diff --git a/build.gradle b/build.gradle index 88a1badc..9edc68e9 100755 --- a/build.gradle +++ b/build.gradle @@ -105,7 +105,10 @@ dependencies { // reading, writing, and manipulating SBML files implementation("org.sbml.jsbml:jsbml:1.6.1") { exclude group: "org.apache.logging.log4j", module: "log4j-core" + exclude group: "org.apache.logging.log4j", module: "log4j-api" + exclude group: "org.apache.logging.log4j", module: "log4j-1.2-api " exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl" + exclude group: "org.apache.commons", module: "logging" } // ontology support within BioJava implementation "org.biojava:biojava-ontology:7.1.1" @@ -120,7 +123,7 @@ dependencies { 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:${jacksonVersion}" // data binding for Jackson implementation "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}" @@ -141,7 +144,14 @@ dependencies { // runtime engine for executing tests with JUnit 5 testRuntimeOnly 'org.junit.platform:junit-platform-launcher:1.10.2' testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine:${jupiterVersion}" +} +configurations { + runtime.exclude group: "org.apache.logging.log4j", module: "log4j-core" + runtime.exclude group: "org.apache.logging.log4j", module: "log4j-api" + runtime.exclude group: "org.apache.logging.log4j", module: "log4j-1.2-api" + runtime.exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl" + runtime.exclude group: "org.apache.commons", module: "logging" } /** === Configuration for pre-existing Tasks === **/ diff --git a/docs/allclasses-index.html b/docs/allclasses-index.html index ca3e5f93..361c4229 100644 --- a/docs/allclasses-index.html +++ b/docs/allclasses-index.html @@ -59,13 +59,13 @@

All Classes and Interfaces<
Class
Description
-
AbstractADBAnnotator<SBMLElement>
+
AbstractADBAnnotator
 
-
AbstractAnnotator<SBMLElement>
+
AbstractAnnotator
 
-
AbstractBiGGAnnotator<SBMLElement>
+
AbstractBiGGAnnotator
 
-
AbstractPolisher<SBMLElement>
+
AbstractPolisher
 
ADBAnnotationParameters
 
@@ -105,7 +105,7 @@

All Classes and Interfaces<
This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
-
BiGGCVTermAnnotator<T extends org.sbml.jsbml.AbstractSBase>
+
BiGGCVTermAnnotator<T extends org.sbml.jsbml.SBase>
Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
@@ -166,42 +166,50 @@

All Classes and Interfaces<

CommandLineParameters
 
-
CompartmentPolisher
-
+
CompartmentFixer
+
 
+
CompartmentPolisher
+
This class is responsible for polishing the properties of a compartment in an SBML model to ensure compliance with standards and completeness.
-
Compartments
+
Compartments
+
 
+
DAG
 
-
DAG
+
DBParameters
 
-
DBParameters
+
DeleteOnCloseFileInputStream
 
-
DeleteOnCloseFileInputStream
+
ECOParserCLILauncher
 
-
ECOparser
+
FBCPolisher
 
-
FBCPolisher
+
FBCReactionPolisher
 
-
FluxObjectivesPolisher
+
FluxObjectivesPolishingParameters
 
-
FluxObjectivesPolishingParameters
+
Gene
 
-
Gene
+
GeneParser
 
-
GeneParser
+
GeneProductAssociationsProcessor
 
-
GeneProductAssociationsProcessor
+
GeneProductsPolisher
 
-
GeneProductsPolisher
+
GPRParser
-
This class is responsible for polishing GeneProduct instances by processing their annotations and adjusting their identifiers and names.
-
-
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
+
 
+
GroupsUtils
+
+
A collection of helpful functions for dealing with SBML data structures.
+
+
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.
@@ -215,28 +223,56 @@

All Classes and Interfaces<
 
IdentifiersOrgURIUtils
 
+
IFixSBases<SBMLElement extends org.sbml.jsbml.SBase>
+
 
+
IFixSpeciesReferences
+
 
Institution
 
IOOptions
 
+
IPolishAnnotations
+
 
+
IPolishSBaseAttributes
+
 
+
IPolishSBases<SBMLElement extends org.sbml.jsbml.SBase>
+
 
+
IPolishSpeciesReferences
+
 
+
IProcessNotes
+
 
+
IReadModelsFromFile
+
 
+
IReportDiffs
+
 
+
IReportStatus
+
 
+
IWriteModels
+
 
+
IWriteModelsToFile
+
 
JSONConverter
 
JSONParser
 
-
Location
+
ListOfObjectivesFixer
 
-
MatlabParser
+
Location
 
-
Metabolite
+
MatlabParser
 
-
Metabolites
+
Metabolite
 
-
ModelField
-
+
Metabolites
+
 
+
ModelField
+
For more information about COBRA model fields, see the following Supplementary Material.
+
ModelFixer
+
 
ModelPolisher
This class provides functionality to polish an SBML (Systems Biology Markup Language) document.
@@ -245,23 +281,31 @@

All Classes and Interfaces<
The ModelPolisher class is the entry point of this application.
-
ModelPolisherOptions
+
ModelPolisherOptions
 
-
ModelPolisherOptions.OutputType
+
ModelPolisherOptions.OutputType
 
ModelReader
 
-
ModelReaderException
-
 
-
ModelValidator
+
ModelReaderException
+
 
+
ModelValidator
 
-
ModelValidatorException
+
ModelValidatorException
 
ModelWriter
 
ModelWriterException
 
-
Namespace
+
NamePolisher
+
 
+
Namespace
+
 
+
Node
+
 
+
ObjectiveFixer
+
 
+
ObjectivesPolisher
 
Parameters
 
@@ -273,25 +317,25 @@

All Classes and Interfaces<
 
PolishingParameters
 
-
PolishingUtils
+
PostgresConnectionPool
 
-
PostgresConnectionPool
-
 
-
ProgressFinalization
-
 
-
ProgressInitialization
+
ProgressFinalization
 
-
ProgressObserver
-
 
-
ProgressUpdate
-
 
-
Publication
+
ProgressInitialization
+
 
+
ProgressObserver
+
 
+
ProgressUpdate
 
-
RawIdentifiersOrgRegistry
+
Publication
+
 
+
RawIdentifiersOrgRegistry
+
 
+
Reaction
 
-
Reaction
+
ReactionFixer
 
-
ReactionNamePatterns
+
ReactionNamePatterns
Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
@@ -319,43 +363,42 @@

All Classes and Interfaces<
Possible FileTypes of input file
-
SBMLFix
-
+
SBMLFixer
+
 
+
SBMLFixerCLILauncher
+
This is a stand-alone bug-fix program.
-
SBMLPolisher
-
 
-
SBMLUtils
-
-
A collection of helpful functions for dealing with SBML data structures.
-
-
SBMLValidator
+
SBMLPolisher
+
 
+
SBMLValidatorCLILauncher
 
SBOParameters
 
-
SpeciesParser
+
SpeciesFixer
+
 
+
SpeciesParser
+
 
+
SpeciesPolisher
+
 
+
SpeciesReferenceFixer
+
 
+
SpeciesReferencesPolisher
 
-
SpeciesPolisher
+
StrictnessPredicate
-
This class is responsible for polishing Species objects in an SBML model to ensure they conform to - specific standards and completeness.
-
-
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.
-
XHTMLBuilder
-
 
diff --git a/docs/allpackages-index.html b/docs/allpackages-index.html index 8c1122ea..2eb95511 100644 --- a/docs/allpackages-index.html +++ b/docs/allpackages-index.html @@ -71,29 +71,41 @@

All Packages

 
edu.ucsd.sbrg.eco
 
-
edu.ucsd.sbrg.io
+
edu.ucsd.sbrg.fixing
 
-
edu.ucsd.sbrg.io.parsers.cobra
+
edu.ucsd.sbrg.fixing.ext.fbc
 
-
edu.ucsd.sbrg.io.parsers.json
+
edu.ucsd.sbrg.fixing.ext.groups
 
-
edu.ucsd.sbrg.io.parsers.json.mapping
+
edu.ucsd.sbrg.io
 
-
edu.ucsd.sbrg.parameters
+
edu.ucsd.sbrg.io.parsers.cobra
 
-
edu.ucsd.sbrg.polishing
+
edu.ucsd.sbrg.io.parsers.json
 
-
edu.ucsd.sbrg.polishing.fbc
+
edu.ucsd.sbrg.io.parsers.json.mapping
 
-
edu.ucsd.sbrg.reporting
+
edu.ucsd.sbrg.parameters
 
-
edu.ucsd.sbrg.resolver
+
edu.ucsd.sbrg.polishing
 
-
edu.ucsd.sbrg.resolver.identifiersorg
+
edu.ucsd.sbrg.polishing.fbc
 
-
edu.ucsd.sbrg.resolver.identifiersorg.mapping
+
edu.ucsd.sbrg.reporting
 
-
edu.ucsd.sbrg.util
+
edu.ucsd.sbrg.resolver
+
 
+
edu.ucsd.sbrg.resolver.identifiersorg
+
 
+
edu.ucsd.sbrg.resolver.identifiersorg.mapping
+
 
+
edu.ucsd.sbrg.util
+
 
+
edu.ucsd.sbrg.util.ext.fbc
+
 
+
edu.ucsd.sbrg.util.ext.groups
+
 
+
edu.ucsd.sbrg.validation
 
diff --git a/docs/constant-values.html b/docs/constant-values.html index 923dae49..346e7add 100644 --- a/docs/constant-values.html +++ b/docs/constant-values.html @@ -195,13 +195,13 @@

edu.ucsd.*

  • -
    edu.ucsd.sbrg.util.SBMLUtils
    +
    edu.ucsd.sbrg.util.ext.groups.GroupsUtils
    Modifier and Type
    Constant Field
    Value
    -
    public static final String
    -
    SUBSYSTEM_LINK
    +
    public static final String
    +
    SUBSYSTEM_LINK
    "SUBSYSTEM_LINK"
    • diff --git a/docs/edu/ucsd/sbrg/eco/ECOparser.html b/docs/edu/ucsd/sbrg/ECOParserCLILauncher.html similarity index 81% rename from docs/edu/ucsd/sbrg/eco/ECOparser.html rename to docs/edu/ucsd/sbrg/ECOParserCLILauncher.html index 7dbe1a68..20d42e97 100644 --- a/docs/edu/ucsd/sbrg/eco/ECOparser.html +++ b/docs/edu/ucsd/sbrg/ECOParserCLILauncher.html @@ -2,24 +2,24 @@ -ECOparser (ModelPolisher 2.1 API) +ECOParserCLILauncher (ModelPolisher 2.1 API) - + - - - - - - + + + + + +
Specified by:
-
annotate in class AbstractADBAnnotator<org.sbml.jsbml.Reaction>
+
annotate in interface IAnnotateSBases<org.sbml.jsbml.Reaction>
Throws:
SQLException
diff --git a/docs/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.html b/docs/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.html index 357e2c2a..ca36662e 100644 --- a/docs/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.html @@ -71,16 +71,19 @@

Class ADBSBMLAnnotator

java.lang.Object -
edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> -
edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator<org.sbml.jsbml.SBMLDocument> +
edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator
edu.ucsd.sbrg.annotation.adb.ADBSBMLAnnotator
-
+
+
All Implemented Interfaces:
+
IAnnotateSBases<org.sbml.jsbml.SBMLDocument>
+
public class ADBSBMLAnnotator -extends AbstractADBAnnotator<org.sbml.jsbml.SBMLDocument>
+extends AbstractADBAnnotator +implements IAnnotateSBases<org.sbml.jsbml.SBMLDocument>
-

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

-annotate, 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
@@ -166,7 +169,7 @@

annotate

throws SQLException
Specified by:
-
annotate in class AbstractADBAnnotator<org.sbml.jsbml.SBMLDocument>
+
annotate in interface IAnnotateSBases<org.sbml.jsbml.SBMLDocument>
Throws:
SQLException
diff --git a/docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html b/docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html index 89519185..9504ffe1 100644 --- a/docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html @@ -71,16 +71,19 @@

Class ADBSpeciesAnnotator

java.lang.Object -
edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> -
edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator<org.sbml.jsbml.Species> +
edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator
edu.ucsd.sbrg.annotation.adb.ADBSpeciesAnnotator
-
+
+
All Implemented Interfaces:
+
IAnnotateSBases<org.sbml.jsbml.Species>
+
public class ADBSpeciesAnnotator -extends AbstractADBAnnotator<org.sbml.jsbml.Species>
+extends AbstractADBAnnotator +implements IAnnotateSBases<org.sbml.jsbml.Species>
@@ -168,8 +168,8 @@

annotate

public void annotate(List<org.sbml.jsbml.Species> species) throws SQLException
-
Overrides:
-
annotate in class AbstractAnnotator<org.sbml.jsbml.Species>
+
Specified by:
+
annotate in interface IAnnotateSBases<org.sbml.jsbml.Species>
Throws:
SQLException
@@ -182,7 +182,7 @@

annotate

throws SQLException
Specified by:
-
annotate in class AbstractADBAnnotator<org.sbml.jsbml.Species>
+
annotate in interface IAnnotateSBases<org.sbml.jsbml.Species>
Throws:
SQLException
diff --git a/docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html b/docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html index f4baf9cb..48a8f1dd 100644 --- a/docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html @@ -68,12 +68,10 @@
Package edu.ucsd.sbrg.annotation.adb
-

Class AbstractADBAnnotator<SBMLElement>

+

Class AbstractADBAnnotator

java.lang.Object -
edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> -
edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator<SBMLElement>
-
+
edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator
@@ -81,8 +79,8 @@

Class AbstractADBAnnotator&
ADBReactionsAnnotator, ADBSBMLAnnotator, ADBSpeciesAnnotator

-
public abstract class AbstractADBAnnotator<SBMLElement> -extends AbstractAnnotator<SBMLElement>
+
public abstract class AbstractADBAnnotator +extends Object
@@ -170,7 +178,7 @@

annotate

throws SQLException
Specified by:
-
annotate in class AbstractAnnotator<org.sbml.jsbml.Model>
+
annotate in interface IAnnotateSBases<org.sbml.jsbml.Model>
Throws:
SQLException
diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.html index 3e62934d..179136b5 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.html @@ -71,8 +71,8 @@

Class BiGGReactionsAnnotator

java.lang.Object -
edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> -
edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator<T> +
edu.ucsd.sbrg.annotation.AbstractAnnotator +
edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator
edu.ucsd.sbrg.annotation.bigg.BiGGCVTermAnnotator<org.sbml.jsbml.Reaction>
edu.ucsd.sbrg.annotation.bigg.BiGGReactionsAnnotator
@@ -80,9 +80,14 @@

Class BiGGReactionsAnnota

+
+
All Implemented Interfaces:
+
IAnnotateSBases<org.sbml.jsbml.Reaction>, IReportDiffs, IReportStatus
+
public class BiGGReactionsAnnotator -extends BiGGCVTermAnnotator<org.sbml.jsbml.Reaction>
+extends BiGGCVTermAnnotator<org.sbml.jsbml.Reaction> +implements IAnnotateSBases<org.sbml.jsbml.Reaction>
This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers. It extends the BiGGCVTermAnnotator class, allowing it to manage controlled vocabulary (CV) terms associated with the reaction. The class handles various aspects of reaction annotation including setting @@ -143,7 +148,7 @@

Method Summary

Annotates a reaction by setting its name, SBO term, and additional annotations.
-
Optional<BiGGId>
+
BiGGId
findBiGGId(org.sbml.jsbml.Reaction reaction)
This method checks if the ID of the reaction is a valid BiGG ID and attempts to retrieve a corresponding @@ -226,8 +231,8 @@

annotate

This method iterates over all reactions in the model, updates the progress display, and invokes the annotation for each reaction.
-
Overrides:
-
annotate in class AbstractAnnotator<org.sbml.jsbml.Reaction>
+
Specified by:
+
annotate in interface IAnnotateSBases<org.sbml.jsbml.Reaction>
Throws:
SQLException
@@ -244,7 +249,7 @@

annotate

annotation and parsing processes.
Specified by:
-
annotate in class AbstractAnnotator<org.sbml.jsbml.Reaction>
+
annotate in interface IAnnotateSBases<org.sbml.jsbml.Reaction>
Throws:
SQLException
@@ -253,8 +258,8 @@

annotate

  • findBiGGId

    -
    public Optional<BiGGId> findBiGGId(org.sbml.jsbml.Reaction reaction) - throws SQLException
    +
    public BiGGId findBiGGId(org.sbml.jsbml.Reaction reaction) + throws SQLException
    This method checks if the ID of the reaction is a valid BiGG ID and attempts to retrieve a corresponding BiGG ID based on existing annotations. It first checks if the reaction ID matches the expected BiGG ID format and verifies its existence in the database. If the ID does not match or is not found, it then attempts to @@ -277,8 +282,9 @@

    setName

    public void setName(org.sbml.jsbml.Reaction reaction, BiGGId biggId) throws SQLException
    -
    Sets the name of the reaction based on the provided BiGGId. It retrieves the reaction name using the abbreviation - from the BiGGId, polishes the name, and updates the reaction's name if the new name is different from the current name.
    +
    Sets the name of the reaction based on the provided BiGGId. It retrieves the reaction name + using the abbreviation from the BiGGId, polishes the name, and updates the reaction's name + if the new name is different from the current name.
    Parameters:
    biggId - The BiGGId object containing the abbreviation used to fetch and potentially update the reaction's name.
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.html index 0888282c..aa380f63 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.html @@ -71,16 +71,21 @@

    Class BiGGSBMLAnnotator

    java.lang.Object -
    edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> -
    edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator<org.sbml.jsbml.SBMLDocument> +
    edu.ucsd.sbrg.annotation.AbstractAnnotator +
    edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator
    edu.ucsd.sbrg.annotation.bigg.BiGGSBMLAnnotator
    +
    +
    All Implemented Interfaces:
    +
    IAnnotateSBases<org.sbml.jsbml.SBMLDocument>, IReportDiffs, IReportStatus
    +
    public class BiGGSBMLAnnotator -extends AbstractBiGGAnnotator<org.sbml.jsbml.SBMLDocument>
    +extends AbstractBiGGAnnotator +implements IAnnotateSBases<org.sbml.jsbml.SBMLDocument>
    This class is responsible for annotating SBML models using data from the BiGG database. It handles the addition of annotations related to compartments, species, reactions, and gene products.
    @@ -141,10 +146,13 @@

    getBiGGIdFromResources

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

    -annotate, diffReport, getObservers, statusReport
    +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
    @@ -194,7 +202,7 @@

    annotate

    It also handles the addition of publications and notes related to the model.
    Specified by:
    -
    annotate in class AbstractAnnotator<org.sbml.jsbml.SBMLDocument>
    +
    annotate in interface IAnnotateSBases<org.sbml.jsbml.SBMLDocument>
    Parameters:
    doc - The SBMLDocument that contains the model to be annotated.
    Throws:
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSpeciesAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSpeciesAnnotator.html index 2c93929e..c79806ca 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSpeciesAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSpeciesAnnotator.html @@ -71,8 +71,8 @@

    Class BiGGSpeciesAnnotator

    java.lang.Object -
    edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> -
    edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator<T> +
    edu.ucsd.sbrg.annotation.AbstractAnnotator +
    edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator
    edu.ucsd.sbrg.annotation.bigg.BiGGCVTermAnnotator<org.sbml.jsbml.Species>
    edu.ucsd.sbrg.annotation.bigg.BiGGSpeciesAnnotator
    @@ -80,9 +80,14 @@

    Class BiGGSpeciesAnnotator<

    +
    +
    All Implemented Interfaces:
    +
    IAnnotateSBases<org.sbml.jsbml.Species>, IReportDiffs, IReportStatus
    +
    public class BiGGSpeciesAnnotator -extends BiGGCVTermAnnotator<org.sbml.jsbml.Species>
    +extends BiGGCVTermAnnotator<org.sbml.jsbml.Species> +implements IAnnotateSBases<org.sbml.jsbml.Species>
    This class provides functionality to annotate a species in an SBML model using BiGG database identifiers. It extends the BiGGCVTermAnnotator class, allowing it to manage controlled vocabulary (CV) terms associated with the species. The class handles various aspects of species annotation including setting @@ -146,7 +151,7 @@

    Method Summary

    This method annotates a species with various details fetched from the BiGG Knowledgebase.
    -
    Optional<BiGGId>
    +
    BiGGId
    findBiGGId(org.sbml.jsbml.Species species)
    Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations.
    @@ -215,8 +220,8 @@

    annotate

    Delegates annotation processing for all chemical species contained in the Model. This method iterates over each species in the model and applies specific annotations.
    -
    Overrides:
    -
    annotate in class AbstractAnnotator<org.sbml.jsbml.Species>
    +
    Specified by:
    +
    annotate in interface IAnnotateSBases<org.sbml.jsbml.Species>
    Throws:
    SQLException
    @@ -236,7 +241,7 @@

    annotate

    The BiGGId used for these operations is either derived from the species' URI list or directly from its ID if available.
    Specified by:
    -
    annotate in class AbstractAnnotator<org.sbml.jsbml.Species>
    +
    annotate in interface IAnnotateSBases<org.sbml.jsbml.Species>
    Throws:
    SQLException
    @@ -245,8 +250,8 @@

    annotate

  • findBiGGId

    -
    public Optional<BiGGId> findBiGGId(org.sbml.jsbml.Species species) - throws SQLException
    +
    public BiGGId findBiGGId(org.sbml.jsbml.Species species) + throws SQLException
    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.
    @@ -266,8 +271,9 @@

    setName

    public void setName(org.sbml.jsbml.Species species, BiGGId biggId) throws SQLException
    -
    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 +
    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:
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html index 47aac20c..b7989665 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html @@ -71,16 +71,21 @@

    Class BiGGFBCAnnotator

    java.lang.Object -
    edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> -
    edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator<org.sbml.jsbml.Model> +
    edu.ucsd.sbrg.annotation.AbstractAnnotator +
    edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator
    edu.ucsd.sbrg.annotation.bigg.fbc.BiGGFBCAnnotator
    +
    +
    All Implemented Interfaces:
    +
    IAnnotateSBases<org.sbml.jsbml.Model>, IReportDiffs, IReportStatus
    +
    public class BiGGFBCAnnotator -extends AbstractBiGGAnnotator<org.sbml.jsbml.Model>
    +extends AbstractBiGGAnnotator +implements IAnnotateSBases<org.sbml.jsbml.Model>
      @@ -131,10 +136,13 @@

      getBiGGIdFromResources

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

    -annotate, diffReport, getObservers, statusReport
    +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
    @@ -170,7 +178,7 @@

    annotate

    throws SQLException
    Specified by:
    -
    annotate in class AbstractAnnotator<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/fbc/BiGGGeneProductAnnotator.html index 9150e136..441cca3b 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html @@ -71,8 +71,8 @@

    Class BiGGGeneProductAnnotator

    java.lang.Object -
    edu.ucsd.sbrg.annotation.AbstractAnnotator<SBMLElement> -
    edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator<T> +
    edu.ucsd.sbrg.annotation.AbstractAnnotator +
    edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator
    edu.ucsd.sbrg.annotation.bigg.BiGGCVTermAnnotator<org.sbml.jsbml.ext.fbc.GeneProduct>
    edu.ucsd.sbrg.annotation.bigg.fbc.BiGGGeneProductAnnotator
    @@ -80,9 +80,14 @@

    Class BiGGGeneProductAn

    +
    +
    All Implemented Interfaces:
    +
    IAnnotateSBases<org.sbml.jsbml.ext.fbc.GeneProduct>, IReportDiffs, IReportStatus
    +
    public class BiGGGeneProductAnnotator -extends BiGGCVTermAnnotator<org.sbml.jsbml.ext.fbc.GeneProduct>
    +extends BiGGCVTermAnnotator<org.sbml.jsbml.ext.fbc.GeneProduct> +implements IAnnotateSBases<org.sbml.jsbml.ext.fbc.GeneProduct>
    Provides functionality to annotate gene products in an SBML model using data from the BiGG database. This class extends BiGGCVTermAnnotator 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.
    @@ -151,7 +156,7 @@

    Method Summary

    Annotates a gene product by adding relevant metadata and references.
    -
    Optional<BiGGId>
    +
    BiGGId
    findBiGGId(org.sbml.jsbml.ext.fbc.GeneProduct geneProduct)
    Validates the ID of a GeneProduct against the expected BiGG ID format and attempts to retrieve a @@ -241,8 +246,8 @@

    annotate

    set and then proceeds to annotate each gene product found within the model. The progress bar is updated to reflect the number of gene products being annotated.
    -
    Overrides:
    -
    annotate in class AbstractAnnotator<org.sbml.jsbml.ext.fbc.GeneProduct>
    +
    Specified by:
    +
    annotate in interface IAnnotateSBases<org.sbml.jsbml.ext.fbc.GeneProduct>
    Throws:
    SQLException
    @@ -260,7 +265,7 @@

    annotate

    and sets the gene product's metaId if it has any CV terms. Finally, it sets the gene product's label name.
    Specified by:
    -
    annotate in class AbstractAnnotator<org.sbml.jsbml.ext.fbc.GeneProduct>
    +
    annotate in interface IAnnotateSBases<org.sbml.jsbml.ext.fbc.GeneProduct>
    Throws:
    SQLException
    @@ -269,8 +274,8 @@

    annotate

  • findBiGGId

    -
    public Optional<BiGGId> findBiGGId(org.sbml.jsbml.ext.fbc.GeneProduct geneProduct) - throws SQLException
    +
    public BiGGId findBiGGId(org.sbml.jsbml.ext.fbc.GeneProduct geneProduct) + throws SQLException
    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 diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/package-tree.html b/docs/edu/ucsd/sbrg/annotation/bigg/fbc/package-tree.html index b112aef8..0074298e 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/package-tree.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/fbc/package-tree.html @@ -58,16 +58,16 @@

    Class Hierarchy

    +
    +

    Interface Hierarchy

    + +
    • diff --git a/docs/edu/ucsd/sbrg/db/bigg/BiGGId.html b/docs/edu/ucsd/sbrg/db/bigg/BiGGId.html index f20fb7c2..959a9df1 100644 --- a/docs/edu/ucsd/sbrg/db/bigg/BiGGId.html +++ b/docs/edu/ucsd/sbrg/db/bigg/BiGGId.html @@ -128,36 +128,23 @@

    Method Summary

    Modifier and Type
    Method
    Description
    -
    static Optional<BiGGId>
    +
    static BiGGId
    createGeneId(String id)
    -
    Creates a BiGG ID for a gene using the default correction behavior.
    -
    -
    static Optional<BiGGId>
    -
    createGeneId(String id, - boolean correct)
    -
    Creates a BiGG ID for a gene, with an option to correct the ID to conform to BiGG standards.
    -
    static Optional<BiGGId>
    -
    createMetaboliteId(String id)
    -
    -
    Creates a BiGG ID for a metabolite with default correction behavior.
    -
    -
    static Optional<BiGGId>
    -
    createMetaboliteId(String id, - boolean correct)
    +
    static BiGGId
    +
    createMetaboliteId(String id)
    Creates a BiGG ID for a metabolite based on the provided string identifier.
    -
    static Optional<BiGGId>
    +
    static BiGGId
    createReactionId(String id)
    Creates a BiGG ID for a reaction based on the provided string identifier.
    -
    static Optional<BiGGId>
    -
    createReactionId(String id, - boolean correct, +
    static BiGGId
    +
    createReactionId(String id, boolean isPseudo)
    Creates a BiGG ID for a reaction based on the provided string identifier.
    @@ -297,27 +284,12 @@

    Method Details

  • createMetaboliteId

    -
    public static Optional<BiGGId> createMetaboliteId(String id)
    -
    Creates a BiGG ID for a metabolite with default correction behavior.
    -
    -
    Parameters:
    -
    id - The raw metabolite ID string.
    -
    Returns:
    -
    An Optional containing the BiGGId if the ID is non-empty and valid, or an empty Optional otherwise.
    -
    -
    -
    • -
  • -
    -

    createMetaboliteId

    -
    public static Optional<BiGGId> createMetaboliteId(String id, - boolean correct)
    +
    public static BiGGId createMetaboliteId(String id)
    Creates a BiGG ID for a metabolite based on the provided string identifier. This method handles the correction and standardization of the metabolite ID according to BiGG database standards.
    Parameters:
    id - The raw metabolite ID string.
    -
    correct - A boolean flag indicating whether to correct the ID to conform to BiGG standards.
    Returns:
    An Optional containing the BiGGId if the ID is non-empty and valid, or an empty Optional otherwise.
    @@ -326,21 +298,7 @@

