org.colomoto.biolqm

Interface LogicalModel

All Known Implementing Classes:

LogicalModelImpl

public interface LogicalModel

A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

Author:

Aurelien Naldi

Method Summary

Modifier and Type	Method and Description
LogicalModel	clone() Make a copy of this model.
LogicalModel	clone(boolean keepExtra)
void	fillExtraValues(byte[] state, byte[] extra) Compute the value of all extra components for a given state.
Map<String,NodeInfo[]>	getBooleanizedMap() Get the Boolean - multi-valued mapping information for booleanized models.
NodeInfo	getComponent(String s_source) Retrieve a component by name.
int	getComponentIndex(String s_source) Retrieve a component by name.
List<NodeInfo>	getComponents() Get the list of core nodes in this model.
List<NodeInfo>	getExtraComponents() Get the list of extra components in this model.
int[]	getExtraLogicalFunctions() Get the logical function of extra components in this model.
byte	getExtraValue(int componentIdx, byte[] state) Compute the value of an extra component for a given state.
ModelLayout	getLayout() Retrieve the associated layout information.
int[]	getLogicalFunctions() Get the logical function of core components in this model.
org.colomoto.mddlib.MDDManager	getMDDManager() Get the MDD factory holding logical functions for this model.
byte	getTargetValue(int componentIdx, byte[] state) Compute the target value of a core component for a given state.
LogicalModel	getView(List<NodeInfo> neworder) Get a logical model with the same nodes but a different order for the core components.
boolean	hasExtraComponents() Check if the model has extra component(s).
boolean	hasLayout() Check if this model has associated layout information.
boolean	isBoolean() Check if this model is Boolean.

Method Detail

getMDDManager

org.colomoto.mddlib.MDDManager getMDDManager()

Get the MDD factory holding logical functions for this model.

Returns:

the MDD factory in which logical function are stored.

getComponents

List<NodeInfo> getComponents()

Get the list of core nodes in this model. Logical functions for these nodes (in the same order) can be obtained with the getLogicalFunctions() method.

Returns:

the list of nodeInfo objects for core components.

getLogicalFunctions

int[] getLogicalFunctions()

Get the logical function of core components in this model. The order used is the same as for getNodeOrder(). These functions are just identifiers, actual functions are stored in the MDD factory provided by getMDDManager.

Returns:

the list of logical function identifiers for core components

getExtraComponents

List<NodeInfo> getExtraComponents()

Get the list of extra components in this model. Extra components have logical functions, but do not regulate any component, they are thus NOT considered as variables in the MDDManager. Logical functions for these nodes (in the same order) can be obtained with the getExtraLogicalFunctions() method.

Returns:

the list of nodeInfo objects for extra components.

getExtraLogicalFunctions

int[] getExtraLogicalFunctions()

Get the logical function of extra components in this model. The order used is the same as for getExtraNodes(). These functions are just identifiers, actual functions are stored in the MDD factory provided by getMDDManager().

Returns:

the list of logical function identifiers for extra components

getTargetValue

byte getTargetValue(int componentIdx,
                    byte[] state)

Compute the target value of a core component for a given state.

Parameters:

componentIdx - index of the component in the core node order

state - value of components

Returns:

the target value reached for this state

hasExtraComponents

boolean hasExtraComponents()

Check if the model has extra component(s). If this returns true, then the getExtraComponents() and getExtraLogicalFunctions() methods should not return null.

Returns:

true is there is at least one extra component

getExtraValue

byte getExtraValue(int componentIdx,
                   byte[] state)

Compute the value of an extra component for a given state.

Parameters:

componentIdx - index of the component in the extra node order

state - value of components

Returns:

the computed value for this state

fillExtraValues

void fillExtraValues(byte[] state,
                     byte[] extra)

Compute the value of all extra components for a given state.

Parameters:

state - value of components

extra - an array of the right size to fill

clone

LogicalModel clone()

Make a copy of this model. This will duplicate logical functions pointers, but not the actual MDD Factory.

Returns:

a copy of this model.

clone

LogicalModel clone(boolean keepExtra)

getView

LogicalModel getView(List<NodeInfo> neworder)

Get a logical model with the same nodes but a different order for the core components.

Parameters:

neworder - the desired ordered list of components

Returns:

a re-ordered view of the same model

isBoolean

boolean isBoolean()

Check if this model is Boolean.

Returns:

true if the model has no multivalued components, false otherwise.

getComponent

NodeInfo getComponent(String s_source)

Retrieve a component by name.

Parameters:

s_source - the name of the component

Returns:

the component or null if not found

getComponentIndex

int getComponentIndex(String s_source)

Retrieve a component by name.

Parameters:

s_source - the name of the component

Returns:

the component or null if not found

getBooleanizedMap

Map<String,NodeInfo[]> getBooleanizedMap()

Get the Boolean - multi-valued mapping information for booleanized models.

Returns:

a list of booleanized groups

hasLayout

boolean hasLayout()

Check if this model has associated layout information.

Returns:

true if some layout information is available

getLayout

ModelLayout getLayout()

Retrieve the associated layout information.

Returns:

the existing layout information. Create it if it does not exist.