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Packages that use MathExpr | |
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sbrt.ext.cplex | Provides a class that allows communication with CPLEX. |
sbrt.ext.glpk | Provides a class that allows communication with GLPK. |
sbrt.kernel.fba | Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. |
sbrt.kernel.fba.comp | Provides classes and interfaces for performing Flux Balance Analysis computations. |
sbrt.kernel.fba.proc | Provides classes and interfaces for executing Flux Balance Analysis processes. |
sbrt.kernel.math | Provides classes and interfaces for creating objects relevant to mathematics. |
sbrt.kernel.math.optimization | Provides classes and interfaces for creating objects relevant to solving optimization problems. |
sbrt.kernel.utilities.proc | Provides classes and interfaces for performing utility processes. |
sbrt.shell.io.fba | Provides classes and interfaces for reading and writing files relevant to Flux Balance Analysis. |
sbrt.shell.text.fba | Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis. |
sbrt.shell.text.math | Provides classes and interfaces for defining formats for mathematical objects. |
Uses of MathExpr in sbrt.ext.cplex |
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Methods in sbrt.ext.cplex with parameters of type MathExpr | |
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void |
CplexSolver.setConstraint(MathExpr<? extends C> expression,
Interval c)
Sets a constraint on the provided mathematical expression of column variables. |
void |
CplexSolver.setObjectiveFunction(MathExpr<? extends C> objective)
Sets the objective function to the provided mathematical expression of column variables. |
void |
CplexSolver.setObjectiveFunction(MathExpr<? extends C> objective,
OptSense sense)
Sets the objective function and optimization sense to the provided values. |
Method parameters in sbrt.ext.cplex with type arguments of type MathExpr | |
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void |
CplexSolver.setConstraints(java.util.Map<? extends MathExpr<? extends C>,Interval> exprConstraints)
Sets constraints on the provided mathematical expressions of column variables. |
Uses of MathExpr in sbrt.ext.glpk |
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Methods in sbrt.ext.glpk with parameters of type MathExpr | |
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void |
GlpkSolver.setConstraint(MathExpr<? extends C> expression,
Interval c)
Sets a constraint on the provided mathematical expression of column variables. |
void |
GlpkSolver.setObjectiveFunction(MathExpr<? extends C> expression)
Sets the objective function to the provided mathematical expression of column variables. |
void |
GlpkSolver.setObjectiveFunction(MathExpr<? extends C> expression,
OptSense sense)
Sets the objective function and optimization sense to the provided values. |
Method parameters in sbrt.ext.glpk with type arguments of type MathExpr | |
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void |
GlpkSolver.setConstraints(java.util.Map<? extends MathExpr<? extends C>,Interval> expressionConstraints)
Sets constraints on the provided mathematical expressions of column variables. |
Uses of MathExpr in sbrt.kernel.fba |
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Methods in sbrt.kernel.fba that return types with arguments of type MathExpr | |
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UnmodifiableMap<MathExpr<java.lang.String>,Interval> |
FluxConstraints.getExprConstraints()
Returns the constraints for mathematical expressions of fluxes. |
Methods in sbrt.kernel.fba with parameters of type MathExpr | |
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Interval |
FluxConstraints.getConstraint(MathExpr<java.lang.String> rxnExpr)
Returns the constraint of the provided mathematical expression of reaction names. |
Interval |
MixedFluxomeV1.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the constraint associated with the expression provided. |
Interval |
Fluxome.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the constraint corresponding to the provided mathematical expression of reaction names. |
Interval |
IrrevRxnFluxomeV1.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the constraint associated with the expression provided. |
Constructor parameters in sbrt.kernel.fba with type arguments of type MathExpr | |
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FluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints,
java.util.Map<? extends MathExpr<java.lang.String>,Interval> exprConstraints)
Constructs a set of FBA constraints from the provided arguments. |
Uses of MathExpr in sbrt.kernel.fba.comp |
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Methods in sbrt.kernel.fba.comp with type parameters of type MathExpr | ||
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FbaOptimizer.getMaxima(java.util.Collection<E> objectives)
Computes the maximum value of each provided objective function. |
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FbaOptimizer.getMinima(java.util.Collection<E> objectives)
Computes the minimum value of each provided objective function. |
Methods in sbrt.kernel.fba.comp that return MathExpr | |
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MathExpr<java.lang.String> |
FluxCapException.getFluxCap()
Returns the invalid flux cap. |
MathExpr<java.lang.String> |
RxnDeletionComputer.getObjectiveFunction()
Returns the current objective function. |
MathExpr<?> |
FbaOptException.getObjFunction()
Returns the objective function whose optimal value could not be found. |
Methods in sbrt.kernel.fba.comp that return types with arguments of type MathExpr | |
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java.util.Map<MathExpr<?>,Interval> |
FbaOptimizer.getColExprConstraints()
Returns all current constraints on mathematical expressions of column variables. |
java.util.Set<MathExpr<?>> |
FbaOptimizer.getColExprs()
Returns the set of all mathematical expressions of column variables. |
java.util.Map<MathExpr<java.lang.String>,Interval> |
RxnDeletionComputer.getRxnExprConstraints()
Returns the set of all constraints on mathematical expressions of fluxes. |
java.util.Map<MathExpr<java.lang.String>,Interval> |
InitialPointComputer.getRxnExprConstraints()
Returns all current flux expression constraints. |
java.util.Map<? extends MathExpr<java.lang.String>,Interval> |
FluxCvComputer.getRxnExprConstraints()
Returns all current flux expression constraints. |
java.util.Map<MathExpr<java.lang.String>,Interval> |
AbstractFluxIntervalComputer.getRxnExprConstraints()
Returns all current flux expression constraints. |
java.util.Map<MathExpr<java.lang.String>,Interval> |
FbaOptimizer.getRxnExprConstraints()
Returns all current constraints on mathematical expressions of reaction names. |
java.util.Set<MathExpr<java.lang.String>> |
FbaOptimizer.getRxnExprs()
Returns the set of all mathematical expressions of reaction names. |
Methods in sbrt.kernel.fba.comp with parameters of type MathExpr | |
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protected void |
FbaOptimizer.checkColExpr(MathExpr<?> e)
Ensures all the variables in the provided expression are valid column variables. |
protected void |
AbstractCvComputer.checkRxnExpr(MathExpr<java.lang.String> e)
Ensures the expression is valid for the fluxome provided. |
protected void |
FbaOptimizer.checkRxnExpr(MathExpr<java.lang.String> e)
Ensures all the variables in the provided expression are reaction names. |
protected double |
AbstractFluxIntervalComputer.getBoundedMax(MathExpr<java.lang.String> rxnNameExpr)
Computes the maximum value of the provided objective function. |
protected double |
AbstractFluxIntervalComputer.getBoundedMin(MathExpr<java.lang.String> rxnNameExpr)
Computes the minimum value of the provided objective function. |
Interval |
FbaOptimizer.getColExprConstraint(MathExpr<?> columnVariableExpr)
Returns the current constraint on the provided expression. |
FbaOptimizer.Results |
FbaOptimizer.getMax(MathExpr<?> objective)
Returns the results of computing the maximum value of the provided objective function. |
double |
FbaOptimizer.getMaximum(MathExpr<?> objective)
Computes the maximum value of the provided objective function. |
protected double |
AbstractFluxIntervalComputer.getMaximum(MathExpr<java.lang.String> rxnNameExpr)
Computes the maximum value of the provided objective function. |
FbaOptimizer.Results |
FbaOptimizer.getMin(MathExpr<?> objective)
Returns the results of computing the minimum value of the provided objective function. |
double |
FbaOptimizer.getMinimum(MathExpr<?> objective)
Computes the minimum value of the provided objective function. |
protected double |
AbstractFluxIntervalComputer.getMinimum(MathExpr<java.lang.String> rxnNameExpr)
Computes the minimum value of the provided objective function. |
FbaOptimizer.Results |
FbaOptimizer.getOptimal(MathExpr<?> objective,
OptSense sense)
Returns the results of computing the optimal value of the provided objective function. |
Interval |
RxnDeletionComputer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the constraint on the provided mathematical expression of fluxes. |
Interval |
InitialPointComputer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
Interval |
FluxCvComputer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
Interval |
AbstractFluxIntervalComputer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
Interval |
CdHarFluxComp.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
Interval |
FbaOptimizer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the current constraint on the provided expression. |
void |
FbaOptimizer.restoreColExprConstraint(MathExpr<?> columnVarExpr)
Restores the constraint on the provided expression of column variables to the value contained in the fluxome. |
void |
RxnDeletionComputer.restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Restores the constraint on the provided flux expression to the value contained in the fluxome. |
void |
InitialPointComputer.restoreRxnExprConstraint(MathExpr<java.lang.String> expr)
Restores the constraint on the provided flux expression to the value contained in the fluxome. |
void |
FluxCvComputer.restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Restores the constraint on the provided flux expression to the value contained in the fluxome. |
void |
AbstractFluxIntervalComputer.restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Restores the constraint on the provided flux expression to the value contained in the fluxome. |
void |
CdHarFluxComp.restoreRxnExprConstraint(MathExpr<java.lang.String> expr)
Restores the constraint on the provided flux expression to the value contained in the fluxome. |
void |
FbaOptimizer.restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Restores the constraint on the provided flux expression to the value contained in the fluxome. |
void |
FbaOptimizer.setColExprConstraint(MathExpr<?> expr,
Interval c)
Changes the constraint on the provided mathematical expression of column variables. |
void |
RxnDeletionComputer.setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
RxnDeletionComputer.setRxnExprConstraint(MathExpr<java.lang.String> e,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
InitialPointComputer.setRxnExprConstraint(MathExpr<java.lang.String> e,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
FluxCvComputer.setRxnExprConstraint(MathExpr<java.lang.String> e,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
AbstractFluxIntervalComputer.setRxnExprConstraint(MathExpr<java.lang.String> e,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
CdHarFluxComp.setRxnExprConstraint(MathExpr<java.lang.String> rxnExpr,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
FbaOptimizer.setRxnExprConstraint(MathExpr<java.lang.String> expr,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
Method parameters in sbrt.kernel.fba.comp with type arguments of type MathExpr | |
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void |
FbaOptimizer.restoreColExprConstraints(java.util.Collection<? extends MathExpr<?>> colVarExprs)
Restores the constraints for the provided column variable expressions to those in the provided fluxome. |
void |
InitialPointComputer.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 |
FluxCvComputer.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 |
AbstractCvComputer.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 |
AbstractFluxIntervalComputer.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 |
FbaOptimizer.restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExprs)
Restores the constraints for the provided reaction name expressions to those in the provided fluxome. |
void |
FbaOptimizer.setColExprConstraints(java.util.Map<? extends MathExpr<?>,Interval> exprConstraints)
Changes the constraints on more than one mathematical expression of column variables. |
void |
InitialPointComputer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
Changes the constraints on more than one mathematical expression of fluxes. |
void |
FluxCvComputer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
Changes the constraints on more than one mathematical expression of fluxes. |
void |
AbstractCvComputer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
Changes the constraints on more than one mathematical expression of fluxes. |
void |
AbstractFluxIntervalComputer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
Changes the constraints on more than one mathematical expression of fluxes. |
void |
FbaOptimizer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> exprConstraints)
Changes the constraints on more than one mathematical expression of fluxes. |
Constructors in sbrt.kernel.fba.comp with parameters of type MathExpr | |
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FbaOptException(MathExpr<?> objectiveFunction,
OptSense sense,
ProgramSolverStatus status)
Constructs a new FBA optimization exception. |
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FbaOptException(MathExpr<?> objectiveFunction,
OptSense sense,
ProgramSolverStatus status,
java.lang.String message)
Constructs a new FBA optimization exception. |
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FluxCapException(MathExpr<java.lang.String> fluxCap,
java.lang.String reactionName)
Constructs a new flux cap exception. |
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FluxCapException(MathExpr<java.lang.String> fluxCap,
java.lang.String reactionName,
java.lang.Throwable cause)
Constructs a new flux cap exception. |
Uses of MathExpr in sbrt.kernel.fba.proc |
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Methods in sbrt.kernel.fba.proc that return MathExpr | |
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MathExpr<java.lang.String> |
CvFbaOptProcess.getObjectiveFunction()
Returns the current objective function. |
MathExpr<java.lang.String> |
CatalystDeletionProcess.getObjectiveFunction()
Returns the current objective function. |
MathExpr<java.lang.String> |
RxnDeletionProcess.getObjectiveFunction()
Returns the current objective function. |
MathExpr<java.lang.String> |
CvRxnDeletionProcess.getObjectiveFunction()
Returns the current objective function. |
MathExpr<java.lang.String> |
CvCatalystDeletionProcess.getObjectiveFunction()
Returns the current objective function. |
Methods in sbrt.kernel.fba.proc with parameters of type MathExpr | |
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void |
CvFbaOptProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
CatalystDeletionProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
RxnDeletionProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
CvRxnDeletionProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
void |
CvCatalystDeletionProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
Sets the objective function to the provided mathematical expression. |
Method parameters in sbrt.kernel.fba.proc with type arguments of type MathExpr | |
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void |
CvObjectiveFunctionProcess.setObjectiveFunctionSource(java.lang.Iterable<? extends MathExpr<java.lang.String>> objectiveSource)
Sets the objective function input source. |
void |
ObjFunAnalysis.setObjectiveFunctionSource(java.lang.Iterable<? extends MathExpr<java.lang.String>> objectiveSource)
Sets the objective function input source. |
Uses of MathExpr in sbrt.kernel.math |
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Subinterfaces of MathExpr in sbrt.kernel.math | |
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interface |
LinearComb<V>
This interface is used to represent linear combinations. |
interface |
Polynomial<V>
This interface is used to represent polynomials. |
interface |
QuadraticExpr<V>
This interface is used to represent quadratic expressions. |
Classes in sbrt.kernel.math that implement MathExpr | |
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class |
AbstractLinearComb<V>
This abstract class is a skeleton implementation of LinearComb. |
class |
AbstractPolynomial<V>
This abstract class is a skeleton implementation of Polynomial. |
class |
HashLinearComb<V>
This class is a concrete implemenation of LinearComb. |
Methods in sbrt.kernel.math that return MathExpr | |
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MathExpr<V> |
MathExpr.plugInNumbers(java.util.Map<?,java.lang.Double> variableValues)
Plugs in the provided numerical values to produce a new mathematical expression. |
Uses of MathExpr in sbrt.kernel.math.optimization |
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Methods in sbrt.kernel.math.optimization with parameters of type MathExpr | |
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void |
ProgramSolver.setConstraint(MathExpr<? extends C> expression,
Interval c)
Sets a constraint on the provided mathematical expression of column variables. |
void |
ProgramSolver.setObjectiveFunction(MathExpr<? extends C> expression)
Sets the objective function to the provided mathematical expression of column variables. |
void |
ProgramSolver.setObjectiveFunction(MathExpr<? extends C> expression,
OptSense sense)
Sets the objective function and optimization sense to the provided values. |
Method parameters in sbrt.kernel.math.optimization with type arguments of type MathExpr | |
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void |
ProgramSolver.setConstraints(java.util.Map<? extends MathExpr<? extends C>,Interval> expressionConstraints)
Sets constraints on the provided mathematical expressions of column variables. |
Uses of MathExpr in sbrt.kernel.utilities.proc |
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Classes in sbrt.kernel.utilities.proc with type parameters of type MathExpr | |
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class |
VariableParticipation<E extends MathExpr<V>,V>
This class is used to organize a collection of mathematical expressions according to the variables they contain. |
Uses of MathExpr in sbrt.shell.io.fba |
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Classes in sbrt.shell.io.fba with type parameters of type MathExpr | |
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class |
RxnNamExprSetInputFile<E extends MathExpr<S>,S>
This class is used to read files containing a set of reaction name expressions. |
Uses of MathExpr in sbrt.shell.text.fba |
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Classes in sbrt.shell.text.fba with type parameters of type MathExpr | |
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interface |
RxnNameExprFormat<E extends MathExpr<S>,S>
This interface is used to represent formats for mathematical expressions of reaction names. |
Uses of MathExpr in sbrt.shell.text.math |
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Classes in sbrt.shell.text.math with type parameters of type MathExpr | |
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interface |
MathExprFormat<E extends MathExpr<V>,V>
This interface is used to represent formats for linear combinations. |
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