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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectsbrt.kernel.fba.comp.FbaOptComputer
public final class FbaOptComputer
This class is the workhorse of all Flux Balance Analysis optimizations. It provides an interface for communication between FBA experiments and program solvers.
Nested Class Summary | |
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class |
FbaOptComputer.Results
This class is used to store the results of an FBA optimization problem. |
Field Summary | |
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static double |
DEFAULT_CONST_TOL
The default constraint tolerance. |
static int |
DEFAULT_SAFETY_LEVEL
The default saftey level. |
Constructor Summary | |
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FbaOptComputer(IrrevRxnFluxome fluxome,
ProgramSolver<java.lang.Object,java.lang.Object> solver)
Constructs a new FBA optimization computer from the provided fluxome and program solver. |
|
FbaOptComputer(IrrevRxnFluxome fluxome,
ProgramSolver<java.lang.Object,java.lang.Object> solver,
double constraintTolerance)
Constructs a new FBA optimization computer from the provided fluxome, program solver, and constraint tolerance. |
Method Summary | ||
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protected void |
checkChemSpecies(java.lang.String string)
Ensures the provided string is the name of a chemical species in the fluxome used by this optimization computer. |
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protected void |
checkColExpr(MathExpr<?> e)
Ensures all the variables in the provided expression are valid column variables. |
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protected void |
checkColumnValue(java.lang.Object columnVariable,
double value)
Ensures the provided numerical value does not violate the defined constraint of the provided column variable. |
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protected void |
checkColumnValue(java.lang.Object columnVariable,
java.lang.Double value)
Ensures the provided numerical value does not violate the defined constraint of the provided column variable. |
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protected void |
checkColumnVariable(java.lang.Object obj)
Ensures the provided object is column variable. |
|
protected void |
checkColumnVariables(java.util.Collection<?> c)
Ensures each element of the provided collection is column variable. |
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protected void |
checkFluxConstraint(Interval c,
java.lang.String rxnName,
double tolerance)
Ensures the provided constraint is a valid flux constraint in the fluxome used by this optimization computer. |
|
protected void |
checkNumber(double number)
Ensures the provided number is finite and not NaN. |
|
protected void |
checkRowVariable(java.lang.Object obj)
Ensures the provided object is row variable. |
|
protected void |
checkRxnExpr(MathExpr<java.lang.String> e)
Ensures all the variables in the provided expression are reaction names. |
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protected void |
checkRxnExprConstraint(Interval c)
Ensures the provided constraint is valid for reaction name-expressions for the fluxome used by this optimization computer. |
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protected void |
checkRxnName(java.lang.String string)
Ensures the provided string is the name of a reaction in the fluxome used by this optimization computer. |
|
protected void |
checkRxnNames(java.util.Collection<java.lang.String> c)
Ensures each element of the provided collection is reaction name. |
|
protected void |
checkSolutionVector(java.util.Map<?,java.lang.Double> solutionVector)
Ensures the provided solution vector does not violate the defined constraints of the system. |
|
Interval |
getColExprConstraint(MathExpr<?> columnVariableExpr)
Returns the current constraint on the provided expression. |
|
java.util.Map<MathExpr<?>,Interval> |
getColExprConstraints()
Returns all current constraints on mathematical expressions of column variables. |
|
java.util.Set<MathExpr<?>> |
getColExprs()
Returns the set of all mathematical expressions of column variables. |
|
Interval |
getColumnConstraint(java.lang.Object columnVariable)
Returns the current constraint on the provided column variable. |
|
java.util.Map<?,Interval> |
getColumnConstraints()
Returns the current constraints for each column variable in the program matrix. |
|
double |
getColumnMax(java.lang.Object columnVariable)
Computes the maximum value of the provided column variable. |
|
|
getColumnMaxima(java.util.Collection<T> columnVariables)
Computes the maximum values of each provided column variable. |
|
double |
getColumnMin(java.lang.Object columnVariable)
Computes the minimum value of the provided column variable. |
|
|
getColumnMinima(java.util.Collection<T> columnVariables)
Computes the minimum values of each provided column variable. |
|
java.util.Set<?> |
getColumnVariables()
Returns the set of all column variables in the program matrix. |
|
protected
|
getExpr(java.util.Collection<V> columnVariables)
Converts a collection of column variables to a linear combination. |
|
protected
|
getExpr(V columnVariable)
Converts a column variable to a single-term linear combination. |
|
Interval |
getFluxConstraint(java.lang.String reactionName)
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 for each reaction in the fluxome used by this optimization computer. |
|
double |
getFluxMax(java.lang.String reactionName)
Computes the maximum flux of the reaction with the provided name. |
|
java.util.Map<java.lang.String,java.lang.Double> |
getFluxMaxima(java.util.Collection<java.lang.String> reactionNames)
Computes the maximum flux of each reaction with the provided names. |
|
double |
getFluxMin(java.lang.String reactionName)
Computes the minimum flux of the reaction with the provided name. |
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java.util.Map<java.lang.String,java.lang.Double> |
getFluxMinima(java.util.Collection<java.lang.String> reactionNames)
Computes the minimum flux of each reaction with the provided names. |
|
IrrevRxnFluxome |
getFluxome()
Returns the fluxome used by this optimization computer. |
|
FbaOptComputer.Results |
getMax(MathExpr<?> objective)
Returns the results of computing the maximum value of the provided objective function. |
|
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getMaxima(java.util.Collection<E> objectives)
Computes the maximum value of each provided objective function. |
|
double |
getMaximum(MathExpr<?> objective)
Computes the maximum value of the provided objective function. |
|
FbaOptComputer.Results |
getMin(MathExpr<?> objective)
Returns the results of computing the minimum value of the provided objective function. |
|
|
getMinima(java.util.Collection<E> objectives)
Computes the minimum value of each provided objective function. |
|
double |
getMinimum(MathExpr<?> objective)
Computes the minimum value of the provided objective function. |
|
FbaOptComputer.Results |
getOptimal(MathExpr<?> objective,
OptimizationSense sense)
Returns the results of computing the optimal value of the provided objective function. |
|
FbaOptComputer.Results |
getOptimal(java.lang.String reactionName,
OptimizationSense sense)
Returns the results of computing the optimal flux of the reaction with the provided name. |
|
java.lang.Class |
getProgramSolverType()
Returns the Class of the program solver used by this
optimization computer. |
|
Interval |
getRowConstraint(java.lang.Object rowVariable)
Returns the current constraint on the provided row variable. |
|
java.util.Map<?,Interval> |
getRowConstraints()
Returns all the current constraints on row variables. |
|
java.util.Set<?> |
getRowVariables()
Returns the set of all row variables in the program matrix. |
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protected LinearComb<java.lang.String> |
getRxnExpr(java.util.Collection<java.lang.String> rxnNames)
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. |
|
Interval |
getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the current constraint on the provided expression. |
|
java.util.Map<MathExpr<java.lang.String>,Interval> |
getRxnExprConstraints()
Returns all current constraints on mathematical expressions of reaction names. |
|
java.util.Set<MathExpr<java.lang.String>> |
getRxnExprs()
Returns the set of all mathematical expressions of reaction names. |
|
double |
getTolerance()
Returns the allowable amount by which column variables may violate their defined constraints. |
|
void |
restoreColExprConstraint(MathExpr<?> columnVarExpr)
Restores the constraint on the provided expression of column variables to the value contained in the fluxome. |
|
void |
restoreColExprConstraints()
Restores the constraints on all mathematical expressions of column variables. |
|
void |
restoreColExprConstraints(java.util.Collection<? extends MathExpr<?>> colVarExprs)
Restores the constraints for the provided column variable expressions to those in the provided fluxome. |
|
void |
restoreColumnConstraint(java.lang.Object columnVariable)
Restores the constraint for the provided column variable to the value contained in the fluxome. |
|
void |
restoreColumnConstraints()
Restores the constraints on all column variables to those contained in the fluxome used by this optimization computer. |
