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java.lang.Objectsbrt.kernel.fba.comp.AbstractCvComputer
sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
sbrt.kernel.fba.comp.FastMsFluxRangeComputer
public class FastMsFluxRangeComputer
This class is used to compute Mahadevan-Schilling flux intervals in a
(sometimes) faster way than MsFluxIntervalComputer
can.
Field Summary |
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Fields inherited from class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer |
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ZERO_CUTOFF |
Constructor Summary | |
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FastMsFluxRangeComputer(FbaOptComputer computer,
java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps,
LinearSystemSolution<java.lang.String> systemSolution,
double zeroCutoff)
Constructs a new flux interval computer. |
Method Summary | |
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double |
getConstraintTolerance()
Returns the constraint tolerance used by this flux interval computer. |
Interval |
getFluxConstraint(java.lang.String rxnName)
Returns the current flux constraint on the reaction with the provided name. |
java.util.Map<java.lang.String,Interval> |
getFluxConstraints()
Returns all current flux constraints. |
java.util.Map<java.lang.String,Interval> |
getIntervals()
Computes and returns the intervals of every flux in the fluxome used to construct this flux interval computer. |
java.util.Map<java.lang.String,Interval> |
getIntervals(java.util.Collection<java.lang.String> reactionNames)
Computes and returns the flux intervals of the reactions with the provided names. |
ProgressMonitor |
getProgress()
Returns a progress monitor for this flux interval computer. |
Interval |
getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
java.util.Map<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> rxnNameExpr)
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>> rxnNameExprs)
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. |
Methods inherited from class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer |
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getBoundedMax, getBoundedMax, getBoundedMaxWithReverseConstrained, getBoundedMin, getBoundedMin, getInterval, getIntervals, getMaximum, getMaximum, getMaxWithReverseConstrained, getMinimum, getMinimum, getReverseRxnNames, getZeroCutoff |
Methods inherited from class sbrt.kernel.fba.comp.AbstractCvComputer |
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checkFluxConstraint, checkNumber, checkRxnExpr, checkRxnExprConstraint, checkRxnName, checkRxnNames, getFluxome, getRxnExpr, getRxnExpr |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface sbrt.kernel.fba.comp.FluxCvComputer |
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getFluxome |
Constructor Detail |
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public FastMsFluxRangeComputer(FbaOptComputer computer, java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps, LinearSystemSolution<java.lang.String> systemSolution, double zeroCutoff)
computer
- the computer with which all optimizations will be
performed.fluxCaps
- the flux caps used to constrain all unbounded fluxes.systemSolution
- the solution to the system of linear equations
formed by the fluxome contained in the provided FBA optimization
computer.zeroCutoff
- the zero cutoff to be used by this computer.Method Detail |
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public double getConstraintTolerance()
getConstraintTolerance
in interface FluxIntervalComputer
getConstraintTolerance
in class AbstractFluxIntervalComputer
public ProgressMonitor getProgress()
public java.util.Map<java.lang.String,Interval> getIntervals()
public java.util.Map<java.lang.String,Interval> getIntervals(java.util.Collection<java.lang.String> reactionNames)
reactionNames
- a collection of reaction names.
public void setFluxConstraint(java.lang.String reactionName, Interval c)
setFluxConstraint
in interface FluxCvComputer
setFluxConstraint
in class AbstractFluxIntervalComputer
reactionName
- the name of the reaction whose flux constraint
is to be changed.c
- the new constraint.public final void setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
setFluxConstraints
in interface FluxCvComputer
setFluxConstraints
in class AbstractFluxIntervalComputer
fluxConstraints
- reaction names mapped to their respective flux
constraints.public final void setRxnExprConstraint(MathExpr<java.lang.String> e, Interval c)
setRxnExprConstraint
in interface FluxCvComputer
setRxnExprConstraint
in class AbstractFluxIntervalComputer
e
- a matheamtical expression of reaction names.c
- the new constraint.public final void setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
setRxnExprConstraints
in interface FluxCvComputer
setRxnExprConstraints
in class AbstractFluxIntervalComputer
constraints
- mathematical expressions of reaction names mapped
to their new respective constraints.public final void restoreFluxConstraint(java.lang.String reactionName)
restoreFluxConstraint
in interface FluxCvComputer
restoreFluxConstraint
in class AbstractFluxIntervalComputer
reactionName
- the name of the reaction whose flux constraint
is to be restored.public final void restoreFluxConstraints(java.util.Collection<java.lang.String> reactionNames)
restoreFluxConstraints
in interface FluxCvComputer
restoreFluxConstraints
in class AbstractFluxIntervalComputer
reactionNames
- the reaction names whose flux constraints are to
be restored.public void restoreFluxConstraints()
restoreFluxConstraints
in interface FluxCvComputer
restoreFluxConstraints
in class AbstractFluxIntervalComputer
public final void restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
restoreRxnExprConstraint
in interface FluxCvComputer
restoreRxnExprConstraint
in class AbstractFluxIntervalComputer
rxnNameExpr
- the expression of reaction names whose contraint
is to be restored.public final void restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExprs)
restoreRxnExprConstraints
in interface FluxCvComputer
restoreRxnExprConstraints
in class AbstractFluxIntervalComputer
rxnNameExprs
- the reaction name expressions whose contraints
are to be restored.public final void restoreRxnExprConstraints()
restoreRxnExprConstraints
in interface FluxCvComputer
restoreRxnExprConstraints
in class AbstractFluxIntervalComputer
public java.util.Map<MathExpr<java.lang.String>,Interval> getRxnExprConstraints()
getRxnExprConstraints
in interface FluxCvComputer
getRxnExprConstraints
in class AbstractFluxIntervalComputer
public java.util.Map<java.lang.String,Interval> getFluxConstraints()
getFluxConstraints
in interface FluxCvComputer
getFluxConstraints
in class AbstractFluxIntervalComputer
public Interval getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
getRxnExprConstraint
in interface FluxCvComputer
getRxnExprConstraint
in class AbstractFluxIntervalComputer
rxnNameExp
- the mathematical expression of reaction names
whose constraint is to be returned.
public Interval getFluxConstraint(java.lang.String rxnName)
getFluxConstraint
in interface FluxCvComputer
getFluxConstraint
in class AbstractFluxIntervalComputer
rxnName
- the name of the reaction whose flux constraint
is to be returned.
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