sbrt.kernel.fba.comp
Interface FluxCvComputer<F extends Fluxome>

Type Parameters:
F - a type of fluxome.
All Known Subinterfaces:
FluxIntervalComputer<F>
All Known Implementing Classes:
AbstractCvComputer, AbstractFluxIntervalComputer, CdHarFluxComp, FbaOptimizer, InitialPointComputer, MsFluxIntervalComputer, ReverseRxnIntervalComp, RxnDeletionComputer, SimpleFluxIntervalComputer

public interface FluxCvComputer<F extends Fluxome>

This interface is used to represent a flux constraint variation computer. A constraint-variation computer uses a particular fluxome, and it allows one to compute the effect of varying the constraints within that fluxome.

Author:
This interface was written and documented by Jeremiah Wright while in the Wagner lab.

Method Summary
 Interval getFluxConstraint(java.lang.String rxnName)
          Returns the current flux constraint for the reaction with the provided name.
 java.util.Map<java.lang.String,Interval> getFluxConstraints()
          Returns all current flux constraints.
 F getFluxome()
          Returns the fluxome that this flux constraint-variation computer uses.
 Interval getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
          Returns the current constraint on the provided expression.
 java.util.Map<? extends MathExpr<java.lang.String>,Interval> getRxnExprConstraints()
          Returns all current flux expression constraints.
 void restoreFluxConstraint(java.lang.String reactionName)
          Restores the flux constraint for the reaction with the provided name to the value contained in the fluxome.
 void restoreFluxConstraints()
          Restores the flux constraints for all reactions in the fluxome to those values contained in the fluxome.
 void restoreFluxConstraints(java.util.Collection<java.lang.String> reactionNames)
          Restores the flux constraints for the provided reaction names to the values contained in the fluxome.
 void restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
          Restores the constraint on the provided flux expression to the value contained in the fluxome.
 void restoreRxnExprConstraints()
          Restores the constraints on all flux expressions to the values contained in the fluxome.
 void restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExps)
          Restores the constraints on the provided expressions to the values contained in the fluxome.
 void setFluxConstraint(java.lang.String reactionName, Interval c)
          Changes the flux constraint of the reaction with the provided name.
 void setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
          Changes the flux constraints on more than one reaction.
 void setRxnExprConstraint(MathExpr<java.lang.String> e, Interval c)
          Changes the constraint on the provided mathematical expression of fluxes.
 void setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
          Changes the constraints on more than one mathematical expression of fluxes.
 

Method Detail

getFluxome

F getFluxome()
Returns the fluxome that this flux constraint-variation computer uses.

Returns:
the fluxome that this flux constraint-variation computer uses.

getRxnExprConstraints

java.util.Map<? extends MathExpr<java.lang.String>,Interval> getRxnExprConstraints()
Returns all current flux expression constraints.

Returns:
mathematical expressions of reaction names mapped to their respective constraint.

getFluxConstraints

java.util.Map<java.lang.String,Interval> getFluxConstraints()
Returns all current flux constraints.

Returns:
reaction names mapped to their respective flux constraint.

getRxnExprConstraint

Interval getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression.

Parameters:
rxnNameExp - the mathematical expression of reaction names whose constraint is to be returned.
Returns:
the current constraint on the provided expression.

getFluxConstraint

Interval getFluxConstraint(java.lang.String rxnName)
Returns the current flux constraint for the reaction with the provided name.

Parameters:
rxnName - the name of the reaction whose flux constraint is to be returned.
Returns:
the current flux constraint for the reaction with the provided name.

setFluxConstraint

void setFluxConstraint(java.lang.String reactionName,
                       Interval c)
Changes the flux constraint of the reaction with the provided name.

Parameters:
reactionName - the name of the reaction whose flux constraint is to be changed.
c - the new constraint.

setFluxConstraints

void setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
Changes the flux constraints on more than one reaction.

Parameters:
fluxConstraints - reaction names mapped to their respective flux constraints.

setRxnExprConstraint

void setRxnExprConstraint(MathExpr<java.lang.String> e,
                          Interval c)
Changes the constraint on the provided mathematical expression of fluxes.

Parameters:
e - a matheamtical expression of reaction names.
c - the new constraint.

setRxnExprConstraints

void setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
Changes the constraints on more than one mathematical expression of fluxes.

Parameters:
constraints - mathematical expressions of reaction names mapped to their new respective constraints.

restoreFluxConstraints

void restoreFluxConstraints()
Restores the flux constraints for all reactions in the fluxome to those values contained in the fluxome.


restoreFluxConstraint

void restoreFluxConstraint(java.lang.String reactionName)
Restores the flux constraint for the reaction with the provided name to the value contained in the fluxome.

Parameters:
reactionName - the name of the reaction whose flux constraint is to be restored.

restoreFluxConstraints

void restoreFluxConstraints(java.util.Collection<java.lang.String> reactionNames)
Restores the flux constraints for the provided reaction names to the values contained in the fluxome.

Parameters:
reactionNames - the reaction names whose flux constraints are to be restored.

restoreRxnExprConstraints

void restoreRxnExprConstraints()
Restores the constraints on all flux expressions to the values contained in the fluxome.


restoreRxnExprConstraint

void restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Restores the constraint on the provided flux expression to the value contained in the fluxome.

Parameters:
rxnNameExp - the expression of reaction names whose contraint is to be restored.

restoreRxnExprConstraints

void restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExps)
Restores the constraints on the provided expressions to the values contained in the fluxome.

Parameters:
rxnNameExps - the reaction name expressions whose contraints are to be restored.