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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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