Uses of Interface
sbrt.kernel.math.LinearComb

Packages that use LinearComb
sbrt.ext.cplex Provides a class that allows communication with CPLEX. 
sbrt.ext.glpk Provides a class that allows communication with GLPK. 
sbrt.ext.mma.algebra Provides classes that allow communication with Mathematica for the purposes of algebra. 
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.algebra Provides classes and interfaces for creating objects relevant to algebra. 
sbrt.kernel.math.algebra.proc Provides classes and interfaces for executing algebra-related processes. 
sbrt.kernel.math.geom Provides classes and interfaces for creating objects relevant to computational geometry. 
sbrt.kernel.math.optimization Provides classes and interfaces for creating objects relevant to solving optimization problems. 
sbrt.shell.io.fba Provides classes and interfaces for reading and writing files relevant to Flux Balance Analysis. 
sbrt.shell.mng.algebra Provides classes for creating algebra process managers. 
sbrt.shell.mng.fba Provides classes and interfaces for creating Flux Balance Analysis process managers. 
sbrt.shell.mng.utilities Provides classes and interfaces for creating mathematical process managers. 
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 LinearComb in sbrt.ext.cplex
 

Methods in sbrt.ext.cplex with parameters of type LinearComb
 void CplexSolver.setConstraint(LinearComb<? extends C> linComb, Interval c)
          Sets a constraint on the provided mathematical expression of column variables.
 void CplexSolver.setObjectiveFunction(LinearComb<? extends C> objective)
          Sets the objective function to the provided mathematical expression of column variables.
 void CplexSolver.setObjectiveFunction(LinearComb<? extends C> objective, OptSense sense)
          Sets the objective function and optimization sense to the provided values.
 

Uses of LinearComb in sbrt.ext.glpk
 

Methods in sbrt.ext.glpk with parameters of type LinearComb
 void GlpkSolver.setConstraint(LinearComb<? extends C> expression, Interval c)
          Sets a constraint on the provided mathematical expression of column variables.
 void GlpkSolver.setObjectiveFunction(LinearComb<? extends C> expression)
          Sets the objective function to the provided mathematical expression of column variables.
 void GlpkSolver.setObjectiveFunction(LinearComb<? extends C> expression, OptSense sense)
          Sets the objective function and optimization sense to the provided values.
 

Uses of LinearComb in sbrt.ext.mma.algebra
 

Methods in sbrt.ext.mma.algebra that return types with arguments of type LinearComb
protected static java.util.Map<java.lang.String,LinearComb<java.lang.String>> MMaExprInterpretter.interpretSolution(com.wolfram.jlink.Expr solution)
          Converts the provided Mathematica expression to a Map.
 

Method parameters in sbrt.ext.mma.algebra with type arguments of type LinearComb
 LinearSystemSolution<V> MathematicaSolver.solve(java.util.Map<LinearComb<V>,java.lang.Double> equations)
          Computes and returns a solution to the provided system of linear equations.
 

Uses of LinearComb in sbrt.kernel.fba
 

Methods in sbrt.kernel.fba that return LinearComb
 LinearComb<java.lang.String> RevExchRxn.getProducts()
          Returns a linear combination representing the products of this exchange reaction.
 LinearComb<java.lang.String> AbstractExchangeRxn.getProducts()
          Returns an empty linear combination.
 LinearComb<java.lang.String> AbstractRxn.getProducts()
          Returns the products of this reaction.
 LinearComb<java.lang.String> SourceRxn.getProducts()
          Returns a single-term linear combination.
 LinearComb<java.lang.String> ChemRxn.getProducts()
          Returns the products of this chemical reaction.
 LinearComb<java.lang.String> RevExchRxn.getReactants()
          Returns a linear combination representing the reactants of this exchange reaction.
 LinearComb<java.lang.String> AbstractExchangeRxn.getReactants()
          Returns an empty linear combination.
 LinearComb<java.lang.String> AbstractRxn.getReactants()
          Returns the reactants of this reaction.
 LinearComb<java.lang.String> SinkRxn.getReactants()
          Returns a single-term linear combination.
 LinearComb<java.lang.String> ChemRxn.getReactants()
          Returns the reactants of this chemical reaction.
 

