Uses of Interface
sbrt.shell.text.Parser

Packages that use Parser
sbrt.shell.io Provides classes and interfaces for reading and writing files. 
sbrt.shell.text Provides classes and interfaces for defining formats for basic objects. 
sbrt.shell.text.chem Provides classes and interfaces for defining formats for chemistry related objects. 
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 Parser in sbrt.shell.io
 

Methods in sbrt.shell.io that return Parser
 Parser<E> TextInputFile.getLineFormat()
          Returns the format used to parse lines of this file.
 

Constructors in sbrt.shell.io with parameters of type Parser
TextInputFile(java.lang.String fileName, FileFormat fileFormat, Parser<E> fileLineFormat)
          Constructs a new text input file using the provided arguments.
TextInputFile(java.lang.String fileName, FileFormat fileFormat, Parser<E> fileLineFormat, java.util.Collection<java.lang.Character> commentCharacters)
          Constructs a new text input file using the provided arguments.
TextInputFile(java.lang.String fileName, Parser<E> fileLineFormat)
          Constructs a new text input file using the provided arguments.
 

Uses of Parser in sbrt.shell.text
 

Subinterfaces of Parser in sbrt.shell.text
 interface BooleanFormat
          This interface is used to represent a format for boolean values.
 interface CollectionFormat<E>
          This interface is used to represent collection formats.
 interface DoubleFormat
          This interface is used to represent a format for double precision numbers.
 interface IntegerFormat
          This interface is used to represent a format for integers.
 interface LinkedHashSetFormat<E>
          This interface is used to represent LinkedHashSet formats.
 interface ListFormat<E>
          This interface is used to represent list formats.
 interface LongFormat
          This interface is used to represent a format for longs.
 interface PercentFormat
          This interface is used to represent a format for percentages.
 interface SimpleFormat<T>
          This interface is used to represent simple formats.
 

Classes in sbrt.shell.text that implement Parser
 class AbstractLinkedHashSetFormat<E>
          This abstract class is a skeleton implementation of LinkedHashSetFormat.
 class AbstractListFormat<E>
          This abstract class is a skeleton implementation of ListFormat.
 class AmpersandSetFormat<E>
          This class is used to define a format for ampersand-delimited sets.
 class BoolRelFormatV1<E>
          This interface is used to represent boolean relationship formats.
 class DoubleFormatV1
          This class is a concrete implementation of DoubleFormat.
 class DoubleFormatV2
          This class is a concrete implementation of DoubleFormat.
 class FileFormatFormat
          This class is used to represent formats for types of file formats.
 class IntegerFormatV1
          This class is a concrete implementation of IntegerFormat.
 class LongFormatV1
          This class is a concrete implementation of LongFormat.
 class NonEmptyStringFormat
          This class is used to define a format for String objects.
 class PercentFormatVersion1
          This class is a concrete implementation of PercentFormat.
 class PipeListFormat<E>
          This class is used to define a format for pipe-delimited lists.
 class PipeSetFormat<E>
          This class is used to define a format for pipe-delimited sets.
 class SimpleListFormat<E>
          This interface is used to wrap ListFormat objects as SimpleFormat objects.
 class SimpleSetFormat<E>
          This interface is used to wrap ListFormat objects as SimpleFormat objects.
 class StringFormat
          This class is used to define a format for String objects.
 class TabListFormat<E>
          This class is used to define a format for tab-delimited lists.
 class TabSetFormat<E>
          This class is used to define a format for tab-delimited sets.
 class TrueFalseFormat
          This class is used to define a format for true/false values.
 class WhitespaceListFormat<E>
          This class is used to define a format for whitespace-delimited lists.
 class WhitespaceSetFormat<E>
          This class is used to define a format for whitespace-delimited sets.
 class YesNoFormat
          This class is used to define a format for yes/no values.
 

Methods in sbrt.shell.text that return Parser
 Parser<E> ListFormat.getElementParser()
          Returns the parser for the elements of this list format.
 Parser<E> AbstractListFormat.getElementParser()
          Returns the parser for the elements of this set format.
 Parser<E> BoolRelFormatV1.getElementParser()
          Returns the parser for the elements of this set format.
 Parser<E> SimpleSetFormat.getElementParser()
          Returns the parser for the elements of this set format.
 Parser<E> SimpleListFormat.getElementParser()
          Returns the parser for the elements of this list format.
 Parser<E> AbstractLinkedHashSetFormat.getElementParser()
          Returns the parser for the elements of this set format.
 Parser<E> LinkedHashSetFormat.getElementParser()
          Returns the parser for the elements of this set format.
 Parser<K> AbstractMapFormat.getKeyParser()
          Returns the parser used for keys.
 Parser<V> AbstractMapFormat.getValueParser()
          Returns the parser used for values.
 

Constructors in sbrt.shell.text with parameters of type Parser
AbstractLinkedHashSetFormat(java.lang.String delimiter, java.util.regex.Pattern regex, Formatter<E> elementFormatter, Parser<E> elementParser)
          Constructs a new LinkedHashSet format from the provided arguments.
AbstractListFormat(java.lang.String delimiter, java.util.regex.Pattern regex, Formatter<E> elementFormatter, Parser<E> elementParser)
          Constructs a new list format from the provided arguments.
AmpersandSetFormat(Formatter<E> elementFormatter, Parser<E> elementParser)
          Constructs a new ampersand-delimited set format with the provided element format.
EqualsMapFormatV1(Formatter<K> keyFormatter, Parser<K> keyParser, Formatter<V> valueFormatter, Parser<V> valueParser)
          Constructs a new map format using the provided key and value formats.
EqualsMapFormatV1(Formatter<K> keyFormatter, Parser<K> keyParser, Formatter<V> valueFormatter, Parser<V> valueParser)
          Constructs a new map format using the provided key and value formats.
PipeListFormat(Formatter<E> elementFormatter, Parser<E> elementParser)
          Constructs a new pipe-delimited list format with the provided element format.
PipeSetFormat(Formatter<E> elementFormatter, Parser<E> elementParser)
          Constructs a new pipe-delimited set format with the provided element format.
TabListFormat(Formatter<E> elementFormatter, Parser<E> elementParser)
          Constructs a new tab-delimited list format with the provided element format.
TabSetFormat(Formatter<E> elementFormatter, Parser<E> elementParser)
          Constructs a new tab-delimited set format with the provided element format.
WhitespaceListFormat(Formatter<E> elementFormatter, Parser<E> elementParser)
          Constructs a new whitespace-delimited list format with the provided element format.
WhitespaceSetFormat(Formatter<E> elementFormatter, Parser<E> elementParser)
          Constructs a new whitespace-delimited set format with the provided element format.
 

Uses of Parser in sbrt.shell.text.chem
 

Subinterfaces of Parser in sbrt.shell.text.chem
 interface CatalystFormat
          This interface is used to represent the formats of catalysts in chemical reactions.
 interface ChemSpeciesFormat
          This interface is used to represent the formats of chemical species.
 interface RxnNameFormat<T>
          This interface is used to represent formats for the names of chemical reactions.
 

Classes in sbrt.shell.text.chem that implement Parser
 class CatalystFormatV1
          This class is a concrete implementation of CatalystFormat.
 class CatalystFormatV2
          This class is a concrete implementation of CatalystFormat.
 class ChemSpeciesFormatV1
          This class is a concrete implemenation of ChemSpeciesFormat.
 class IrrevRxnFormatV1
          This class is used to format irreversible chemical reactions.
 class RevRxnFormatV1
          This class is used to format reversible chemical reactions.
 class RxnNameFormatV1
          This class is a concrete implementation of RxnNameFormat.
 

Uses of Parser in sbrt.shell.text.fba
 

Subinterfaces of Parser in sbrt.shell.text.fba
 interface CatalystListFormat
          This interface is used to represent the formats of lists of catalyst names.
 interface CatalystSetFormat
          This interface is used to represent the formats of sets of enzyme names.
 interface FbaOptHeaderParser
          This interface is used to represent parsers for headers used in writing files of FBA optimization data.
 interface RxnNameExprFormat<E extends MathExpr<S>,S>
          This interface is used to represent formats for mathematical expressions of reaction names.
 interface RxnNameListFormat
          This interface is used to represent the formats of collections of reaction names.
 interface RxnNameOrExprFormat
          This interface is used to represent formats for reaction names and mathematical expressions of reaction names.
 interface RxnNameSetFormat
          This interface is used to represent the formats of collections of reaction names.
 

Classes in sbrt.shell.text.fba that implement Parser
 class CatalystListFormatV1
          This class is a concrete implemenation of CatalystListFormat.
 class CatalystSetFormatV1
          This class is a concrete implemenation of CatalystSetFormat.
 class CatalystVerifier
          This class is used to ensure catalysts exist in a given CatalyzedFluxome.
 class ChemSpeciesVerifier
          This class is used to ensure chemical species exist in a given Fluxome.
 class FbaOptHeaderParserV1
          This class is a concrete implemenation of FbaOptHeaderParser.
 class IrrevRxnFormatV2
          This class is used to format irreversible reactions for use in flux balance analysis.
 class RevRxnFormatV2
          This class is used to format reversible reactions for use in flux balance analysis.
 class RxnFormatV1
          This class is used to format reactions for use in flux balance analysis.
 class RxnNameExprFormatV1
          This class is used to format linear combinations of reaction names.
 class RxnNameListFormatV1
          This class is a concrete implemenation of RxnNameListFormat.
 class RxnNameOrExprFormatV1
          This class is a concrete implemenation of RxnNameOrExprFormat.
 class RxnNameSetFormatV1
          This class is a concrete implemenation of RxnNameSetFormat.
 class RxnNameVerifier
          This class is used to ensure reaction names exist in a given Fluxome.
 

Uses of Parser in sbrt.shell.text.math
 

Subinterfaces of Parser in sbrt.shell.text.math
 interface CoeffFormat
          This interface is used to represent the format of coefficients of mathematical expressions.
 interface DirEdgeFormat<N>
          This interface is used to represent formats for the edges of directed graphs.
 interface IndexPairFormat<R,C>
          This interface is used to represent formats for pairs of indices.
 interface IntervalFormat
          This interface is used to represent formats for intervals.
 interface LinearCombFormat<V>
          This interface is used to represent formats for linear combinations.
 interface LinearCombTermFormat<V>
          This interface is used to represent the formats of terms from linear combinations.
 interface MathExprFormat<E extends MathExpr<V>,V>
          This interface is used to represent formats for linear combinations.
 interface MatrixElementFormat<R,C,E>
          This interface is used to represent formats for matrix elements.
 

Classes in sbrt.shell.text.math that implement Parser
 class BoundedIntervalFormatV1
          This class is a concrete implementation of IntervalFormat.
 class CoeffFormatV1
          This class is a concrete implementation of CoeffFormat.
 class CoeffFormatV2
          This class is a concrete implementation of CoeffFormat.
 class DirEdgeFormatV1<N>
          This class is a concrete implementation of DirEdgeFormat.
 class IndexPairFormatV1<R,C>
          This class is a concrete implementation of IndexPairFormat.
 class IntervalFormatV1
          This class is a concrete implementation of IntervalFormat.
 class LinCombTermFormatV1<V>
          This class is a concrete implementation of LinearCombTermFormat.
 class LinCombTermFormatV2<V>
          This class is a concrete implementation of LinearCombTermFormat.
 class LinearCombFormatV1<V>
          This class is a concrete implementation of LinearCombFormat.
 class LinearCombFormatV2<V>
          This class is a concrete implementation of LinearCombFormat.
 class MatrixElementFormatV1<R,C>
          This class is a concrete implementation of MatrixElementFormat.
 class SenseFormat
          This class is used to represent formats of optimization senses.