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void |
restoreColumnConstraints(java.util.Collection<?> columnVariables)
Restores the constraints for the provided column variables to those in the provided fluxome. |
|
void |
restoreFluxConstraint(java.lang.String reactionName)
Restores the flux constraint for the reaction with the provided name to the value contained in the fluxome. |
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void |
restoreFluxConstraints()
Restores the flux constraints for all reactions to those contained in the fluxome used by this optimization computer. |
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void |
restoreFluxConstraints(java.util.Collection<java.lang.String> reactionNames)
Restores the constraints for the provided reaction names to those in the provided fluxome. |
|
void |
restoreMatrixElements()
Restores the program matrix to the stoichiometry matrix of the fluxome used by this computer. |
|
void |
restoreRowConstraint(java.lang.Object rowVariable)
Restores the constraint on the provided row variable. |
|
void |
restoreRowConstraints()
Restores the constraints on all row variables to those contained in the fluxome used by this optimization computer. |
|
void |
restoreRowConstraints(java.util.Collection<?> rowVariables)
Restores the constraints for the provided row variables to those in the provided 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 mathematical expressions of reaction names. |
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void |
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 |
setColExprConstraint(MathExpr<?> expr,
Interval c)
Changes the constraint on the provided mathematical expression of column variables. |
|
void |
setColExprConstraints(java.util.Map<? extends MathExpr<?>,Interval> exprConstraints)
Changes the constraints on more than one mathematical expression of column variables. |
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void |
setColumnConstraint(java.lang.Object columnVar,
Interval c)
Changes the constraint of the provided column variable. |
|
void |
setColumnConstraints(java.util.Map<?,Interval> columnConstraints)
Changes the constraints on more than one column variable. |
|
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 |
setMatrixElement(java.lang.Object rowVar,
java.lang.Object columnVar,
double value)
Sets the specified element of the program matrix to the one provided. |
|
void |
setMatrixElements(DoubleMatrix<?,?> elements)
Sets the specified elements of the program matrix to those provided. |
|
void |
setRowConstraint(java.lang.Object rowVariable,
Interval c)
Changes the constraint of the provided row variable. |
|
void |
setRowConstraints(java.util.Map<?,Interval> rowConstraints)
Changes the constraints on more than one row variable. |
|
void |
setRxnExprConstraint(MathExpr<java.lang.String> expr,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
|
void |
setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> exprConstraints)
Changes the constraints on more than one mathematical expression of fluxes. |
|
void |
setSafetyLevel(int level)
Sets the safety level. |
|
void |
setTolerance(double constraintTolerance)
Sets the constraint tolerance. |
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 int DEFAULT_SAFETY_LEVEL
public static final double DEFAULT_CONST_TOL
Constructor Detail |
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public FbaOptComputer(IrrevRxnFluxome fluxome, ProgramSolver<java.lang.Object,java.lang.Object> solver)
fluxome
- the fluxome for which all values will be computed.solver
- the program solver used to compute all values.public FbaOptComputer(IrrevRxnFluxome fluxome, ProgramSolver<java.lang.Object,java.lang.Object> solver, double constraintTolerance)
fluxome
- the fluxome for which all values will be computed.solver
- the program solver used to compute all values.constraintTolerance
- the allowed amount by which
computed values can violate their defined constraints.Method Detail |
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public void setSafetyLevel(int level)
level
- the saftey level.
java.lang.IllegalArgumentException
- if the provided value does not
equal 0 or 1.DEFAULT_SAFETY_LEVEL
,
setTolerance(double)
public void setTolerance(double constraintTolerance)
constraintTolerance
- the amount by which computed values can
violate their defined constraints.
java.lang.IllegalArgumentException
- if the provided value is NaN,
infinite, or less than 0.setSafetyLevel(int)
public double getTolerance()
public java.lang.Class getProgramSolverType()
Class
of the program solver used by this
optimization computer.
Class
of the program solver used by this
optimization computer.public IrrevRxnFluxome getFluxome()
getFluxome
in interface FluxCvComputer
public final void setMatrixElement(java.lang.Object rowVar, java.lang.Object columnVar, double value)
rowVar
- the row variable.columnVar
- the column variable.value
- the new value.
java.lang.IllegalArgumentException
- if value
is infinite or NaN.
java.lang.NullPointerException
- if either variable is null
.public final void setMatrixElements(DoubleMatrix<?,?> elements)
elements
- a matrix containing the elements to be set.
java.lang.IllegalArgumentException
- if value
is infinite or NaN.
java.lang.NullPointerException
- if either variable is null
.public final void restoreMatrixElements()
public final void setColumnConstraint(java.lang.Object columnVar, Interval c)
columnVar
- the column variable in the program matrix whose
constraint is to be changed.c
- the new constraint.
java.lang.IllegalArgumentException
- if columnVar
is not a column
variable in the program matrix.
java.lang.NullPointerException
- if the provided constraint is null
.setFluxConstraint(String, Interval)
public final void setFluxConstraint(java.lang.String reactionName, Interval c)
setFluxConstraint
in interface FluxCvComputer
reactionName
- the name of the reaction whose flux constraint
is to be changed.c
- the new constraint.
java.lang.IllegalArgumentException
- if reactionName
is not the name
of a reaction in the fluxome used by this computer.
java.lang.NullPointerException
- if the provided constraint is null
.setColumnConstraint(Object, Interval)
public final void setRxnExprConstraint(MathExpr<java.lang.String> expr, Interval c)
setRxnExprConstraint
in interface FluxCvComputer
expr
- a matheamtical expression of reaction names.c
- the new constraint.
java.lang.IllegalArgumentException
- if the variables in the provided
expressions are not the names of reactions in the fluxome used by this
computer.
java.lang.NullPointerException
- if either argument is null
.public final void setColExprConstraint(MathExpr<?> expr, Interval c)
expr
- a mathematical expression of column variables from the
program matrix.c
- the new constraint.
java.lang.IllegalArgumentException
- if the variables in the provided
expressions are not column variables of the program matrix.
java.lang.NullPointerException
- if either argument is null
.public final void setRowConstraint(java.lang.Object rowVariable, Interval c)
rowVariable
- the row variable in the program matrix whose
constraint is to be changed.c
- the new constraint.
java.lang.IllegalArgumentException
- if rowVariable
is not a row
variable of the program matrix.
java.lang.NullPointerException
- if the provided constraint is null
.public final void setColumnConstraints(java.util.Map<?,Interval> columnConstraints)
columnConstraints
- column variables mapped to their respective
constraints.public final void setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
setFluxConstraints
in interface FluxCvComputer
fluxConstraints
- reaction names mapped to their respective flux
constraints.public final void setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> exprConstraints)
setRxnExprConstraints
in interface FluxCvComputer
exprConstraints
- mathematical expressions of reaction names
mapped to their new respective constraints.public final void setColExprConstraints(java.util.Map<? extends MathExpr<?>,Interval> exprConstraints)
exprConstraints
- mathematical expressions of column variables
mapped to their new respective constraints.public final void setRowConstraints(java.util.Map<?,Interval> rowConstraints)
rowConstraints
- row variables mapped to their respective
constraints.public final void restoreColumnConstraint(java.lang.Object columnVariable)
columnVariable
- the column variable whose constraint
is to be restored.public final void restoreFluxConstraint(java.lang.String reactionName)
restoreFluxConstraint
in interface FluxCvComputer
reactionName
- the name of the reaction whose flux constraint
is to be restored.public final void restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
restoreRxnExprConstraint
in interface FluxCvComputer
rxnNameExpr
- the expression of reaction names whose contraint
is to be restored.public final void restoreColExprConstraint(MathExpr<?> columnVarExpr)
columnVarExpr
- the expression of column variables whose contraint
is to be restored.public final void restoreRowConstraint(java.lang.Object rowVariable)
rowVariable
- a row variable from the program matrix.public final void restoreColumnConstraints(java.util.Collection<?> columnVariables)
columnVariables
- a collection of column variables.restoreColumnConstraint(Object)
public final void restoreFluxConstraints(java.util.Collection<java.lang.String> reactionNames)
restoreFluxConstraints
in interface FluxCvComputer
reactionNames
- a collection of reaction names.restoreFluxConstraint(String)
public final void restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExprs)
restoreRxnExprConstraints
in interface FluxCvComputer
rxnNameExprs
- a collection of mathematical expressions of reaction
names.restoreRxnExprConstraint(MathExpr)
public final void restoreColExprConstraints(java.util.Collection<? extends MathExpr<?>> colVarExprs)
colVarExprs
- a collection of mathematical expressions of column
variables.restoreColExprConstraint(MathExpr)
public final void restoreRowConstraints(java.util.Collection<?> rowVariables)
rowVariables
- a collection of row variables.restoreRowConstraint(Object)
public final void restoreColumnConstraints()
restoreColumnConstraint(Object)
public final void restoreFluxConstraints()
restoreFluxConstraints
in interface FluxCvComputer
restoreFluxConstraint(String)
public final void restoreRxnExprConstraints()
restoreRxnExprConstraints
in interface FluxCvComputer
restoreRxnExprConstraint(MathExpr)
public final void restoreColExprConstraints()
restoreColExprConstraint(MathExpr)
public final void restoreRowConstraints()
restoreRowConstraint(Object)
public java.util.Set<?> getColumnVariables()
public java.util.Set<MathExpr<java.lang.String>> getRxnExprs()
public java.util.Set<MathExpr<?>> getColExprs()
public java.util.Set<?> getRowVariables()
public Interval getColumnConstraint(java.lang.Object columnVariable)
columnVariable
- the column variable whose constraint
is to be returned.
public Interval getFluxConstraint(java.lang.String reactionName)
getFluxConstraint
in interface FluxCvComputer
reactionName
- the name of the reaction whose flux constraint
is to be returned.
public Interval getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
getRxnExprConstraint
in interface FluxCvComputer
rxnNameExpr
- the mathematical expression of reaction names
whose constraint is to be returned.
public Interval getColExprConstraint(MathExpr<?> columnVariableExpr)
columnVariableExpr
- the mathematical expression of column
variables whose constraint is to be returned.
public Interval getRowConstraint(java.lang.Object rowVariable)
rowVariable
- the row variable whose constraint
is to be returned.
public java.util.Map<?,Interval> getColumnConstraints()
public java.util.Map<java.lang.String,Interval> getFluxConstraints()
getFluxConstraints
in interface FluxCvComputer
public java.util.Map<MathExpr<?>,Interval> getColExprConstraints()
public java.util.Map<MathExpr<java.lang.String>,Interval> getRxnExprConstraints()
getRxnExprConstraints
in interface FluxCvComputer
public java.util.Map<?,Interval> getRowConstraints()
public final FbaOptComputer.Results getOptimal(java.lang.String reactionName, OptimizationSense sense)
reactionName
- the name of the reaction whose flux is to be
optimized.sense
- the sense, or direction, of optimization.
public final FbaOptComputer.Results getOptimal(MathExpr<?> objective, OptimizationSense sense)
objective
- a mathematical expression of column variables.sense
- the sense, or direction, of optimization.
public final FbaOptComputer.Results getMax(MathExpr<?> objective)
objective
- a mathematical expression of column variables.
public final FbaOptComputer.Results getMin(MathExpr<?> objective)
objective
- a mathematical expression of column variables.
public double getMaximum(MathExpr<?> objective)
objective
- a mathematical expression
whose variables are column variables in the program matrix.
java.lang.NullPointerException
- if the provided expression is null.