Constructors in sbrt.kernel.fba with parameters of type LinearComb
AbstractRxn(LinearComb<java.lang.String> reactants, LinearComb<java.lang.String> products)
          Constructs a new chemical reaction from the provided reactants and products with the given name.
AbstractRxn(LinearComb<java.lang.String> reactants, LinearComb<java.lang.String> products)
          Constructs a new chemical reaction from the provided reactants and products with the given name.
IrrevRxn(LinearComb<java.lang.String> reactants, LinearComb<java.lang.String> products)
          Constructs a new irreversible reaction from the provided reactants and products.
IrrevRxn(LinearComb<java.lang.String> reactants, LinearComb<java.lang.String> products)
          Constructs a new irreversible reaction from the provided reactants and products.
RevRxn(LinearComb<java.lang.String> reactants, LinearComb<java.lang.String> products)
          Constructs a new reversible reaction from the provided reactants and products.
RevRxn(LinearComb<java.lang.String> reactants, LinearComb<java.lang.String> products)
          Constructs a new reversible reaction from the provided reactants and products.
 

Uses of LinearComb in sbrt.kernel.fba.comp
 

Methods in sbrt.kernel.fba.comp that return LinearComb
protected
<V> LinearComb<V>
FbaOptimizer.getExpr(java.util.Collection<V> columnVariables)
          Converts a collection of column variables to a linear combination.
protected
<V> LinearComb<V>
FbaOptimizer.getExpr(V columnVariable)
          Converts a column variable to a single-term linear combination.
protected  LinearComb<java.lang.String> AbstractCvComputer.getRxnExpr(java.util.Collection<java.lang.String> reactionNames)
          Converts a collection of reaction names to a linear combination.
protected  LinearComb<java.lang.String> FbaOptimizer.getRxnExpr(java.util.Collection<java.lang.String> rxnNames)
          Converts a collection of reaction names to a linear combination.
protected  LinearComb<java.lang.String> AbstractCvComputer.getRxnExpr(java.lang.String reactionName)
          Converts a reaction name to a single-term linear combination.
protected  LinearComb<java.lang.String> FbaOptimizer.getRxnExpr(java.lang.String reactionName)
          Converts a reaction name to a single-term linear combination.
 

Methods in sbrt.kernel.fba.comp that return types with arguments of type LinearComb
 java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> FluxCapComputer.getFluxCaps()
          Computes and returns all flux caps.
 java.util.Map<LinearComb<java.lang.String>,Interval> CdHarFluxComp.getRxnExprConstraints()
          Returns all current flux expression constraints.
 

Methods in sbrt.kernel.fba.comp with parameters of type LinearComb
 void CdHarFluxComp.restoreRxnExprConstraint(LinearComb<java.lang.String> expr)
          Restores the constraint on the provided flux expression to the value contained in the fluxome.
 void CdHarFluxComp.setRxnExprConstraint(LinearComb<java.lang.String> rxnExpr, Interval c)
          Changes the constraint on the provided linear combination of fluxes.
 

Constructor parameters in sbrt.kernel.fba.comp with type arguments of type LinearComb
FluxCapComputer(IrrevRxnFluxome fluxome, java.util.Collection<LinearComb<java.lang.String>> allCycles)
          Constructs a new flux cap computer from the cycles contained in the provided fluxome.
MsFluxIntervalComputer(FbaOptimizer<F> computer, java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps)
          Constructs a new Mahadevan-Schilling flux interval computer.
MsFluxIntervalComputer(FbaOptimizer<F> computer, java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> fluxCaps, double zeroCutoff)
          Constructs a new Mahadevan-Schilling flux interval computer.
 

Uses of LinearComb in sbrt.kernel.fba.proc
 

Methods in sbrt.kernel.fba.proc that return LinearComb
 LinearComb<java.lang.String> FbaOptProcess.getObjectiveFunction()
          Returns the current objective function.
 

Methods in sbrt.kernel.fba.proc with parameters of type LinearComb
 void FbaOptProcess.setObjectiveFunction(LinearComb<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 LinearComb
 void RandomObjectiveGenerator.run(ResultsManager<LinearComb<java.lang.String>> resultsManager)
          Generates random objective functions and adds them to the provided results manager.
 void FluxCapProcess.run(ResultsManager<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>> resultsManager)
          Computes the flux caps and adds the result to the provided manager.
 

Uses of LinearComb in sbrt.kernel.math
 

Classes in sbrt.kernel.math that implement LinearComb
 class AbstractLinearComb<V>
          This abstract class is a skeleton implementation of LinearComb.
 class HashLinearComb<V>
          This class is a concrete implemenation of LinearComb.
 

Methods in sbrt.kernel.math that return LinearComb
 LinearComb<V> LinearComb.add(double constant)
          Adds, in the mathematical sense, the provided constant to this linear combination.
 LinearComb<V> LinearComb.add(LinearComb<? extends V> linComb)
          Adds, in the mathematical sense, the provided linear combination to this linear combination.
 LinearComb<V> LinearComb.multiply(double constant)
          Multiplies this linear combination by the provided constant.
 LinearComb<V> LinearComb.plugIn(java.util.Map<?,? extends LinearComb<? extends V>> linearCombs)
          Plugs in the provided linear combinations to produce a new linear combination.
 LinearComb<V> LinearComb.plugIn(java.util.Map<?,java.lang.Double> numbers, java.util.Map<?,? extends LinearComb<? extends V>> linearCombs)
          Plugs in the provided numerical values and linear combinations to produce a new linear combination.
 LinearComb<V> LinearComb.plugIn(java.lang.Object variable, double constant)
          Assigns the value of the provided variable to the provided constant.
 LinearComb<V> LinearComb.plugIn(java.lang.Object variable, LinearComb<? extends V> expr)
          Assigns the value of the provided variable to the provided linear combination.
 LinearComb<V> LinearComb.plugInNumbers(java.util.Map<?,java.lang.Double> numbers)
          Plugs in the provided numerical values to produce a new linear combination.
 LinearComb<V> LinearComb.solveFor(java.lang.Object variable, double constant)
          Equates this linear combination to the provided constant and solves for the provided variable.
 

Methods in sbrt.kernel.math with parameters of type LinearComb
 LinearComb<V> LinearComb.add(LinearComb<? extends V> linComb)
          Adds, in the mathematical sense, the provided linear combination to this linear combination.
 HashLinearComb<V> HashLinearComb.add(LinearComb<? extends V> expression)
          Adds, in the mathematical sense, the provided linear combination to this linear combination.
 LinearComb<V> LinearComb.plugIn(java.lang.Object variable, LinearComb<? extends V> expr)
          Assigns the value of the provided variable to the provided linear combination.
 HashLinearComb<V> HashLinearComb.plugIn(java.lang.Object variable, LinearComb<? extends V> expr)
          Plugs the provided linear combination into the provided variable to produce a new linear combination.
 

Method parameters in sbrt.kernel.math with type arguments of type LinearComb
 LinearComb<V> LinearComb.plugIn(java.util.Map<?,? extends LinearComb<? extends V>> linearCombs)
          Plugs in the provided linear combinations to produce a new linear combination.
 HashLinearComb<V> HashLinearComb.plugIn(java.util.Map<?,? extends LinearComb<? extends V>> variableValues)
          Plugs in the provided linear combinations to produce a new linear combination.
 LinearComb<V> LinearComb.plugIn(java.util.Map<?,java.lang.Double> numbers, java.util.Map<?,? extends LinearComb<? extends V>> linearCombs)
          Plugs in the provided numerical values and linear combinations to produce a new linear combination.
 HashLinearComb<V> HashLinearComb.plugIn(java.util.Map<?,java.lang.Double> numbers, java.util.Map<?,? extends LinearComb<? extends V>> linearCombs)
          Plugs in the provided numerical values and linear combinations to produce a new linear combination.
 

