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

A

AbstractCvComputer<F extends Fluxome> - Class in sbrt.kernel.fba.comp
This abstract class is a skeleton implementation of FluxCvComputer.
AbstractCvComputer(F) - Constructor for class sbrt.kernel.fba.comp.AbstractCvComputer
Constructs a new constraint-variation computer.
AbstractCvFbaOptProcess<F extends Fluxome,R> - Class in sbrt.kernel.fba.proc
This class is used to represent constraint-variation Flux Balance Analysis processes.
AbstractCvFbaOptProcess() - Constructor for class sbrt.kernel.fba.proc.AbstractCvFbaOptProcess
 
AbstractExchangeRxn - Class in sbrt.kernel.fba
This class is a skeleton implementation of ExchangeRxn.
AbstractExchangeRxn(String) - Constructor for class sbrt.kernel.fba.AbstractExchangeRxn
Constructs a new exchange reaction for the provided chemical species.
AbstractFluxIntervalComputer<F extends Fluxome> - Class in sbrt.kernel.fba.comp
This abstract class is a skeleton implemenation of FluxIntervalComputer.
AbstractFluxIntervalComputer(FbaOptimizer<F>) - Constructor for class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Constructs a new flux interval computer with the default zero cutoff.
AbstractFluxIntervalComputer(FbaOptimizer<F>, double) - Constructor for class sbrt.kernel.fba.comp.AbstractFluxIntervalComputer
Constructs a new flux interval computer with the provided zero cutoff.
AbstractLinearComb<V> - Class in sbrt.kernel.math
This abstract class is a skeleton implementation of LinearComb.
AbstractLinearComb(double, double) - Constructor for class sbrt.kernel.math.AbstractLinearComb
Constructs a new linear combination with the provided constant and zero cutoff.
AbstractLinearComb(double) - Constructor for class sbrt.kernel.math.AbstractLinearComb
Constructs a new linear combination with the provided constant.
AbstractLinearComb.Term<V> - Class in sbrt.kernel.math
This class is a skeleton implementation of LinearComb.Term.
AbstractLinearComb.Term(double, V) - Constructor for class sbrt.kernel.math.AbstractLinearComb.Term
Constructs a new linear combination term with the provided coefficient and variable.
AbstractLinearComb.Term(V, double) - Constructor for class sbrt.kernel.math.AbstractLinearComb.Term
Constructs a new linear combination term with the provided coefficient and variable.
AbstractLinearComb.Term(V) - Constructor for class sbrt.kernel.math.AbstractLinearComb.Term
Constructs a new linear combination term with the provided variable.
AbstractLinkedHashSetFormat<E> - Class in sbrt.shell.text
This abstract class is a skeleton implementation of LinkedHashSetFormat.
AbstractLinkedHashSetFormat(String, Pattern, SimpleFormat<E>) - Constructor for class sbrt.shell.text.AbstractLinkedHashSetFormat
Constructs a new LinkedHashSet format from the provided arguments.
AbstractLinkedHashSetFormat(String, Pattern, Formatter<E>, Parser<E>) - Constructor for class sbrt.shell.text.AbstractLinkedHashSetFormat
Constructs a new LinkedHashSet format from the provided arguments.
AbstractListFormat<E> - Class in sbrt.shell.text
This abstract class is a skeleton implementation of ListFormat.
AbstractListFormat(String, Pattern, SimpleFormat<E>) - Constructor for class sbrt.shell.text.AbstractListFormat
Constructs a new list format from the provided arguments.
AbstractListFormat(String, Pattern, Formatter<E>, Parser<E>) - Constructor for class sbrt.shell.text.AbstractListFormat
Constructs a new list format from the provided arguments.
AbstractMapEntryFormat<K,V> - Class in sbrt.shell.text
This abstract class is a skeleton implementation of MapEntryFormat.
AbstractMapEntryFormat(String, String, String) - Constructor for class sbrt.shell.text.AbstractMapEntryFormat
Constructs a new map entry format from the provided arguments.
AbstractMapEntryFormat(String) - Constructor for class sbrt.shell.text.AbstractMapEntryFormat
Constructs a new map entry format using the provided delimiter and zero-length strings as left and right paddings.
AbstractMapFormat<K,V> - Class in sbrt.shell.text
This abstract class is a skeleton implementation of MapFormat.
AbstractMapFormat() - Constructor for class sbrt.shell.text.AbstractMapFormat
 
AbstractMapInputFile<K,V> - Class in sbrt.shell.io
This abstract class is a skeleton implemenation of text-based map input files.
AbstractMapInputFile(String, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.AbstractMapInputFile
Constructs a new map input file from the provided arguments.
AbstractMapInputFile(String, FileFormat, MapFormat<K, V>) - Constructor for class sbrt.shell.io.AbstractMapInputFile
Constructs a new map input file from the provided arguments.
AbstractMapOutputFile<K,V> - Class in sbrt.shell.io
This abstract class is a skeleton implementation of MapTextOutputFile.
AbstractMapOutputFile(String, FileFormat, Set<? extends K>, MapFormat<K, V>) - Constructor for class sbrt.shell.io.AbstractMapOutputFile
Constructs a new map output file from the provided arguments.
AbstractMapOutputFile(String, FileFormat, String, MapFormat<K, V>) - Constructor for class sbrt.shell.io.AbstractMapOutputFile
Constructs a new map output file from the provided arguments.
AbstractMapOutputFile(String, FileFormat, MapFormat<K, V>) - Constructor for class sbrt.shell.io.AbstractMapOutputFile
Constructs a new vector output file from the provided arguments.
AbstractMdMatrix<R,C> - Class in sbrt.kernel.math.algebra
This abstract class is a skeleton implementation of DoubleMatrixBuilder.
AbstractMdMatrix() - Constructor for class sbrt.kernel.math.algebra.AbstractMdMatrix
 
AbstractPolynomial<V> - Class in sbrt.kernel.math
This abstract class is a skeleton implementation of Polynomial.
AbstractPolynomial(double) - Constructor for class sbrt.kernel.math.AbstractPolynomial
Constructs a new polynomial with the provided constant.
AbstractProcessManager - Class in sbrt.shell.mng
This class is a skeleton implemenation of KernelProcessManager.
AbstractProcessManager() - Constructor for class sbrt.shell.mng.AbstractProcessManager
 
AbstractProgressMonitor - Class in sbrt.kernel.utilities
This abstract class is a skeleton implementation of ProgressMonitor.
AbstractProgressMonitor() - Constructor for class sbrt.kernel.utilities.AbstractProgressMonitor
Constructs a new progress monitor.
AbstractResultsManager<R> - Class in sbrt.kernel.io
This class is a skeleton implemenation of ResultsManager.
AbstractResultsManager() - Constructor for class sbrt.kernel.io.AbstractResultsManager
Constructs a new results manager.
AbstractRxn - Class in sbrt.kernel.fba
This class is a skeleton implementation of ChemicalRxn.
AbstractRxn(LinearComb<String>, LinearComb<String>) - Constructor for class sbrt.kernel.fba.AbstractRxn
Constructs a new chemical reaction from the provided reactants and products with the given name.
AbstractSbrtFile - Class in sbrt.shell.io
This class provides a helper method for SBRT files.
AbstractSbrtFile() - Constructor for class sbrt.shell.io.AbstractSbrtFile
 
AbstractSmdMatrix<R,C> - Class in sbrt.kernel.math.algebra
This abstract class is a skeleton implementation of SmdMatrix.
AbstractSmdMatrix() - Constructor for class sbrt.kernel.math.algebra.AbstractSmdMatrix
 
actionPerformed(ActionEvent) - Method in class sbrt.shell.gui.TextPaneGui
Responds to the provided action event.
active() - Method in class sbrt.kernel.fba.proc.FluxActivityProcess.Results
Returns the number of active fluxes.
ACTIVITY_COUNT_FILE_NAME - Static variable in class sbrt.shell.mng.fba.FluxActivityManager
The keyword used to denote the name of the activity count output file.
ACTIVITY_VECTOR_FILE_NAME - Static variable in class sbrt.shell.mng.fba.FluxActivityManager
The keyword used to denote the name of the activity vector output file.
add(double) - Method in class sbrt.kernel.math.HashLinearComb
Adds, in the mathematical sense, the provided constant to this linear combination.
add(LinearComb<? extends V>) - Method in class sbrt.kernel.math.HashLinearComb
Adds, in the mathematical sense, the provided linear combination to this linear combination.
add(LinearComb<? extends V>) - Method in interface sbrt.kernel.math.LinearComb
Adds, in the mathematical sense, the provided linear combination to this linear combination.
add(double) - Method in interface sbrt.kernel.math.LinearComb
Adds, in the mathematical sense, the provided constant to this linear combination.
add(E) - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.add(Object).
add(E) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.add(Object).
add(int, E) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.add(int, Object).
add(E) - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.add(Object).
addAll(Collection<? extends E>) - Method in class sbrt.kernel.utilities.UnmodifiableCollection
See Collection.addAll(Collection).
addAll(Collection<? extends E>) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.addAll(Collection).
addAll(int, Collection<? extends E>) - Method in class sbrt.kernel.utilities.UnmodifiableList
See List.addAll(int, Collection).
addAll(Collection<? extends E>) - Method in class sbrt.kernel.utilities.UnmodifiableSet
See Set.addAll(Collection).
addData(S) - Method in class sbrt.kernel.io.ListResultsManager
Adds the provided results to this results manager.
addData(S) - Method in interface sbrt.kernel.io.ResultsManager
Adds data to this results manager.
addData(S) - Method in class sbrt.kernel.io.SingleRm
Adds the provided results to this results manager.
addData(Map<? extends K, ? extends V>) - Method in class sbrt.shell.io.ComoFile
Writes the appropriate values of the provided vector to this file.
addData(S) - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Writes the appropriate values in the provided FbaOptimizer.Results to this file.
addData(Map<String, Double>) - Method in class sbrt.shell.io.fba.ColumnOrFbaOptOutputFile
Writes the appropriate values in the provided map to this file.
addData(FbaOptimizer<F>.Results) - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Writes the appropriate values in the provided FbaOptimizer.Results to this file.
addData(Map<String, Double>) - Method in class sbrt.shell.io.fba.RowOrFbaOptOutputFile
Writes the appropriate values in the provided map to this file.
addData(FbaOptimizer<F>.Results) - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Writes the appropriate values in the provided FbaOptimizer.Results to this file.
addData(Map<String, Double>) - Method in class sbrt.shell.io.fba.SerFbaOptOutputFile
Writes the appropriate values in the provided map to this file.
addData(Map<? extends K, ? extends V>) - Method in interface sbrt.shell.io.MapOutputFile
Writes the appropriate values of the provided map to this file.
addData(S) - Method in class sbrt.shell.io.MultiOutputFiles
Adds the provided results to the current file.
addData(Map.Entry<? extends K, ? extends V>) - Method in class sbrt.shell.io.RomoFile
Writes the provided value to this file if the variable is contained in the set returned by AbstractMapOutputFile.getFilterKeys().
addData(Map<? extends K, ? extends V>) - Method in class sbrt.shell.io.RomoFile
Writes the appropriate values of the provided vector to this file.
addData(S) - Method in class sbrt.shell.io.SerializedOutputFile
Adds data to this output file.
addData(Map<? extends K, ? extends V>) - Method in class sbrt.shell.io.SmoFile
Writes the appropriate values of the provided map to this file.
addData(S) - Method in class sbrt.shell.io.TextOutputFile
Adds data to this output file.
addData(DoubleMatrix<?, String>) - Method in class sbrt.shell.mng.fba.ExtremeCurrentManager.Rm
Adds data to this results manager.
addedConstraints() - Method in interface sbrt.kernel.fba.Fluxome
Returns the total number of constraints added to this fluxome.
addedConstraints() - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Returns the total number of constraints added to this fluxome.
addedConstraints() - Method in class sbrt.kernel.fba.MixedFluxomeV1
Returns the total number of constraints added to this fluxome.
ALGORITHM - Static variable in class sbrt.shell.mng.AbstractProcessManager
The keyword used to denote an algorithm.
ALGORITHM - Static variable in class sbrt.shell.mng.fba.RandomFluxVectorManager
The keyword used to denote a random flux vector algorithm.
ALL_RXNS - Static variable in class sbrt.shell.text.fba.RxnNameSetFormatV1
The string used to indicate every reaction in a fluxome.
ALWAYS_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 always-active reactions.
alwaysActive() - Method in class sbrt.kernel.fba.proc.FluxPlasticityProcess.Results
Returns the number of fluxes that are always active.
AMPERSAND - Static variable in class sbrt.shell.text.SpecialChars
&
AmpersandSetFormat<E> - Class in sbrt.shell.text
This class is used to define a format for ampersand-delimited sets.
AmpersandSetFormat(SimpleFormat<E>) - Constructor for class sbrt.shell.text.AmpersandSetFormat
Constructs a new ampersand-delimited set format with the provided element format.
AmpersandSetFormat(Formatter<E>, Parser<E>) - Constructor for class sbrt.shell.text.AmpersandSetFormat
Constructs a new ampersand-delimited set format with the provided element format.
And<C> - Class in sbrt.kernel.utilities
This class is used to represent the logical relationship "and".
And(Collection<C>) - Constructor for class sbrt.kernel.utilities.And
Constructs a new "and" relationship.
AppInputFileLineFormat - Interface in sbrt.shell.text
This interface is used to represent the format of lines in process input files.
AppInputFileLineFormatVersion1 - Class in sbrt.shell.text
This class is a concrete implementation of AppInputFileLineFormat.
AppInputFileLineFormatVersion1() - Constructor for class sbrt.shell.text.AppInputFileLineFormatVersion1
Constructs a new process input file line format.
ApplicationException - Exception in sbrt.shell
This class is the superclass of those exceptions that are expected to be thrown from the SBRT shell.
ApplicationException(String) - Constructor for exception sbrt.shell.ApplicationException
Constructs a new process exception with the provided error message.
ApplicationException(String, Throwable) - Constructor for exception sbrt.shell.ApplicationException
Constructs a new process exception with the provided error message and cause.
areEquiv(Double, Double) - Method in class sbrt.kernel.math.DoubleEquiv
Indicates if the provided values are equivalent.
areEquiv(double, double) - Method in class sbrt.kernel.math.DoubleEquiv
Indicates if the provided values are equivalent.
areEquiv(A, B) - Method in interface sbrt.kernel.math.EquivTester
Tests the provided objects for equivalence.
areEquiv(Interval, Interval) - Method in class sbrt.kernel.math.IntervalEquiv
Indicates if the provided intervals are equivalent.
areReqCatalysts(Collection<String>, String) - Method in interface sbrt.kernel.fba.CatalyzedFluxome
Indicates if the reaction with the provided name could function if each of the catalysts in the provided collection were simultaneously absent.
areReqCatalysts(Collection<String>, String) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if the reaction with the provided name could function if each of the catalysts in the provided collection were simultaneously absent.
areReqCatalysts(Collection<String>, String) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if the reaction with the provided name could function if each of the catalysts in the provided collection were simultaneously absent.
areRxnNames(Collection<String>) - Method in interface sbrt.kernel.fba.Fluxome
Indicates if every string in the provided collection is the name of a reaction contained in this fluxome.
areRxnNames(Collection<String>) - Method in class sbrt.kernel.fba.IrrevRxnFluxomeV1
Indicates if every string in the provided collection is the name of a reaction contained in this fluxome.
areRxnNames(Collection<String>) - Method in class sbrt.kernel.fba.MixedFluxomeV1
Indicates if every string in the provided collection is the name of a reaction contained in this fluxome.
areSame(Map<?, Double>, Map<?, Double>, double) - Method in class sbrt.kernel.math.VectorComparer
Indicates if the provided numerical vectors are equivalent.
ARROW - Static variable in class sbrt.shell.text.chem.IrrevRxnFormatV1
The arrow used to signify an irreversible reaction.
ARROW - Static variable in class sbrt.shell.text.chem.RevRxnFormatV1
The arrow used to signify a reversible reaction.
ARROW - Static variable in class sbrt.shell.text.fba.IrrevRxnFormatV1
The arrow used to signify an irreversible reaction.
ARROW - Static variable in class sbrt.shell.text.fba.IrrevRxnFormatV2
The arrow used to signify an irreversible reaction.
ARROW - Static variable in class sbrt.shell.text.fba.RevRxnFormatV1
The arrow used to signify an irreversible reaction.
ARROW - Static variable in class sbrt.shell.text.fba.RevRxnFormatV2
The arrow used to signify an irreversible reaction.
ASTERICK - Static variable in class sbrt.shell.text.SpecialChars
*
asUnmodifiable() - Method in class sbrt.kernel.utilities.DiscreteProgressMonitor
Returns this progress monitor as an immutable object.
asUnmodifiable() - Method in interface sbrt.kernel.utilities.MutableProgressMonitor
Returns this progress monitor as an immutable object.
asUnmodifiable() - Method in class sbrt.kernel.utilities.PercentProgressMonitor
Returns this progress monitor as an immutable object.
AT - Static variable in class sbrt.shell.text.SpecialChars
@

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