Uses of Class
general.Constraint

Packages that use Constraint

Package	Description
analyses
general
interaction
operation
thread

Uses of Constraint in analyses

Fields in analyses with type parameters of type Constraint

Modifier and Type	Field and Description
private java.util.List<Constraint>	FVAAnalysis.constraints List of contraints to add before the FVA.

Constructor parameters in analyses with type arguments of type Constraint

Constructor and Description
FVAAnalysis(Bind b, java.util.Map<java.lang.String,parsebionet.biodata.BioEntity> mapEntities, java.util.List<Constraint> constraints)

Uses of Constraint in general

Fields in general with type parameters of type Constraint

Modifier and Type	Field and Description
protected java.util.List<Constraint>	Bind.constraints All problem's constraints.
protected java.util.Map<Interaction,java.util.List<Constraint>>	Bind.intToConstraint Links an interactions to a list of constraints to check if the interaction is true.
protected java.util.Map<parsebionet.biodata.BioEntity,Constraint>	Bind.simpleConstraints Contains the constraints of just one entity and with coeff = 1, it make it easier to get and change them.
protected java.util.Map<parsebionet.biodata.BioEntity,java.util.List<Constraint>>	Bind.steadyStateConstraints Contains all the constraints caused by the steady state assumption.

Methods in general that return types with arguments of type Constraint

Modifier and Type	Method and Description
java.util.Map<Constraint,Interaction>	Bind.checkInteractions() Checks all interactions.
java.util.List<Constraint>	Bind.checkInteractionsForEntities(java.util.Map<parsebionet.biodata.BioEntity,double[]> entititesMap) Returns list of true interactions when setting the given entities to the given values. double[0]=lb, double[1]=ub.
java.util.List<Constraint>	Bind.getConstraints()
java.util.Map<Interaction,java.util.List<Constraint>>	Bind.getIntToConstraint()
java.util.Map<parsebionet.biodata.BioEntity,Constraint>	Bind.getSimpleConstraints()

Methods in general with parameters of type Constraint

Modifier and Type	Method and Description
void	CplexBind.makeSolverConstraint(Constraint constraint, java.util.List<java.lang.Object> toRemoveFromModel, java.util.Map<java.lang.String,double[]> oldBounds)
protected void	GLPKBind.makeSolverConstraint(Constraint constraint, java.util.List<java.lang.Object> toRemoveFromModel, java.util.Map<java.lang.String,double[]> oldBounds)
protected abstract void	Bind.makeSolverConstraint(Constraint c, java.util.List<java.lang.Object> toRemoveFromModel, java.util.Map<java.lang.String,double[]> oldBounds) Creates a constraint for the solver.

Method parameters in general with type arguments of type Constraint

Modifier and Type	Method and Description
DoubleResult	Bind.FBAWithConstraints(java.util.List<Constraint> constraintsToAdd, boolean saveResults, boolean chechInt) Takes constraints, checks interactions for those constraints, and performs FBA.
private DoubleResult	Bind.goWithConstraints(java.util.List<Constraint> constraints, boolean saveResults) Performs the solver solve with constraints.

Constructor parameters in general with type arguments of type Constraint

Constructor and Description
Bind(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet, parsebionet.biodata.BioNetwork bioNet, boolean interactionInSolver) Constructor used to copy the bind.
Bind(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet, parsebionet.biodata.BioNetwork bioNet, boolean interactionInSolver) Constructor used to copy the bind.
CplexBind(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet, parsebionet.biodata.BioNetwork bioNet, boolean interactionInSolver)
CplexBind(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet, parsebionet.biodata.BioNetwork bioNet, boolean interactionInSolver)
GLPKBind(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet, parsebionet.biodata.BioNetwork bioNet, boolean interactionInSolver)
GLPKBind(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet, parsebionet.biodata.BioNetwork bioNet, boolean interactionInSolver)

Uses of Constraint in interaction

Fields in interaction with type parameters of type Constraint

Modifier and Type	Field and Description
(package private) java.util.List<Constraint>	Relation.constraints Constraints corresponding to the relation.

Methods in interaction that return types with arguments of type Constraint

Modifier and Type	Method and Description
java.util.List<Constraint>	Relation.createConstraints() Used when interaction are not in the solver

Method parameters in interaction with type arguments of type Constraint

Modifier and Type	Method and Description
abstract boolean	Relation.isTrue(java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints)
boolean	Unique.isTrue(java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints)
boolean	Or.isTrue(java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints)
boolean	And.isTrue(java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints)
boolean	InversedRelation.isTrue(java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints) Return the opposite of the isTrue function of rel.

Uses of Constraint in operation

Methods in operation that return types with arguments of type Constraint

Modifier and Type	Method and Description
java.util.List<Constraint>	OperationLe.makeConstraint(parsebionet.biodata.BioEntity entity, double value)
java.util.List<Constraint>	OperationGt.makeConstraint(parsebionet.biodata.BioEntity entity, double value)
java.util.List<Constraint>	OperationEq.makeConstraint(parsebionet.biodata.BioEntity entity, double value)
java.util.List<Constraint>	OperationGe.makeConstraint(parsebionet.biodata.BioEntity entity, double value)
java.util.List<Constraint>	OperationLt.makeConstraint(parsebionet.biodata.BioEntity entity, double value)
java.util.List<Constraint>	OperationNotEq.makeConstraint(parsebionet.biodata.BioEntity entity, double value)
abstract java.util.List<Constraint>	Operation.makeConstraint(parsebionet.biodata.BioEntity entity, double value) Make constraint from an entity and a value.

Methods in operation with parameters of type Constraint

Modifier and Type	Method and Description
boolean	OperationLe.isTrue(Constraint cons, double value)
boolean	OperationGt.isTrue(Constraint cons, double value)
boolean	OperationEq.isTrue(Constraint cons, double value)
boolean	OperationGe.isTrue(Constraint cons, double value)
boolean	OperationLt.isTrue(Constraint cons, double value)
boolean	OperationNotEq.isTrue(Constraint cons, double value)
abstract boolean	Operation.isTrue(Constraint cons, double value) Checks if the combination of the constraint, the operation and the value is true or not.

Uses of Constraint in thread

Fields in thread with type parameters of type Constraint

Modifier and Type	Field and Description
protected java.util.List<Constraint>	ThreadFactory.constraints Bind constraints to copy.
protected java.util.Map<Constraint,java.lang.Boolean>	ResolveThread.constraintsToAdd Constraints to add.
protected java.util.Map<parsebionet.biodata.BioEntity,Constraint>	ThreadFactory.simpleConstraints Bind simple constraints to copy.

Method parameters in thread with type arguments of type Constraint

Modifier and Type	Method and Description
void	ResolveThread.setConstraintsToAdd(java.util.Map<Constraint,java.lang.Boolean> c)

Constructor parameters in thread with type arguments of type Constraint

Constructor and Description
ThreadFactory(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet)
ThreadFactory(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet)
ThreadFactoryCPLEX(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet)
ThreadFactoryCPLEX(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet)
ThreadFactoryGLPK(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet)
ThreadFactoryGLPK(java.util.List<Constraint> constraints, java.util.Map<parsebionet.biodata.BioEntity,Constraint> simpleConstraints, InteractionNetwork intNet)