Uses of LinearComb in sbrt.kernel.math.algebra
 

Methods in sbrt.kernel.math.algebra that return LinearComb
 LinearComb<V> HashLinearSystemSolution.getSolution(java.lang.Object variable)
          Returns the linear combination of free variables to which the provided variable is equal.
 LinearComb<V> LinearSystemSolution.getSolution(java.lang.Object variable)
          Returns the linear combination of free variables to which the provided variable is equal.
 

Methods in sbrt.kernel.math.algebra that return types with arguments of type LinearComb
 java.util.List<LinearComb<C>> DoubleMatrixWrap.toLinearCombs()
          Returns this matrix as a list of linear combinations.
 java.util.List<LinearComb<C>> DoubleMatrix.toLinearCombs()
          Returns this matrix as a list of linear combinations.
 java.util.List<LinearComb<C>> AbstractSmdMatrix.toLinearCombs()
          Returns this matrix as a list of linear combinations.
 java.util.Map<V,LinearComb<V>> HashLinearSystemSolution.toMap()
          Returns this solution as a map.
 java.util.Map<V,LinearComb<V>> LinearSystemSolution.toMap()
          Returns this solution as a map.
 

Method parameters in sbrt.kernel.math.algebra with type arguments of type LinearComb
 LinearSystemSolution<V> LinearSystemSolver.solve(java.util.Map<LinearComb<V>,java.lang.Double> equations)
          Computes and returns a solution to the provided system of linear equations.
 

Constructor parameters in sbrt.kernel.math.algebra with type arguments of type LinearComb
HashLinearSystemSolution(java.util.Map<? extends V,? extends LinearComb<? extends V>> solutions)
          Constructs a new hash code-based linear system solution.
 

Uses of LinearComb in sbrt.kernel.math.algebra.proc
 

Method parameters in sbrt.kernel.math.algebra.proc with type arguments of type LinearComb
 void LinearSolverProcess.setEquations(java.util.Map<LinearComb<V>,java.lang.Double> equations)
          Sets the system of linear equations to be solver.
 

Uses of LinearComb in sbrt.kernel.math.geom
 

Methods in sbrt.kernel.math.geom that return LinearComb
 LinearComb<V> ParallelHyperplanes.getPlane()
          Returns the hyperplane.
 

Constructors in sbrt.kernel.math.geom with parameters of type LinearComb
ParallelHyperplanes(LinearComb<V> hyperplane, Interval bounds)
          Constructs a new pair of bounding parallel hyperplanes.
 

Uses of LinearComb in sbrt.kernel.math.optimization
 

Methods in sbrt.kernel.math.optimization with parameters of type LinearComb
 void LinearProgramSolver.setConstraint(LinearComb<? extends C> expression, Interval c)
          Sets a constraint on the provided linear combination of column variables.
 void LinearProgramSolver.setObjectiveFunction(LinearComb<? extends C> expression)
          Sets the objective function to the provided linear combination of column variables.
 void LinearProgramSolver.setObjectiveFunction(LinearComb<? extends C> expression, OptSense sense)
          Sets the objective function and optimization sense to the provided values.
 

Uses of LinearComb in sbrt.shell.io.fba
 

Methods in sbrt.shell.io.fba that return types with arguments of type LinearComb
static java.util.Set<LinearComb<java.lang.String>> FluxIntervalInputFile.convertVariables(java.util.Set<java.lang.String> rxnNames)
          Converts a set of reaction names to a set of single-term linear combinations.
 UnmodifiableMap<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> FluxCapInputFile.getFluxCaps()
          Returns the flux caps contained in this file.
 MapFormat<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> FluxCapInputFile.getMapFormat()
          Returns the map format used to parse this file.
 java.util.Iterator<java.util.Map<java.lang.String,java.util.Set<LinearComb<java.lang.String>>>> FluxCapInputFile.iterator()
          Returns an iterator over this file.
 

Method parameters in sbrt.shell.io.fba with type arguments of type LinearComb
static FluxConstraints FluxIntervalInputFile.convertConstraints(java.util.Map<LinearComb<java.lang.String>,Interval> intervals, Fluxome fluxome, double tolerance)
          Converts the provided intervals into a FluxConstraints object.
 

Constructor parameters in sbrt.shell.io.fba with type arguments of type LinearComb
FluxIntervalInputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<LinearComb<java.lang.String>> requiredVariables, MapFormat<LinearComb<java.lang.String>,Interval> mapFormat, Fluxome fluxome, double tolerance)
          Constructs a new flux-interval input file.
FluxIntervalInputFile(java.lang.String fileName, FileFormat fileFormat, java.util.Set<LinearComb<java.lang.String>> requiredVariables, MapFormat<LinearComb<java.lang.String>,Interval> mapFormat, Fluxome fluxome, double tolerance)
          Constructs a new flux-interval input file.
 

Uses of LinearComb in sbrt.shell.mng.algebra
 

Methods in sbrt.shell.mng.algebra that return types with arguments of type LinearComb
static java.util.Map<LinearComb<java.lang.String>,java.lang.Double> LinearSolverManager.getEquations(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Returns the set of linear equations contained in the file with the provided name.
static java.util.Map<LinearComb<java.lang.String>,java.lang.Double> LinearSolverManager.getEquations(java.lang.String fileName)
          Returns the set of linear equations contained in the file with the provided name.
static java.util.Map<LinearComb<java.lang.String>,java.lang.Double> LinearSolverManager.getEquations(java.lang.String fileName, java.io.PrintWriter out)
          Returns the set of linear equations contained in the file with the provided name.
 

Uses of LinearComb in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba that return LinearComb
static LinearComb<java.lang.String> FbaOptManager.getObjFunc(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Parses and returns the value for FbaOptManager.OBJECTIVE_FUNCTION in the provided manager input.
 

Methods in sbrt.shell.mng.fba that return types with arguments of type LinearComb
static java.util.List<LinearComb<java.lang.String>> FluxCapManager.getCycles(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Opens the file denoted by FluxCapManager.CYCLE_FILE in the provided manager input and returns the list of cycles it contains.
static UnmodifiableMap<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> MsFluxIntervalManager.getFluxCaps(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Returns the flux caps contained in the file with the name specified by MsFluxIntervalManager.FLUX_CAP_FILE in the provided input.
static TextInputFile<LinearComb<java.lang.String>> ObjectiveFunctionManager.getInputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Returns the file denoted by ObjectiveFunctionManager.OBJ_FUNCT_FILE in the provided manager input.
static TextInputFile<LinearComb<java.lang.String>> ObjectiveFunctionManager.getInputFile(java.lang.String fileName, FileFormat format, Fluxome fluxome)
          Returns the input file with the provided name.
static TextInputFile<LinearComb<java.lang.String>> ObjectiveFunctionManager.getInputFile(java.lang.String fileName, Fluxome fluxome)
          Returns the input file with the provided name.
static TextOutputFile<LinearComb<java.lang.String>> RandomObjectiveManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out, Fluxome fluxome)
          Returns an empty output file that is suitable for storing randomly generated objective functions.
static TextOutputFile<LinearComb<java.lang.String>> RandomObjectiveManager.getOutputFile(java.lang.String fileName, FileFormat format, java.io.PrintWriter out, Fluxome fluxome)
          Returns an empty output file that is suitable for storing randomly generated objective functions.
static RxnNameExprFormat<LinearComb<java.lang.String>,java.lang.String> FbaManager.getRxnNameExprFormat(Fluxome f)
          Returns the default reaction name expression format.
 

