From 8be7743516fd03d6804cea61147ddb93ad936587 Mon Sep 17 00:00:00 2001 From: Dario Date: Mon, 22 Jul 2024 15:42:26 +0200 Subject: [PATCH] updated javadocs --- docs/allclasses-index.html | 302 +-- docs/allpackages-index.html | 34 +- docs/constant-values.html | 52 +- docs/edu/ucsd/sbrg/CommandLineParameters.html | 238 +++ .../ModelPolisherOptions.Compression.html | 3 - docs/edu/ucsd/sbrg/Parameters.html | 406 +++- docs/edu/ucsd/sbrg/XHTMLBuilder.html | 24 - ...Annotation.html => AbstractAnnotator.html} | 163 +- ...lAnnotator.html => AnnotationsSorter.html} | 39 +- .../annotation/GeneProductAnnotation.html | 275 --- .../annotation/adb/ADBReactionsAnnotator.html | 212 ++ .../ADBSBMLAnnotator.html} | 98 +- .../annotation/adb/ADBSpeciesAnnotator.html | 212 ++ .../annotation/adb/AbstractADBAnnotator.html | 231 +++ .../adb}/package-summary.html | 26 +- .../adb}/package-tree.html | 23 +- .../bigg/AbstractBiGGAnnotator.html | 255 +++ .../BiGGAnnotationUtils.html} | 54 +- .../annotation/bigg/BiGGCVTermAnnotator.html | 227 +++ .../BiGGCompartmentsAnnotator.html} | 120 +- .../bigg/BiGGDocumentNotesProcessor.html} | 60 +- .../annotation/bigg/BiGGModelAnnotator.html | 277 +++ .../bigg/BiGGPublicationsAnnotator.html} | 115 +- .../BiGGReactionsAnnotator.html} | 168 +- .../BiGGSBMLAnnotator.html} | 121 +- .../annotation/bigg/BiGGSpeciesAnnotator.html | 291 +++ .../annotation/bigg/fbc/BiGGFBCAnnotator.html | 203 ++ .../bigg/fbc/BiGGGeneProductAnnotator.html | 355 ++++ .../BiGGGeneProductReferencesAnnotator.html} | 52 +- .../annotation/bigg/fbc/package-summary.html | 107 + .../annotation/bigg/fbc/package-tree.html | 84 + .../sbrg/annotation/bigg/package-summary.html | 135 ++ .../sbrg/annotation/bigg/package-tree.html | 89 + .../ucsd/sbrg/annotation/package-summary.html | 36 +- .../ucsd/sbrg/annotation/package-tree.html | 13 +- docs/edu/ucsd/sbrg/db/DBConfig.html | 206 -- ...ector.html => PostgresConnectionPool.html} | 26 +- docs/edu/ucsd/sbrg/db/adb/AnnotateDB.html | 98 +- .../sbrg/db/bigg/BiGGDB.ForeignReaction.html | 2 +- docs/edu/ucsd/sbrg/db/bigg/BiGGDB.html | 350 ++-- docs/edu/ucsd/sbrg/db/bigg/BiGGId.html | 8 +- docs/edu/ucsd/sbrg/db/bigg/Publication.html | 262 +++ .../ucsd/sbrg/db/bigg/package-summary.html | 26 +- docs/edu/ucsd/sbrg/db/bigg/package-tree.html | 14 + docs/edu/ucsd/sbrg/db/package-summary.html | 12 +- docs/edu/ucsd/sbrg/db/package-tree.html | 4 +- .../sbrg/{util => io}/CombineArchive.html | 6 +- docs/edu/ucsd/sbrg/io/ModelReader.html | 49 +- .../{util => io}/SBMLFileUtils.FileType.html | 30 +- .../ucsd/sbrg/{util => io}/SBMLFileUtils.html | 12 +- .../sbrg/{util => io}/UpdateListener.html | 8 +- docs/edu/ucsd/sbrg/io/package-summary.html | 25 +- docs/edu/ucsd/sbrg/io/package-tree.html | 17 + .../{ => io}/parsers/cobra/COBRAParser.html | 47 +- .../{ => io}/parsers/cobra/COBRAUtils.html | 50 +- .../{ => io}/parsers/cobra/GeneParser.html | 26 +- .../{ => io}/parsers/cobra/ModelField.html | 147 +- .../parsers/cobra/ReactionParser.html | 50 +- .../{ => io}/parsers/cobra/SpeciesParser.html | 40 +- .../parsers/cobra/package-summary.html | 40 +- .../{ => io}/parsers/cobra/package-tree.html | 40 +- .../{ => io}/parsers/json/JSONConverter.html | 122 +- .../{ => io}/parsers/json/JSONParser.html | 136 +- .../parsers/json/mapping}/Compartments.html | 30 +- .../parsers/json/mapping}/Gene.html | 26 +- .../parsers/json/mapping}/Metabolite.html | 26 +- .../parsers/json/mapping}/Metabolites.html | 26 +- .../parsers/json/mapping}/Reaction.html | 36 +- .../parsers/json/mapping}/Root.html | 60 +- .../parsers/json/mapping/package-summary.html | 111 ++ .../io/parsers/json/mapping/package-tree.html | 75 + .../sbrg/io/parsers/json/package-summary.html | 103 + .../parsers/json}/package-tree.html | 14 +- .../edu/ucsd/sbrg/miriam/CompactResource.html | 253 --- docs/edu/ucsd/sbrg/miriam/Entries.html | 303 --- docs/edu/ucsd/sbrg/miriam/Registry.html | 351 ---- .../ucsd/sbrg/miriam/RegistryProvider.html | 181 -- docs/edu/ucsd/sbrg/miriam/models/Miriam.html | 190 -- docs/edu/ucsd/sbrg/package-summary.html | 36 +- docs/edu/ucsd/sbrg/package-tree.html | 6 +- .../ucsd/sbrg/polishing/AbstractPolisher.html | 295 +++ .../sbrg/polishing/AnnotationPolisher.html | 214 ++ .../sbrg/polishing/CompartmentPolisher.html | 219 ++ .../GeneProductAssociationsProcessor.html} | 34 +- .../ucsd/sbrg/polishing/MiscPolishing.html | 291 --- .../ucsd/sbrg/polishing/ModelPolisher.html | 136 +- .../sbrg/polishing/ParametersPolisher.html | 218 ++ ...atterns.html => ReactionNamePatterns.html} | 42 +- ...nPolishing.html => ReactionsPolisher.html} | 163 +- .../edu/ucsd/sbrg/polishing/SBMLPolisher.html | 210 ++ .../ucsd/sbrg/polishing/SpeciesPolisher.html | 247 +++ .../{UnitPolishing.html => UnitPolisher.html} | 64 +- .../ucsd/sbrg/polishing/fbc/FBCPolisher.html | 193 ++ .../polishing/fbc/FluxObjectivesPolisher.html | 227 +++ .../polishing/fbc/GeneProductsPolisher.html | 215 ++ .../polishing/fbc/StrictnessPredicate.html | 311 +++ .../fbc}/package-summary.html | 22 +- .../json => polishing/fbc}/package-tree.html | 16 +- .../ucsd/sbrg/polishing/package-summary.html | 44 +- .../edu/ucsd/sbrg/polishing/package-tree.html | 20 +- .../PolisherProgressBar.html | 34 +- .../ProgressFinalization.html | 6 +- .../ProgressInitialization.html | 6 +- .../{util => reporting}/ProgressObserver.html | 24 +- .../{util => reporting}/ProgressUpdate.html | 49 +- docs/edu/ucsd/sbrg/reporting/ReportType.html | 222 +++ .../package-summary.html | 43 +- .../edu/ucsd/sbrg/reporting/package-tree.html | 106 + .../Node.html => resolver/Registry.html} | 68 +- .../RegistryURI.html} | 64 +- .../identifiersorg/IdentifiersOrg.html} | 201 +- .../IdentifiersOrgRegistryParser.html} | 69 +- .../identifiersorg/IdentifiersOrgURI.html | 326 +++ .../IdentifiersOrgURIUtils.html} | 129 +- .../identifiersorg/mapping}/Institution.html | 36 +- .../identifiersorg/mapping}/Location.html | 26 +- .../identifiersorg/mapping}/Namespace.html | 34 +- .../mapping/RawIdentifiersOrgRegistry.html} | 46 +- .../identifiersorg/mapping}/Resource.html | 46 +- .../mapping}/package-summary.html | 22 +- .../identifiersorg/mapping/package-tree.html | 74 + .../identifiersorg/package-summary.html | 114 ++ .../resolver/identifiersorg/package-tree.html | 73 + .../ucsd/sbrg/resolver/package-summary.html | 105 + .../{miriam => resolver}/package-tree.html | 24 +- docs/edu/ucsd/sbrg/util/SBMLFix.html | 53 +- docs/edu/ucsd/sbrg/util/package-summary.html | 35 +- docs/edu/ucsd/sbrg/util/package-tree.html | 42 - docs/element-list | 16 +- docs/index-all.html | 1755 +++++++++-------- docs/index.html | 34 +- docs/member-search-index.js | 2 +- docs/overview-tree.html | 168 +- docs/package-search-index.js | 2 +- docs/serialized-form.html | 14 +- docs/type-search-index.js | 2 +- 136 files changed, 10680 insertions(+), 5351 deletions(-) create mode 100644 docs/edu/ucsd/sbrg/CommandLineParameters.html rename docs/edu/ucsd/sbrg/annotation/{SpeciesAnnotation.html => AbstractAnnotator.html} (54%) rename docs/edu/ucsd/sbrg/annotation/{ModelAnnotator.html => AnnotationsSorter.html} (85%) delete mode 100644 docs/edu/ucsd/sbrg/annotation/GeneProductAnnotation.html create mode 100644 docs/edu/ucsd/sbrg/annotation/adb/ADBReactionsAnnotator.html rename docs/edu/ucsd/sbrg/annotation/{ModelAnnotation.html => adb/ADBSBMLAnnotator.html} (61%) create mode 100644 docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html create mode 100644 docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html rename docs/edu/ucsd/sbrg/{miriam/models => annotation/adb}/package-summary.html (77%) rename docs/edu/ucsd/sbrg/{miriam/models => annotation/adb}/package-tree.html (70%) create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html rename docs/edu/ucsd/sbrg/annotation/{CVTermAnnotation.html => bigg/BiGGAnnotationUtils.html} (69%) create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/BiGGCVTermAnnotator.html rename docs/edu/ucsd/sbrg/annotation/{CompartmentAnnotation.html => bigg/BiGGCompartmentsAnnotator.html} (50%) rename docs/edu/ucsd/sbrg/{polishing/CompartmentPolishing.html => annotation/bigg/BiGGDocumentNotesProcessor.html} (76%) create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html rename docs/edu/ucsd/sbrg/{polishing/SpeciesPolishing.html => annotation/bigg/BiGGPublicationsAnnotator.html} (57%) rename docs/edu/ucsd/sbrg/annotation/{ReactionAnnotation.html => bigg/BiGGReactionsAnnotator.html} (57%) rename docs/edu/ucsd/sbrg/annotation/{BiGGAnnotation.html => bigg/BiGGSBMLAnnotator.html} (54%) create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/BiGGSpeciesAnnotator.html create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html rename docs/edu/ucsd/sbrg/{util/GeneProductReferencesAnnotator.html => annotation/bigg/fbc/BiGGGeneProductReferencesAnnotator.html} (79%) create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/fbc/package-summary.html create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/fbc/package-tree.html create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/package-summary.html create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/package-tree.html delete mode 100644 docs/edu/ucsd/sbrg/db/DBConfig.html rename docs/edu/ucsd/sbrg/db/{PostgreSQLConnector.html => PostgresConnectionPool.html} (91%) create mode 100644 docs/edu/ucsd/sbrg/db/bigg/Publication.html rename docs/edu/ucsd/sbrg/{util => io}/CombineArchive.html (98%) rename docs/edu/ucsd/sbrg/{util => io}/SBMLFileUtils.FileType.html (90%) rename docs/edu/ucsd/sbrg/{util => io}/SBMLFileUtils.html (96%) rename docs/edu/ucsd/sbrg/{util => io}/UpdateListener.html (98%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/cobra/COBRAParser.html (79%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/cobra/COBRAUtils.html (92%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/cobra/GeneParser.html (90%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/cobra/ModelField.html (85%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/cobra/ReactionParser.html (80%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/cobra/SpeciesParser.html (83%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/cobra/package-summary.html (77%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/cobra/package-tree.html (63%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/json/JSONConverter.html (80%) rename docs/edu/ucsd/sbrg/{ => io}/parsers/json/JSONParser.html (72%) rename docs/edu/ucsd/sbrg/{parsers/json/models => io/parsers/json/mapping}/Compartments.html (93%) rename docs/edu/ucsd/sbrg/{parsers/json/models => io/parsers/json/mapping}/Gene.html (94%) rename docs/edu/ucsd/sbrg/{parsers/json/models => io/parsers/json/mapping}/Metabolite.html (96%) rename docs/edu/ucsd/sbrg/{parsers/json/models => io/parsers/json/mapping}/Metabolites.html (92%) rename docs/edu/ucsd/sbrg/{parsers/json/models => io/parsers/json/mapping}/Reaction.html (94%) rename docs/edu/ucsd/sbrg/{parsers/json/models => io/parsers/json/mapping}/Root.html (90%) create mode 100644 docs/edu/ucsd/sbrg/io/parsers/json/mapping/package-summary.html create mode 100644 docs/edu/ucsd/sbrg/io/parsers/json/mapping/package-tree.html create mode 100644 docs/edu/ucsd/sbrg/io/parsers/json/package-summary.html rename docs/edu/ucsd/sbrg/{parsers/json/models => io/parsers/json}/package-tree.html (69%) delete mode 100644 docs/edu/ucsd/sbrg/miriam/CompactResource.html delete mode 100644 docs/edu/ucsd/sbrg/miriam/Entries.html delete mode 100644 docs/edu/ucsd/sbrg/miriam/Registry.html delete mode 100644 docs/edu/ucsd/sbrg/miriam/RegistryProvider.html delete mode 100644 docs/edu/ucsd/sbrg/miriam/models/Miriam.html create mode 100644 docs/edu/ucsd/sbrg/polishing/AbstractPolisher.html create mode 100644 docs/edu/ucsd/sbrg/polishing/AnnotationPolisher.html create mode 100644 docs/edu/ucsd/sbrg/polishing/CompartmentPolisher.html rename docs/edu/ucsd/sbrg/{util/GeneProductAssociationsPolisher.html => polishing/GeneProductAssociationsProcessor.html} (86%) delete mode 100644 docs/edu/ucsd/sbrg/polishing/MiscPolishing.html create mode 100644 docs/edu/ucsd/sbrg/polishing/ParametersPolisher.html rename docs/edu/ucsd/sbrg/polishing/{ReactionPolishing.Patterns.html => ReactionNamePatterns.html} (86%) rename docs/edu/ucsd/sbrg/polishing/{ReactionPolishing.html => ReactionsPolisher.html} (56%) create mode 100644 docs/edu/ucsd/sbrg/polishing/SBMLPolisher.html create mode 100644 docs/edu/ucsd/sbrg/polishing/SpeciesPolisher.html rename docs/edu/ucsd/sbrg/polishing/{UnitPolishing.html => UnitPolisher.html} (77%) create mode 100644 docs/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.html create mode 100644 docs/edu/ucsd/sbrg/polishing/fbc/FluxObjectivesPolisher.html create mode 100644 docs/edu/ucsd/sbrg/polishing/fbc/GeneProductsPolisher.html create mode 100644 docs/edu/ucsd/sbrg/polishing/fbc/StrictnessPredicate.html rename docs/edu/ucsd/sbrg/{parsers/json => polishing/fbc}/package-summary.html (73%) rename docs/edu/ucsd/sbrg/{parsers/json => polishing/fbc}/package-tree.html (69%) rename docs/edu/ucsd/sbrg/{util => reporting}/PolisherProgressBar.html (83%) rename docs/edu/ucsd/sbrg/{util => reporting}/ProgressFinalization.html (98%) rename docs/edu/ucsd/sbrg/{util => reporting}/ProgressInitialization.html (98%) rename docs/edu/ucsd/sbrg/{util => reporting}/ProgressObserver.html (84%) rename docs/edu/ucsd/sbrg/{util => reporting}/ProgressUpdate.html (81%) create mode 100644 docs/edu/ucsd/sbrg/reporting/ReportType.html rename docs/edu/ucsd/sbrg/{miriam => reporting}/package-summary.html (73%) create mode 100644 docs/edu/ucsd/sbrg/reporting/package-tree.html rename docs/edu/ucsd/sbrg/{miriam/Node.html => resolver/Registry.html} (68%) rename docs/edu/ucsd/sbrg/{miriam/RegistryParser.html => resolver/RegistryURI.html} (50%) rename docs/edu/ucsd/sbrg/{miriam/CompactEntry.html => resolver/identifiersorg/IdentifiersOrg.html} (50%) rename docs/edu/ucsd/sbrg/{polishing/GeneProductPolishing.html => resolver/identifiersorg/IdentifiersOrgRegistryParser.html} (70%) create mode 100644 docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURI.html rename docs/edu/ucsd/sbrg/{db/MemorizedQuery.html => resolver/identifiersorg/IdentifiersOrgURIUtils.html} (56%) rename docs/edu/ucsd/sbrg/{miriam/models => resolver/identifiersorg/mapping}/Institution.html (92%) rename docs/edu/ucsd/sbrg/{miriam/models => resolver/identifiersorg/mapping}/Location.html (92%) rename docs/edu/ucsd/sbrg/{miriam/models => resolver/identifiersorg/mapping}/Namespace.html (95%) rename docs/edu/ucsd/sbrg/{miriam/models/Root.html => resolver/identifiersorg/mapping/RawIdentifiersOrgRegistry.html} (89%) rename docs/edu/ucsd/sbrg/{miriam/models => resolver/identifiersorg/mapping}/Resource.html (93%) rename docs/edu/ucsd/sbrg/{parsers/json/models => resolver/identifiersorg/mapping}/package-summary.html (80%) create mode 100644 docs/edu/ucsd/sbrg/resolver/identifiersorg/mapping/package-tree.html create mode 100644 docs/edu/ucsd/sbrg/resolver/identifiersorg/package-summary.html create mode 100644 docs/edu/ucsd/sbrg/resolver/identifiersorg/package-tree.html create mode 100644 docs/edu/ucsd/sbrg/resolver/package-summary.html rename docs/edu/ucsd/sbrg/{miriam => resolver}/package-tree.html (62%) diff --git a/docs/allclasses-index.html b/docs/allclasses-index.html index a69dca11..235f0651 100644 --- a/docs/allclasses-index.html +++ b/docs/allclasses-index.html @@ -55,31 +55,51 @@

All Classes and Interfaces<
Class
Description
-
AnnotateDB
+
AbstractADBAnnotator<SBMLElement>
 
-
AnnotateDBContract
+
AbstractAnnotator<SBMLElement>
 
-
AnnotateDBContract.Constants
+
AbstractBiGGAnnotator<SBMLElement>
 
-
AnnotateDBContract.Constants.Column
+
AbstractPolisher<SBMLElement>
 
-
AnnotateDBContract.Constants.Table
+
ADBReactionsAnnotator
 
-
AnnotateDBOptions
-
+
ADBSBMLAnnotator
+
 
+
ADBSpeciesAnnotator
+
 
+
AnnotateDB
+
 
+
AnnotateDBContract
+
 
+
AnnotateDBContract.Constants
+
 
+
AnnotateDBContract.Constants.Column
+
 
+
AnnotateDBContract.Constants.Table
+
 
+
AnnotateDBOptions
+
This interface provides options for connecting to the ADB database.
-
BiGGAnnotation
+
AnnotationPolisher
+
 
+
AnnotationsSorter
+
 
+
BiGGAnnotationUtils
+
 
+
BiGGCompartmentsAnnotator
-
This class is responsible for annotating SBML models using data from the BiGG database.
+
This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
-
BiGGDB
+
BiGGCVTermAnnotator<T>
-
This class provides a connection to the BiGG database.
+
Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
-
BiGGDB.ForeignReaction
+
BiGGDB
-
Represents a reaction from an external data source mapped to the BiGG database, including its compartment details.
+
This class provides a connection to the BiGG database.
BiGGDBContract
 
@@ -91,218 +111,214 @@

All Classes and Interfaces<
 
BiGGDBOptions
 
+
BiGGDocumentNotesProcessor
+
 
+
BiGGFBCAnnotator
+
 
+
BiGGGeneProductAnnotator
+
+
Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
+
+
BiGGGeneProductReferencesAnnotator
+
 
BiGGId
Represents a BiGG identifier used to uniquely identify various biological entities such as reactions, metabolites, and genes within the BiGG database.
-
COBRAParser
-
 
-
COBRAUtils
-
 
-
CombineArchive
+
BiGGModelAnnotator
-
The CombineArchive class provides functionality to create a COMBINE archive from an SBML document.
+
This class is responsible for annotating an SBML Model with relevant metadata and references.
-
CompactEntry
+
BiGGPublicationsAnnotator
 
-
CompactResource
+
BiGGReactionsAnnotator
-
Represents a compact version of a Resource with essential fields only.
+
This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
-
CompartmentAnnotation
+
BiGGSBMLAnnotator
-
This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
+
This class is responsible for annotating SBML models using data from the BiGG database.
-
CompartmentPolishing
+
BiGGSpeciesAnnotator
-
This class is responsible for polishing the properties of a compartment in an SBML model to ensure - compliance with standards and completeness.
+
This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
-
Compartments
+
COBRAParser
 
-
CVTermAnnotation
-
-
Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
+
COBRAUtils
+
 
+
CombineArchive
+
+
The CombineArchive class provides functionality to create a COMBINE archive from an SBML document.
-
DAG
-
 
-
DBConfig
-
-
This class provides configuration and initialization methods for database connections.
+
CommandLineParameters
+
 
+
CompartmentPolisher
+
+
This class is responsible for polishing the properties of a compartment in an SBML model to ensure + compliance with standards and completeness.
-
ECOparser
+
Compartments
+
 
+
DAG
 
-
Entries
-
-
The singleton Entries class serves as a central repository for managing and querying MIRIAM namespaces and their associated resources.
-
-
Gene
+
ECOparser
+
 
+
FBCPolisher
 
-
GeneParser
+
FluxObjectivesPolisher
 
-
GeneProductAnnotation
-
-
Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
-
-
GeneProductAssociationsPolisher
+
Gene
+
 
+
GeneParser
 
-
GeneProductPolishing
-
+
GeneProductAssociationsProcessor
+
 
+
GeneProductsPolisher
+
This class is responsible for polishing GeneProduct instances by processing their annotations and adjusting their identifiers and names.
-
GeneProductReferencesAnnotator
-
 
GPRParser
The GPRParser class provides methods to parse gene product associations (GPRs) from gene reaction rules and integrate them into SBML models using JSBML.
-
Institution
+
IdentifiersOrg
+
+
The IdentifiersOrg class serves as a central hub for managing and processing identifiers related to the MIRIAM registry.
+
+
IdentifiersOrgRegistryParser
+
+
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.
+
+
IdentifiersOrgURI
+
 
+
IdentifiersOrgURIUtils
+
 
+
Institution
 
IOOptions
 
-
JSONConverter
+
JSONConverter
 
-
JSONParser
+
JSONParser
 
-
Location
+
Location
 
-
MemorizedQuery
+
Metabolite
 
-
Metabolite
+
Metabolites
 
-
Metabolites
-
 
-
Miriam
-
-
The Miriam class is a singleton that manages a collection of namespaces.
-
-
MiscPolishing
-
-
This class provides methods to polish an SBML model to conform to specific standards and conventions.
-
-
ModelAnnotation
-
-
This class is responsible for annotating an SBML Model with relevant metadata and references.
-
-
ModelAnnotator
-
 
-
ModelField
-
+
ModelField
+
For more information about COBRA model fields, see the following Supplementary Material.
-
ModelPolisher
-
+
ModelPolisher
+
This class provides functionality to polish an SBML (Systems Biology Markup Language) document.
-
ModelPolisherCLILauncher
-
+
ModelPolisherCLILauncher
+
The ModelPolisher class is the entry point of this application.
-
ModelPolisherOptions
-
 
-
ModelPolisherOptions.Compression
-
 
-
ModelReader
-
 
-
ModelValidator
+
ModelPolisherOptions
+
 
+
ModelPolisherOptions.Compression
+
 
+
ModelReader
 
-
ModelWriter
+
ModelValidator
 
-
Namespace
+
ModelWriter
 
-
Node
-
 
+
Namespace
+
 
Parameters
Helper class to store all parameters for running ModelPolisher in batch mode.
-
PolisherProgressBar
+
ParametersPolisher
 
-
PolishingUtils
+
PolisherProgressBar
 
-
PostgreSQLConnector
-
-
Created by mephenor on 05.05.17.
-
-
ProgressFinalization
-
 
-
ProgressInitialization
+
PolishingUtils
+
 
+
PostgresConnectionPool
+
 
+
ProgressFinalization
 
-
ProgressObserver
-
 
-
ProgressUpdate
+
ProgressInitialization
+
 
+
ProgressObserver
+
 
+
ProgressUpdate
+
 
+
Publication
 
-
Reaction
+
RawIdentifiersOrgRegistry
 
-
ReactionAnnotation
-
-
This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
-
-
ReactionParser
-
 
-
ReactionPolishing
-
-
This class provides methods to polish and validate SBML reactions according to specific rules and patterns.
-
-
ReactionPolishing.Patterns
+
Reaction
+
 
+
ReactionNamePatterns
Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
-
Registry
-
-
The Registry class serves as a central hub for managing and processing identifiers related to the MIRIAM registry.
-
-
RegistryParser
+
ReactionParser
+
 
+
ReactionsPolisher
-
The RegistryParser class is a singleton that provides functionality to parse the MIRIAM registry - from a JSON file and convert it into a Miriam object.
+
This class provides methods to polish and validate SBML reactions according to specific rules and patterns.
-
RegistryProvider
-
 
-
Resource
+
Registry
+
 
+
RegistryURI
+
 
+
ReportType
+
 
+
Resource
 
-
Root
+
Root
 
-
Root
+
SBMLFileUtils
 
-
SBMLFileUtils
-
 
-
SBMLFileUtils.FileType
-
+
SBMLFileUtils.FileType
+
Possible FileTypes of input file
-
SBMLFix
-
+
SBMLFix
+
This is a stand-alone bug-fix program.
+
SBMLPolisher
+
 
SBMLUtils
A collection of helpful functions for dealing with SBML data structures.
SBMLValidator
 
-
SpeciesAnnotation
-
-
This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
-
-
SpeciesParser
-
 
-
SpeciesPolishing
-
+
SpeciesParser
+
 
+
SpeciesPolisher
+
This class is responsible for polishing Species objects in an SBML model to ensure they conform to specific standards and completeness.
-
UnitPolishing
+
StrictnessPredicate
+
+
From ...:
+
+
UnitPolisher
This class is responsible for ensuring that all necessary UnitDefinitions and Units are correctly defined and present in the SBML model.
-
UpdateListener
+
UpdateListener
The UpdateListener class implements the TreeNodeChangeListener to monitor and respond to changes within an SBML model's structure.
diff --git a/docs/allpackages-index.html b/docs/allpackages-index.html index 4c268bfa..f4d24b16 100644 --- a/docs/allpackages-index.html +++ b/docs/allpackages-index.html @@ -57,27 +57,39 @@

All Packages

 
edu.ucsd.sbrg.annotation
 
-
edu.ucsd.sbrg.db
+
edu.ucsd.sbrg.annotation.adb
 
-
edu.ucsd.sbrg.db.adb
+
edu.ucsd.sbrg.annotation.bigg
 
-
edu.ucsd.sbrg.db.bigg
+
edu.ucsd.sbrg.annotation.bigg.fbc
 
-
edu.ucsd.sbrg.eco
+
edu.ucsd.sbrg.db
 
-
edu.ucsd.sbrg.io
+
edu.ucsd.sbrg.db.adb
 
-
edu.ucsd.sbrg.miriam
+
edu.ucsd.sbrg.db.bigg
 
-
edu.ucsd.sbrg.miriam.models
+
edu.ucsd.sbrg.eco
 
-
edu.ucsd.sbrg.parsers.cobra
+
edu.ucsd.sbrg.io
 
-
edu.ucsd.sbrg.parsers.json
+
edu.ucsd.sbrg.io.parsers.cobra
 
-
edu.ucsd.sbrg.parsers.json.models
+
edu.ucsd.sbrg.io.parsers.json
 
-
edu.ucsd.sbrg.polishing
+
edu.ucsd.sbrg.io.parsers.json.mapping
+
 
+
edu.ucsd.sbrg.polishing
+
 
+
edu.ucsd.sbrg.polishing.fbc
+
 
+
edu.ucsd.sbrg.reporting
+
 
+
edu.ucsd.sbrg.resolver
+
 
+
edu.ucsd.sbrg.resolver.identifiersorg
+
 
+
edu.ucsd.sbrg.resolver.identifiersorg.mapping
 
edu.ucsd.sbrg.util
 
diff --git a/docs/constant-values.html b/docs/constant-values.html index 57e1c774..a866b60f 100644 --- a/docs/constant-values.html +++ b/docs/constant-values.html @@ -59,6 +59,35 @@

Contents

edu.ucsd.*

+ + + diff --git a/docs/edu/ucsd/sbrg/Parameters.html b/docs/edu/ucsd/sbrg/Parameters.html index b09ee7b3..ecd793ad 100644 --- a/docs/edu/ucsd/sbrg/Parameters.html +++ b/docs/edu/ucsd/sbrg/Parameters.html @@ -38,7 +38,7 @@

Summary:

@@ -46,7 +46,7 @@

  • Detail:

    @@ -58,13 +58,13 @@ @@ -88,6 +88,10 @@

    Class Parameters

    edu.ucsd.sbrg.Parameters
    • +
    +
    Direct Known Subclasses:
    +
    CommandLineParameters
    +
    public class Parameters extends Object
    @@ -96,6 +100,63 @@

    Class Parameters

    Methods inherited from class java.lang.Object

    -clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/XHTMLBuilder.html b/docs/edu/ucsd/sbrg/XHTMLBuilder.html index 0cdfd6dc..88594f96 100644 --- a/docs/edu/ucsd/sbrg/XHTMLBuilder.html +++ b/docs/edu/ucsd/sbrg/XHTMLBuilder.html @@ -147,14 +147,6 @@

    table

    Object[][] data, String caption, Map<String,String> attributes)
    -
    -
    Parameters:
    -
    header -
    -
    data -
    -
    caption -
    -
    attributes -
    -
    Returns:
    -
  • @@ -162,11 +154,6 @@

    table

    appendAttribute

    public static void appendAttribute(StringBuilder sb, Map.Entry<String,String> entry)
    -
    -
    Parameters:
    -
    sb -
    -
    entry -
    -
  • @@ -175,23 +162,12 @@

    appendAttribute

    public static void appendAttribute(StringBuilder sb, String key, String value)
    -
    -
    Parameters:
    -
    sb -
    -
    key -
    -
    value -
    -

  • p

    public static String p(String content)
    -
    -
    Parameters:
    -
    content -
    -
    Returns:
    -
    • diff --git a/docs/edu/ucsd/sbrg/annotation/SpeciesAnnotation.html b/docs/edu/ucsd/sbrg/annotation/AbstractAnnotator.html similarity index 54% rename from docs/edu/ucsd/sbrg/annotation/SpeciesAnnotation.html rename to docs/edu/ucsd/sbrg/annotation/AbstractAnnotator.html index 6e90fa46..9b1251b3 100644 --- a/docs/edu/ucsd/sbrg/annotation/SpeciesAnnotation.html +++ b/docs/edu/ucsd/sbrg/annotation/AbstractAnnotator.html @@ -2,10 +2,10 @@ -SpeciesAnnotation (ModelPolisher 2.1 API) +AbstractAnnotator (ModelPolisher 2.1 API) - + @@ -38,7 +38,7 @@

    Summary:

    @@ -46,7 +46,7 @@

  • Detail:

    @@ -58,13 +58,13 @@ @@ -82,25 +82,37 @@
    Package edu.ucsd.sbrg.annotation
    -

    Class SpeciesAnnotation

    +

    Class AbstractAnnotator<SBMLElement>

    java.lang.Object -
    edu.ucsd.sbrg.annotation.CVTermAnnotation -
    edu.ucsd.sbrg.annotation.SpeciesAnnotation
    -
    +
    edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement>
    +
    +
    Direct Known Subclasses:
    +
    AbstractADBAnnotator, AbstractBiGGAnnotator
    +
    -
    public class SpeciesAnnotation -extends CVTermAnnotation
    -
    This class provides functionality to annotate a species in an SBML model using BiGG database identifiers. - It extends the CVTermAnnotation class, allowing it to manage controlled vocabulary (CV) terms - associated with the species. The class handles various aspects of species annotation including setting - the species' name, SBO term, and additional annotations. It also sets the chemical formula and charge - for the species using FBC (Flux Balance Constraints) extensions.
    +
    public abstract class AbstractAnnotator<SBMLElement> +extends Object
      + +
    • +
      +

      Field Summary

      +
      Fields
      +
      +
      Modifier and Type
      +
      Field
      +
      Description
      +
      protected final Parameters
      +
      parameters
      +
       
      +
      +
      +
    • @@ -109,9 +121,11 @@

      Constructor Summary

      Constructor
      Description
      -
      SpeciesAnnotation(org.sbml.jsbml.Species species, - Parameters parameters)
      +
      AbstractAnnotator(Parameters parameters)
       
      +
      AbstractAnnotator(Parameters parameters, + List<ProgressObserver> observers)
      +
       
      • @@ -120,32 +134,25 @@

      Constructor Summary

      Method Summary

      -
      +
      Modifier and Type
      Method
      Description
      void
      -
      addAnnotations(BiGGId biggId)
      -
      -
      This method delegates the task of adding annotations to the species based on the provided BiGGId.
      -
      -
      void
      -
      annotate()
      -
      -
      This method annotates a species with various details fetched from the BiGG Knowledgebase.
      -
      -
      Optional<BiGGId>
      -
      checkId()
      -
      -
      Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations.
      -
      -
      void
      -
      setName(BiGGId biggId)
      -
      -
      Updates the name of the species based on data retrieved from the BiGG Knowledgebase.
      -
      +
      annotate(List<SBMLElement> elementsToAnnotate)
      +
       
      +
      abstract void
      +
      annotate(SBMLElement elementToAnnotate)
      +
       
      +
      List<ProgressObserver>
      +
      getObservers()
      +
       
      +
      protected void
      +
      statusReport(String text, + Object element)
      +
       
      @@ -158,16 +165,36 @@

      Methods inherited from cl

        + +
      • +
        +

        Field Details

        +
          +
        • +
          +

          parameters

          +
          protected final Parameters parameters
          +
          +
          • +
        +
        +

      • Constructor Details

        • -
          -

          SpeciesAnnotation

          -
          public SpeciesAnnotation(org.sbml.jsbml.Species species, - Parameters parameters)
          +
          +

          AbstractAnnotator

          +
          public AbstractAnnotator(Parameters parameters)
          +
          +
          • +
        • +
          +

          AbstractAnnotator

          +
          public AbstractAnnotator(Parameters parameters, + List<ProgressObserver> observers)
        @@ -179,54 +206,28 @@

        SpeciesAnnotation

        Method Details

        • -
          +

          annotate

          -
          public void annotate()
          -
          This method annotates a species with various details fetched from the BiGG Knowledgebase. It performs the following: - 1. Sets the species name based on the BiGGId. If the species does not have a name, it uses the BiGGId as the name. - 2. Assigns an SBO (Systems Biology Ontology) term to the species based on the BiGGId. - 3. Adds additional annotations to the species, such as database cross-references. - 4. Sets the chemical formula and charge for the species using FBC (Flux Balance Constraints) extensions. -

          - The BiGGId used for these operations is either derived from the species' URI list or directly from its ID if available.

          +
          public void annotate(List<SBMLElement> elementsToAnnotate)
        • -
          -

          checkId

          -
          public Optional<BiGGId> checkId()
          -
          Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations. - This method first tries to create a BiGGId from the species ID. If the species ID does not correspond to a known - BiGGId in the database, it then searches through the species' annotations to find a valid BiGGId.
          -
          -
          Returns:
          -
          An Optional containing the BiGGId if a valid one is found or created, otherwise Optional.empty()
          -
          +
          +

          annotate

          +
          public abstract void annotate(SBMLElement elementToAnnotate)
        • -
          -

          setName

          -
          public void setName(BiGGId biggId)
          -
          Updates the name of the species based on data retrieved from the BiGG Knowledgebase. The species name is set only if it - has not been previously set or if the current name follows a default format that combines the BiGGId abbreviation and - compartment code. This method relies on the availability of a valid BiGGId for the species.
          -
          -
          Parameters:
          -
          biggId - The BiGGId associated with the species, used to fetch the component name from the BiGG database.
          -
          +
          +

          statusReport

          +
          protected void statusReport(String text, + Object element)
        • -
          -

          addAnnotations

          -
          public void addAnnotations(BiGGId biggId)
          -
          This method delegates the task of adding annotations to the species based on the provided BiGGId. - It ensures that annotations are added to the species, updates HTTP URIs to HTTPS in MIRIAM URIs, and merges any duplicate annotations.
          -
          -
          Parameters:
          -
          biggId - the BiGGId associated with the species ID, used for fetching and adding annotations.
          -
          +
          +

          getObservers

          +
          public List<ProgressObserver> getObservers()
        diff --git a/docs/edu/ucsd/sbrg/annotation/ModelAnnotator.html b/docs/edu/ucsd/sbrg/annotation/AnnotationsSorter.html similarity index 85% rename from docs/edu/ucsd/sbrg/annotation/ModelAnnotator.html rename to docs/edu/ucsd/sbrg/annotation/AnnotationsSorter.html index 6a451cf8..8642b514 100644 --- a/docs/edu/ucsd/sbrg/annotation/ModelAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/AnnotationsSorter.html @@ -2,10 +2,10 @@ -ModelAnnotator (ModelPolisher 2.1 API) +AnnotationsSorter (ModelPolisher 2.1 API) - + @@ -82,14 +82,14 @@
        Package edu.ucsd.sbrg.annotation
        -

        Class ModelAnnotator

        +

        Class AnnotationsSorter

        java.lang.Object -
        edu.ucsd.sbrg.annotation.ModelAnnotator
        +
        edu.ucsd.sbrg.annotation.AnnotationsSorter
        -
        public class ModelAnnotator +
        public class AnnotationsSorter extends Object
        @@ -102,7 +102,7 @@

        Constructor Summary

        Constructor
        Description
        -
        ModelAnnotator(Parameters parameters)
        +
        AnnotationsSorter()
         
        @@ -119,8 +119,11 @@

        Method Summary

        Method
        Description
        void
        -
        annotate(org.sbml.jsbml.SBMLDocument doc)
        -
         
        +
        groupAndSortAnnotations(org.sbml.jsbml.SBase sbase)
        +
        +
        Recursively goes through all annotations in the given SBase and + alphabetically sort annotations after grouping them by CVTerm.Qualifier.
        +
    • @@ -139,9 +142,9 @@

    Methods inherited from cl

    Constructor Details

    • -
      -

      ModelAnnotator

      -
      public ModelAnnotator(Parameters parameters)
      +
      +

      AnnotationsSorter

      +
      public AnnotationsSorter()
    @@ -153,9 +156,17 @@

    ModelAnnotator

    Method Details

    • -
      -

      annotate

      -
      public void annotate(org.sbml.jsbml.SBMLDocument doc)
      +
      +

      groupAndSortAnnotations

      +
      public void groupAndSortAnnotations(org.sbml.jsbml.SBase sbase)
      +
      Recursively goes through all annotations in the given SBase and + alphabetically sort annotations after grouping them by CVTerm.Qualifier.
      +
      +
      Parameters:
      +
      sbase - : + SBase to start the merging process at, corresponding to an instance of SBMLDocument here, + though also used to pass current SBase during recursion
      +
    diff --git a/docs/edu/ucsd/sbrg/annotation/GeneProductAnnotation.html b/docs/edu/ucsd/sbrg/annotation/GeneProductAnnotation.html deleted file mode 100644 index a04d7b07..00000000 --- a/docs/edu/ucsd/sbrg/annotation/GeneProductAnnotation.html +++ /dev/null @@ -1,275 +0,0 @@ - - - - -GeneProductAnnotation (ModelPolisher 2.1 API) - - - - - - - - - - - - - -
    - -
    -
    - -
    -
    Package edu.ucsd.sbrg.annotation
    -

    Class GeneProductAnnotation

    -
    -
    java.lang.Object -
    edu.ucsd.sbrg.annotation.CVTermAnnotation -
    edu.ucsd.sbrg.annotation.GeneProductAnnotation
    -
    -
    -
    -
    -
    public class GeneProductAnnotation -extends CVTermAnnotation
    -
    Provides functionality to annotate gene products in an SBML model using data from the BiGG database. - This class extends CVTermAnnotation and specifically handles the annotation of GeneProduct instances. - It includes methods to validate gene product IDs, retrieve and set labels, and add annotations based on BiGG IDs.
    -
    -
    - -
    -
    -
      - -
    • -
      -

      Constructor Details

      -
        -
      • -
        -

        GeneProductAnnotation

        -
        public GeneProductAnnotation(org.sbml.jsbml.ext.fbc.GeneProduct geneProduct, - GeneProductReferencesAnnotator gprAnnotator, - Parameters parameters)
        -
        Constructs a new GeneProductAnnotation instance for a given GeneProduct.
        -
        -
        Parameters:
        -
        geneProduct - The GeneProduct to be annotated.
        -
        -
        -
        • -
      -
      -
      • - -
    • -
      -

      Method Details

      -
        -
      • -
        -

        annotate

        -
        public void annotate()
        -
        Annotates a gene product by adding relevant metadata and references. - This method first checks the gene product's ID for validity and retrieves a corresponding BiGGId if available. - It then attempts to get a label for the gene product. If no label is found, the method returns early. - If a label is present, it updates the gene product reference in the association, adds annotations using the BiGGId, - and sets the gene product's metaId if it has any CV terms. Finally, it sets the gene product's label name.
        -
        -
        • -
      • -
        -

        checkId

        -
        public Optional<BiGGId> checkId()
        -
        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. - The method first checks if the gene product's ID matches the BiGG ID pattern. If it does not match, it then - tries to find a valid BiGG ID from the gene product's annotations. If a valid BiGG ID is found among the annotations, - it updates the ID; otherwise, it retains the original ID.
        -
        -
        Returns:
        -
        An Optional<BiGGId> containing the validated or retrieved BiGG ID, or an empty Optional if no valid ID is found.
        -
        -
        -
        • -
      • -
        -

        getLabel

        -
        public Optional<String> getLabel(Optional<BiGGId> biggId)
        -
        Retrieves the label for a gene product based on the provided BiGGId. If the gene product has a label set and it is not "None", - that label is returned. If no label is set but the gene product has an ID, the BiGGId is converted to a string and returned. - If neither condition is met, an empty string is returned.
        -
        -
        Parameters:
        -
        biggId - An Optional containing the BiGGId of the gene product, which may be used to generate a label if the gene product's own label is not set.
        -
        Returns:
        -
        An Optional<String> containing the label of the gene product, or an empty string if no appropriate label is found.
        -
        -
        -
        • -
      • -
        -

        setGPLabelName

        -
        public void setGPLabelName(String label)
        -
        Updates the label of a gene product and sets its name based on the retrieved gene name from the BiGG database. - If the current label is set to "None", it updates the label to the provided one. It then attempts to fetch - the gene name corresponding to this label from the BiGG database. If a gene name is found, it checks if the - current gene product name is different from the fetched name. If they differ, it logs a warning and updates - the gene product name. If no gene name is found, it logs this as a fine-level message.
        -
        -
        Parameters:
        -
        label - The label to set or use for fetching the gene name. This label should correspond to a BiGGId - or be derived from AbstractSBase.getId().
        -
        -
        -
        • -
      • -
        -

        addAnnotations

        -
        public void addAnnotations(BiGGId biggId)
        -
        Adds annotations to a gene product based on a given BiGGId. This method differentiates between - annotations that specify what the gene product 'is' and what it 'is encoded by'. Resources are fetched - from the BiGG database using the abbreviation from the provided BiGGId. Each resource URL is checked and - parsed to determine the appropriate category ('is' or 'is encoded by') based on predefined prefixes.
        -
        -
        Parameters:
        -
        biggId - The BiGGId associated with the gene product, typically derived from a species ID.
        -
        -
        -
        • -
      -
      -
      • -
    -
    - -
    -
    -
    - - diff --git a/docs/edu/ucsd/sbrg/annotation/adb/ADBReactionsAnnotator.html b/docs/edu/ucsd/sbrg/annotation/adb/ADBReactionsAnnotator.html new file mode 100644 index 00000000..f37fd228 --- /dev/null +++ b/docs/edu/ucsd/sbrg/annotation/adb/ADBReactionsAnnotator.html @@ -0,0 +1,212 @@ + + + + +ADBReactionsAnnotator (ModelPolisher 2.1 API) + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.annotation.adb
    +

    Class ADBReactionsAnnotator

    +
    +
    java.lang.Object +
    edu.ucsd.sbrg.annotation.AbstractAnnotator<org.sbml.jsbml.Reaction> +
    edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator<org.sbml.jsbml.Reaction> +
    edu.ucsd.sbrg.annotation.adb.ADBReactionsAnnotator
    +
    +
    +
    +
    +
    +
    public class ADBReactionsAnnotator +extends AbstractADBAnnotator<org.sbml.jsbml.Reaction>
    +
    +
    + +
    +
    +
      + +
    • +
      +

      Constructor Details

      +
        +
      • +
        +

        ADBReactionsAnnotator

        +
        public ADBReactionsAnnotator(AnnotateDB adb, + Parameters parameters)
        +
        +
        • +
      +
      +
      • + +
    • +
      +

      Method Details

      +
        +
      • +
        +

        annotate

        +
        public void annotate(List<org.sbml.jsbml.Reaction> reactions)
        +
        +
        Overrides:
        +
        annotate in class AbstractAnnotator<org.sbml.jsbml.Reaction>
        +
        +
        +
        • +
      • +
        +

        annotate

        +
        public void annotate(org.sbml.jsbml.Reaction reaction)
        +
        +
        Specified by:
        +
        annotate in class AbstractADBAnnotator<org.sbml.jsbml.Reaction>
        +
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/annotation/ModelAnnotation.html b/docs/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.html similarity index 61% rename from docs/edu/ucsd/sbrg/annotation/ModelAnnotation.html rename to docs/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.html index f08e05ee..33b89fd3 100644 --- a/docs/edu/ucsd/sbrg/annotation/ModelAnnotation.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.html @@ -2,19 +2,19 @@ -ModelAnnotation (ModelPolisher 2.1 API) +ADBSBMLAnnotator (ModelPolisher 2.1 API) - + - - - - - + + + + + -

    +

    Methods inherited from class edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator

    +addBQB_IS_AnnotationsFromADB
    +
    +

    Methods inherited from class edu.ucsd.sbrg.annotation.AbstractAnnotator

    +annotate, getObservers, statusReport
    +

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -147,10 +162,10 @@

    Methods inherited from cl

    Constructor Details

    • -
      -

      ModelAnnotation

      -
      public ModelAnnotation(org.sbml.jsbml.Model model, - Parameters parameters)
      +
      +

      ADBSBMLAnnotator

      +
      public ADBSBMLAnnotator(AnnotateDB adb, + Parameters parameters)
    @@ -162,16 +177,13 @@

    ModelAnnotation

    Method Details

    • -
      +

      annotate

      -
      public void annotate()
      -
      Annotates the Model with relevant metadata and delegates the annotation of contained elements such as - Compartment, Species, Reaction, and GeneProduct. - - Steps: - 1. Retrieves the model's ID and uses it to fetch and add a taxonomy annotation if available. - 2. Checks if the model exists in the database and adds specific BiGG database annotations. - 3. Sets the model's MetaId to its ID if MetaId is not already set and the model has at least one CVTerm.
      +
      public void annotate(org.sbml.jsbml.SBMLDocument doc)
      +
      +
      Specified by:
      +
      annotate in class AbstractADBAnnotator<org.sbml.jsbml.SBMLDocument>
      +
    diff --git a/docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html b/docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html new file mode 100644 index 00000000..3a098bac --- /dev/null +++ b/docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html @@ -0,0 +1,212 @@ + + + + +ADBSpeciesAnnotator (ModelPolisher 2.1 API) + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.annotation.adb
    +

    Class ADBSpeciesAnnotator

    +
    +
    java.lang.Object +
    edu.ucsd.sbrg.annotation.AbstractAnnotator<org.sbml.jsbml.Species> +
    edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator<org.sbml.jsbml.Species> +
    edu.ucsd.sbrg.annotation.adb.ADBSpeciesAnnotator
    +
    +
    +
    +
    +
    +
    public class ADBSpeciesAnnotator +extends AbstractADBAnnotator<org.sbml.jsbml.Species>
    +
    +
    + +
    +
    +
      + +
    • +
      +

      Constructor Details

      +
        +
      • +
        +

        ADBSpeciesAnnotator

        +
        public ADBSpeciesAnnotator(AnnotateDB adb, + Parameters parameters)
        +
        +
        • +
      +
      +
      • + +
    • +
      +

      Method Details

      +
        +
      • +
        +

        annotate

        +
        public void annotate(List<org.sbml.jsbml.Species> species)
        +
        +
        Overrides:
        +
        annotate in class AbstractAnnotator<org.sbml.jsbml.Species>
        +
        +
        +
        • +
      • +
        +

        annotate

        +
        public void annotate(org.sbml.jsbml.Species species)
        +
        +
        Specified by:
        +
        annotate in class AbstractADBAnnotator<org.sbml.jsbml.Species>
        +
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html b/docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html new file mode 100644 index 00000000..15ca86e3 --- /dev/null +++ b/docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html @@ -0,0 +1,231 @@ + + + + +AbstractADBAnnotator (ModelPolisher 2.1 API) + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.annotation.adb
    +

    Class AbstractADBAnnotator<SBMLElement>

    +
    +
    java.lang.Object +
    edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> +
    edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator<SBMLElement>
    +
    +
    +
    +
    +
    Direct Known Subclasses:
    +
    ADBReactionsAnnotator, ADBSBMLAnnotator, ADBSpeciesAnnotator
    +
    +
    +
    public abstract class AbstractADBAnnotator<SBMLElement> +extends AbstractAnnotator<SBMLElement>
    +
    +
    + +
    +
    +
      + +
    • +
      +

      Field Details

      + +
      +
      • + +
    • +
      +

      Constructor Details

      +
        +
      • +
        +

        AbstractADBAnnotator

        +
        public AbstractADBAnnotator(AnnotateDB adb, + Parameters parameters)
        +
        +
        • +
      +
      +
      • + +
    • +
      +

      Method Details

      +
        +
      • +
        +

        annotate

        +
        public abstract void annotate(SBMLElement element)
        +
        +
        Specified by:
        +
        annotate in class AbstractAnnotator<SBMLElement>
        +
        +
        +
        • +
      • +
        +

        addBQB_IS_AnnotationsFromADB

        +
        protected void addBQB_IS_AnnotationsFromADB(org.sbml.jsbml.Annotation annotation, + String type, + BiGGId biggId)
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/miriam/models/package-summary.html b/docs/edu/ucsd/sbrg/annotation/adb/package-summary.html similarity index 77% rename from docs/edu/ucsd/sbrg/miriam/models/package-summary.html rename to docs/edu/ucsd/sbrg/annotation/adb/package-summary.html index 9533bf78..973e7a32 100644 --- a/docs/edu/ucsd/sbrg/miriam/models/package-summary.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/package-summary.html @@ -2,10 +2,10 @@ -edu.ucsd.sbrg.miriam.models (ModelPolisher 2.1 API) +edu.ucsd.sbrg.annotation.adb (ModelPolisher 2.1 API) - + @@ -64,10 +64,10 @@
    -

