From 6dc07e1ed088566c5ea41672c0e3f8eb7b93ea29 Mon Sep 17 00:00:00 2001 From: Dario Date: Mon, 19 Aug 2024 18:43:24 +0200 Subject: [PATCH] OCD and CLI mode debugging --- build.gradle | 12 +- docs/allclasses-index.html | 201 +++---- docs/allpackages-index.html | 34 +- docs/constant-values.html | 49 +- docs/edu/ucsd/sbrg/SBMLFixerCLILauncher.html | 172 ------ .../AnnotationOptions.html} | 164 +----- .../ucsd/sbrg/annotation/IAnnotateSBases.html | 2 +- .../bigg/AbstractBiGGAnnotator.html | 2 +- .../annotation/bigg/BiGGCVTermAnnotator.html | 2 +- .../bigg/{ => ext}/fbc/BiGGFBCAnnotator.html | 70 +-- .../fbc/BiGGGeneProductAnnotator.html | 108 ++-- .../BiGGGeneProductReferencesAnnotator.html | 26 +- .../bigg/ext/fbc/package-summary.html | 87 +++ .../annotation/bigg/ext/fbc/package-tree.html | 84 +++ .../sbrg/annotation/bigg/package-summary.html | 4 +- .../ucsd/sbrg/annotation/package-summary.html | 18 +- .../ucsd/sbrg/annotation/package-tree.html | 5 + .../ucsd/sbrg/cli/CommandLineIOOptions.html | 167 ++++++ docs/edu/ucsd/sbrg/cli/ConfigOptions.html | 129 +++++ .../sbrg/{ => cli}/ECOParserCLILauncher.html | 26 +- .../{ => cli}/ModelPolisherCLILauncher.html | 28 +- docs/edu/ucsd/sbrg/cli/package-summary.html | 95 ++++ .../edu/ucsd/sbrg/{ => cli}/package-tree.html | 49 +- docs/edu/ucsd/sbrg/db/adb/AnnotateDB.html | 35 +- docs/edu/ucsd/sbrg/db/bigg/BiGGDB.html | 66 +-- docs/edu/ucsd/sbrg/db/bigg/BiGGId.html | 42 +- docs/edu/ucsd/sbrg/db/package-summary.html | 6 +- docs/edu/ucsd/sbrg/eco/package-summary.html | 13 +- ...ObjectiveFixer.html => AbstractFixer.html} | 94 +-- .../ucsd/sbrg/fixing/CompartmentFixer.html | 41 +- docs/edu/ucsd/sbrg/fixing/FixingOptions.html | 156 +++++ docs/edu/ucsd/sbrg/fixing/IFixSBases.html | 2 +- docs/edu/ucsd/sbrg/fixing/ModelFixer.html | 17 +- docs/edu/ucsd/sbrg/fixing/ReactionFixer.html | 41 +- docs/edu/ucsd/sbrg/fixing/SBMLFixer.html | 17 +- docs/edu/ucsd/sbrg/fixing/SpeciesFixer.html | 41 +- .../fixing/ext/fbc/ListOfObjectivesFixer.html | 21 +- .../sbrg/fixing/ext/fbc/package-summary.html | 2 - .../sbrg/fixing/ext/fbc/package-tree.html | 5 +- .../sbrg/fixing/ext/groups/GroupsFixer.html | 54 +- .../sbrg/fixing/ext/groups/package-tree.html | 6 +- .../edu/ucsd/sbrg/fixing/package-summary.html | 19 +- docs/edu/ucsd/sbrg/fixing/package-tree.html | 9 + .../IOOptions.OutputType.html} | 34 +- docs/edu/ucsd/sbrg/io/IOOptions.html | 55 +- docs/edu/ucsd/sbrg/io/ModelWriter.html | 6 +- docs/edu/ucsd/sbrg/io/package-summary.html | 47 +- docs/edu/ucsd/sbrg/io/package-tree.html | 1 + docs/edu/ucsd/sbrg/logging/BundleNames.html | 282 +++++++++ .../ucsd/sbrg/logging/package-summary.html | 81 +++ docs/edu/ucsd/sbrg/logging/package-tree.html | 70 +++ docs/edu/ucsd/sbrg/package-summary.html | 122 ---- .../parameters/ADBAnnotationParameters.html | 57 +- .../sbrg/parameters/AnnotationParameters.html | 41 +- .../parameters/BiGGAnnotationParameters.html | 41 +- .../parameters/CommandLineParameters.html | 107 +--- .../ucsd/sbrg/parameters/DBParameters.html | 43 +- .../sbrg/parameters/FixingParameters.html | 228 ++++++++ ...ml => FluxObjectivesFixingParameters.html} | 62 +- .../ucsd/sbrg/parameters/GeneralOptions.html | 159 ++++++ docs/edu/ucsd/sbrg/parameters/Parameters.html | 94 ++- .../sbrg/parameters/ParametersException.html | 145 +++++ .../sbrg/parameters/ParametersParser.html | 14 + .../sbrg/parameters/PolishingParameters.html | 29 +- .../ucsd/sbrg/parameters/SBOParameters.html | 49 +- .../ucsd/sbrg/parameters/package-summary.html | 31 +- .../ucsd/sbrg/parameters/package-tree.html | 32 +- .../ucsd/sbrg/polishing/AbstractPolisher.html | 2 +- .../ucsd/sbrg/polishing/IPolishSBases.html | 2 +- .../PolisherFactory.html} | 57 +- .../ucsd/sbrg/polishing/PolishingOptions.html | 138 +++++ .../polishing/{ => ext}/fbc/FBCPolisher.html | 64 +-- .../{ => ext}/fbc/FBCReactionPolisher.html | 74 +-- .../fbc/GeneProductAssociationsProcessor.html | 42 +- .../{ => ext}/fbc/GeneProductsPolisher.html | 58 +- .../{ => ext}/fbc/ObjectivesPolisher.html | 68 +-- .../{ => ext}/fbc/StrictnessPredicate.html | 26 +- .../ext}/fbc/package-summary.html | 37 +- .../ext}/fbc/package-tree.html | 25 +- .../sbrg/polishing/fbc/package-summary.html | 104 ---- .../ucsd/sbrg/polishing/fbc/package-tree.html | 79 --- .../ucsd/sbrg/polishing/package-summary.html | 19 +- .../edu/ucsd/sbrg/polishing/package-tree.html | 6 + .../DiffListener.html} | 131 ++--- .../edu/ucsd/sbrg/reporting/IReportDiffs.html | 2 +- .../ucsd/sbrg/reporting/IReportStatus.html | 2 +- .../sbrg/reporting/ProgressFinalization.html | 34 +- .../ucsd/sbrg/reporting/package-summary.html | 41 +- .../edu/ucsd/sbrg/reporting/package-tree.html | 1 + .../ucsd/sbrg/resolver/package-summary.html | 4 +- .../edu/ucsd/sbrg/util/ext/fbc/GPRParser.html | 108 +--- .../sbrg/util/ext/fbc/package-summary.html | 5 +- docs/edu/ucsd/sbrg/util/package-summary.html | 13 +- .../ucsd/sbrg/validation/package-summary.html | 13 +- docs/element-list | 7 +- docs/index-all.html | 534 ++++++++++-------- docs/index.html | 34 +- docs/member-search-index.js | 2 +- docs/overview-tree.html | 79 ++- docs/package-search-index.js | 2 +- docs/serialized-form.html | 79 +-- docs/type-search-index.js | 2 +- examples/config.json | 53 ++ .../edu/ucsd/sbrg/SBMLFixerCLILauncher.java | 106 ---- .../ucsd/sbrg/SBMLValidatorCLILauncher.java | 27 - .../sbrg/annotation/AnnotationOptions.java | 75 +++ .../sbrg/annotation/AnnotationsSorter.java | 5 +- .../bigg/BiGGDocumentNotesProcessor.java | 3 +- .../bigg/BiGGReactionsAnnotator.java | 3 +- .../annotation/bigg/BiGGSpeciesAnnotator.java | 3 +- .../ext/fbc/BiGGGeneProductAnnotator.java | 3 +- .../ucsd/sbrg/cli/CommandLineIOOptions.java | 54 ++ .../java/edu/ucsd/sbrg/cli/ConfigOptions.java | 11 + .../sbrg/{ => cli}/ECOParserCLILauncher.java | 2 +- .../{ => cli}/ModelPolisherCLILauncher.java | 191 ++++--- .../java/edu/ucsd/sbrg/db/bigg/BiGGDB.java | 5 +- .../edu/ucsd/sbrg/db/bigg/BiGGDBOptions.java | 15 - .../java/edu/ucsd/sbrg/db/bigg/BiGGId.java | 5 +- .../edu/ucsd/sbrg/fixing/AbstractFixer.java | 29 + .../ucsd/sbrg/fixing/CompartmentFixer.java | 18 +- .../edu/ucsd/sbrg/fixing/FixingOptions.java | 27 + .../java/edu/ucsd/sbrg/fixing/IFixSBases.java | 8 +- .../java/edu/ucsd/sbrg/fixing/ModelFixer.java | 39 +- .../edu/ucsd/sbrg/fixing/ReactionFixer.java | 15 +- .../java/edu/ucsd/sbrg/fixing/SBMLFixer.java | 15 +- .../edu/ucsd/sbrg/fixing/SpeciesFixer.java | 17 +- .../fixing/ext/fbc/ListOfObjectivesFixer.java | 104 +++- .../sbrg/fixing/ext/fbc/ObjectiveFixer.java | 90 --- .../sbrg/fixing/ext/groups/GroupsFixer.java | 39 +- .../java/edu/ucsd/sbrg/io/CombineArchive.java | 3 +- src/main/java/edu/ucsd/sbrg/io/IOOptions.java | 76 ++- .../java/edu/ucsd/sbrg/io/ModelWriter.java | 14 +- .../java/edu/ucsd/sbrg/io/SBMLFileUtils.java | 15 +- .../java/edu/ucsd/sbrg/io/UpdateListener.java | 3 +- .../sbrg/io/parsers/cobra/COBRAUtils.java | 3 +- .../sbrg/io/parsers/cobra/MatlabFields.java | 12 +- .../sbrg/io/parsers/cobra/MatlabParser.java | 29 +- .../sbrg/io/parsers/cobra/ReactionParser.java | 6 +- .../sbrg/io/parsers/cobra/SpeciesParser.java | 3 +- .../ucsd/sbrg/io/parsers/json/JSONParser.java | 39 +- .../edu/ucsd/sbrg/logging/BundleNames.java | 13 + .../parameters/ADBAnnotationParameters.java | 5 +- .../parameters/BiGGAnnotationParameters.java | 13 +- .../sbrg/parameters/BiGGNotesParameters.java | 13 +- .../parameters/CommandLineParameters.java | 50 +- .../ucsd/sbrg/parameters/DBParameters.java | 10 +- .../sbrg/parameters/FixingParameters.java | 19 + ...va => FluxObjectivesFixingParameters.java} | 22 +- .../ucsd/sbrg/parameters/GeneralOptions.java | 39 ++ .../sbrg/parameters/ModelPolisherOptions.java | 153 ----- .../edu/ucsd/sbrg/parameters/Parameters.java | 35 +- .../sbrg/parameters/ParametersException.java | 8 + .../sbrg/parameters/ParametersParser.java | 10 + .../sbrg/parameters/PolishingParameters.java | 45 +- .../ReactionPolishingParameters.java | 51 -- .../ucsd/sbrg/parameters/SBOParameters.java | 6 +- .../sbrg/polishing/CompartmentPolisher.java | 3 +- .../ucsd/sbrg/polishing/ModelPolisher.java | 3 +- .../edu/ucsd/sbrg/polishing/NamePolisher.java | 3 +- .../sbrg/polishing/ParametersPolisher.java | 2 +- .../ucsd/sbrg/polishing/PolisherFactory.java | 22 + .../ucsd/sbrg/polishing/PolishingOptions.java | 31 + .../sbrg/polishing/ReactionsPolisher.java | 2 +- .../edu/ucsd/sbrg/polishing/SBMLPolisher.java | 4 +- .../ucsd/sbrg/polishing/SpeciesPolisher.java | 3 +- .../sbrg/polishing/ext/fbc/FBCPolisher.java | 3 +- .../fbc/GeneProductAssociationsProcessor.java | 3 +- .../ext/fbc/GeneProductsPolisher.java | 2 +- .../sbrg/reporting/PolisherProgressBar.java | 1 + .../sbrg/reporting/ProgressFinalization.java | 2 +- .../identifiersorg/IdentifiersOrg.java | 8 + .../edu/ucsd/sbrg/util/ext/fbc/GPRParser.java | 7 +- .../ucsd/sbrg/validation/ModelValidator.java | 3 +- .../edu/ucsd/sbrg/annotation/Messages.xml | 15 + .../edu/ucsd/sbrg/annotation/adb/Messages.xml | 4 + .../ucsd/sbrg/annotation/bigg/Messages.xml | 10 + .../resources/edu/ucsd/sbrg/cli/Messages.xml | 14 + .../resources/edu/ucsd/sbrg/db/Messages.xml | 16 + .../edu/ucsd/sbrg/fixing/Messages.xml | 15 + .../resources/edu/ucsd/sbrg/io/Messages.xml | 51 ++ .../edu/ucsd/sbrg/polisher/Messages.xml | 210 ------- .../edu/ucsd/sbrg/polisher/Messages_de.xml | 210 ------- .../edu/ucsd/sbrg/polishing/Messages.xml | 27 + .../IdentifiersOrg-Registry.json | 56 ++ src/main/resources/logback.xml | 20 + .../bigg/BiGGSBMLAnnotatorTest.java | 4 +- .../fixing/fbc/ListOfObjectivesFixerTest.java | 20 +- .../sbrg/parameters/ParametersParserTest.java | 53 +- .../polishing/fbc/ObjectivesPolisherTest.java | 10 +- src/test/resources/logback.xml | 20 + 190 files changed, 4924 insertions(+), 3535 deletions(-) delete mode 100644 docs/edu/ucsd/sbrg/SBMLFixerCLILauncher.html rename docs/edu/ucsd/sbrg/{parameters/ModelPolisherOptions.html => annotation/AnnotationOptions.html} (57%) rename docs/edu/ucsd/sbrg/annotation/bigg/{ => ext}/fbc/BiGGFBCAnnotator.html (68%) rename docs/edu/ucsd/sbrg/annotation/bigg/{ => ext}/fbc/BiGGGeneProductAnnotator.html (73%) rename docs/edu/ucsd/sbrg/annotation/bigg/{ => ext}/fbc/BiGGGeneProductReferencesAnnotator.html (90%) create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/ext/fbc/package-summary.html create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/ext/fbc/package-tree.html create mode 100644 docs/edu/ucsd/sbrg/cli/CommandLineIOOptions.html create mode 100644 docs/edu/ucsd/sbrg/cli/ConfigOptions.html rename docs/edu/ucsd/sbrg/{ => cli}/ECOParserCLILauncher.html (94%) rename docs/edu/ucsd/sbrg/{ => cli}/ModelPolisherCLILauncher.html (96%) create mode 100644 docs/edu/ucsd/sbrg/cli/package-summary.html rename docs/edu/ucsd/sbrg/{ => cli}/package-tree.html (52%) rename docs/edu/ucsd/sbrg/fixing/{ext/fbc/ObjectiveFixer.html => AbstractFixer.html} (52%) create mode 100644 docs/edu/ucsd/sbrg/fixing/FixingOptions.html rename docs/edu/ucsd/sbrg/{parameters/ModelPolisherOptions.OutputType.html => io/IOOptions.OutputType.html} (84%) create mode 100644 docs/edu/ucsd/sbrg/logging/BundleNames.html create mode 100644 docs/edu/ucsd/sbrg/logging/package-summary.html create mode 100644 docs/edu/ucsd/sbrg/logging/package-tree.html delete mode 100644 docs/edu/ucsd/sbrg/package-summary.html create mode 100644 docs/edu/ucsd/sbrg/parameters/FixingParameters.html rename docs/edu/ucsd/sbrg/parameters/{FluxObjectivesPolishingParameters.html => FluxObjectivesFixingParameters.html} (80%) create mode 100644 docs/edu/ucsd/sbrg/parameters/GeneralOptions.html create mode 100644 docs/edu/ucsd/sbrg/parameters/ParametersException.html rename docs/edu/ucsd/sbrg/{SBMLValidatorCLILauncher.html => polishing/PolisherFactory.html} (74%) create mode 100644 docs/edu/ucsd/sbrg/polishing/PolishingOptions.html rename docs/edu/ucsd/sbrg/polishing/{ => ext}/fbc/FBCPolisher.html (69%) rename docs/edu/ucsd/sbrg/polishing/{ => ext}/fbc/FBCReactionPolisher.html (72%) rename docs/edu/ucsd/sbrg/polishing/{ => ext}/fbc/GeneProductAssociationsProcessor.html (84%) rename docs/edu/ucsd/sbrg/polishing/{ => ext}/fbc/GeneProductsPolisher.html (73%) rename docs/edu/ucsd/sbrg/polishing/{ => ext}/fbc/ObjectivesPolisher.html (70%) rename docs/edu/ucsd/sbrg/polishing/{ => ext}/fbc/StrictnessPredicate.html (96%) rename docs/edu/ucsd/sbrg/{annotation/bigg => polishing/ext}/fbc/package-summary.html (66%) rename docs/edu/ucsd/sbrg/{annotation/bigg => polishing/ext}/fbc/package-tree.html (51%) delete mode 100644 docs/edu/ucsd/sbrg/polishing/fbc/package-summary.html delete mode 100644 docs/edu/ucsd/sbrg/polishing/fbc/package-tree.html rename docs/edu/ucsd/sbrg/{parameters/ReactionPolishingParameters.html => reporting/DiffListener.html} (62%) create mode 100644 examples/config.json delete mode 100644 src/main/java/edu/ucsd/sbrg/SBMLFixerCLILauncher.java delete mode 100644 src/main/java/edu/ucsd/sbrg/SBMLValidatorCLILauncher.java