Method parameters in sbrt.shell.mng.fba with type arguments of type LinearComb
static FluxIntervalInputFile IntervalVariationManager.getIntervalInputFile(java.lang.String fileName, Fluxome fluxome, MapFormat<LinearComb<java.lang.String>,Interval> mapFormat, double tolerance)
          Returns the flux interval input file with the provided name.
 

Uses of LinearComb in sbrt.shell.mng.utilities
 

Methods in sbrt.shell.mng.utilities that return types with arguments of type LinearComb
static java.util.List<LinearComb<java.lang.String>> VariableParticipationManager.getExpressions(ManagerInput<java.lang.String,java.lang.String> input, java.io.PrintWriter out)
          Opens the file denoted by VariableParticipationManager.EXPRESSION_FILE in the provided manager input and returns the list of mathematical expressions it contains.
 VariableParticipation<LinearComb<java.lang.String>,java.lang.String> VariableParticipationManager.getProcess()
          Returns the process this process manager controls.
 

Uses of LinearComb in sbrt.shell.text.fba
 

Methods in sbrt.shell.text.fba that return LinearComb
 LinearComb<java.lang.String> PalssonRxnNodeParser.getProducts(org.w3c.dom.Node reactionNode)
          Returns the products of the provided reaction node.
 LinearComb<java.lang.String> BiggRxnNodeParser.getProducts(org.w3c.dom.Node reactionNode)
          Returns the products of the provided reaction node.
 LinearComb<java.lang.String> PalssonRxnNodeParser.getReactants(org.w3c.dom.Node reactionNode)
          Returns the reactants of the provided reaction node.
 LinearComb<java.lang.String> BiggRxnNodeParser.getReactants(org.w3c.dom.Node reactionNode)
          Returns the reactants of the provided reaction node.
 LinearComb<java.lang.String> RxnNameExprFormatV1.parse(java.lang.String rxnNameExpr)
          Parses the provided string and returns its corresponding linear combination of reaction names.
 

Methods in sbrt.shell.text.fba that return types with arguments of type LinearComb
 PipeListFormat<java.util.Set<LinearComb<java.lang.String>>> FluxCapFormatV1.getListFormat()
          Returns the format used for lists of values.
 PipeListFormat<LinearComb<java.lang.String>> FluxomeSolFileLineFormatV1.getListFormat()
          Returns the format used for lists of values.
 PipeSetFormat<LinearComb<java.lang.String>> ConstraintsFileLineFormatV2.getSetFormat()
          Returns the format used for sets of variables.
 

Methods in sbrt.shell.text.fba with parameters of type LinearComb
 java.lang.String RxnNameExprFormatV1.format(LinearComb<java.lang.String> rxnNameExpr)
          Returns a formatted string representation of the provided linear combination of reaction names.
 

Uses of LinearComb in sbrt.shell.text.math
 

Methods in sbrt.shell.text.math that return LinearComb
 LinearComb<V> LinearCombFormat.parse(java.lang.String expression)
          Parses the provided string and returns its corresponding linear combination.
 LinearComb<V> LinearCombFormatV2.parse(java.lang.String expression)
          Parses the provided string and returns its corresponding linear combination.
 LinearComb<V> LinearCombFormatV1.parse(java.lang.String expression)
          Parses the provided string and returns its corresponding linear combination.
 

Methods in sbrt.shell.text.math with parameters of type LinearComb
 java.lang.String LinearCombFormat.format(LinearComb<V> expression)
          Returns a formatted string representation of the provided linear combination.
 java.lang.String LinearCombFormatV2.format(LinearComb<V> expression)
          Returns a formatted string representation of the provided linear combination.
 java.lang.String LinearCombFormatV1.format(LinearComb<V> expression)
          Returns a formatted string representation of the provided linear combination.