FbaOptException
- if an optimal solution cannot be found.
java.lang.IllegalArgumentException
- if the provided expression
contains a variable that is not a column variable
in the program matrix.public double getFluxMax(java.lang.String reactionName)
reactionName
- the name of the reaction whose
maximum flux will be computed.
java.lang.IllegalArgumentException
- if the provided string
is not a reaction name of the fluxome used by this optimization
computer.public double getColumnMax(java.lang.Object columnVariable)
columnVariable
- a column variable from the program
matrix whose maximum value is to be computed.
java.lang.IllegalArgumentException
- if the provided object
is not a column variable in the program matrix.public <V,E extends MathExpr<V>> java.util.Map<E,java.lang.Double> getMaxima(java.util.Collection<E> objectives)
V
- the variable type.E
- the mathematical expression type.objectives
- a collection of mathematical
expressions whose variables are column variables in the program
matrix.
java.lang.NullPointerException
- if the provided collection, or any
of its elements, is null
.
java.lang.IllegalArgumentException
- if one of the provided
mathematical expressions contains a variable that is not a
column variable.public java.util.Map<java.lang.String,java.lang.Double> getFluxMaxima(java.util.Collection<java.lang.String> reactionNames)
reactionNames
- a collection of reaction names from
the fluxome used by this optimization computer.
java.lang.NullPointerException
- if the provided collection
is null
.
java.lang.IllegalArgumentException
- if an element in the provided
collection is not a reaction name.public <T> java.util.Map<T,java.lang.Double> getColumnMaxima(java.util.Collection<T> columnVariables)
T
- the column variable type.columnVariables
- a collection of column variables in
the program matrix.
java.lang.IllegalArgumentException
- if an element in the provided
collection is not a legitimate column variable.public double getMinimum(MathExpr<?> objective)
objective
- a mathematical expression
whose variables are column variables in the program matrix.
java.lang.IllegalArgumentException
- if a variable in the
provided expression is not a column variable
in the program matrix.public double getFluxMin(java.lang.String reactionName)
reactionName
- a reaction name from the fluxome
used by this optimization computer.
java.lang.IllegalArgumentException
- if the provided string
is not a reaction name.public double getColumnMin(java.lang.Object columnVariable)
columnVariable
- a column variable from the program
matrix.
java.lang.IllegalArgumentException
- if the provided object
is not a column variable in the program matrix.public <V,E extends MathExpr<V>> java.util.Map<E,java.lang.Double> getMinima(java.util.Collection<E> objectives)
V
- the variable type.E
- the mathematical expression type.objectives
- a collection of mathematical
expressions whose variables are column variables in the program
matrix.
java.lang.NullPointerException
- if the provided collection, or any
of its elements, is null
.
java.lang.IllegalArgumentException
- if one of the provided
mathematical expressions contains a variable that is not a
column variable.public java.util.Map<java.lang.String,java.lang.Double> getFluxMinima(java.util.Collection<java.lang.String> reactionNames)
reactionNames
- a collection of reaction names from
the fluxome used by this optimization computer.
java.lang.NullPointerException
- if the provided collection
is null
.
java.lang.IllegalArgumentException
- if an element in the provided
collection is not a reaction name.public <T> java.util.Map<T,java.lang.Double> getColumnMinima(java.util.Collection<T> columnVariables)
T
- the column variable type.columnVariables
- a collection of column variables in
the program matrix.
java.lang.IllegalArgumentException
- if an element in the provided
collection is not a legitimate column variable.protected void checkRowVariable(java.lang.Object obj)
obj
- the object to check.
java.lang.IllegalArgumentException
- if the provided object is not a row
variable in the program matrix.protected void checkColumnVariable(java.lang.Object obj)
obj
- the object to check.
java.lang.IllegalArgumentException
- if the provided object is not a column
variable in the program matrix.protected void checkColumnVariables(java.util.Collection<?> c)
c
- the collection of objects to check.
java.lang.IllegalArgumentException
- if an element in the provided
collection is not a column variable in the program matrix.protected void checkColExpr(MathExpr<?> e)
e
- the expression to check.
java.lang.IllegalArgumentException
- if a variable in the provided
expression is not a column variable in the program matrix.protected void checkRxnName(java.lang.String string)
string
- the string to check.
java.lang.IllegalArgumentException
- if the provided string
is not the name of a reaction in the fluxome used by this optimization
computer.protected void checkRxnNames(java.util.Collection<java.lang.String> c)
c
- the collection of strings to check.
java.lang.IllegalArgumentException
- if a string in the provided
collection is not the name of a reaction in the fluxome used by this
optimization computer.protected void checkRxnExpr(MathExpr<java.lang.String> e)
e
- the expression to check.
java.lang.IllegalArgumentException
- if a variable in the provided
expression is not the name of a reaction in the fluxome used by this
optimization computer.protected void checkNumber(double number)
number
- the number to check.
java.lang.IllegalArgumentException
- if the provided number is infinite
or NaN.protected void checkChemSpecies(java.lang.String string)
string
- the string to check.
java.lang.IllegalArgumentException
- if the provided string
is not the name of a chemical species in the fluxome used by this optimization
computer.protected void checkRxnExprConstraint(Interval c)
c
- the constraint to check.
java.lang.NullPointerException
- if the provided constraint is null
.protected void checkFluxConstraint(Interval c, java.lang.String rxnName, double tolerance)
c
- the constraint to check.rxnName
- the name of the reaction for which this constraint
applies.tolerance
- the allowable amount by which the bounds of the
provided constraint can violate the maximum bounds defined the
fluxome used by this optimization computer.
java.lang.IllegalArgumentException
- if the provided
constraint is not a valid flux constraint.protected <V> LinearComb<V> getExpr(V columnVariable)
V
- the column variable type.columnVariable
- a column variable from the
program matrix.
java.lang.IllegalArgumentException
- if the provided object
is not a column variable in the program matrix.protected LinearComb<java.lang.String> getRxnExpr(java.lang.String reactionName)
reactionName
- a reaction name from the fluxome
used to create this optimization computer.
java.lang.IllegalArgumentException
- if the provided string
is not a reaction name in the fluxome used by
this optimization computer.protected LinearComb<java.lang.String> getRxnExpr(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- a collection of reaction names from the fluxome
used by this optimization computer.
java.lang.IllegalArgumentException
- if an element in the provided
collection is not a reaction name in the fluxome used by
this optimization computer.protected <V> LinearComb<V> getExpr(java.util.Collection<V> columnVariables)
V
- the column variable type.columnVariables
- a collection of column variables contained
in the program matrix.
java.lang.IllegalArgumentException
- if an element in the provided
collection is not a column variable in the program matrix.protected void checkSolutionVector(java.util.Map<?,java.lang.Double> solutionVector)
solutionVector
- column variables mapped to their respective
numerical values.
ConstraintViolationException
- if a value in the
provided vector violates its defined constraints
by more than the defined constraint tolerance.
java.lang.IllegalArgumentException
- if a key in the provided
map is not a legitimate column variable in the program matrix.
java.lang.NullPointerException
- if a value in the provided
map is null
.protected void checkColumnValue(java.lang.Object columnVariable, java.lang.Double value)
columnVariable
- the column variable whose value and
constraint will be compared.value
- the numerical value of the provided column
variable.
ConstraintViolationException
- if the provided value
violates the defined constraint for the provided column variable
by more than the defined constraint tolerance.
java.lang.IllegalArgumentException
- if the provided
column variable does not exist in the program matrix.
java.lang.NullPointerException
- if the provided value is null
.protected void checkColumnValue(java.lang.Object columnVariable, double value)
columnVariable
- the column variable whose value and
constraint will be compared.value
- the numerical value of the provided column
variable.
ConstraintViolationException
- if the provided value
violates the defined constraint for the provided column variable
by more than the defined constraint tolerance.
java.lang.IllegalArgumentException
- if the provided
column variable does not exist in the program matrix.
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