create mode 100644 src/main/java/edu/ucsd/sbrg/annotation/AnnotationOptions.java create mode 100644 src/main/java/edu/ucsd/sbrg/cli/CommandLineIOOptions.java create mode 100644 src/main/java/edu/ucsd/sbrg/cli/ConfigOptions.java rename src/main/java/edu/ucsd/sbrg/{ => cli}/ECOParserCLILauncher.java (99%) rename src/main/java/edu/ucsd/sbrg/{ => cli}/ModelPolisherCLILauncher.java (68%) create mode 100644 src/main/java/edu/ucsd/sbrg/fixing/AbstractFixer.java create mode 100644 src/main/java/edu/ucsd/sbrg/fixing/FixingOptions.java delete mode 100644 src/main/java/edu/ucsd/sbrg/fixing/ext/fbc/ObjectiveFixer.java create mode 100644 src/main/java/edu/ucsd/sbrg/logging/BundleNames.java rename src/main/java/edu/ucsd/sbrg/parameters/{FluxObjectivesPolishingParameters.java => FluxObjectivesFixingParameters.java} (53%) create mode 100644 src/main/java/edu/ucsd/sbrg/parameters/GeneralOptions.java delete mode 100644 src/main/java/edu/ucsd/sbrg/parameters/ModelPolisherOptions.java create mode 100644 src/main/java/edu/ucsd/sbrg/parameters/ParametersException.java delete mode 100644 src/main/java/edu/ucsd/sbrg/parameters/ReactionPolishingParameters.java create mode 100644 src/main/java/edu/ucsd/sbrg/polishing/PolisherFactory.java create mode 100644 src/main/java/edu/ucsd/sbrg/polishing/PolishingOptions.java create mode 100644 src/main/resources/edu/ucsd/sbrg/annotation/Messages.xml create mode 100644 src/main/resources/edu/ucsd/sbrg/annotation/adb/Messages.xml create mode 100644 src/main/resources/edu/ucsd/sbrg/annotation/bigg/Messages.xml create mode 100644 src/main/resources/edu/ucsd/sbrg/cli/Messages.xml create mode 100644 src/main/resources/edu/ucsd/sbrg/db/Messages.xml create mode 100644 src/main/resources/edu/ucsd/sbrg/fixing/Messages.xml create mode 100644 src/main/resources/edu/ucsd/sbrg/io/Messages.xml delete mode 100644 src/main/resources/edu/ucsd/sbrg/polisher/Messages.xml delete mode 100644 src/main/resources/edu/ucsd/sbrg/polisher/Messages_de.xml create mode 100644 src/main/resources/edu/ucsd/sbrg/polishing/Messages.xml create mode 100644 src/main/resources/logback.xml create mode 100644 src/test/resources/logback.xml diff --git a/build.gradle b/build.gradle index 165f6130..9d01a0e4 100755 --- a/build.gradle +++ b/build.gradle @@ -127,15 +127,18 @@ dependencies { implementation "org.slf4j:log4j-over-slf4j:2.0.9" implementation "org.slf4j:osgi-over-slf4j:2.0.9" + // TODO: this needs to be fixed - this dependency should only be included in the uberjar + implementation group: 'ch.qos.logback', name: 'logback-classic', version: '1.5.7' + // JDBC connection pool implementation "com.zaxxer:HikariCP:5.1.0" // https://mvnrepository.com/artifact/commons-io/commons-io implementation group: 'commons-io', name: 'commons-io', version: '2.16.1' // https://mvnrepository.com/artifact/org.apache.commons/commons-lang3 implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.15.0' -// JSON processor + // JSON processor implementation "com.fasterxml.jackson.core:jackson-core:${jacksonVersion}" -// data binding for Jackson + // data binding for Jackson implementation "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}" // Java port of HTML Tidy, for cleaning up malformed HTML implementation "net.sf.jtidy:jtidy:r938" @@ -179,13 +182,14 @@ tasks.withType(Jar).configureEach { "Specification-Title": "ModelPolisher", "Implementation-Vendor-Id": "edu.ucsd.sbrg", "Implementation-Vendor": "University of California, San Diego", - "Main-Class": "edu.ucsd.sbrg.ModelPolisherCLILauncher" + "Main-Class": "edu.ucsd.sbrg.cli.ModelPolisherCLILauncher" ) } into("META-INF/maven/${project.group}/${project.name}") { from generatePomFileForMavenPublication rename { it.replace('pom-default.xml', 'pom.xml') } } + archiveFileName = "${project.name}-${project.version}.jar" } @@ -272,6 +276,8 @@ processResources.dependsOn(downloadMIRIAM) tasks.register('uberjar', Jar) { duplicatesStrategy = DuplicatesStrategy.EXCLUDE + archiveFileName = "${project.name}-${project.version}-STANDALONE.jar" + from sourceSets.main.output dependsOn configurations.runtimeClasspath from { diff --git a/docs/allclasses-index.html b/docs/allclasses-index.html index 361c4229..eb6dea24 100644 --- a/docs/allclasses-index.html +++ b/docs/allclasses-index.html @@ -65,32 +65,36 @@

All Classes and Interfaces<
 
AbstractBiGGAnnotator
 
-
AbstractPolisher
+
AbstractFixer
 
-
ADBAnnotationParameters
+
AbstractPolisher
 
-
ADBReactionsAnnotator
+
ADBAnnotationParameters
 
-
ADBSBMLAnnotator
+
ADBReactionsAnnotator
 
-
ADBSpeciesAnnotator
+
ADBSBMLAnnotator
 
-
AnnotateDB
+
ADBSpeciesAnnotator
 
-
AnnotateDBContract
+
AnnotateDB
 
-
AnnotateDBContract.Constants
+
AnnotateDBContract
 
-
AnnotateDBContract.Constants.Column
+
AnnotateDBContract.Constants
 
-
AnnotateDBContract.Constants.Table
+
AnnotateDBContract.Constants.Column
 
-
AnnotateDBOptions
-
+
AnnotateDBContract.Constants.Table
+
 
+
AnnotateDBOptions
+
This interface provides options for connecting to the ADB database.
-
AnnotationException
-
 
+
AnnotationException
+
 
+
AnnotationOptions
+
 
AnnotationParameters
 
AnnotationPolisher
@@ -125,13 +129,13 @@

All Classes and Interfaces<
 
BiGGDocumentNotesProcessor
 
-
BiGGFBCAnnotator
+
BiGGFBCAnnotator
 
-
BiGGGeneProductAnnotator
+
BiGGGeneProductAnnotator
Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
-
BiGGGeneProductReferencesAnnotator
+
BiGGGeneProductReferencesAnnotator
 
BiGGId
@@ -158,12 +162,16 @@

All Classes and Interfaces<
This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
-
COBRAUtils
+
BundleNames
 
-
CombineArchive
-
+
COBRAUtils
+
 
+
CombineArchive
+
The CombineArchive class provides functionality to create a COMBINE archive from an SBML document.
+
CommandLineIOOptions
+
 
CommandLineParameters
 
CompartmentFixer
@@ -175,62 +183,71 @@

All Classes and Interfaces<

Compartments
 
-
DAG
+
ConfigOptions
+
 
+
DAG
+
 
+
DBParameters
 
-
DBParameters
+
DeleteOnCloseFileInputStream
 
-
DeleteOnCloseFileInputStream
+
DiffListener
 
-
ECOParserCLILauncher
+
ECOParserCLILauncher
 
-
FBCPolisher
+
FBCPolisher
 
-
FBCReactionPolisher
+
FBCReactionPolisher
+
 
+
FixingOptions
+
 
+
FixingParameters
 
-
FluxObjectivesPolishingParameters
+
FluxObjectivesFixingParameters
 
Gene
 
GeneParser
 
-
GeneProductAssociationsProcessor
+
GeneProductAssociationsProcessor
 
-
GeneProductsPolisher
+
GeneProductsPolisher
 
-
GPRParser
-
-
The GPRParser class provides methods to parse gene product associations (GPRs) from gene reaction rules - and integrate them into SBML models using JSBML.
-
-
GroupsFixer
+
GeneralOptions
+
 
+
GPRParser
 
-
GroupsUtils
-
+
GroupsFixer
+
 
+
GroupsUtils
+
A collection of helpful functions for dealing with SBML data structures.
-
IAnnotateSBases<SBMLElement extends org.sbml.jsbml.SBase>
-
 
-
IdentifiersOrg
-
+
IAnnotateSBases<SBMLElement extends org.sbml.jsbml.SBase>
+
 
+
IdentifiersOrg
+
The IdentifiersOrg class serves as a central hub for managing and processing identifiers related to the MIRIAM registry.
-
IdentifiersOrgRegistryParser
-
+
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
+
IdentifiersOrgURI
 
-
IFixSBases<SBMLElement extends org.sbml.jsbml.SBase>
-
 
-
IFixSpeciesReferences
-
 
-
Institution
+
IdentifiersOrgURIUtils
 
-
IOOptions
+
IFixSBases<SBMLElement extends org.sbml.jsbml.SBase>
 
+
IFixSpeciesReferences
+
 
+
Institution
+
 
+
IOOptions
+
 
+
IOOptions.OutputType
+
 
IPolishAnnotations
 
IPolishSBaseAttributes
@@ -277,14 +294,10 @@

All Classes and Interfaces<
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.OutputType
-
 
ModelReader
 
ModelReaderException
@@ -303,18 +316,22 @@

All Classes and Interfaces<
 
Node
 
-
ObjectiveFixer
+
ObjectivesPolisher
 
-
ObjectivesPolisher
+
Parameters
 
-
Parameters
+
ParametersException
 
ParametersParser
 
ParametersPolisher
 
-
PolisherProgressBar
+
PolisherFactory
 
+
PolisherProgressBar
+
 
+
PolishingOptions
+
 
PolishingParameters
 
PostgresConnectionPool
@@ -341,61 +358,53 @@

All Classes and Interfaces<

ReactionParser
 
-
ReactionPolishingParameters
-
 
-
ReactionsPolisher
-
+
ReactionsPolisher
+
This class provides methods to polish and validate SBML reactions according to specific rules and patterns.
-
Registry
-
 
-
RegistryURI
+
Registry
 
-
ReportType
-
 
-
Resource
-
 
-
Root
+
RegistryURI
+
 
+
ReportType
+
 
+
Resource
 
-
SBMLFileUtils
+
Root
 
-
SBMLFileUtils.FileType
-
+
SBMLFileUtils
+
 
+
SBMLFileUtils.FileType
+
Possible FileTypes of input file
-
SBMLFixer
-
 
-
SBMLFixerCLILauncher
-
-
This is a stand-alone bug-fix program.
-
+
SBMLFixer
+
 
SBMLPolisher
 
-
SBMLValidatorCLILauncher
+
SBOParameters
 
-
SBOParameters
+
SpeciesFixer
 
-
SpeciesFixer
+
SpeciesParser
 
-
SpeciesParser
+
SpeciesPolisher
 
-
SpeciesPolisher
+
SpeciesReferenceFixer
 
-
SpeciesReferenceFixer
+
SpeciesReferencesPolisher
 
-
SpeciesReferencesPolisher
-
 
-
StrictnessPredicate
-
+
StrictnessPredicate
+
From ...:
-
UnitPolisher
-
+
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 2eb95511..da460566 100644 --- a/docs/allpackages-index.html +++ b/docs/allpackages-index.html @@ -53,15 +53,15 @@

All Packages

Package
Description
-
edu.ucsd.sbrg
+
edu.ucsd.sbrg.annotation
 
-
edu.ucsd.sbrg.annotation
+
edu.ucsd.sbrg.annotation.adb
 
-
edu.ucsd.sbrg.annotation.adb
+
edu.ucsd.sbrg.annotation.bigg
 
-
edu.ucsd.sbrg.annotation.bigg
+
edu.ucsd.sbrg.annotation.bigg.ext.fbc
 
-
edu.ucsd.sbrg.annotation.bigg.fbc
+
edu.ucsd.sbrg.cli
 
edu.ucsd.sbrg.db
 
@@ -85,28 +85,30 @@

All Packages

 
edu.ucsd.sbrg.io.parsers.json.mapping
 
-
edu.ucsd.sbrg.parameters
+
edu.ucsd.sbrg.logging
 
-
edu.ucsd.sbrg.polishing
+
edu.ucsd.sbrg.parameters
 
-
edu.ucsd.sbrg.polishing.fbc
+
edu.ucsd.sbrg.polishing
 
-
edu.ucsd.sbrg.reporting
+
edu.ucsd.sbrg.polishing.ext.fbc
 
-
edu.ucsd.sbrg.resolver
+
edu.ucsd.sbrg.reporting
 
-
edu.ucsd.sbrg.resolver.identifiersorg
+
edu.ucsd.sbrg.resolver
 
-
edu.ucsd.sbrg.resolver.identifiersorg.mapping
+
edu.ucsd.sbrg.resolver.identifiersorg
 
-
edu.ucsd.sbrg.util
+
edu.ucsd.sbrg.resolver.identifiersorg.mapping
 
-
edu.ucsd.sbrg.util.ext.fbc
+
edu.ucsd.sbrg.util
 
-
edu.ucsd.sbrg.util.ext.groups
+
edu.ucsd.sbrg.util.ext.fbc
 
-
edu.ucsd.sbrg.validation
+
edu.ucsd.sbrg.util.ext.groups
 
+
edu.ucsd.sbrg.validation
+
 
diff --git a/docs/constant-values.html b/docs/constant-values.html index 346e7add..7fe23e34 100644 --- a/docs/constant-values.html +++ b/docs/constant-values.html @@ -75,13 +75,13 @@

edu.ucsd.*

diff --git a/docs/edu/ucsd/sbrg/SBMLFixerCLILauncher.html b/docs/edu/ucsd/sbrg/SBMLFixerCLILauncher.html deleted file mode 100644 index de921611..00000000 --- a/docs/edu/ucsd/sbrg/SBMLFixerCLILauncher.html +++ /dev/null @@ -1,172 +0,0 @@ - - - - -SBMLFixerCLILauncher (ModelPolisher 2.1 API) - - - - - - - - - - - - - - -
- -
-
- -
-
Package edu.ucsd.sbrg
-

Class SBMLFixerCLILauncher

-
-
java.lang.Object -
edu.ucsd.sbrg.SBMLFixerCLILauncher
-
-
-
-
public class SBMLFixerCLILauncher -extends Object
-
This is a stand-alone bug-fix program. It recursively traverses a directory - of SBML files and applies fixes to each model found. The result is saved to - a target directory, which can be in-place, i.e., identical to the input - directory. Otherwise, an identical directory structure will be created within - the target directory. -

- This program became necessary as a temporary solution for invalid SBML models - in BiGG database before a new version of ModelPolisherCLILauncher could be - released. -

- The methods in this class can also be used in other parts of ModelPolisher, - and are used in fact. This class can become a collection of repair functions - for invalid SBML models. -

- Date: 2016-02-19

-
-
- -
-
-
    - -
  • -
    -

    Constructor Details

    -
      -
    • -
      -

      SBMLFixerCLILauncher

      -
      public SBMLFixerCLILauncher()
      -
      -
      • -
    -
    -
    • - -
  • -
    -

    Method Details

    -
      -
    • -
      -

      main

      -
      public static void main(String[] args)
      -
      -
      • -
    -
    -
    • -
-
- -
-
-
- - diff --git a/docs/edu/ucsd/sbrg/parameters/ModelPolisherOptions.html b/docs/edu/ucsd/sbrg/annotation/AnnotationOptions.html similarity index 57% rename from docs/edu/ucsd/sbrg/parameters/ModelPolisherOptions.html rename to docs/edu/ucsd/sbrg/annotation/AnnotationOptions.html index 922f5999..7e841b4f 100644 --- a/docs/edu/ucsd/sbrg/parameters/ModelPolisherOptions.html +++ b/docs/edu/ucsd/sbrg/annotation/AnnotationOptions.html @@ -2,10 +2,10 @@ -ModelPolisherOptions (ModelPolisher 2.1 API) +AnnotationOptions (ModelPolisher 2.1 API) - + @@ -63,8 +63,8 @@
-
Package edu.ucsd.sbrg.parameters
-

Interface ModelPolisherOptions

+
Package edu.ucsd.sbrg.annotation
+

Interface AnnotationOptions

@@ -72,7 +72,7 @@

Interface ModelPolisher
de.zbit.util.prefs.KeyProvider

-
public interface ModelPolisherOptions +
public interface AnnotationOptions extends de.zbit.util.prefs.KeyProvider
@@ -81,15 +81,6 @@

Interface ModelPolisher

  • Nested Class Summary

    -
    Nested Classes
    -
    -
    Modifier and Type
    -
    Interface
    -
    Description
    -
    static enum 
    -
    ModelPolisherOptions.OutputType
    -
     
    -

    Nested classes/interfaces inherited from interface de.zbit.util.prefs.KeyProvider

    de.zbit.util.prefs.KeyProvider.Entry<T extends Object>, de.zbit.util.prefs.KeyProvider.Tools
    @@ -110,23 +101,11 @@

    Field Summary

    If set to true, annotations will be added to species and reactions from AnnotateDB also.

    • static final de.zbit.util.prefs.Option<Boolean>
    -
    ADD_GENERIC_TERMS
    +
    ANNOTATE_WITH_BIGG
    -
    Set this option to true if generic top-level annotations, such as 'process' - should not be applied.
    -
    -
    static final de.zbit.util.prefs.Option<Boolean>
    -
    ANNOTATE_WITH_BIGG
    -
    If set to true, the model will be annotated with data from BiGG Models database.
    -
    static final de.zbit.util.prefs.Option<Boolean>
    -
    CHECK_MASS_BALANCE
    -
    -
    When set to true, the mass balance of each reaction will be checked where - possible.
    -
    static final de.zbit.util.prefs.Option<File>
    DOCUMENT_NOTES_FILE
    @@ -140,12 +119,6 @@

    Field Summary

    description and hence the headline when the file is displayed in a web browser.
    -
    static final de.zbit.util.prefs.Option<Double[]>
    -
    FLUX_COEFFICIENTS
    -
     
    -
    static final de.zbit.util.prefs.Option<String[]>
    -
    FLUX_OBJECTIVES
    -
     
    static final de.zbit.util.prefs.Option<Boolean>
    INCLUDE_ANY_URI
    @@ -155,9 +128,7 @@

    Field Summary

    static final ResourceBundle
    MESSAGES
    -
    -
    Bundle for ModelPolisher logger messages
    -
    +
     
    static final de.zbit.util.prefs.Option<File>
    MODEL_NOTES_FILE
    @@ -170,28 +141,6 @@

    Field Summary

    If set to true, no web content will be inserted in the SBML container nor into the model within the SBML file.
    -
    static final de.zbit.util.prefs.Option<Boolean>
    -
    OUTPUT_COMBINE
    -
    -
    Produce output as a single COMBINE Archive.
    -
    -
    static final de.zbit.util.prefs.Option<ModelPolisherOptions.OutputType>
    -
    OUTPUT_TYPE
    -
    -
    Decides whether or not the output file should directly be compressed and if - so, which archive type should be used.
    -
    -
    static final de.zbit.util.prefs.Option<Boolean>
    -
    SBML_VALIDATION
    -
    -
    If true, the created SBML file will be validated through the online - validator service at http://sbml.org.
    -
    -
    static final de.zbit.util.prefs.Option<Boolean>
    -
    WRITE_JSON
    -
    -
    TODO
    -
    @@ -208,7 +157,6 @@

    Field Details

    MESSAGES

    static final ResourceBundle MESSAGES
    -
    Bundle for ModelPolisher logger messages
  • @@ -228,63 +176,6 @@

    ANNOTATE_WITH_BIGG

  • -
    -

    CHECK_MASS_BALANCE

    -
    static final de.zbit.util.prefs.Option<Boolean> CHECK_MASS_BALANCE
    -
    When set to true, the mass balance of each reaction will be checked where - possible. Reactions that are recognized as peudoreactions are excluded from - this check, also are reactions that lack information about elementary - composition of their participants.
    -
    -
    • -
  • -
    -

    OUTPUT_TYPE

    -
    static final de.zbit.util.prefs.Option<ModelPolisherOptions.OutputType> OUTPUT_TYPE
    -
    Decides whether or not the output file should directly be compressed and if - so, which archive type should be used.
    -
    -
    • -
  • -
    -

    DOCUMENT_NOTES_FILE

    -
    static final de.zbit.util.prefs.Option<File> DOCUMENT_NOTES_FILE
    -
    This XHTML file defines alternative document notes and makes them - exchangeable.
    -
    -
    • -
  • -
    -

    DOCUMENT_TITLE_PATTERN

    -
    static final de.zbit.util.prefs.Option<String> DOCUMENT_TITLE_PATTERN
    -
    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.
    -
    -
    • -
  • -
    -

    FLUX_COEFFICIENTS

    -
    static final de.zbit.util.prefs.Option<Double[]> FLUX_COEFFICIENTS
    -
    -
    • -
  • -
    -

    FLUX_OBJECTIVES

    -
    static final de.zbit.util.prefs.Option<String[]> FLUX_OBJECTIVES
    -
    -
    • -
  • -
    -

    INCLUDE_ANY_URI

    -
    static final de.zbit.util.prefs.Option<Boolean> INCLUDE_ANY_URI
    -
    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. If set to true, ModelPolisher also includes URIs that - do not contain the pattern identifiers.org.
    -
    -
    • -

  • MODEL_NOTES_FILE

    static final de.zbit.util.prefs.Option<File> MODEL_NOTES_FILE
    @@ -301,35 +192,30 @@

    NO_MODEL_NOTES

  • -
    -

    ADD_GENERIC_TERMS

    -
    static final de.zbit.util.prefs.Option<Boolean> ADD_GENERIC_TERMS
    -
    Set this option to true if generic top-level annotations, such as 'process' - should not be applied. Not using those terms will reduce the size of the - resulting output file.
    -
    -
    • -
  • -
    -

    OUTPUT_COMBINE

    -
    static final de.zbit.util.prefs.Option<Boolean> OUTPUT_COMBINE
    -
    Produce output as a single COMBINE Archive.
    +
    +

    INCLUDE_ANY_URI

    +
    static final de.zbit.util.prefs.Option<Boolean> INCLUDE_ANY_URI
    +
    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. If set to true, ModelPolisher also includes URIs that + do not contain the pattern identifiers.org.
  • -
    -

    SBML_VALIDATION

    -
    static final de.zbit.util.prefs.Option<Boolean> SBML_VALIDATION
    -
    If true, the created SBML file will be validated through the online - validator service at http://sbml.org. This option is only used - if the output is GZIP compressed.
    +
    +

    DOCUMENT_NOTES_FILE

    +
    static final de.zbit.util.prefs.Option<File> DOCUMENT_NOTES_FILE
    +
    This XHTML file defines alternative document notes and makes them + exchangeable.
  • -
    -

    WRITE_JSON

    -
    static final de.zbit.util.prefs.Option<Boolean> WRITE_JSON
    -
    TODO
    +
    +

    DOCUMENT_TITLE_PATTERN

    +
    static final de.zbit.util.prefs.Option<String> DOCUMENT_TITLE_PATTERN
    +
    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.
    • diff --git a/docs/edu/ucsd/sbrg/annotation/IAnnotateSBases.html b/docs/edu/ucsd/sbrg/annotation/IAnnotateSBases.html index 088f215e..243583e1 100644 --- a/docs/edu/ucsd/sbrg/annotation/IAnnotateSBases.html +++ b/docs/edu/ucsd/sbrg/annotation/IAnnotateSBases.html @@ -73,7 +73,7 @@

    Interface IAnnotateSBases<
    All Known Implementing Classes:
    -
    ADBReactionsAnnotator, ADBSBMLAnnotator, ADBSpeciesAnnotator, BiGGCompartmentsAnnotator, BiGGFBCAnnotator, BiGGGeneProductAnnotator, BiGGModelAnnotator, BiGGPublicationsAnnotator, BiGGReactionsAnnotator, BiGGSBMLAnnotator, BiGGSpeciesAnnotator
    +
    ADBReactionsAnnotator, ADBSBMLAnnotator, ADBSpeciesAnnotator, BiGGCompartmentsAnnotator, BiGGFBCAnnotator, BiGGGeneProductAnnotator, BiGGModelAnnotator, BiGGPublicationsAnnotator, BiGGReactionsAnnotator, BiGGSBMLAnnotator, BiGGSpeciesAnnotator
    public interface IAnnotateSBases<SBMLElement extends org.sbml.jsbml.SBase>
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html index 07e58296..2afac83b 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html @@ -82,7 +82,7 @@

    Class AbstractBiGGAnnotato
    Direct Known Subclasses:
    -
    BiGGCompartmentsAnnotator, BiGGCVTermAnnotator, BiGGFBCAnnotator, BiGGModelAnnotator, BiGGPublicationsAnnotator, BiGGSBMLAnnotator
    +
    BiGGCompartmentsAnnotator, BiGGCVTermAnnotator, BiGGFBCAnnotator, BiGGModelAnnotator, BiGGPublicationsAnnotator, BiGGSBMLAnnotator
    public abstract class AbstractBiGGAnnotator diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCVTermAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCVTermAnnotator.html index 1fb70236..f1d22bd5 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCVTermAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCVTermAnnotator.html @@ -84,7 +84,7 @@

    Class BiGGCVTermAnnotator<
    Direct Known Subclasses:
    -
    BiGGGeneProductAnnotator, BiGGReactionsAnnotator, BiGGSpeciesAnnotator
    +
    BiGGGeneProductAnnotator, BiGGReactionsAnnotator, BiGGSpeciesAnnotator
    public abstract class BiGGCVTermAnnotator<T extends org.sbml.jsbml.SBase> diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGFBCAnnotator.html similarity index 68% rename from docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html rename to docs/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGFBCAnnotator.html index b7989665..ec415bdf 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGFBCAnnotator.html @@ -5,21 +5,21 @@ BiGGFBCAnnotator (ModelPolisher 2.1 API) - + - - - - - - + + + + + +

    @@ -106,10 +106,10 @@

    Constructor Summary

    Constructor
    Description
    -
    BiGGFBCAnnotator(BiGGDB bigg, - BiGGAnnotationParameters parameters, - Registry registry, - List<ProgressObserver> observers)
    +
    BiGGFBCAnnotator(BiGGDB bigg, + BiGGAnnotationParameters parameters, + Registry registry, + List<ProgressObserver> observers)
     
    @@ -132,17 +132,17 @@

    Method Summary

    -

    Methods inherited from class edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator

    -getBiGGIdFromResources
    +

    Methods inherited from class edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator

    +getBiGGIdFromResources
    -

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

    -diffReport, getObservers, statusReport
    +

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

    +diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -

    Methods inherited from interface edu.ucsd.sbrg.annotation.IAnnotateSBases

    -annotate
    +

    Methods inherited from interface edu.ucsd.sbrg.annotation.IAnnotateSBases

    +annotate @@ -157,10 +157,10 @@

    Constructor Details

  • BiGGFBCAnnotator

    -
    public BiGGFBCAnnotator(BiGGDB bigg, - BiGGAnnotationParameters parameters, - Registry registry, - List<ProgressObserver> observers)
    +
    public BiGGFBCAnnotator(BiGGDB bigg, + BiGGAnnotationParameters parameters, + Registry registry, + List<ProgressObserver> observers)
    • @@ -178,7 +178,7 @@

    annotate

    throws SQLException
    Specified by:
    -
    annotate in interface IAnnotateSBases<org.sbml.jsbml.Model>
    +
    annotate in interface IAnnotateSBases<org.sbml.jsbml.Model>
    Throws:
    SQLException
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGGeneProductAnnotator.html similarity index 73% rename from docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html rename to docs/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGGeneProductAnnotator.html index 441cca3b..c01fc9d3 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGGeneProductAnnotator.html @@ -5,21 +5,21 @@ BiGGGeneProductAnnotator (ModelPolisher 2.1 API) - + - - - - - - + + + + + +