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See:
Description
Interface Summary | |
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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 | |
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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 . |
Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis.
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