|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectsbrt.kernel.fba.comp.AbstractCvComputer<F>
F
- a type of fluxome.public abstract class AbstractCvComputer<F extends Fluxome>
This abstract class is a skeleton implementation of FluxCvComputer.
Constructor Summary | |
---|---|
AbstractCvComputer(F fluxome)
Constructs a new constraint-variation computer. |
Method Summary | |
---|---|
protected void |
checkFluxConstraint(Interval c,
java.lang.String rxnName,
double tolerance)
Ensures the flux constraint is valid for the fluxome provided. |
protected void |
checkNumber(double number)
Ensures the provided number is not NaN or infinite. |
protected void |
checkRxnExpr(MathExpr<java.lang.String> e)
Ensures the expression is valid for the fluxome provided. |
protected void |
checkRxnExprConstraint(Interval c)
Ensures the expression constraint is valid for the fluxome provided. |
protected void |
checkRxnName(java.lang.String reactionName)
Ensures the reaction name is valid for the fluxome provided. |
protected void |
checkRxnNames(java.util.Collection<java.lang.String> reactionNames)
Ensures the reaction names are valid for the fluxome provided. |
F |
getFluxome()
Returns the fluxome for which values will be computed. |
protected LinearComb<java.lang.String> |
getRxnExpr(java.util.Collection<java.lang.String> reactionNames)
Converts a collection of reaction names to a linear combination. |
protected LinearComb<java.lang.String> |
getRxnExpr(java.lang.String reactionName)
Converts a reaction name to a single-term linear combination. |
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 |
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 |
setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
Changes the flux constraints on more than one reaction. |
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 java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface sbrt.kernel.fba.comp.FluxCvComputer |
---|
getFluxConstraint, getFluxConstraints, getRxnExprConstraint, getRxnExprConstraints, restoreFluxConstraint, restoreRxnExprConstraint, restoreRxnExprConstraints, setFluxConstraint, setRxnExprConstraint |
Constructor Detail |
---|
public AbstractCvComputer(F fluxome)
fluxome
- the fluxome for which values will be computed.
java.lang.NullPointerException
- if the provided fluxome is null.Method Detail |
---|
public F getFluxome()
getFluxome
in interface FluxCvComputer<F extends Fluxome>
protected void checkRxnName(java.lang.String reactionName)
reactionName
- String The reaction name to check.
java.lang.IllegalArgumentException
- if the reaction name is not
present in the fluxome.protected void checkRxnNames(java.util.Collection<java.lang.String> reactionNames)
reactionNames
- the reaction names to check.
java.lang.IllegalArgumentException
- if a reaction name in the provided
collection is not present in the fluxome.
java.lang.NullPointerException
- if the provided Collection is
null
.protected void checkRxnExpr(MathExpr<java.lang.String> e)
e
- the expression to check.
java.lang.IllegalArgumentException
- if the expression contains variables
that are not valid reaction names in the fluoxme.
java.lang.NullPointerException
- if the provided expression is
null
.protected void checkFluxConstraint(Interval c, java.lang.String rxnName, double tolerance)
c
- the constraint to check.rxnName
- the name of the reaction whose flux this constraint
applies to.tolerance
- the numerical tolerance to use during the comparison.
java.lang.IllegalArgumentException
- if the flux constraint is not
valid for the fluoxme provided.
java.lang.NullPointerException
- if the provided constraint is
null
.protected void checkRxnExprConstraint(Interval c)
c
- the constraint to check.
java.lang.NullPointerException
- if the provided constraint is
null
.protected void checkNumber(double number)
NaN
or infinite.
number
- the number to check.
java.lang.IllegalArgumentException
- if the provided number is
NaN
or infinite.protected LinearComb<java.lang.String> getRxnExpr(java.lang.String reactionName)
reactionName
- the reaction name to convert.
protected LinearComb<java.lang.String> getRxnExpr(java.util.Collection<java.lang.String> reactionNames)
reactionNames
- the reaction names to appear as variables.
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 respective constraints.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 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 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>
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |