Package sbrt.shell.text.fba

Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis.

See:
          Description

Interface Summary
CatalystListFormat This interface is used to represent the formats of lists of catalyst names.
CatalystSetFormat This interface is used to represent the formats of sets of enzyme names.
ConstraintsFileLineFormat<E> This interface is used to represent formats for flux constraints files.
FbaOptFileLineFormat This interface is used to represent formats of FBA optimization file lines.
FbaOptHeaderFormatter This interface is used to represent formatters for headers used in writing files of FBA optimization data.
FbaOptHeaderParser This interface is used to represent parsers for headers used in writing files of FBA optimization data.
FluxCapFormat This interface is used to represent the formats of lines of flux cap-containing files.
FluxomeSolutionFileLineFormat This interface is used to represent formats for solutions to the linear system of equations formed by a fluxome.
FluxVectorFormat This interface is used to represent formats for flux vectors.
RxnNameExprFormat<E extends MathExpr<S>,S> This interface is used to represent formats for mathematical expressions of reaction names.
RxnNameListFormat This interface is used to represent the formats of collections of reaction names.
RxnNameOrExprFormat This interface is used to represent formats for reaction names and mathematical expressions of reaction names.
RxnNameSetFormat This interface is used to represent the formats of collections of reaction names.
 

Class Summary
BiggBracketParserV1 This class is used to parse bracketed expressions contained in SBML files from the BiGG Database.
BiggRxnNodeParser This class is used to make a direct translation from SBML 'reaction' nodes into Systems Biology Research Tool objects.
CatalystListFormatV1 This class is a concrete implemenation of CatalystListFormat.
CatalystSetFormatV1 This class is a concrete implemenation of CatalystSetFormat.
CatalystVerifier This class is used to ensure catalysts exist in a given CatalyzedFluxome.
ChemSpeciesVerifier This class is used to ensure chemical species exist in a given Fluxome.
ConstraintsFileLineFormatV1 This class is a concrete implemenation of ConstraintsFileLineFormat.
ConstraintsFileLineFormatV2 This class is a concrete implemenation of ConstraintsFileLineFormat.
FbaOptFileLineFormatV1 This class is a concrete implementation of FbaOptFileLineFormat.
FbaOptHeaderFormatterV1 This class is a concrete implemenation of FbaOptHeaderFormatter.
FbaOptHeaderParserV1 This class is a concrete implemenation of FbaOptHeaderParser.
FluxCapFormatV1 This class is a concrete implementation of FluxCapFormat.
FluxomeSolFileLineFormatV1 This class is a concrete implemenation of FluxomeSolutionFileLineFormat.
FluxVectorFormatV1 This class is a concrete implemenation of FluxVectorFormat.
IrfFormatV1 This class is used to format irreversible reaction fluxome files.
IrrevRxnFormatV1 This class is used to format irreversible reactions for use in flux balance analysis.
IrrevRxnFormatV2 This class is used to format irreversible reactions for use in flux balance analysis.
MixedFluxomeFormatV1 This class is used to format irreversible reaction fluxome files.
PalssonRxnNodeParser This class is used to make a direct translation from SBML 'reaction' nodes into Systems Biology Research Tool objects.
RevRxnFormatV1 This class is used to format reversible reactions for use in flux balance analysis.
RevRxnFormatV2 This class is used to format reversible reactions for use in flux balance analysis.
RxnFormatV1 This class is used to format reactions for use in flux balance analysis.
RxnNameExprFormatV1 This class is used to format linear combinations of reaction names.
RxnNameListFormatV1 This class is a concrete implemenation of RxnNameListFormat.
RxnNameOrExprFormatV1 This class is a concrete implemenation of RxnNameOrExprFormat.
RxnNameSetFormatV1 This class is a concrete implemenation of RxnNameSetFormat.
RxnNameVerifier This class is used to ensure reaction names exist in a given Fluxome.
 

Package sbrt.shell.text.fba Description

Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis.