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java.lang.Objectsbrt.kernel.fba.comp.AbstractCvComputer<F>
sbrt.kernel.fba.comp.RxnDeletionComputer<F>
F
- a type of fluxome.public class RxnDeletionComputer<F extends Fluxome>
This class is used to compute the effect of deleting reactions in a fluxome.
Constructor Summary | |
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RxnDeletionComputer(FbaOptimizer<F> computer)
Constructs a new reaction deletion computer. |
Method Summary | |
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FbaOptimizer.Results |
delete(java.util.Set<java.lang.String> rxnNames)
Computes and returns the results of deleting the reactions whose names appear in the provided set. |
Interval |
getFluxConstraint(java.lang.String rxnName)
Returns the flux constraint of the reaction with the provided name. |
java.util.Map<java.lang.String,Interval> |
getFluxConstraints()
Returns the set of all constraints on single fluxes. |
MathExpr<java.lang.String> |
getObjectiveFunction()
Returns the current objective function. |
OptSense |
getOptimizationSense()
Returns the current optimization sense. |
Interval |
getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the constraint on the provided mathematical expression of fluxes. |
java.util.Map<MathExpr<java.lang.String>,Interval> |
getRxnExprConstraints()
Returns the set of all constraints on mathematical expressions of fluxes. |
double |
getTolerance()
Returns the constraint tolerance. |
double |
getZeroCutoff()
Returns the current zero cutoff. |
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 |
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 |
setFluxConstraint(java.lang.String reactionName,
Interval c)
Changes the flux constraint of the reaction with the provided name. |
void |
setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
setOptimizationSense(OptSense sense)
Sets the optimization sense to the provided value. |
void |
setRxnExprConstraint(MathExpr<java.lang.String> e,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
setTolerance(double tolerance)
Sets the constraint tolerance. |
void |
setZeroCutoff(double zeroCutoff)
Sets the zero cutoff to the provided value. |
Methods inherited from class sbrt.kernel.fba.comp.AbstractCvComputer |
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checkFluxConstraint, checkNumber, checkRxnExpr, checkRxnExprConstraint, checkRxnName, checkRxnNames, getFluxome, getRxnExpr, getRxnExpr, restoreFluxConstraints, restoreFluxConstraints, restoreRxnExprConstraints, setFluxConstraints, setRxnExprConstraints |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public RxnDeletionComputer(FbaOptimizer<F> computer)
computer
- the FBA optimization computer to use for all
optimizations.Method Detail |
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public void setZeroCutoff(double zeroCutoff)
zeroCutoff
- the zero cutoff.public void setTolerance(double tolerance)
tolerance
- the amount by which computed values can
violate their defined constraints.
java.lang.IllegalArgumentException
- if the provided value is NaN,
infinite, or less than 0.public void setOptimizationSense(OptSense sense)
sense
- an optimization sense.public void setObjectiveFunction(MathExpr<java.lang.String> objective)
objective
- a mathematical expression of reaction names.public MathExpr<java.lang.String> getObjectiveFunction()
public OptSense getOptimizationSense()
public double getZeroCutoff()
setZeroCutoff(double)
public double getTolerance()
public FbaOptimizer.Results delete(java.util.Set<java.lang.String> rxnNames)
rxnNames
- the names of reactions whose effect upon deletion
will be computed.
java.lang.IllegalStateException
- if no objective function or optimization
sense were provided.public java.util.Map<MathExpr<java.lang.String>,Interval> getRxnExprConstraints()
public java.util.Map<java.lang.String,Interval> getFluxConstraints()
public Interval getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
rxnNameExp
- a mathematical expression of reaction names.
public Interval getFluxConstraint(java.lang.String rxnName)
rxnName
- the name of the reaction whose flux constraint is to
be returned.
public void setFluxConstraint(java.lang.String reactionName, Interval c)
reactionName
- the name of the reaction whose flux constraint
is to be changed.c
- the new constraint.public void setRxnExprConstraint(MathExpr<java.lang.String> e, Interval c)
e
- a matheamtical expression of reaction names.c
- the new constraint.public void restoreRxnExprConstraints()
public void restoreFluxConstraint(java.lang.String reactionName)
reactionName
- the name of the reaction whose flux constraint
is to be restored.public void restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
rxnNameExp
- the expression of reaction names whose contraint
is to be restored.
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