Index (lib 2.1 API)

A B C D E F G H I J L M N O P R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v = 0 or g(μ) ⋅ A ⋅ v + B ⋅ v = 0 with g(μ) being some continuous nonlinear function of μ;
AbstractADBAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.adb
AbstractADBAnnotator(AnnotateDB, ADBAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.adb.AbstractADBAnnotator
AbstractAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation
AbstractAnnotator() - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
AbstractAnnotator(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
AbstractBiGGAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
AbstractBiGGAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
AbstractBiGGAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
AbstractFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
AbstractFixer() - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer
AbstractFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer
AbstractPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
AbstractPolisher(PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
AbstractPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
adb - Variable in class de.uni_halle.informatik.biodata.mp.annotation.adb.AbstractADBAnnotator
adbAnnotationParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
ADBAnnotationParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
ADBAnnotationParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
ADBAnnotationParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
ADBReactionsAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.adb
ADBReactionsAnnotator(AnnotateDB, ADBAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBReactionsAnnotator
ADBSBMLAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.adb
ADBSBMLAnnotator(AnnotateDB, ADBAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSBMLAnnotator
ADBSpeciesAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.adb
ADBSpeciesAnnotator(AnnotateDB, ADBAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSpeciesAnnotator
add(String, double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
add(String, String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
ADD_ADB_ANNOTATIONS - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions: If set to true, annotations will be added to species and reactions from AnnotateDB also.
ADD_GENERIC_TERMS - Static variable in interface de.uni_halle.informatik.biodata.mp.parameters.GeneralOptions: Set this option to true if generic top-level annotations, such as 'process' should not be applied.
addAll(Map<String, String>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
addAnnotations(GeneProduct, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator: Adds annotations to a gene product based on a given BiGGId.
addBQB_IS_AnnotationsFromADB(Annotation, String, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.AbstractADBAnnotator
addChild(Node) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
addChild(Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
addGenericTerms - Variable in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
addGenericTerms() - Method in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
addJavaRegexCaptureGroup(String) - Static method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURIUtils
addParent(Node) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
addParent(Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
addResource(String, CVTerm, String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ReactionParser: Tries to update a resource according to pre-defined rules.
annotate(List<Compartment>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCompartmentsAnnotator
annotate(List<GeneProduct>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator: This method handles the annotation of gene products in a given SBML model.
annotate(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBReactionsAnnotator
annotate(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator: Delegates the annotation process for each reaction in the given SBML model.
annotate(List<Species>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSpeciesAnnotator
annotate(List<Species>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator: Delegates annotation processing for all chemical species contained in the Model.
annotate(List<SBMLElement>) - Method in interface de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases
annotate(Compartment) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCompartmentsAnnotator: Annotates the compartment with BiGG and SBO terms.
annotate(GeneProduct) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator: Annotates a gene product by adding relevant metadata and references.
annotate(Model) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator: Annotates the Model with relevant metadata and delegates the annotation of contained elements such as Compartment, Species, Reaction, and GeneProduct.
annotate(Model) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGPublicationsAnnotator
annotate(Model) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCAnnotator
annotate(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBReactionsAnnotator
annotate(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator: Annotates a reaction by setting its name, SBO term, and additional annotations.
annotate(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSBMLAnnotator
annotate(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSBMLAnnotator: Annotates an SBMLDocument using data from the BiGG Knowledgebase.
annotate(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSpeciesAnnotator
annotate(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator: This method annotates a species with various details fetched from the BiGG Knowledgebase.
annotate(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCSpeciesAnnotator
annotate(SBMLElement) - Method in interface de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases
ANNOTATE_WITH_BIGG - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions: If set to true, the model will be annotated with data from BiGG Models database.
AnnotateDB - Class in de.uni_halle.informatik.biodata.mp.db.adb
AnnotateDB() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB
AnnotateDBContract - Class in de.uni_halle.informatik.biodata.mp.db.adb
AnnotateDBContract() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract
AnnotateDBContract.Constants - Class in de.uni_halle.informatik.biodata.mp.db.adb
AnnotateDBContract.Constants.Column - Class in de.uni_halle.informatik.biodata.mp.db.adb
AnnotateDBContract.Constants.Table - Class in de.uni_halle.informatik.biodata.mp.db.adb
AnnotateDBOptions - Interface in de.uni_halle.informatik.biodata.mp.db.adb: This interface provides options for connecting to the ADB database.
annotateWithAdb - Variable in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
annotateWithAdb() - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
annotateWithBiGG - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
annotateWithBiGG() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
annotation() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
ANNOTATION_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
AnnotationException - Exception in de.uni_halle.informatik.biodata.mp.annotation
AnnotationException(String, Exception) - Constructor for exception de.uni_halle.informatik.biodata.mp.annotation.AnnotationException
AnnotationOptions - Interface in de.uni_halle.informatik.biodata.mp.annotation
AnnotationParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
AnnotationParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
AnnotationParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
AnnotationPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
AnnotationPolisher(PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.AnnotationPolisher
AnnotationPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.AnnotationPolisher
AnnotationsSorter - Class in de.uni_halle.informatik.biodata.mp.annotation
AnnotationsSorter() - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.AnnotationsSorter
archiveFile() - Method in exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException
asString(Array) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
asString(Array, String, int) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
ATP_MAINTENANCE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Pattern for ATP maintenance reactions, which are typically denoted by IDs containing 'ATPM' in any case.
author - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Can be part of the ModelField.description.

B

b - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: The bound vector of metabolite concentration change rates (usually but not always all zero, i.e., steady-state): S ⋅ v = b.
B - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v = 0 or g(μ) ⋅ A ⋅ v + B ⋅ v = 0 with g(μ) being some continuous nonlinear function of μ;
BASE_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
bigg - Variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
BIGG_ANNOTATION_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
BIGG_GENE_ID_PATTERN - Static variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
BIGG_METABOLITE - Static variable in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants
BIGG_REACTION - Static variable in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants
BiGGAnnotationException - Exception in de.uni_halle.informatik.biodata.mp.annotation.bigg
BiGGAnnotationException(String, Exception, Object) - Constructor for exception de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGAnnotationException
biggAnnotationParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
biGGAnnotationParameters - Variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
BiGGAnnotationParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
BiGGAnnotationParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
BiGGAnnotationParameters(boolean, boolean, String, BiGGNotesParameters, DBParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
BiGGAnnotationParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
BiGGCompartmentsAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg: This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
BiGGCompartmentsAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCompartmentsAnnotator
BiGGCompartmentsAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCompartmentsAnnotator
BiGGCVTermAnnotator<T extends org.sbml.jsbml.SBase> - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg: Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
BiGGCVTermAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCVTermAnnotator
BiGGCVTermAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCVTermAnnotator
BiGGDB - Class in de.uni_halle.informatik.biodata.mp.db.bigg: This class provides a connection to the BiGG database.
BiGGDB() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
BiGGDB.ForeignReaction - Class in de.uni_halle.informatik.biodata.mp.db.bigg: Represents a reaction from an external data source mapped to the BiGG database, including its compartment details.
BiGGDBContract - Class in de.uni_halle.informatik.biodata.mp.db.bigg
BiGGDBContract.Constants - Class in de.uni_halle.informatik.biodata.mp.db.bigg
BiGGDBContract.Constants.Column - Class in de.uni_halle.informatik.biodata.mp.db.bigg
BiGGDBContract.Constants.Table - Class in de.uni_halle.informatik.biodata.mp.db.bigg
BiGGDBOptions - Interface in de.uni_halle.informatik.biodata.mp.db.bigg
BiGGDocumentNotesProcessor - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
BiGGDocumentNotesProcessor(BiGGDB, BiGGAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGDocumentNotesProcessor
BiGGFBCAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
BiGGFBCAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCAnnotator
BiGGFBCSpeciesAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
BiGGFBCSpeciesAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCSpeciesAnnotator
BiGGGeneProductAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc: Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
BiGGGeneProductAnnotator(BiGGGeneProductReferencesAnnotator, BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
BiGGGeneProductReferencesAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
BiGGGeneProductReferencesAnnotator() - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductReferencesAnnotator
BiGGId - Class in de.uni_halle.informatik.biodata.mp.db.bigg: Represents a BiGG identifier used to uniquely identify various biological entities such as reactions, metabolites, and genes within the BiGG database.
BiGGId() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
BiGGId(String) - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
BiGGId(String, String, String, String) - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
BiGGModelAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg: This class is responsible for annotating an SBML Model with relevant metadata and references.
BiGGModelAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator
BiGGModelAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator
BiGGNotesParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
BiGGNotesParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
BiGGNotesParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
BiGGPublicationsAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
BiGGPublicationsAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGPublicationsAnnotator
BiGGReactionsAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg: This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
BiGGReactionsAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
BiGGReactionsAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
BiGGSBMLAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg: This class is responsible for annotating SBML models using data from the BiGG database.
BiGGSBMLAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSBMLAnnotator
BiGGSBMLAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSBMLAnnotator
BiGGSpeciesAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg: This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
BiGGSpeciesAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator
BiGGSpeciesAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator
BIOMASS_CASE_INSENSITIVE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Case-insensitive pattern for biomass reactions, matching IDs that include the word 'biomass' in any case.
BIOMASS_CASE_SENSITIVE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Case-sensitive pattern for biomass reactions, matching IDs that specifically contain 'BIOMASS'.
BundleNames - Class in de.uni_halle.informatik.biodata.mp.logging
BundleNames() - Constructor for class de.uni_halle.informatik.biodata.mp.logging.BundleNames

C

c - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: The objective function vector for max(c' ⋅ v) for corresponding reactions.
checkCreateOutDir(File) - Static method in class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils: Creates output directory or output parent directory, if necessary
checkId(String) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils: Necessary to check for a special whitespace (code 160) at beginning of id (iCHOv1.mat, possibly other models) and to remove trailing ';'
citations - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Literature references for the reactions.
CLI_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
close() - Method in class de.uni_halle.informatik.biodata.mp.db.PostgresConnectionPool
close() - Method in class de.uni_halle.informatik.biodata.mp.io.DeleteOnCloseFileInputStream
COBRAUtils - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
COBRAUtils() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
coefficients - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: TODO
Column() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Column
Column() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.Column
COMBINE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
COMBINE_SPECIFICATION - Static variable in class de.uni_halle.informatik.biodata.mp.io.CombineArchive
CombineArchive - Class in de.uni_halle.informatik.biodata.mp.io: The CombineArchive class provides functionality to create a COMBINE archive from an SBML document.
CombineArchive(SBMLDocument, File) - Constructor for class de.uni_halle.informatik.biodata.mp.io.CombineArchive
comments - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: These are human-readable notes for reactions.
compareTo(IdentifiersOrgURI) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
CompartmentFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
CompartmentFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.CompartmentFixer
compartmentId - Variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB.ForeignReaction
compartmentName - Variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB.ForeignReaction
CompartmentPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing: This class is responsible for polishing the properties of a compartment in an SBML model to ensure compliance with standards and completeness.
CompartmentPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.CompartmentPolisher
Compartments - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
Compartments() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
confidenceScores - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Confidence score for each reaction.
Constants() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants
Constants() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants
convertAssociationsToFBCV2(Reaction, boolean) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductAssociationsProcessor
convertGene(GeneProduct) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
convertGenes(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
convertMetabolite(Species) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
convertMetabolites(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
convertModel(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
convertReaction(Reaction) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
convertReactions(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
createGeneId(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
createMetaboliteId(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
createReactionId(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
createReactionId(String, boolean) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId: Creates a BiGG ID for a reaction based on the provided string identifier.
createSubsystemLink(Reaction, Member) - Static method in class de.uni_halle.informatik.biodata.mp.util.ext.groups.GroupsUtils: Establishes a link between a reaction and a subsystem member by setting the member's reference to the reaction.
csense - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: The csense field expresses equality constraints in the model.
CV_TERM_DESCRIBED_BY_PUBMED_GROWTH_UNIT - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
CV_TERM_IS_SUBSTANCE_UNIT - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
CV_TERM_IS_TIME_UNIT - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
CV_TERM_IS_UO_GRAM - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
CV_TERM_IS_UO_HOUR - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
CV_TERM_IS_UO_MMOL - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
CV_TERM_IS_UO_SECOND - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
CV_TERM_IS_VERSION_OF_UO_MOLE - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
CV_TERM_IS_VERSION_OF_UO_SECOND - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
CV_TERM_IS_VOLUME_UNIT - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher

D

DAG - Class in de.uni_halle.informatik.biodata.mp.eco
DAG(Term) - Constructor for class de.uni_halle.informatik.biodata.mp.eco.DAG
data() - Method in exception de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGAnnotationException
DATA - Enum constant in enum class de.uni_halle.informatik.biodata.mp.reporting.ReportType
DB_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
dbName() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
DBNAME - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
DBNAME - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions
dbParameters - Variable in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
dbParameters - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
dbParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
dbParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
DBParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
DBParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
DBParameters(String, String, String, Integer, String) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
de.uni_halle.informatik.biodata.mp.annotation - package de.uni_halle.informatik.biodata.mp.annotation
de.uni_halle.informatik.biodata.mp.annotation.adb - package de.uni_halle.informatik.biodata.mp.annotation.adb
de.uni_halle.informatik.biodata.mp.annotation.bigg - package de.uni_halle.informatik.biodata.mp.annotation.bigg
de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc - package de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
de.uni_halle.informatik.biodata.mp.db - package de.uni_halle.informatik.biodata.mp.db
de.uni_halle.informatik.biodata.mp.db.adb - package de.uni_halle.informatik.biodata.mp.db.adb
de.uni_halle.informatik.biodata.mp.db.bigg - package de.uni_halle.informatik.biodata.mp.db.bigg
de.uni_halle.informatik.biodata.mp.eco - package de.uni_halle.informatik.biodata.mp.eco
de.uni_halle.informatik.biodata.mp.fixing - package de.uni_halle.informatik.biodata.mp.fixing
de.uni_halle.informatik.biodata.mp.fixing.ext.fbc - package de.uni_halle.informatik.biodata.mp.fixing.ext.fbc
de.uni_halle.informatik.biodata.mp.fixing.ext.groups - package de.uni_halle.informatik.biodata.mp.fixing.ext.groups
de.uni_halle.informatik.biodata.mp.io - package de.uni_halle.informatik.biodata.mp.io
de.uni_halle.informatik.biodata.mp.io.parsers.cobra - package de.uni_halle.informatik.biodata.mp.io.parsers.cobra
de.uni_halle.informatik.biodata.mp.io.parsers.json - package de.uni_halle.informatik.biodata.mp.io.parsers.json
de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping - package de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
de.uni_halle.informatik.biodata.mp.logging - package de.uni_halle.informatik.biodata.mp.logging
de.uni_halle.informatik.biodata.mp.parameters - package de.uni_halle.informatik.biodata.mp.parameters
de.uni_halle.informatik.biodata.mp.polishing - package de.uni_halle.informatik.biodata.mp.polishing
de.uni_halle.informatik.biodata.mp.polishing.ext.fbc - package de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
de.uni_halle.informatik.biodata.mp.reporting - package de.uni_halle.informatik.biodata.mp.reporting
de.uni_halle.informatik.biodata.mp.resolver - package de.uni_halle.informatik.biodata.mp.resolver
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg - package de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping - package de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
de.uni_halle.informatik.biodata.mp.util - package de.uni_halle.informatik.biodata.mp.util
de.uni_halle.informatik.biodata.mp.util.ext.fbc - package de.uni_halle.informatik.biodata.mp.util.ext.fbc
de.uni_halle.informatik.biodata.mp.util.ext.groups - package de.uni_halle.informatik.biodata.mp.util.ext.groups
de.uni_halle.informatik.biodata.mp.validation - package de.uni_halle.informatik.biodata.mp.validation
DEFAULT_FLUX_BOUND - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Pattern for default flux bound reactions, matching IDs that typically start with a prefix followed by 'default_'.
DeleteOnCloseFileInputStream - Class in de.uni_halle.informatik.biodata.mp.io
DeleteOnCloseFileInputStream(File) - Constructor for class de.uni_halle.informatik.biodata.mp.io.DeleteOnCloseFileInputStream
DeleteOnCloseFileInputStream(String) - Constructor for class de.uni_halle.informatik.biodata.mp.io.DeleteOnCloseFileInputStream
DEMAND_REACTION - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Pattern for demand reactions, identified by IDs starting with 'DM_'.
description - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Human-redable information about the model, e.g., the model name.
DiffListener - Class in de.uni_halle.informatik.biodata.mp.reporting
DiffListener() - Constructor for class de.uni_halle.informatik.biodata.mp.reporting.DiffListener
diffReport(String, Object, Object) - Method in class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
diffReport(String, Object, Object) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.IReportDiffs
disabled - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: The "disabled" field comes from the reconstruction tool rBioNet.
doc() - Method in exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException
DOCUMENT_NOTES_FILE - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions: This XHTML file defines alternative document notes and makes them exchangeable.
DOCUMENT_TITLE_PATTERN - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions: This option allows you to define the title of the SBML document's description and hence the headline when the file is displayed in a web browser.
documentNotesFile - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
documentNotesFile() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
documentTitlePattern - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
documentTitlePattern() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
DONT_FIX - Static variable in interface de.uni_halle.informatik.biodata.mp.fixing.FixingOptions
dontFix() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters

E

ecNumbers - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: The Enzyme Commission codes for the reactions.
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
equals(Object) - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
equals(Object) - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
EXCHANGE_REACTION - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Pattern for exchange reactions, identified by IDs starting with 'EX_'.
exists(Array, int) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
extractCompartmentCode(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId: Extracts the compartment code from a given identifier if it matches the expected pattern.

F

FBCPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
FBCPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCPolisher
FBCReactionPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
FBCReactionPolisher(FBCModelPlugin, PolishingParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher
FBCReactionPolisher(FBCModelPlugin, PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher
FBCSpeciesFixer - Class in de.uni_halle.informatik.biodata.mp.fixing.ext.fbc
FBCSpeciesFixer() - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.FBCSpeciesFixer
findBiGGId(GeneProduct) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator: Validates the ID of a GeneProduct against the expected BiGG ID format and attempts to retrieve a corresponding BiGGId from existing annotations if the initial ID does not conform to the BiGG format.
findBiGGId(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator: This method checks if the ID of the reaction is a valid BiGG ID and attempts to retrieve a corresponding BiGG ID based on existing annotations.
findBiGGId(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator: Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations.
findBiGGId(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCSpeciesAnnotator
findBiGGId(T) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCVTermAnnotator: Abstract method to check the validity of a BiGG ID.
findChild(Node, Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
findParent(Node, Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
findTerm(Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node: Returns the Node containing the specified Term or null, if not present
finish(ProgressFinalization) - Method in class de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar
finish(ProgressFinalization) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver
fix(List<Compartment>) - Method in class de.uni_halle.informatik.biodata.mp.fixing.CompartmentFixer
fix(List<Group>) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ext.groups.GroupsFixer
fix(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ReactionFixer
fix(List<Species>) - Method in class de.uni_halle.informatik.biodata.mp.fixing.SpeciesFixer
fix(List<SpeciesReference>) - Method in interface de.uni_halle.informatik.biodata.mp.fixing.IFixSpeciesReferences
fix(List<SBMLElement>) - Method in interface de.uni_halle.informatik.biodata.mp.fixing.IFixSBases
fix(Compartment, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.CompartmentFixer
fix(ListOfObjectives, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.ListOfObjectivesFixer
fix(Group, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ext.groups.GroupsFixer
fix(Model, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ModelFixer
fix(Reaction, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ReactionFixer
fix(SBMLDocument, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.SBMLFixer
fix(Species, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.FBCSpeciesFixer
fix(Species, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.SpeciesFixer
fix(SpeciesReference) - Method in interface de.uni_halle.informatik.biodata.mp.fixing.IFixSpeciesReferences
fix(SpeciesReference) - Method in class de.uni_halle.informatik.biodata.mp.fixing.SpeciesReferenceFixer
fix(SBMLElement, int) - Method in interface de.uni_halle.informatik.biodata.mp.fixing.IFixSBases
fixIdentifiersOrgUri(IdentifiersOrgURI) - Static method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
fixing() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
FIXING_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
FixingOptions - Interface in de.uni_halle.informatik.biodata.mp.fixing
FixingParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
FixingParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
FixingParameters(boolean, FluxObjectivesFixingParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
FixingParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
FLUX_COEFFICIENTS - Static variable in interface de.uni_halle.informatik.biodata.mp.fixing.FixingOptions
FLUX_OBJECTIVES - Static variable in interface de.uni_halle.informatik.biodata.mp.fixing.FixingOptions
fluxCoefficients - Variable in class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
fluxCoefficients() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
fluxObjectiveHasValidCoefficients(FluxObjective) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate: 5) All defined FluxObjective objects must have their coefficient attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'.
fluxObjectives - Variable in class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
fluxObjectives() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
FluxObjectivesFixingParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
FluxObjectivesFixingParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
FluxObjectivesFixingParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
FluxObjectivesFixingParameters(List<Double>, List<String>) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
fluxObjectivesPolishingParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
ForeignReaction(String, String, String) - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB.ForeignReaction: Constructs a new ForeignReaction instance.

G

Gene - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
Gene() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
genedate - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Can be part of the ModelField.description.
geneindex - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Can be part of the ModelField.description.
GeneParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
GeneParser(FBCModelPlugin, int) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.GeneParser
GeneProductAssociationsProcessor - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
GeneProductAssociationsProcessor() - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductAssociationsProcessor
GeneProductsPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
GeneProductsPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductsPolisher
GeneralOptions - Interface in de.uni_halle.informatik.biodata.mp.parameters
genes - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: The list of all genes in the model, where each contained gene corresponds to a AbstractSBase.getId().
genesource - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Can be part of the ModelField.description.
GENOME_ASSEMBLY_ID_PATTERN - Static variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator
get() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
get() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
getAbbreviation() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
getAllBiggIds(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves a set of unique BiGG IDs from a specified table in the database.
getAnnotation() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
getAnnotation() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
getAnnotation() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getAnnotation() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
getAnnotations(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB: Retrieves a set of annotated URLs based on the type and BiGG ID provided.
getApiVersion() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
getBiGGIdFromResources(List<String>, String) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator: Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase.
getBiggIdFromSynonym(String, String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the BiGG ID associated with a given synonym and type from the specified data source.
getBiggIdsForReactionForeignId(RegistryURI) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves a collection of ForeignReaction objects for a given synonym and data source ID.
getBiGGVersion() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the version date of the BiGG database.
getBound() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
getCharge() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
getCharge(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the charge for a given component and model from the database.
getChargeByCompartment(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the charge associated with a specific component in a given compartment when the model ID is unknown.
getChemicalFormula(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the chemical formula for a given component within a specific model in the BiGG database.
getChemicalFormulaByCompartment(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the unique chemical formula for a given component within a specific compartment.
getChildren() - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
getCompartment() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
getCompartmentCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
getCompartmentName(BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the name of the compartment associated with the given BiGG ID from the database.
getCompartments() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
getComponentName(BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the name of the component associated with the given BiGG ID from the database.
getComponentType(BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the type of the component associated with the given BiGG ID from the database.
getConnection() - Method in class de.uni_halle.informatik.biodata.mp.db.PostgresConnectionPool
getCorrectName(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies, if case can't be matched
getCountryCode() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
getCountryName() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
getCreated() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getDeprecationDate() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getDeprecationDate() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getDescription() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
getDescription() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
getDescription() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getDescription() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getErrorMessage() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
getFileExtension() - Method in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
getFileType(File) - Static method in class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils: Determines the type of the input file based on its extension or content.
getFormula() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
getGeneIds(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves all possible MIRIAM-compliant gene identifiers from the database based on a given label.
getGeneName(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the gene name from the database based on a given label.
getGeneReactionRule() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getGeneReactionRule(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves formatted gene reaction rules for a specific reaction and model from the database.
getGenes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
getGenomeAccesion(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the genome accession for a given model ID from the BiGG database.
getHomeUrl() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
getId() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
getId() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
getId() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getId() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
getId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
getId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
getId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getId() - Method in interface de.uni_halle.informatik.biodata.mp.resolver.RegistryURI
getInstitution() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getJSONDocument(SBMLDocument) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
getJSONModel(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
getLabel(GeneProduct, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator: Retrieves the label for a gene product based on the provided BiGGId.
getLocation() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
getLocation() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getLowerBound() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getMetabolites() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getMetabolites() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
getMirId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getMirId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getModified() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getName() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
getName() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
getName() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getName() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
getName() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
getName() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getName() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getNameForPrefix(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies using struct field as prefix of knwon model field
getNamespaceForPrefix(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
getNamespaceForPrefix(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
getNotes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
getNotes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
getNotes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getNotes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
getObjectiveCoefficient() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getObservers() - Method in class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
getObservers() - Method in class de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer
getObservers() - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
getOrganism(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the organism associated with a given BiGG model abbreviation from the database.
getOutputFileName(File, File) - Static method in class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils: Fix output file name to contain xml extension
getParents() - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
getPattern() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getPattern() - Method in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Retrieves the compiled Pattern object for this enum constant.
getPatternByNamespaceName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
getPatternByNamespaceName(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
getPayload() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
getPrefix() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
getPrefix() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
getPrefix() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getPrefix() - Method in interface de.uni_halle.informatik.biodata.mp.resolver.RegistryURI
getPrefixByNamespaceName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
getPrefixByNamespaceName(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
getProviderCode() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getPublications(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves a list of publications associated with a given BiGG model abbreviation from the database.
getReactionName(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the name of a reaction based on its BiGG ID abbreviation, ensuring the name is not empty.
getReactionRules(String, String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Executes a provided SQL query to retrieve gene reaction rules from the database.
getReactions() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
getResourceHomeUrl() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getResources() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getResources(BiGGId, boolean, boolean) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves a set of resource URLs for a given BiGG ID, optionally filtering to include only those containing 'identifiers.org'.
getRoot() - Method in class de.uni_halle.informatik.biodata.mp.eco.DAG
getRorId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
getSampleId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
getSampleId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getSubsystem() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getSubsystems(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves a list of distinct subsystems associated with a specific model and reaction BiGG IDs.
getSubsystemsForReaction(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves a list of distinct subsystems associated with a specific reaction BiGG ID.
getTaxonId(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Retrieves the taxonomic identifier (taxon ID) for a given model based on its abbreviation.
getTerm() - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
getTissueCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
getUpperBound() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
getURI() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
getURI() - Method in interface de.uni_halle.informatik.biodata.mp.resolver.RegistryURI
getUrlPattern() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
getVersion() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
GPRParser - Class in de.uni_halle.informatik.biodata.mp.util.ext.fbc
GPRParser() - Constructor for class de.uni_halle.informatik.biodata.mp.util.ext.fbc.GPRParser
groupAndSortAnnotations(SBase) - Method in class de.uni_halle.informatik.biodata.mp.annotation.AnnotationsSorter: Recursively goes through all annotations in the given SBase and alphabetically sort annotations after grouping them by CVTerm.Qualifier.
GroupsFixer - Class in de.uni_halle.informatik.biodata.mp.fixing.ext.groups
GroupsFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ext.groups.GroupsFixer
GroupsUtils - Class in de.uni_halle.informatik.biodata.mp.util.ext.groups: A collection of helpful functions for dealing with SBML data structures.
GroupsUtils() - Constructor for class de.uni_halle.informatik.biodata.mp.util.ext.groups.GroupsUtils
GROWTH_UNIT_ID - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
GROWTH_UNIT_NAME - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
grRules - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Boolean gene-protein-reaction (GPR) rules in a readable format (AND/OR).

H

hashCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
hashCode() - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication: Returns a hash code value for this object.
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
hashCode() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization: Returns a hash code value for this object.
hashCode() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization: Returns a hash code value for this object.
hashCode() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate: Returns a hash code value for this object.
hashCode() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
host() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
HOST - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
HOST - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions

I

IAnnotateSBases<SBMLElement extends org.sbml.jsbml.SBase> - Interface in de.uni_halle.informatik.biodata.mp.annotation
IDENTIFIERS_ORG_ID_PATTERN - Static variable in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
IdentifiersOrg - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg: The IdentifiersOrg class serves as a central hub for managing and processing identifiers related to the MIRIAM registry.
IdentifiersOrg() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
IdentifiersOrgRegistryParser - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg: The IdentifiersOrgRegistryParser class is a singleton that provides functionality to parse the MIRIAM registry from a JSON file and convert it into a Miriam object.
IdentifiersOrgRegistryParser() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgRegistryParser
IdentifiersOrgURI - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
IdentifiersOrgURI(String) - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
IdentifiersOrgURI(String, BiGGId) - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
IdentifiersOrgURI(String, Object) - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
IdentifiersOrgURI(String, String) - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
IdentifiersOrgURIUtils - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
IdentifiersOrgURIUtils() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURIUtils
IFixSBases<SBMLElement extends org.sbml.jsbml.SBase> - Interface in de.uni_halle.informatik.biodata.mp.fixing
IFixSpeciesReferences - Interface in de.uni_halle.informatik.biodata.mp.fixing
INCLUDE_ANY_URI - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions: This switch allows users to specify if also those database cross-links should be extracted from BiGG Models database for which currently no entry in the MIRIAM exists.
includeAnyURI - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
includeAnyURI() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
init(DBParameters) - Static method in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB
init(DBParameters) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
init(String, Integer, String, String, String) - Static method in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB
init(String, Integer, String, String, String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
initialAssignmentDoesNotReferenceBoundParameters(InitialAssignment) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate: 4) InitialAssignment objects may not target the Parameter objects referenced by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.
initialAssignmentDoesNotReferenceSpeciesReferences(InitialAssignment) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate: 4) InitialAssignment objects may not target the Parameter objects referenced by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.
initialize(ProgressInitialization) - Method in class de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar
initialize(ProgressInitialization) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver
input() - Method in class de.uni_halle.informatik.biodata.mp.io.ModelReaderException
Institution - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
Institution() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
IO_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
IOOptions - Interface in de.uni_halle.informatik.biodata.mp.io
IOOptions.OutputType - Enum Class in de.uni_halle.informatik.biodata.mp.io
IPolishAnnotations - Interface in de.uni_halle.informatik.biodata.mp.polishing
IPolishSBaseAttributes - Interface in de.uni_halle.informatik.biodata.mp.polishing
IPolishSBases<SBMLElement extends org.sbml.jsbml.SBase> - Interface in de.uni_halle.informatik.biodata.mp.polishing
IPolishSpeciesReferences - Interface in de.uni_halle.informatik.biodata.mp.polishing
IProcessNotes - Interface in de.uni_halle.informatik.biodata.mp.annotation
IReadModelsFromFile - Interface in de.uni_halle.informatik.biodata.mp.io
IReportDiffs - Interface in de.uni_halle.informatik.biodata.mp.reporting
IReportStatus - Interface in de.uni_halle.informatik.biodata.mp.reporting
isBoundSet(Parameter) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
isCompartment(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
isDataSource(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
isDeprecated() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
isDeprecated() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
isDirectory(File) - Static method in class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils: Check if file is directory by calling File.isDirectory() on an existing file or check presence of '.' in output.getName(), if this is not the case
isEmptyString(String) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
isMetabolite(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
isModel(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
isNamespaceEmbeddedInLui() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
isOfficial() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
isPseudoreaction(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Determines if a given reaction ID corresponds to a pseudoreaction in the database.
isReaction(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
isSetAbbreviation() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
isSetCompartmentCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
isSetPrefix() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
isSetTissueCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
isValid(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
isValid(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
isValid(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
IWriteModels - Interface in de.uni_halle.informatik.biodata.mp.io
IWriteModelsToFile - Interface in de.uni_halle.informatik.biodata.mp.io

J

JSON - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
JSON_FILE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
JSONConverter - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json
JSONConverter() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
JSONParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json
JSONParser(Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser

L

lb - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Lower reaction flux bounds for corresponding reactions
linkNodes(Node, Node) - Static method in class de.uni_halle.informatik.biodata.mp.eco.Node
ListOfObjectivesFixer - Class in de.uni_halle.informatik.biodata.mp.fixing.ext.fbc
ListOfObjectivesFixer(FixingParameters, FBCModelPlugin, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.ListOfObjectivesFixer
Location - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
Location() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location

M

MAT_FILE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
MatlabParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
MatlabParser(SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.MatlabParser
message() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization: Returns the value of the message record component.
MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions
MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.fixing.FixingOptions
MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.io.IOOptions
MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.SpeciesParser
MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.parameters.GeneralOptions
MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.polishing.PolishingOptions
Metabolite - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
Metabolite() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
Metabolites - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
Metabolites() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
metCharge - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Value of charge for corresponding metabolite.
metCHEBIID - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Optional: if present, it must have same dimension as ModelField.mets.
metFormulas - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Elemental formula for each metabolite.
metHMDB - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Optional: if present, it must have same dimension as ModelField.mets.
metInchiString - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Inichi String for each corresponding metabolite.
metKeggID - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: KEGG ID for each corresponding metabolite.
metNames - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Descriptive metabolite names, must have same dimension as ModelField.mets.
metPubChemID - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Pub Chem ID for each corresponding metabolite.
mets - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Metabolite name abbreviation; metabolite ID; order corresponds to S matrix.
metSmile - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Optional: if present, it must have same dimension as ModelField.mets.
MODEL_NOTES_FILE - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions: This XHTML file defines alternative model notes and makes them exchangeable.
ModelField - Enum Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra: For more information about COBRA model fields, see the following Supplementary Material.
ModelFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
ModelFixer(FixingParameters, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ModelFixer
modelNotesFile - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
modelNotesFile() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
ModelPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing: This class provides functionality to polish an SBML (Systems Biology Markup Language) document.
ModelPolisher(PolishingParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ModelPolisher
ModelPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ModelPolisher
ModelReader - Class in de.uni_halle.informatik.biodata.mp.io
ModelReader(SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.ModelReader
ModelReaderException - Class in de.uni_halle.informatik.biodata.mp.io
ModelReaderException(String, File) - Constructor for class de.uni_halle.informatik.biodata.mp.io.ModelReaderException
ModelReaderException(String, Exception, File) - Constructor for class de.uni_halle.informatik.biodata.mp.io.ModelReaderException
ModelValidator - Class in de.uni_halle.informatik.biodata.mp.validation
ModelValidator() - Constructor for class de.uni_halle.informatik.biodata.mp.validation.ModelValidator
ModelValidatorException - Exception in de.uni_halle.informatik.biodata.mp.validation
ModelValidatorException(Exception, File) - Constructor for exception de.uni_halle.informatik.biodata.mp.validation.ModelValidatorException
ModelWriter - Class in de.uni_halle.informatik.biodata.mp.io
ModelWriter(IOOptions.OutputType) - Constructor for class de.uni_halle.informatik.biodata.mp.io.ModelWriter
ModelWriterException - Exception in de.uni_halle.informatik.biodata.mp.io
ModelWriterException(String, Exception, SBMLDocument, File) - Constructor for exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException
ModelWriterException(String, SBMLDocument, File, File) - Constructor for exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException

N

name - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Can be part of the ModelField.description.
NamePolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
NamePolisher() - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.NamePolisher
Namespace - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
Namespace() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
NO_MODEL_NOTES - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions: If set to true, no web content will be inserted in the SBML container nor into the model within the SBML file.
Node - Class in de.uni_halle.informatik.biodata.mp.eco
Node(Term) - Constructor for class de.uni_halle.informatik.biodata.mp.eco.Node
nodeAdded(TreeNode) - Method in class de.uni_halle.informatik.biodata.mp.io.UpdateListener: Handles the event when a new node is added to the TreeNode structure.
nodeAdded(TreeNode) - Method in class de.uni_halle.informatik.biodata.mp.reporting.DiffListener
nodeRemoved(TreeNodeRemovedEvent) - Method in class de.uni_halle.informatik.biodata.mp.io.UpdateListener
nodeRemoved(TreeNodeRemovedEvent) - Method in class de.uni_halle.informatik.biodata.mp.reporting.DiffListener
noModelNotes() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
notes - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Can be part of the ModelField.description.
notesParameters - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
notesParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters

O

obj() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate: Returns the value of the obj record component.
ObjectivesPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
ObjectivesPolisher(FBCModelPlugin, PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.ObjectivesPolisher
ObjectivesPolisher(FBCModelPlugin, PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.ObjectivesPolisher
organism - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Can be part of the ModelField.description.
osense - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Objective sense, i.e., to minimize or maximize the objective.
output() - Method in exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException
OUTPUT_TYPE - Static variable in interface de.uni_halle.informatik.biodata.mp.io.IOOptions: Decides whether the output file should directly be compressed and if so, which archive type should be used.
outputFile() - Method in exception de.uni_halle.informatik.biodata.mp.validation.ModelValidatorException
outputType - Variable in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
outputType() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters

P

parameters - Variable in class de.uni_halle.informatik.biodata.mp.annotation.adb.AbstractADBAnnotator
Parameters - Class in de.uni_halle.informatik.biodata.mp.parameters
Parameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.Parameters
Parameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.Parameters
ParametersException - Class in de.uni_halle.informatik.biodata.mp.parameters
ParametersException(String, Parameters) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.ParametersException
ParametersParser - Class in de.uni_halle.informatik.biodata.mp.parameters
ParametersParser() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.ParametersParser
ParametersPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
ParametersPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ParametersPolisher
parse() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.GeneParser
parse() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ReactionParser
parse() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.SpeciesParser
parse(File) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.MatlabParser
parse(File) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser: Creates the ModelBuilder, SBMLDocument and reads the jsonFile as a tree
parse(InputStream) - Method in class de.uni_halle.informatik.biodata.mp.parameters.ParametersParser
parse(InputStream) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgRegistryParser
parseAnnotation(SBase, Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
parseCompartments(ModelBuilder, Map<String, String>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
parseGene(Model, Gene, String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
parseGeneReactionRules(Reaction, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator: Parses gene reaction rules for a given reaction based on the BiGG database identifier.
parseMetabolite(Model, Metabolite, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
parseNotes(SBase, Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
parseReaction(ModelBuilder, Reaction, String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
passwd() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
PASSWD - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
PASSWD - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions
polish(String) - Method in class de.uni_halle.informatik.biodata.mp.polishing.NamePolisher
polish(List<Compartment>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.CompartmentPolisher: Polishes all compartments in the given SBML model.
polish(List<GeneProduct>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductsPolisher
polish(List<Parameter>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ParametersPolisher
polish(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher
polish(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ReactionsPolisher
polish(List<SBase>) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSBaseAttributes
polish(List<Species>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.SpeciesPolisher
polish(List<SpeciesReference>) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSpeciesReferences
polish(List<SBMLElement>) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSBases
polish(Annotation) - Method in class de.uni_halle.informatik.biodata.mp.polishing.AnnotationPolisher: Processes the annotations of an SBML entity to potentially correct identifiers and/or retrieve additional identifiers.org URLs.
polish(Annotation) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishAnnotations
polish(Compartment) - Method in class de.uni_halle.informatik.biodata.mp.polishing.CompartmentPolisher: Polishes the properties of a compartment to ensure compliance with standards and completeness.
polish(GeneProduct) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductsPolisher
polish(Objective) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.ObjectivesPolisher
polish(Model) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCPolisher
polish(Model) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ModelPolisher: This method orchestrates the polishing of an SBML model by delegating tasks to specific polishing methods for different components of the model.
polish(Model) - Method in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher: Ensures that all necessary UnitDefinitions and Units are present in the model.
polish(Parameter) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ParametersPolisher
polish(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher
polish(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ReactionsPolisher: Polishes the reaction by applying various checks and modifications to ensure it conforms to the expected standards and conventions.
polish(SBase) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSBaseAttributes
polish(SBase) - Method in class de.uni_halle.informatik.biodata.mp.polishing.NamePolisher
polish(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.polishing.SBMLPolisher: This method serves as the entry point from the ModelPolisher class to polish an SBML document.
polish(Species) - Method in class de.uni_halle.informatik.biodata.mp.polishing.SpeciesPolisher
polish(SpeciesReference) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSpeciesReferences
polish(SpeciesReference) - Method in class de.uni_halle.informatik.biodata.mp.polishing.SpeciesReferencesPolisher
polish(SBMLElement) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSBases
POLISH_EVEN_IF_MODEL_INVALID - Static variable in interface de.uni_halle.informatik.biodata.mp.polishing.PolishingOptions
PolisherFactory - Class in de.uni_halle.informatik.biodata.mp.polishing
PolisherFactory() - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.PolisherFactory
PolisherProgressBar - Class in de.uni_halle.informatik.biodata.mp.reporting
PolisherProgressBar() - Constructor for class de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar
polishEvenIfModelInvalid() - Method in class de.uni_halle.informatik.biodata.mp.parameters.PolishingParameters
polishing() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
POLISHING_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
PolishingOptions - Interface in de.uni_halle.informatik.biodata.mp.polishing
polishingParameters - Variable in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
PolishingParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
PolishingParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.PolishingParameters
PolishingParameters(boolean) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.PolishingParameters
PolishingParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.PolishingParameters
port() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
PORT - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
PORT - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions
PostgresConnectionPool - Class in de.uni_halle.informatik.biodata.mp.db
PostgresConnectionPool(String, int, String, String, String) - Constructor for class de.uni_halle.informatik.biodata.mp.db.PostgresConnectionPool
processNotes(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGDocumentNotesProcessor
ProgressFinalization - Record Class in de.uni_halle.informatik.biodata.mp.reporting
ProgressFinalization(String) - Constructor for record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization: Creates an instance of a ProgressFinalization record class.
ProgressInitialization - Record Class in de.uni_halle.informatik.biodata.mp.reporting
ProgressInitialization(int) - Constructor for record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization: Creates an instance of a ProgressInitialization record class.
ProgressObserver - Interface in de.uni_halle.informatik.biodata.mp.reporting
ProgressUpdate - Record Class in de.uni_halle.informatik.biodata.mp.reporting
ProgressUpdate(String, Object, ReportType) - Constructor for record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate: Creates an instance of a ProgressUpdate record class.
propertyChange(PropertyChangeEvent) - Method in class de.uni_halle.informatik.biodata.mp.io.UpdateListener: Responds to property change events, specifically focusing on changes to the ID property of tree nodes.
propertyChange(PropertyChangeEvent) - Method in class de.uni_halle.informatik.biodata.mp.reporting.DiffListener
proteins - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Proteins associated with each reaction.
Publication - Record Class in de.uni_halle.informatik.biodata.mp.db.bigg
Publication(String, String) - Constructor for record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication: Creates an instance of a Publication record class.

R

RawIdentifiersOrgRegistry - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
RawIdentifiersOrgRegistry() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
RDF_MEDIATYPE - Static variable in class de.uni_halle.informatik.biodata.mp.io.CombineArchive
Reaction - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
Reaction() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
ReactionFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
ReactionFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ReactionFixer
reactionHasValidBounds(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate: 1) Each Reaction in a Model must define values for the attributes 'lowerFluxBound' and 'upperFluxBound', with each attribute pointing to a valid Parameter object defined in the current Model.
reactionId - Variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB.ForeignReaction
ReactionNamePatterns - Enum Class in de.uni_halle.informatik.biodata.mp.util: Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
ReactionParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
ReactionParser(ModelBuilder, int, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ReactionParser
reactionSpeciesReferencesHaveValidAttributes(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate: see StrictnessPredicate.strictnessOfSpeciesReferences(org.sbml.jsbml.ListOf<org.sbml.jsbml.SpeciesReference>)
ReactionsPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing: This class provides methods to polish and validate SBML reactions according to specific rules and patterns.
ReactionsPolisher(PolishingParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ReactionsPolisher
ReactionsPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ReactionsPolisher
read(File) - Method in interface de.uni_halle.informatik.biodata.mp.io.IReadModelsFromFile
read(File) - Method in class de.uni_halle.informatik.biodata.mp.io.ModelReader
REF_SEQ_ACCESSION_NUMBER_PATTERN - Static variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator
referenceId() - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication: Returns the value of the referenceId record component.
referenceType() - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication: Returns the value of the referenceType record component.
registry - Variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
registry - Variable in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
Registry - Interface in de.uni_halle.informatik.biodata.mp.resolver
RegistryURI - Interface in de.uni_halle.informatik.biodata.mp.resolver
removeHttpProtocolFromUrl(String) - Static method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURIUtils
replaceIdTag(String, String) - Static method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURIUtils: Replaces the identifier placeholder "{$id}" in a URL pattern with a specified regex pattern.
reportType() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate: Returns the value of the reportType record component.
ReportType - Enum Class in de.uni_halle.informatik.biodata.mp.reporting
resolveBackwards(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg: Checks and processes a given resource URL to ensure it conforms to expected formats and corrections.
resolveBackwards(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
Resource - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
Resource() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
rev - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: A vector consisting of zeros and ones that translate to binary and determine if the corresponding reaction of that index is reversible (1) or not (0).
Root - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
Root() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
rules - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Boolean rule for the corresponding reaction which defines gene-reaction relationship.
rxnCOG - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: TODO: description COG
rxnConfidenceEcoIDA - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Cell array of strings, can any value in a range of 0 to 4.
rxnConfidenceScores - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: .
rxnECNumbers - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: E.
rxnGeneMat - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: A matrix with rows corresponding to reaction list and columns corresponding to gene list.
rxnKeggID - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Reaction identifiers in KEGG, but sometimes also contains ModelField.ecNumbers.
rxnKeggOrthology - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: TODO: description KEGG Orthology
rxnNames - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Descriptive reaction names, length of this array must be identical to the number of reactions.
rxnNotes - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Cell array of strings.
rxnReferences - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Cell array of strings which can contain optional information on references for each specific reaction.
rxns - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Reaction BiGG ids.
rxnsboTerm - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: The Systems Biology Ontology Term to describe the role of a reaction.

S

S - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Stoichiometric matrix in sparse format.
SBML - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
SBML_FILE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
SBML_VALIDATION - Static variable in interface de.uni_halle.informatik.biodata.mp.parameters.GeneralOptions: If true, the created SBML file will be validated through the online validator service at http://sbml.org.
SBMLFileUtils - Class in de.uni_halle.informatik.biodata.mp.io
SBMLFileUtils() - Constructor for class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils
SBMLFileUtils.FileType - Enum Class in de.uni_halle.informatik.biodata.mp.io: Possible FileTypes of input file
SBMLFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
SBMLFixer(FixingParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.SBMLFixer
SBMLFixer(FixingParameters, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.SBMLFixer
sbmlPolisher(SBMLDocument, PolishingParameters, SBOParameters) - Static method in class de.uni_halle.informatik.biodata.mp.polishing.PolisherFactory
SBMLPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
SBMLPolisher(PolishingParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SBMLPolisher
SBMLPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SBMLPolisher
sbmlValidation - Variable in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
sbmlValidation() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
sboParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
SBOParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
SBOParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
SBOParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
set(Map<String, Double>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
set(Map<String, String>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
setAbbreviation(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId: Only contain upper and lower case letters, numbers, and underscores /[0-9a-zA-Z][a-zA-Z0-9_]+/, only ASCII and don't start with numbers When converting old BIGG IDs to BIGG2 IDs, replace a dash with two underscores.
setAnnotation(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
setAnnotation(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
setAnnotation(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setAnnotation(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
setApiVersion(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
setBound(double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
setCharge(int) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
setChildren(List<Node>) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
setCompartment(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
setCompartmentCode(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId: One or two characters in length, and contain only lower case letters and numbers, and must begin with a lower case letter.
setCompartments(Compartments) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
setCountryCode(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
setCountryName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
setCreated(Calendar) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setDeprecated(boolean) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setDeprecated(boolean) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setDeprecationDate(Calendar) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setDeprecationDate(Calendar) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setDescription(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
setDescription(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
setDescription(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setDescription(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setErrorMessage(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
setFluxBoundSBOTerm(Parameter) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher: Polishes the SBO term of a flux bound parameter based on its ID.
setFormula(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
setGeneProductAssociation(Reaction, String, boolean) - Static method in class de.uni_halle.informatik.biodata.mp.util.ext.fbc.GPRParser
setGeneReactionRule(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setGenes(List<Gene>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
setGPLabelName(GeneProduct, String) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator: Updates the label of a gene product and sets its name based on the retrieved gene name from the BiGG database.
setHomeUrl(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
setId(long) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
setId(long) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setId(long) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setId(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
setId(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
setId(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setId(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
setInstitution(Institution) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setLocation(Location) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
setLocation(Location) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setLowerBound(double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setMetabolites(Metabolites) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setMetabolites(List<Metabolite>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
setMirId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setMirId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setModified(Calendar) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setName(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
setName(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
setName(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setName(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
setName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
setName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setName(Reaction, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator: Sets the name of the reaction based on the provided BiGGId.
setName(Species, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator: Updates the name of the species based on data retrieved from the BiGG Knowledgebase.
setNamespaceEmbeddedInLui(boolean) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setNotes(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
setNotes(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
setNotes(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setNotes(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
setObjectiveCoefficient(double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setOfficial(boolean) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setParents(List<Node>) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
setPattern(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setPayload(Map<String, List<Namespace>>) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
setPrefix(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId: R: reaction M: metabolite /[RM]/ NOTE: Do we want to have the id entity use R and M, and just remove them when constructing the model, or have them just as [abbreviation]_[compartment code] and add the prefix when they are put into SBML models? Also SBML id's use capital letters (/[RM]/).
setPrefix(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setProviderCode(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setReactions(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
setResourceHomeUrl(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setResources(List<Resource>) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setRorId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
setSampleId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
setSampleId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setSBOTerm(Reaction, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator: Sets the SBO term for a reaction based on the given BiGGId.
setSubsystem(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setTerm(Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
setTissueCode(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId: One or two characters in length, and contain only upper case letters and numbers, and must begin with an upper case letter.
setUpperBound(double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
setUrlPattern(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
setVersion(int) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
singleParamStatement(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB: Executes a SQL query with a single parameter and returns the result as an Optional.
SINK_REACTION - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Pattern for sink reactions, which are reactions that remove metabolites from the system, identified by IDs starting with 'SK_' or 'SINK_'.
SpeciesFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
SpeciesFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.SpeciesFixer
SpeciesParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
SpeciesParser(Model, int, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.SpeciesParser
SpeciesPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
SpeciesPolisher(PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SpeciesPolisher
SpeciesPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SpeciesPolisher
SpeciesReferenceFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
SpeciesReferenceFixer() - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.SpeciesReferenceFixer
SpeciesReferencesPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
SpeciesReferencesPolisher(Integer) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SpeciesReferencesPolisher
STATUS - Enum constant in enum class de.uni_halle.informatik.biodata.mp.reporting.ReportType
statusReport(String, Object) - Method in class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
statusReport(String, Object) - Method in class de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer
statusReport(String, Object) - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
statusReport(String, Object) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.IReportStatus
strictnessOfSpeciesReferences(ListOf<SpeciesReference>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate: 3) SpeciesReference objects in Reaction objects must have their 'stoichiometry' attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'.
StrictnessPredicate - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc: From ...:
StrictnessPredicate() - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
stringify(Association) - Static method in class de.uni_halle.informatik.biodata.mp.util.ext.fbc.GPRParser
SUBSYSTEM_LINK - Static variable in class de.uni_halle.informatik.biodata.mp.util.ext.groups.GroupsUtils: Key to link from Reaction directly to Members referencing that reaction.
subSystems - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: This defines groups of reactions that belong to a common reaction subsystem.

T

Table() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Table
Table() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.Table
test(Model) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
text() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate: Returns the value of the text record component.
toBiGGId() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId: Generates a BiGG ID for this object based on its properties.
toBiGGId(String, String, String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId: Constructs a BiGG ID using the provided components.
toString() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
toString() - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication: Returns a string representation of this record class.
toString() - Method in class de.uni_halle.informatik.biodata.mp.eco.DAG
toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
toString() - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
toString() - Method in class de.uni_halle.informatik.biodata.mp.polishing.ModelPolisher
toString() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization: Returns a string representation of this record class.
toString() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization: Returns a string representation of this record class.
toString() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate: Returns a string representation of this record class.
toString() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
totalCalls() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization: Returns the value of the totalCalls record component.
traverse(Node, int, StringBuilder) - Method in class de.uni_halle.informatik.biodata.mp.eco.DAG
TYPE_GENE_PRODUCT - Static variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants
TYPE_REACTION - Static variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants
TYPE_SPECIES - Static variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants

U

ub - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Upper reaction flux bounds for corresponding reactions
UnitPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing: This class is responsible for ensuring that all necessary UnitDefinitions and Units are correctly defined and present in the SBML model.
UnitPolisher(PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
UnitPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
UNKNOWN - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
update(ProgressUpdate) - Method in class de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar
update(ProgressUpdate) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver
update(GeneProduct) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductReferencesAnnotator: Updates the reference of a gene product in the geneProductReferences map using the gene product's ID.
UpdateListener - Class in de.uni_halle.informatik.biodata.mp.io: The UpdateListener class implements the TreeNodeChangeListener to monitor and respond to changes within an SBML model's structure.
UpdateListener() - Constructor for class de.uni_halle.informatik.biodata.mp.io.UpdateListener: Constructs an UpdateListener instance and initializes the geneIdToAssociation map.
user() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
USER - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
USER - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions

V

validate(File) - Method in class de.uni_halle.informatik.biodata.mp.validation.ModelValidator
validate(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.validation.ModelValidator
validRegistryUrlPrefix(RegistryURI) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg: Existing models on BiGG and Biomodels use some namespaces that were removed from identifiers.org.
validRegistryUrlPrefix(RegistryURI) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.reporting.ReportType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Returns the enum constant of this class with the specified name.
values() - Static method in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class de.uni_halle.informatik.biodata.mp.reporting.ReportType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns: Returns an array containing the constants of this enum class, in the order they are declared.

W

write() - Method in class de.uni_halle.informatik.biodata.mp.io.CombineArchive
write(SBMLDocument) - Method in interface de.uni_halle.informatik.biodata.mp.io.IWriteModels
write(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.io.ModelWriter
write(SBMLDocument, File) - Method in interface de.uni_halle.informatik.biodata.mp.io.IWriteModelsToFile
write(SBMLDocument, File) - Method in class de.uni_halle.informatik.biodata.mp.io.ModelWriter

A B C D E F G H I J L M N O P R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form