    Package edu.ucsd.sbrg.miriam.models

    +

    Package edu.ucsd.sbrg.annotation.adb

    -
    package edu.ucsd.sbrg.miriam.models
    +
    package edu.ucsd.sbrg.annotation.adb
    @@ -87,19 +89,13 @@

    Package edu.ucsd.s
    Class
    Description
    -
    Institution
    +
    AbstractADBAnnotator<SBMLElement>
     
    -
    Location
    +
    ADBReactionsAnnotator
     
    -
    Miriam
    -
    -
    The Miriam class is a singleton that manages a collection of namespaces.
    -
    -
    Namespace
    -
     
    -
    Resource
    +
    ADBSBMLAnnotator
     
    -
    Root
    +
    ADBSpeciesAnnotator
     

    diff --git a/docs/edu/ucsd/sbrg/miriam/models/package-tree.html b/docs/edu/ucsd/sbrg/annotation/adb/package-tree.html similarity index 70% rename from docs/edu/ucsd/sbrg/miriam/models/package-tree.html rename to docs/edu/ucsd/sbrg/annotation/adb/package-tree.html index e12b004e..347ea721 100644 --- a/docs/edu/ucsd/sbrg/miriam/models/package-tree.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/package-tree.html @@ -2,10 +2,10 @@ -edu.ucsd.sbrg.miriam.models Class Hierarchy (ModelPolisher 2.1 API) +edu.ucsd.sbrg.annotation.adb Class Hierarchy (ModelPolisher 2.1 API) - + @@ -47,7 +47,7 @@
    -

    Hierarchy For Package edu.ucsd.sbrg.miriam.models

    +

    Hierarchy For Package edu.ucsd.sbrg.annotation.adb

    Package Hierarchies:
      @@ -58,12 +58,17 @@

      Class Hierarchy

      diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html new file mode 100644 index 00000000..feec5620 --- /dev/null +++ b/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html @@ -0,0 +1,255 @@ + + + + +AbstractBiGGAnnotator (ModelPolisher 2.1 API) + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.annotation.bigg
      +

      Class AbstractBiGGAnnotator<SBMLElement>

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> +
      edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator<SBMLElement>
      +
      +
      +
      +
      +
      Direct Known Subclasses:
      +
      BiGGCompartmentsAnnotator, BiGGCVTermAnnotator, BiGGFBCAnnotator, BiGGModelAnnotator, BiGGPublicationsAnnotator, BiGGSBMLAnnotator
      +
      +
      +
      public abstract class AbstractBiGGAnnotator<SBMLElement> +extends AbstractAnnotator<SBMLElement>
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Field Details

        +
          +
        • +
          +

          bigg

          +
          protected final BiGGDB bigg
          +
          +
          • +
        • +
          +

          registry

          +
          protected final Registry registry
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Constructor Details

        + +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          getBiGGIdFromResources

          +
          public Optional<BiGGId> getBiGGIdFromResources(List<String> resources, + String type)
          +
          Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase. This method + processes annotations for biological entities such as Species, Reaction, or GeneProduct. + Each entity's annotations are provided as a list of URIs, which are then parsed to retrieve the BiGG ID.
          +
          +
          Parameters:
          +
          resources - A list of URIs containing annotations for the biological entity.
          +
          type - The type of the biological entity, which can be one of the following: + BiGGDBContract.Constants.TYPE_SPECIES, BiGGDBContract.Constants.TYPE_REACTION, or + BiGGDBContract.Constants.TYPE_GENE_PRODUCT.
          +
          Returns:
          +
          An containing the BiGG ID if it could be successfully retrieved, otherwise Optional.empty().
          +
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/annotation/CVTermAnnotation.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationUtils.html similarity index 69% rename from docs/edu/ucsd/sbrg/annotation/CVTermAnnotation.html rename to docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationUtils.html index 34f55a9d..c4bbb83d 100644 --- a/docs/edu/ucsd/sbrg/annotation/CVTermAnnotation.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationUtils.html @@ -2,19 +2,19 @@ -CVTermAnnotation (ModelPolisher 2.1 API) +BiGGAnnotationUtils (ModelPolisher 2.1 API) - + - - - - - + + + + + -
    @@ -144,9 +140,10 @@

    Methods inherited from cl

    Constructor Details

    @@ -158,12 +155,9 @@

    CompartmentPolishing

    Method Details

    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html new file mode 100644 index 00000000..38d79623 --- /dev/null +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html @@ -0,0 +1,277 @@ + + + + +BiGGModelAnnotator (ModelPolisher 2.1 API) + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.annotation.bigg
    +

    Class BiGGModelAnnotator

    +
    +
    java.lang.Object +
    edu.ucsd.sbrg.annotation.AbstractAnnotator<org.sbml.jsbml.Model> +
    edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator<org.sbml.jsbml.Model> +
    edu.ucsd.sbrg.annotation.bigg.BiGGModelAnnotator
    +
    +
    +
    +
    +
    +
    public class BiGGModelAnnotator +extends AbstractBiGGAnnotator<org.sbml.jsbml.Model>
    +
    This class is responsible for annotating an SBML Model with relevant metadata and references. + It handles the annotation of the model itself and delegates the annotation of contained elements such as + Compartment, Species, Reaction, and GeneProduct. + The annotations can include taxonomy information, database references, and meta identifiers.
    +
    +
    + +
    +
    +
      + +
    • +
      +

      Field Details

      +
        +
      • +
        +

        REF_SEQ_ACCESSION_NUMBER_PATTERN

        +
        public static final String REF_SEQ_ACCESSION_NUMBER_PATTERN
        +
        +
        See Also:
        +
        + +
        +
        +
        +
        • +
      • +
        +

        GENOME_ASSEMBLY_ID_PATTERN

        +
        public static final String GENOME_ASSEMBLY_ID_PATTERN
        +
        +
        See Also:
        +
        + +
        +
        +
        +
        • +
      +
      +
      • + +
    • +
      +

      Constructor Details

      + +
      +
      • + +
    • +
      +

      Method Details

      +
        +
      • +
        +

        annotate

        +
        public void annotate(org.sbml.jsbml.Model model)
        +
        Annotates the Model with relevant metadata and delegates the annotation of contained elements such as + Compartment, Species, Reaction, and GeneProduct. +

        + Steps: + 1. Retrieves the model's ID and uses it to fetch and add a taxonomy annotation if available. + 2. Checks if the model exists in the database and adds specific BiGG database annotations. + 3. Sets the model's MetaId to its ID if MetaId is not already set and the model has at least one CVTerm.

        +
        +
        Specified by:
        +
        annotate in class AbstractAnnotator<org.sbml.jsbml.Model>
        +
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/polishing/SpeciesPolishing.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGPublicationsAnnotator.html similarity index 57% rename from docs/edu/ucsd/sbrg/polishing/SpeciesPolishing.html rename to docs/edu/ucsd/sbrg/annotation/bigg/BiGGPublicationsAnnotator.html index 6795225e..125e3441 100644 --- a/docs/edu/ucsd/sbrg/polishing/SpeciesPolishing.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGPublicationsAnnotator.html @@ -2,19 +2,19 @@ -SpeciesPolishing (ModelPolisher 2.1 API) +BiGGPublicationsAnnotator (ModelPolisher 2.1 API) - + - - - - - + + + + + -