExport |
PintFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
PintExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
SBMLqualImport.performTask() |
| Modifier and Type | Method and Description |
|---|---|
SBMLqualExport |
SBMLFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
SBMLqualExport(LogicalModel model) |
SBMLqualExport(LogicalModel model,
boolean addLayout) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
TruthTableImport.performTask() |
| Modifier and Type | Method and Description |
|---|---|
TruthTableExport |
TruthTableFormat.getExporter(LogicalModel model) |
| Constructor and Description |
|---|
TruthTableExport(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
default LogicalModel |
ModelModifierService.modify(LogicalModel model)
Apply a modifier with the default parameters.
|
default LogicalModel |
ModelModifierService.modify(LogicalModel model,
String parameters)
Setup a modifier and directly retrieve the modified model.
|
| Modifier and Type | Method and Description |
|---|---|
ModelModifier |
ModelModifierService.getModifier(LogicalModel model)
Get a new modifier object.
|
default ModelModifier |
ModelModifierService.getModifier(LogicalModel model,
String parameters)
Setup a new modifier object.
|
default LogicalModel |
ModelModifierService.modify(LogicalModel model)
Apply a modifier with the default parameters.
|
default LogicalModel |
ModelModifierService.modify(LogicalModel model,
String parameters)
Setup a modifier and directly retrieve the modified model.
|
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
BooleanizeModifier.performTask() |
| Modifier and Type | Method and Description |
|---|---|
ModelModifier |
BooleanizeService.getModifier(LogicalModel model) |
| Constructor and Description |
|---|
BooleanizeModifier(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
BufferingModifier.performTask() |
| Modifier and Type | Method and Description |
|---|---|
ModelModifier |
BufferingService.getModifier(LogicalModel model) |
| Constructor and Description |
|---|
BufferingModifier(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
default LogicalModel |
LogicalModelPerturbation.apply(LogicalModel model)
Apply the perturbation.
|
LogicalModel |
PerturbationModifier.performTask() |
| Modifier and Type | Method and Description |
|---|---|
default LogicalModel |
LogicalModelPerturbation.apply(LogicalModel model)
Apply the perturbation.
|
ModelModifier |
PerturbationService.getModifier(LogicalModel model) |
void |
MultiplePerturbation.update(LogicalModel model) |
void |
RangePerturbation.update(LogicalModel model) |
void |
FixedValuePerturbation.update(LogicalModel model) |
void |
InteractionPerturbation.update(LogicalModel model) |
void |
LogicalModelPerturbation.update(LogicalModel model)
Apply the perturbation to a model directly (do not create a modified model).
|
| Constructor and Description |
|---|
PerturbationModifier(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
ModelReducer.getModel()
Get a logical model for the modified functions.
|
LogicalModel |
ModelReducer.getModel(boolean includeExtra) |
LogicalModel |
ModelReducer.getModel(boolean preserveFixedInputs,
boolean includeExtra) |
LogicalModel |
ReductionModifier.performTask() |
LogicalModel |
PatternReduction.performTask() |
static LogicalModel |
FixedComponentRemover.reduceFixed(LogicalModel model,
boolean removeFixed) |
static LogicalModel |
DuplicateRemover.removeDuplicateComponents(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
ReductionModifier |
ReductionService.getModifier(LogicalModel model) |
static LogicalModel |
FixedComponentRemover.reduceFixed(LogicalModel model,
boolean removeFixed) |
static LogicalModel |
DuplicateRemover.removeDuplicateComponents(LogicalModel model) |
| Constructor and Description |
|---|
ModelReducer(LogicalModel model) |
PatternReduction(LogicalModel model,
StatePattern pattern) |
ReductionModifier(LogicalModel model) |
ReductionModifier(LogicalModel model,
String parameters) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
ReverseModifier.performTask() |
| Modifier and Type | Method and Description |
|---|---|
ModelModifier |
ReverseService.getModifier(LogicalModel model) |
| Constructor and Description |
|---|
ReverseModifier(LogicalModel model)
Prepare a Model modifier for model reversal.
|
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
SanitizeModifier.performTask() |
| Modifier and Type | Method and Description |
|---|---|
ModelModifier |
SanitizeService.getModifier(LogicalModel model) |
| Constructor and Description |
|---|
SanitizeModifier(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
SubmodelModifier.performTask() |
| Modifier and Type | Method and Description |
|---|---|
ModelModifier |
SubmodelService.getModifier(LogicalModel model) |
| Constructor and Description |
|---|
SubmodelModifier(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
SubSpaceModifier.performTask() |
| Modifier and Type | Method and Description |
|---|---|
ModelModifier |
SubSpaceService.getModifier(LogicalModel model) |
| Constructor and Description |
|---|
SubSpaceModifier(LogicalModel model) |
SubSpaceModifier(LogicalModel model,
byte[] pattern) |
| Modifier and Type | Method and Description |
|---|---|
static LogicalModel |
LQMServiceManager.load(String filename)
Load a model guessing the format.
|
static LogicalModel |
LQMServiceManager.load(String filename,
String format)
Load a model from file.
|
static LogicalModel |
LQMServiceManager.modify(LogicalModel model,
String name)
Construct a modified model.
|
static LogicalModel |
LQMServiceManager.modify(LogicalModel model,
String name,
String parameters)
Construct a modified model.
|
| Modifier and Type | Method and Description |
|---|---|
static LogicalModel |
LQMServiceManager.modify(LogicalModel model,
String name)
Construct a modified model.
|
static LogicalModel |
LQMServiceManager.modify(LogicalModel model,
String name,
String parameters)
Construct a modified model.
|
static boolean |
LQMServiceManager.save(LogicalModel model,
String filename,
String format)
Save a model to file
|
| Modifier and Type | Field and Description |
|---|---|
LogicalModel |
AbstractToolTask.model |
| Modifier and Type | Method and Description |
|---|---|
T |
ModelToolService.getTask(LogicalModel model)
Construct a default setting object.
|
default T |
ModelToolService.getTask(LogicalModel model,
String... parameters)
Construct a default setting object.
|
default T |
ModelToolService.getTask(LogicalModel model,
String parameters)
Construct a parsed setting object.
|
| Constructor and Description |
|---|
AbstractToolTask(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
SATAttractorFinder |
AttractorService.getTask(LogicalModel model) |
| Constructor and Description |
|---|
SATAttractorFinder(LogicalModel model) |
| Modifier and Type | Field and Description |
|---|---|
protected LogicalModel |
StructuralNodeOrderer.model |
| Modifier and Type | Method and Description |
|---|---|
static FixpointList |
JBDDModel.getBDD(LogicalModel model) |
FixpointList |
FixpointTask.getMDD(LogicalModel model) |
FixpointList |
FixpointTask.getMDD(LogicalModel model,
boolean pattern) |
FixpointTask |
FixpointService.getTask(LogicalModel model) |
| Constructor and Description |
|---|
FixpointList(LogicalModel model) |
FixpointSearcher(LogicalModel model)
Create a new stable state searcher.
|
FixpointTask(LogicalModel model) |
JBDDModel(LogicalModel lm) |
StableASP(LogicalModel model) |
StructuralNodeOrderer(LogicalModel model) |
| Modifier and Type | Field and Description |
|---|---|
protected LogicalModel |
BaseUpdater.model |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
BaseUpdater.getModel() |
LogicalModel |
LogicalModelUpdater.getModel() |
| Modifier and Type | Method and Description |
|---|---|
static DeterministicUpdater |
UpdaterFactory.getDeterministicUpdater(LogicalModel model,
String s) |
static MultipleSuccessorsUpdater |
UpdaterFactory.getMultipleSuccessorUpdater(LogicalModel model,
String s) |
static RandomUpdater |
UpdaterFactory.getRandomUpdater(LogicalModel model,
String s) |
static byte[] |
InitialStateFactory.parseInitialState(LogicalModel model,
String s) |
| Constructor and Description |
|---|
BaseUpdater(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
TraceTask |
TraceService.getTask(LogicalModel model) |
| Constructor and Description |
|---|
BlockSequentialUpdater(LogicalModel model,
int[][] blocks) |
BlockSequentialUpdater(LogicalModel model,
String config) |
DeterministicPriorityUpdater(LogicalModel model,
int[][] blocks) |
DeterministicPriorityUpdater(LogicalModel model,
String config) |
SequentialUpdater(LogicalModel model)
Create a new sequential updater, using the default order
|
SequentialUpdater(LogicalModel model,
int[] order)
Create a new sequential updater, using a custom order
|
SequentialUpdater(LogicalModel model,
String s_order)
Create a new sequential updater, using a custom order
|
SynchronousUpdater(LogicalModel model)
Create a new synchronous updater
|
TraceTask(LogicalModel model) |
| Modifier and Type | Field and Description |
|---|---|
protected LogicalModel |
ModelGrouping.model |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
ModelGrouping.getModel() |
| Modifier and Type | Method and Description |
|---|---|
ModelGrouping |
ModelGrouping.cloneWithModel(LogicalModel modifiedModel) |
List<List<String>> |
ModelGrouping.RankedClass.getVars(LogicalModel m) |
List<String> |
ModelGrouping.RankedClassGroup.getVars(LogicalModel m) |
| Constructor and Description |
|---|
ModelGrouping(LogicalModel m) |
ModelGrouping(LogicalModel m,
String textFormat) |
RankedClass(LogicalModel m,
String textFormat) |
RankedClassGroup(LogicalModel m,
String textFormat) |
| Constructor and Description |
|---|
AbstractMultipleSuccessorUpdater(LogicalModel model) |
AsynchronousUpdater(LogicalModel model)
Create a new asynchronous random.
|
CompleteUpdater(LogicalModel model)
Create a new full random.
|
PriorityUpdater(LogicalModel model,
String setup) |
| Modifier and Type | Method and Description |
|---|---|
LogicalModel |
RandomUpdaterWrapper.getModel() |
| Modifier and Type | Method and Description |
|---|---|
RandomWalkTask |
RandomWalkService.getTask(LogicalModel model) |
| Constructor and Description |
|---|
AbstractRandomUpdater(LogicalModel model) |
RandomUpdaterWithRates(LogicalModel model)
Create a new random random
|
RandomUpdaterWithRates(LogicalModel model,
double[] rates) |
RandomWalkTask(LogicalModel model) |
| Modifier and Type | Method and Description |
|---|---|
TrapSpaceTask |
TrapSpaceService.getTask(LogicalModel model) |
| Constructor and Description |
|---|
TrapSpaceList(TrapSpaceTask settings,
LogicalModel model) |
TrapSpaceSolverASP(LogicalModel model,
TrapSpaceTask settings) |
TrapSpaceSolverBDD(LogicalModel model,
TrapSpaceTask settings) |
TrapSpaceSolverFunctionASP(LogicalModel model,
TrapSpaceTask settings) |
TrapSpaceTask(LogicalModel model) |
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