A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

P

P_MAX - Static variable in class sbrt.shell.mng.fba.InitialPointManager
The keyword used to denote the P intercept (the value of positioning variables at the edge of the convex poytope).
P_VECTOR_FILE_NAME - Static variable in class sbrt.shell.mng.fba.InitialPointManager
The keyword used to denote the name of the C vector output file.
PalssonRxnNodeParser - Class in sbrt.shell.text.fba
This class is used to make a direct translation from SBML 'reaction' nodes into Systems Biology Research Tool objects.
PalssonRxnNodeParser() - Constructor for class sbrt.shell.text.fba.PalssonRxnNodeParser
Constructs a new SBML reaction node parser.
PalssonSbmlReader - Class in sbrt.shell.proc.fba
This class is used to read SBML files downloaded directly from Dr.
PalssonSbmlReader(String) - Constructor for class sbrt.shell.proc.fba.PalssonSbmlReader
Constructs a new SBML file reader.
PalssonSbmlReaderManager - Class in sbrt.shell.mng.fba
This class is used to manage the reading of SBML files obtained from Palsson's website.
PalssonSbmlReaderManager() - Constructor for class sbrt.shell.mng.fba.PalssonSbmlReaderManager
 
ParallelHyperplanes<V> - Class in sbrt.kernel.math.geom
This class is used to represent a pair of bounding parallel hyperplanes.
ParallelHyperplanes(LinearComb<V>, Interval) - Constructor for class sbrt.kernel.math.geom.ParallelHyperplanes
Constructs a new pair of bounding parallel hyperplanes.
PARAM_FILE - Static variable in class sbrt.shell.ProgramSolverFactory
The keyword used to denote a parameter file for a program solver.
parse(List<String>) - Static method in class sbrt.shell.proc.fba.MetatoolInputReader
Parses the lines of a Metatool input file.
parse(String) - Method in class sbrt.shell.text.AbstractLinkedHashSetFormat
Parses the provided string and returns its corresponding collection of elements as a LinkedHashSet.
parse(String) - Method in class sbrt.shell.text.AbstractListFormat
Parses the provided string and returns its corresponding collection of elements as a list.
parse(String) - Method in interface sbrt.shell.text.BooleanFormat
Parses the provided string and returns its corresponding boolean value.
parse(String) - Method in class sbrt.shell.text.BoolRelFormatV1
Parses the provided string and returns its corresponding collection of elements as a LinkedHashSet.
parse(String) - Method in class sbrt.shell.text.chem.CatalystFormatV1
Parses the provided string and returns its corresponding catalyst name.
parse(String) - Method in class sbrt.shell.text.chem.CatalystFormatV2
Parses the provided string and returns its corresponding catalyst name.
parse(String) - Method in class sbrt.shell.text.chem.ChemSpeciesFormatV1
Parses the provided string and returns its corresponding species name.
parse(String) - Method in class sbrt.shell.text.chem.IrrevRxnFormatV1
Parses the provided string and returns its corresponding irreversible reaction.
parse(String) - Method in class sbrt.shell.text.chem.RevRxnFormatV1
Parses the provided string and returns its corresponding chemical reaction.
parse(String) - Method in class sbrt.shell.text.chem.RxnNameFormatV1
Parses the provided string and returns its corresponding reaction name.
parse(String) - Method in interface sbrt.shell.text.CollectionFormat
Parses the provided string and returns its corresponding collection of elements.
parse(String) - Method in interface sbrt.shell.text.DoubleFormat
Parses the provided string and returns its corresponding double precision number.
parse(String) - Method in class sbrt.shell.text.DoubleFormatV1
Parses the provided string and returns its corresponding double precision number.
parse(String) - Method in class sbrt.shell.text.DoubleFormatV2
Parses the provided string and returns its corresponding double precision number.
parse(String) - Method in class sbrt.shell.text.fba.BiggBracketParserV1
Parses the provided BiGG style bracketed expression.
parse(String) - Method in interface sbrt.shell.text.fba.CatalystListFormat
Parses the provided string and returns the list of catalyst names it contains.
parse(String) - Method in class sbrt.shell.text.fba.CatalystListFormatV1
Parses the provided string and returns the list of catalyst names it contains.
parse(String) - Method in interface sbrt.shell.text.fba.CatalystSetFormat
Parses the provided string and returns the set of enzyme names it contains.
parse(String) - Method in class sbrt.shell.text.fba.CatalystSetFormatV1
Parses the provided string and returns the set of catalyst names it contains.
parse(String) - Method in class sbrt.shell.text.fba.CatalystVerifier
Parses the provided string and returns its corresponding catalyst name.
parse(String) - Method in class sbrt.shell.text.fba.ChemSpeciesVerifier
Parses the provided string and returns its corresponding chemical species.
parse(String) - Method in class sbrt.shell.text.fba.FbaOptHeaderParserV1
Parses the provided string and returns its corresponding set of FBA optimization headers as a LinkedHashSet.
parse(String) - Method in class sbrt.shell.text.fba.IrrevRxnFormatV1
Parses the provided string and returns its corresponding chemical reaction.
parse(String) - Method in class sbrt.shell.text.fba.IrrevRxnFormatV2
Parses the provided string and returns its corresponding chemical reaction.
parse(String) - Method in class sbrt.shell.text.fba.RevRxnFormatV1
Parses the provided string and returns its corresponding chemical reaction.
parse(String) - Method in class sbrt.shell.text.fba.RevRxnFormatV2
Parses the provided string and returns its corresponding chemical reaction.
parse(String) - Method in class sbrt.shell.text.fba.RxnFormatV1
Parses the provided string and returns its corresponding chemical reaction.
parse(String) - Method in class sbrt.shell.text.fba.RxnNameExprFormatV1
Parses the provided string and returns its corresponding linear combination of reaction names.
parse(String) - Method in interface sbrt.shell.text.fba.RxnNameListFormat
Parses the provided string and returns the list of reaction names it contains.
parse(String) - Method in class sbrt.shell.text.fba.RxnNameListFormatV1
Parses the provided string and returns the list of reaction names it contains.
parse(String) - Method in class sbrt.shell.text.fba.RxnNameOrExprFormatV1
Parses the provided string and returns its corresponding object.
parse(String) - Method in interface sbrt.shell.text.fba.RxnNameSetFormat
Parses the provided string and returns the set of reaction names it contains.
parse(String) - Method in class sbrt.shell.text.fba.RxnNameSetFormatV1
Parses the provided string and returns its corresponding collection of reaction names as a LinkedHashSet.
parse(String) - Method in class sbrt.shell.text.fba.RxnNameVerifier
Parses the provided string and returns its corresponding reaction name.
parse(String) - Method in class sbrt.shell.text.FileFormatFormat
Parses the provided string and returns its corresponding file format.
parse(String) - Method in interface sbrt.shell.text.IntegerFormat
Parses the provided string and returns its corresponding integer.
parse(String) - Method in class sbrt.shell.text.IntegerFormatV1
Parses the provided string and returns its corresponding integer.
parse(String) - Method in interface sbrt.shell.text.LinkedHashSetFormat
Parses the provided string and returns its corresponding collection of elements as a LinkedHashSet.
parse(String) - Method in interface sbrt.shell.text.ListFormat
Parses the provided string and returns its corresponding collection of elements as a list.
parse(String) - Method in interface sbrt.shell.text.LongFormat
Parses the provided string and returns its corresponding long.
parse(String) - Method in class sbrt.shell.text.LongFormatV1
Parses the provided string and returns its corresponding long.
parse(String) - Method in class sbrt.shell.text.math.BoundedIntervalFormatV1
Parses the provided string and returns its corresponding interval.
parse(String) - Method in interface sbrt.shell.text.math.CoeffFormat
Parses the provided string and returns its corresponding coefficient.
parse(String) - Method in class sbrt.shell.text.math.CoeffFormatV1
Parses the provided string and returns its corresponding coefficient.
parse(String) - Method in class sbrt.shell.text.math.CoeffFormatV2
Parses the provided string and returns its corresponding coefficient.
parse(String) - Method in class sbrt.shell.text.math.DirEdgeFormatV1
Parses the provided string and returns its corresponding directed edge.
parse(String) - Method in class sbrt.shell.text.math.IndexPairFormatV1
Parses the provided string and returns its corresponding index pair.
parse(String) - Method in class sbrt.shell.text.math.IntervalFormatV1
Parses the provided string and returns its corresponding interval.
parse(String) - Method in class sbrt.shell.text.math.LinCombTermFormatV1
Parses the provided string and returns its corresponding term.
parse(String, String) - Method in class sbrt.shell.text.math.LinCombTermFormatV1
Parses the provided strings and returns their corresponding term.
parse(String) - Method in class sbrt.shell.text.math.LinCombTermFormatV2
Parses the provided string and returns its corresponding term.
parse(String, String) - Method in class sbrt.shell.text.math.LinCombTermFormatV2
Parses the provided strings and returns their corresponding term.
parse(String) - Method in interface sbrt.shell.text.math.LinearCombFormat
Parses the provided string and returns its corresponding linear combination.
parse(String) - Method in class sbrt.shell.text.math.LinearCombFormatV1
Parses the provided string and returns its corresponding linear combination.
parse(String) - Method in class sbrt.shell.text.math.LinearCombFormatV2
Parses the provided string and returns its corresponding linear combination.
parse(String) - Method in interface sbrt.shell.text.math.LinearCombTermFormat
Parses the provided string and returns its corresponding term.
parse(String) - Method in interface sbrt.shell.text.math.MathExprFormat
Parses the provided string and returns its corresponding linear combination.
parse(String) - Method in class sbrt.shell.text.math.MatrixElementFormatV1
Parses the provided string and returns its corresponding matrix element.
parse(String) - Method in class sbrt.shell.text.math.SenseFormat
Parses the provided string and returns its corresponding object.
parse(String) - Method in class sbrt.shell.text.NonEmptyStringFormat
Returns a string equal to the one provided.
parse(String) - Method in interface sbrt.shell.text.Parser
Parses the provided string and returns its corresponding object.
parse(String) - Method in interface sbrt.shell.text.PercentFormat
Parses the provided string and returns its corresponding percentage.
parse(String) - Method in class sbrt.shell.text.PercentFormatVersion1
Parses the provided string and returns its corresponding percentage.
parse(String) - Method in class sbrt.shell.text.SimpleListFormat
Parses the provided string and returns its corresponding collection of elements as a list.
parse(String) - Method in class sbrt.shell.text.SimpleSetFormat
Parses the provided string and returns its corresponding collection of elements as a set.
parse(String) - Method in class sbrt.shell.text.StringFormat
Returns a string equal to the one provided.
parse(String) - Method in class sbrt.shell.text.TrueFalseFormat
Parses the provided string and returns its corresponding boolean value.
parse(String) - Method in class sbrt.shell.text.YesNoFormat
Parses the provided string and returns its corresponding boolean value.
parseAllKeys(String) - Method in class sbrt.shell.text.AbstractMapFormat
Parses the provided string and returns its corresponding set of keys.
parseAllKeys(String) - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Parses the provided string and returns its corresponding set of keys.
parseAllKeys(String) - Method in interface sbrt.shell.text.MapFormat
Parses the provided string and returns its corresponding set of keys.
parseAllPairs(String, String) - Method in class sbrt.shell.text.AbstractMapFormat
Parses the provided set of keys and list of values and returns a corresponding map of variable-value pairs.
parseAllPairs(String, String) - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Parses the provided set of keys and list of values and returns a corresponding map of variable-value pairs.
parseAllPairs(String, String) - Method in interface sbrt.shell.text.MapFormat
Parses the provided set of keys and list of values and returns a corresponding map of key-value pairs.
parseAllValues(String) - Method in class sbrt.shell.text.AbstractMapFormat
Parses the provided string and returns its corresponding list of values.
parseAllValues(LinkedHashSet<? extends K>, String) - Method in class sbrt.shell.text.AbstractMapFormat
Parses the provided string of values and returns a corresponding map of variable-value pairs using the provided set of keys.
parseAllValues(String) - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Parses the provided string and returns its corresponding list of values.
parseAllValues(LinkedHashSet<? extends String>, String) - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Parses the provided string of values and returns a corresponding map of variable-value pairs using the provided set of keys.
parseAllValues(String) - Method in interface sbrt.shell.text.MapFormat
Parses the provided string and returns its corresponding list of values.
parseAllValues(LinkedHashSet<? extends K>, String) - Method in interface sbrt.shell.text.MapFormat
Parses the provided string of values and returns a corresponding map of key-value pairs using the provided set of keys.
parseCorrelator(String) - Static method in class sbrt.shell.mng.stat.CorrelationManager
Returns the correlation computer corresponding to the provided string value.
parseCorrelator(String) - Static method in class sbrt.shell.mng.stat.KendallTauManager
Returns the Kendall's Tau statistic computer corresponding to the provided string value.
parseInt(String) - Static method in class sbrt.shell.mng.AbstractProcessManager
Parses the provided string as a int.
parseKey(String) - Method in class sbrt.shell.text.AbstractMapFormat
Parses the provided string and returns its corresponding key.
parseKey(String) - Method in class sbrt.shell.text.ColonMapEntryFormatV1
Parses the provided string representation of a key object.
parseKey(String) - Method in class sbrt.shell.text.EqualsMapEntryFormatV1
Parses the provided string representation of a key object.
parseKey(String) - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Parses the provided string and returns its corresponding key.
parseKey(String) - Method in interface sbrt.shell.text.MapEntryFormat
Parses the provided string and returns its corresponding key.
parseKey(String) - Method in interface sbrt.shell.text.MapFormat
Parses the provided string and returns its corresponding key.
parseLong(String) - Static method in class sbrt.shell.mng.AbstractProcessManager
Parses the provided string as a long.
parsePair(String) - Method in class sbrt.shell.text.AbstractMapEntryFormat
Parses the provided map entry string, and returns its corresponding map entry.
parsePair(String) - Method in class sbrt.shell.text.AbstractMapFormat
Parses the provided map entry string, and returns its corresponding map entry.
parsePair(String) - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Parses the provided map entry string, and returns its corresponding map entry.
parsePair(String) - Method in interface sbrt.shell.text.MapEntryFormat
Parses the provided string and returns a corresponding map entry.
parsePair(String) - Method in interface sbrt.shell.text.MapFormat
Parses the provided string and returns a corresponding map entry.
parsePrimitive(String) - Method in interface sbrt.shell.text.BooleanFormat
Parses the provided string and returns its corresponding boolean value.
parsePrimitive(String) - Method in interface sbrt.shell.text.DoubleFormat
Parses the provided string and returns its corresponding double precision number.
parsePrimitive(String) - Method in class sbrt.shell.text.DoubleFormatV1
Parses the provided string and returns its corresponding double precision number.
parsePrimitive(String) - Method in class sbrt.shell.text.DoubleFormatV2
Parses the provided string and returns its corresponding double precision number.
parsePrimitive(String) - Method in interface sbrt.shell.text.IntegerFormat
Parses the provided string and returns its corresponding integer.
parsePrimitive(String) - Method in class sbrt.shell.text.IntegerFormatV1
Parses the provided string and returns its corresponding integer.
parsePrimitive(String) - Method in interface sbrt.shell.text.LongFormat
Parses the provided string and returns its corresponding long.
parsePrimitive(String) - Method in class sbrt.shell.text.LongFormatV1
Parses the provided string and returns its corresponding long.
parsePrimitive(String) - Method in interface sbrt.shell.text.math.CoeffFormat
Parses the provided string and returns its corresponding coefficient.
parsePrimitive(String) - Method in class sbrt.shell.text.math.CoeffFormatV1
Parses the provided string and returns its corresponding coefficient.
parsePrimitive(String) - Method in class sbrt.shell.text.math.CoeffFormatV2
Parses the provided string and returns its corresponding coefficient.
parsePrimitive(String) - Method in interface sbrt.shell.text.PercentFormat
Parses the provided string and returns its corresponding percentage.
parsePrimitive(String) - Method in class sbrt.shell.text.PercentFormatVersion1
Parses the provided string and returns its corresponding percentage.
parsePrimitive(String) - Method in class sbrt.shell.text.TrueFalseFormat
Parses the provided string and returns its corresponding boolean value.
parsePrimitive(String) - Method in class sbrt.shell.text.YesNoFormat
Parses the provided string and returns its corresponding boolean value.
Parser<T> - Interface in sbrt.shell.text
This interface is used to represent parsers.
parseValue(String) - Method in class sbrt.shell.text.AbstractMapFormat
Parses the provided string and returns its corresponding value.
parseValue(String) - Method in class sbrt.shell.text.ColonMapEntryFormatV1
Parses the provided string representation of a value object.
parseValue(String) - Method in class sbrt.shell.text.EqualsMapEntryFormatV1
Parses the provided string representation of a value object.
parseValue(String) - Method in class sbrt.shell.text.fba.FbaOptFileLineFormatV1
Parses the provided string and returns its corresponding value.
parseValue(String) - Method in interface sbrt.shell.text.MapEntryFormat
Parses the provided string and returns its corresponding value.
parseValue(String) - Method in interface sbrt.shell.text.MapFormat
Parses the provided string and returns its corresponding value.
Path<N> - Class in sbrt.kernel.math.graph_theory
This class can be used for representing paths in a graph or network.
Path(T[]) - Constructor for class sbrt.kernel.math.graph_theory.Path
Constructs a path containing the nodes from the provided array, in the order they occur starting from index 0.
Path(Collection<? extends N>) - Constructor for class sbrt.kernel.math.graph_theory.Path
Constructs a path containing the nodes from the provided collection, in the order they are returned from the collection's iterator.
PathFinder<N> - Class in sbrt.kernel.math.graph_theory.comp
This class is an implemenation of an algorithm for finding all pathways in a directed graph.
PathFinder(DirectedGraph<N>) - Constructor for class sbrt.kernel.math.graph_theory.comp.PathFinder
Constructs a new path finder for the provided graph.
PathIdManager - Class in sbrt.shell.mng.graph_theory
This class is used to manage simple path identification processes.
PathIdManager() - Constructor for class sbrt.shell.mng.graph_theory.PathIdManager
 
PathIdProcess<N> - Class in sbrt.kernel.math.graph_theory.proc
This class is used to identify all the simple paths in a directed graph.
PathIdProcess() - Constructor for class sbrt.kernel.math.graph_theory.proc.PathIdProcess
Constructs a new path identification process.
paths(T, S) - Method in class sbrt.kernel.math.graph_theory.comp.PathFinder
Returns the number of paths between the provided source and sink nodes.
paths() - Method in class sbrt.kernel.math.graph_theory.comp.PathFinder
Returns the total number of paths.
paths(Collection<? extends N>, Collection<? extends N>) - Method in class sbrt.kernel.math.graph_theory.comp.PathFinder
Returns the number of paths between the provided source and sink nodes.
PEARSONS_R - Static variable in class sbrt.shell.mng.stat.CorrelationManager
The value used to denote a Pearson's r correlation coefficient.
PERCENT - Static variable in class sbrt.shell.mng.AbstractProcessManager
The default format used for percentages.
PERCENT - Static variable in class sbrt.shell.text.SpecialChars
%
PERCENT_COMPLETED - Static variable in class sbrt.shell.mng.AbstractProcessManager
The prefix used to denote the completed percentage of an operation.
PercentFormat - Interface in sbrt.shell.text
This interface is used to represent a format for percentages.
PercentFormatVersion1 - Class in sbrt.shell.text
This class is a concrete implementation of PercentFormat.
PercentFormatVersion1() - Constructor for class sbrt.shell.text.PercentFormatVersion1
Constructs a new percent format.
PercentProgressMonitor - Class in sbrt.kernel.utilities
This class is used to monitor a process whose progress can be measured as a percentage.
PercentProgressMonitor() - Constructor for class sbrt.kernel.utilities.PercentProgressMonitor
Constructs a new percentage-based progress monitor.
PercentProgressMonitor(int) - Constructor for class sbrt.kernel.utilities.PercentProgressMonitor
Constructs a new percentage-based progress monitor.
PIPE - Static variable in class sbrt.shell.text.SpecialChars
|
PipeListFormat<E> - Class in sbrt.shell.text
This class is used to define a format for pipe-delimited lists.
PipeListFormat(SimpleFormat<E>) - Constructor for class sbrt.shell.text.PipeListFormat
Constructs a new pipe-delimited list format with the provided element format.
PipeListFormat(Formatter<E>, Parser<E>) - Constructor for class sbrt.shell.text.PipeListFormat
Constructs a new pipe-delimited list format with the provided element format.
PipeSetFormat<E> - Class in sbrt.shell.text
This class is used to define a format for pipe-delimited sets.
PipeSetFormat(SimpleFormat<E>) - Constructor for class sbrt.shell.text.PipeSetFormat
Constructs a new pipe-delimited set format with the provided element format.
PipeSetFormat(Formatter<E>, Parser<E>) - Constructor for class sbrt.shell.text.PipeSetFormat
Constructs a new pipe-delimited set format with the provided element format.
PLANES_FILE - Static variable in class sbrt.shell.mng.geom.CdHarManager
The keyword used to denote the name of the file containing the collection of sets.
plastic() - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess.Results
Returns the number of plastic fluxes.
plug_in_example.kernel - package plug_in_example.kernel
 
plug_in_example.shell - package plug_in_example.shell
 
plugIn(Map<?, ? extends LinearComb<? extends V>>) - Method in class sbrt.kernel.math.HashLinearComb
Plugs in the provided linear combinations to produce a new linear combination.
plugIn(Map<?, Double>, Map<?, ? extends LinearComb<? extends V>>) - Method in class sbrt.kernel.math.HashLinearComb
Plugs in the provided numerical values and linear combinations to produce a new linear combination.
plugIn(Object, double) - Method in class sbrt.kernel.math.HashLinearComb
Plugs the provided numerical value into the provided variable to produce a new linear combination.
plugIn(Object, LinearComb<? extends V>) - Method in class sbrt.kernel.math.HashLinearComb
Plugs the provided linear combination into the provided variable to produce a new linear combination.
plugIn(Object, LinearComb<? extends V>) - Method in interface sbrt.kernel.math.LinearComb
Assigns the value of the provided variable to the provided linear combination.
plugIn(Object, double) - Method in interface sbrt.kernel.math.LinearComb
Assigns the value of the provided variable to the provided constant.
plugIn(Map<?, ? extends LinearComb<? extends V>>) - Method in interface sbrt.kernel.math.LinearComb
Plugs in the provided linear combinations to produce a new linear combination.
plugIn(Map<?, Double>, Map<?, ? extends LinearComb<? extends V>>) - Method in interface sbrt.kernel.math.LinearComb
Plugs in the provided numerical values and linear combinations to produce a new linear combination.
plugInNumbers(Map<?, Double>) - Method in class sbrt.kernel.math.HashLinearComb
Plugs in the provided numerical values to produce a new linear combination.
plugInNumbers(Map<?, Double>) - Method in interface sbrt.kernel.math.LinearComb
Plugs in the provided numerical values to produce a new linear combination.
plugInNumbers(Map<?, Double>) - Method in interface sbrt.kernel.math.MathExpr
Plugs in the provided numerical values to produce a new mathematical expression.
plugInNumbers(Map<?, Double>) - Method in interface sbrt.kernel.math.Polynomial
Plugs in the provided numerical values to produce a new polynomial.
PLUS - Static variable in class sbrt.shell.text.SpecialChars
+
POINTS_PER_POINT - Static variable in class sbrt.shell.mng.geom.CdHarManager
The keyword used to denote the number of points generated for each point returned.
Polynomial<V> - Interface in sbrt.kernel.math
This interface is used to represent polynomials.
Polynomial.Term<V> - Interface in sbrt.kernel.math
This interface is used to represent the terms of a polynomial.
POT_ACTIVE_FILE_NAME - Static variable in class sbrt.shell.mng.fba.FluxPlasticityManager
The keyword used to denote the name of the output file for the names of potentially-active reactions.
potentiallyActive() - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess.Results
Returns the number of fluxes that are potentially active.
power(Object) - Method in class sbrt.kernel.math.AbstractLinearComb.Term
Returns the power of the provided variable in this term.
power(Object) - Method in interface sbrt.kernel.math.Polynomial.Term
Returns the power of the provided variable in this term.
predecessors(Object) - Method in class sbrt.kernel.math.graph_theory.DirectedGraph
Returns the number of predecessors of the provided node.
print(Collection<?>) - Static method in class sbrt.kernel.utilities.Util
Prints the elements of the provided collection to System.out, one per line.
printBasicInfo(MixedFluxome, PrintWriter) - Static method in class sbrt.shell.mng.fba.NetworkInfoManager
Prints basic information about the provided fluxome.
printBasicInfo(DirectedGraph<?>, PrintWriter) - Static method in class sbrt.shell.mng.graph_theory.GraphInfoManager
Prints basic information about the provided graph.
printFluxomeInfo(Fluxome, PrintWriter) - Static method in class sbrt.shell.mng.fba.FbaManager
Prints basic information about the provided fluxome.
printInput(ManagerInput<String, String>, PrintWriter) - Static method in class sbrt.shell.ProcessManagerFactory
Creates a formatted string representation of the provided input and prints it to the provided print writer.
printProgress(Number, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Prints the provided progress to the provided print writer.
printProgress(Integer, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Prints the provided progress to the provided print writer.
printProgress(Double, PrintWriter) - Static method in class sbrt.shell.mng.AbstractProcessManager
Prints the provided progress to the provided print writer.
PROCESS - Static variable in class sbrt.shell.ProcessManagerFactory
The keyword used to denote a process.
PROCESS_NAME_FILE - Static variable in class sbrt.shell.ProcessManagerFactory
The keyword used to denote a procedure name file.
ProcessInputFile - Class in sbrt.shell.io
This class is used to represent process input files.
ProcessInputFile(String, AppInputFileLineFormat) - Constructor for class sbrt.shell.io.ProcessInputFile
Constructs a new process input file from the provided arguments.
ProcessInputFile(String) - Constructor for class sbrt.shell.io.ProcessInputFile
Constructs a new process input file from the provided argument.
ProcessManager<K,V> - Interface in sbrt.shell.mng
This interface is used to represent process managers.
ProcessManagerFactory - Class in sbrt.shell
This class is used to create ProcessManager objects.
ProcessRunner - Class in sbrt
A class to encapsulate the execution of processes.
ProcessRunner() - Constructor for class sbrt.ProcessRunner
 
ProgramSolver<R,C> - Interface in sbrt.kernel.math.optimization
This interface is used to represent program solvers, as in linear or quadratic program solvers.
ProgramSolverException - Exception in sbrt.kernel.math.optimization
This class is used to wrap exceptions thrown by program solver packages.
ProgramSolverException(Throwable) - Constructor for exception sbrt.kernel.math.optimization.ProgramSolverException
Constructs a wrapped program solver exception.
ProgramSolverException(String, Throwable) - Constructor for exception sbrt.kernel.math.optimization.ProgramSolverException
Constructs a wrapped program solver exception.
ProgramSolverFactory - Class in sbrt.shell
This class is used to create ProgramSolver objects.
ProgramSolverStatus - Enum in sbrt.kernel.math.optimization
This enum type is used to indicate the status of a program solver.
ProgressMonitor - Interface in sbrt.kernel.utilities
This interface is used to represent progress monitors.
PROTEIN_FILE_NAME - Static variable in class sbrt.shell.mng.fba.PalssonSbmlReaderManager
Used to denote the name of the file to which protein-reaction relationships should be written.
put(K, V) - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.put(Object, Object).
putAll(Map<? extends K, ? extends V>) - Method in class sbrt.kernel.utilities.UnmodifiableMap
See Map.putAll(Map).
pVariables() - Method in class sbrt.kernel.fba.comp.InitialPointComputer.Results
Returns the number of created positioning variables.

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