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java.lang.Objectsbrt.kernel.fba.comp.AbstractCvComputer
sbrt.kernel.fba.comp.CdHarFluxVectorComputer
public class CdHarFluxVectorComputer
This class is used to compute randomly distributed vectors within flux space. It uses a coordinate-direction hit-and-run algorithm.
Nested Class Summary | |
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class |
CdHarFluxVectorComputer.Results
This class is used to represent the results of a coordinate-direction hit-and-run flux vector computation. |
Field Summary | |
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static double |
DEFAULT_TOLERANCE
The default constraint tolerance. |
Constructor Summary | |
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CdHarFluxVectorComputer(IrrevRxnFluxome fluxome,
LinearSystemSolution<java.lang.String> systemSolution)
Constructs a new random flux vector computer for the provided fluxome. |
Method Summary | |
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double |
getConstraintTolerance()
Returns the constraint tolerance. |
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. |
double |
getMinChordLength()
Returns the minimum length a computed chord must have to be considered successful. |
Interval |
getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
java.util.Map<LinearComb<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 |
restoreRxnExprConstraint(LinearComb<java.lang.String> expr)
Restores the constraint on the provided flux expression to the value contained in the fluxome. |
void |
restoreRxnExprConstraint(MathExpr<java.lang.String> expr)
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. |
CdHarFluxVectorComputer.Results |
run()
Computes the next random flux vector from within the interior of the convex polytope defined by the current set of constraints. |
void |
setConstraintTolerance(double tolerance)
Sets the constraint tolerance. |
void |
setFluxConstraint(java.lang.String reactionName,
Interval c)
Changes the flux constraint of the reaction with the provided name. |
void |
setInitialFluxVector(java.util.Map<java.lang.String,java.lang.Double> vector)
Sets the initial flux vector to the one provided. |
void |
setMinChordLength(double minChordLength)
Sets the minimum chord length. |
void |
setPointsPerPoint(int pointsPerPoint)
Sets the number of points to generate for each point added to the specified results manager. |
void |
setRandom(java.util.Random random)
Sets the random number generator. |
void |
setRxnExprConstraint(LinearComb<java.lang.String> rxnExpr,
Interval c)
Changes the constraint on the provided linear combination of fluxes. |
void |
setRxnExprConstraint(MathExpr<java.lang.String> rxnExpr,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
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 |
Field Detail |
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public static final double DEFAULT_TOLERANCE
Constructor Detail |
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public CdHarFluxVectorComputer(IrrevRxnFluxome fluxome, LinearSystemSolution<java.lang.String> systemSolution)
fluxome
- the fluxome for which random flux vectors will be
computed.systemSolution
- a solution to the system of linear equations formed
by the provided fluxome.Method Detail |
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public void setRandom(java.util.Random random)
random
- the random number generator with which all psuedorandom
numbers are to be produced.public void setPointsPerPoint(int pointsPerPoint)
pointsPerPoint
- the number of points to generate for each point added to the
specified results manager.public void setConstraintTolerance(double tolerance)
tolerance
- the amount by which constaints can be violated. This
should be a small positive number, like 1E-9 for example.public void setMinChordLength(double minChordLength)
minChordLength
- the minimum length a chord must have to be
considered valid. This should be a small positive number, like 1E-9 for
example.public double getConstraintTolerance()
setConstraintTolerance(double)
public double getMinChordLength()
setMinChordLength(double)
public CdHarFluxVectorComputer.Results run()
public void setInitialFluxVector(java.util.Map<java.lang.String,java.lang.Double> vector)
vector
- reaction names mapped to the flux of their corresponding
reaction.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 restoreFluxConstraint(java.lang.String reactionName)
reactionName
- the name of the reaction whose flux constraint is to
be restored.public void setRxnExprConstraint(MathExpr<java.lang.String> rxnExpr, Interval c)
rxnExpr
- a LinearComb
of reaction names.c
- the new constraint.public void setRxnExprConstraint(LinearComb<java.lang.String> rxnExpr, Interval c)
rxnExpr
- a linear combination of reaction names.c
- the new constraint.public void restoreRxnExprConstraint(MathExpr<java.lang.String> expr)
expr
- the LinearComb
of reaction names whose contraint is
to be restored.public void restoreRxnExprConstraint(LinearComb<java.lang.String> expr)
expr
- the linear combination of reaction names whose contraint is
to be restored.public void restoreRxnExprConstraints()
public java.util.Map<java.lang.String,Interval> getFluxConstraints()
public java.util.Map<LinearComb<java.lang.String>,Interval> getRxnExprConstraints()
public Interval getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
rxnNameExp
- the mathematical expression of reaction names whose
constraint is to be returned.
public Interval getFluxConstraint(java.lang.String rxnName)
rxnName
- the name of the reaction whose flux constraint is to be
returned.
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