|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectsbrt.kernel.fba.comp.InitialPointComputer<F>
F
- the fluxome type.public class InitialPointComputer<F extends Fluxome>
This class is used to compute initial points for coordinate-direction hit-and-run random flux vector algorithms.
Nested Class Summary | |
---|---|
class |
InitialPointComputer.Results
This class is used to represent the results of the initial point computation. |
Field Summary | |
---|---|
double |
DEFAULT_ZERO_CUTOFF
The default zero cutoff. |
Constructor Summary | |
---|---|
InitialPointComputer(FbaOptimizer<F> computer)
Constructs a new initial point, or flux vector, computer. |
Method Summary | |
---|---|
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. |
F |
getFluxome()
Returns the fluxome used by this computer. |
double |
getPIntercept()
Returns the value of each positioning variable at the edges of the convex polytope. |
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. |
double |
getZeroCutoff()
Returns the 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 |
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> 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. |
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. |
InitialPointComputer.Results |
run()
Computes an initial point, or flux vector, in the flux space of the fluxome used by this computer. |
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 |
setPIntercept(double pIntercept)
Sets the value of the positioning variables at the edges of the convex polytope. |
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. |
void |
setZeroCutoff(double zeroCutoff)
Sets the zero cutoff. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public final double DEFAULT_ZERO_CUTOFF
Constructor Detail |
---|
public InitialPointComputer(FbaOptimizer<F> computer)
computer
- the computer with which optimizations will be performed.Method Detail |
---|
public F getFluxome()
getFluxome
in interface FluxCvComputer<F extends Fluxome>
public double getPIntercept()
public double getZeroCutoff()
public void setPIntercept(double pIntercept)
pIntercept
- a finite value >= 10public void setZeroCutoff(double zeroCutoff)
1E-9
.
zeroCutoff
- the zero cutoff.public InitialPointComputer.Results run()
public void setFluxConstraint(java.lang.String reactionName, Interval c)
setFluxConstraint
in interface FluxCvComputer<F extends Fluxome>
reactionName
- the name of the reaction whose flux constraint
is to be changed.c
- the new constraint.public void setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
setFluxConstraints
in interface FluxCvComputer<F extends Fluxome>
fluxConstraints
- reaction names mapped to their respective flux
constraints.public void setRxnExprConstraint(MathExpr<java.lang.String> e, Interval c)
setRxnExprConstraint
in interface FluxCvComputer<F extends Fluxome>
e
- a matheamtical expression of reaction names.c
- the new constraint.public void setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
setRxnExprConstraints
in interface FluxCvComputer<F extends Fluxome>
constraints
- mathematical expressions of reaction names mapped
to their new respective constraints.public void restoreFluxConstraint(java.lang.String reactionName)
restoreFluxConstraint
in interface FluxCvComputer<F extends Fluxome>
reactionName
- the name of the reaction whose flux constraint
is to be restored.public void restoreFluxConstraints(java.util.Collection<java.lang.String> reactionNames)
restoreFluxConstraints
in interface FluxCvComputer<F extends Fluxome>
reactionNames
- the reaction names whose flux constraints are to
be restored.public void restoreFluxConstraints()
restoreFluxConstraints
in interface FluxCvComputer<F extends Fluxome>
public void restoreRxnExprConstraint(MathExpr<java.lang.String> expr)
restoreRxnExprConstraint
in interface FluxCvComputer<F extends Fluxome>
expr
- the expression of reaction names whose contraint
is to be restored.public void restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExps)
restoreRxnExprConstraints
in interface FluxCvComputer<F extends Fluxome>
rxnNameExps
- the reaction name expressions whose contraints
are to be restored.public void restoreRxnExprConstraints()
restoreRxnExprConstraints
in interface FluxCvComputer<F extends Fluxome>
public java.util.Map<MathExpr<java.lang.String>,Interval> getRxnExprConstraints()
getRxnExprConstraints
in interface FluxCvComputer<F extends Fluxome>
public java.util.Map<java.lang.String,Interval> getFluxConstraints()
getFluxConstraints
in interface FluxCvComputer<F extends Fluxome>
public Interval getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
getRxnExprConstraint
in interface FluxCvComputer<F extends Fluxome>
rxnNameExp
- the mathematical expression of reaction names
whose constraint is to be returned.
public Interval getFluxConstraint(java.lang.String rxnName)
getFluxConstraint
in interface FluxCvComputer<F extends Fluxome>
rxnName
- the name of the reaction whose flux constraint
is to be returned.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |