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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectsbrt.kernel.fba.comp.FbaOptimizer<F>
F
- the fluxome type.public final class FbaOptimizer<F extends Fluxome>
This class is the workhorse of all Flux Balance Analysis optimizations. It provides an interface for communication between FBA processes and program solvers.
Nested Class Summary | |
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class |
FbaOptimizer.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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FbaOptimizer(F fluxome,
ProgramSolver<java.lang.Object,java.lang.Object> solver)
Constructs a new FBA optimization computer from the provided fluxome and program solver. |
|
FbaOptimizer(F 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. |
|
protected void |
checkColExpr(MathExpr<?> e)
Ensures all the variables in the provided expression are valid column variables. |
|
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. |
|
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. |
|
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. |
|
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. |
|
protected void |
checkRxnExprConstraint(Interval c)
Ensures the provided constraint is valid for reaction name-expressions for the fluxome used by this optimization computer. |
|
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. |
|
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. |
|
F |
getFluxome()
Returns the fluxome used by this optimization computer. |
|
FbaOptimizer.Results |
getMax(MathExpr<?> objective)
Returns the results of computing the maximum value of the provided objective function. |
|
|
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. |
|
FbaOptimizer.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. |
|
FbaOptimizer.Results |
getOptimal(MathExpr<?> objective,
OptSense sense)
Returns the results of computing the optimal value of the provided objective function. |
|
FbaOptimizer.Results |
getOptimal(java.lang.String reactionName,
OptSense 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. |
|
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. |
|
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. |
|
void |
restoreFluxConstraints()
Restores the flux constraints for all reactions to those contained in the fluxome used by this optimization computer. |
|
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. |
|
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. |
|
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 FbaOptimizer(F 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 FbaOptimizer(F 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 |
---|
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 F getFluxome()
getFluxome
in interface FluxCvComputer<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
restoreFluxConstraint(String)
public final void restoreRxnExprConstraints()
restoreRxnExprConstraints
in interface FluxCvComputer<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
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<F extends Fluxome>
public java.util.Map<MathExpr<?>,Interval> getColExprConstraints()
public java.util.Map<MathExpr<java.lang.String>,Interval> getRxnExprConstraints()
getRxnExprConstraints
in interface FluxCvComputer<F extends Fluxome>
public java.util.Map<?,Interval> getRowConstraints()
public final FbaOptimizer.Results getOptimal(java.lang.String reactionName, OptSense sense)
reactionName
- the name of the reaction whose flux is to be
optimized.sense
- the sense, or direction, of optimization.
public final FbaOptimizer.Results getOptimal(MathExpr<?> objective, OptSense sense)
objective
- a mathematical expression of column variables.sense
- the sense, or direction, of optimization.
public final FbaOptimizer.Results getMax(MathExpr<?> objective)
objective
- a mathematical expression of column variables.
public final FbaOptimizer.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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