    createMetaboliteId

  • createGeneId

    -
    public static Optional<BiGGId> createGeneId(String id)
    -
    Creates a BiGG ID for a gene using the default correction behavior.
    -
    -
    Parameters:
    -
    id - The raw gene ID string.
    -
    Returns:
    -
    An Optional containing the BiGGId if the ID is non-empty and valid, or an empty Optional otherwise.
    -
    -
    -
    • -
  • -
    -

    createGeneId

    -
    public static Optional<BiGGId> createGeneId(String id, - boolean correct)
    +
    public static BiGGId createGeneId(String id)
    Creates a BiGG ID for a gene, with an option to correct the ID to conform to BiGG standards.

    This method first checks if the provided ID is empty, returning an empty Optional if true. @@ -351,7 +309,6 @@

    createGeneId

    Parameters:
    id - The raw gene ID string.
    -
    correct - A boolean flag indicating whether to correct the ID to conform to BiGG standards.
    Returns:
    An Optional containing the BiGGId if the ID is non-empty and valid, or an empty Optional otherwise.
    @@ -360,7 +317,7 @@

    createGeneId

  • createReactionId

    -
    public static Optional<BiGGId> createReactionId(String id)
    +
    public static BiGGId createReactionId(String id)
    Creates a BiGG ID for a reaction based on the provided string identifier. This method handles the prefix stripping and checks if the reaction is a pseudo-reaction. Depending on these checks, it delegates to the overloaded createReactionId method with appropriate flags.
    @@ -373,17 +330,15 @@

    createReactionId

  • -
    +

    createReactionId

    -
    public static Optional<BiGGId> createReactionId(String id, - boolean correct, +
    public static BiGGId createReactionId(String id, boolean isPseudo)
    Creates a BiGG ID for a reaction based on the provided string identifier. The method can correct the ID to conform to BiGG standards and adjust the prefix based on whether it is a pseudo-reaction.
    Parameters:
    id - The raw reaction ID string.
    -
    correct - If true, the ID will be corrected to conform to BiGG standards.
    isPseudo - If true, the ID is treated as a pseudo-reaction, affecting the prefix handling.
    Returns:
    An Optional containing the BiGGId if the ID is non-empty, or an empty Optional if the ID is empty.
    diff --git a/docs/edu/ucsd/sbrg/eco/DAG.html b/docs/edu/ucsd/sbrg/eco/DAG.html index 689224f7..815e2502 100644 --- a/docs/edu/ucsd/sbrg/eco/DAG.html +++ b/docs/edu/ucsd/sbrg/eco/DAG.html @@ -45,13 +45,13 @@
  • Summary: 
  • Nested | 
  • Field | 
    • -
  • Constr | 
    • +
  • Constr | 
  • Method
    • @@ -80,6 +80,19 @@

    Class DAG

      + +
    • +
      +

      Constructor Summary

      +
      Constructors
      +
      +
      Constructor
      +
      Description
      +
      DAG(org.biojava.nbio.ontology.Term term)
      +
       
      +
      +
      +
    • @@ -91,14 +104,14 @@

      Method Summary

      Modifier and Type
      Method
      Description
      -
      edu.ucsd.sbrg.eco.Node
      +
      Node
      getRoot()
       
      String
      toString()
       
      void
      -
      traverse(edu.ucsd.sbrg.eco.Node node, +
      traverse(Node node, int counter, StringBuilder sb)
       
      @@ -114,6 +127,20 @@

      Methods inherited from cl

        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          DAG

          +
          public DAG(org.biojava.nbio.ontology.Term term)
          +
          +
          • +
        +
        +
      • @@ -122,13 +149,13 @@

        Method Details

      • getRoot

        -
        public edu.ucsd.sbrg.eco.Node getRoot()
        +
        public Node getRoot()

      • traverse

        -
        public void traverse(edu.ucsd.sbrg.eco.Node node, +
        public void traverse(Node node, int counter, StringBuilder sb)
        diff --git a/docs/edu/ucsd/sbrg/eco/Node.html b/docs/edu/ucsd/sbrg/eco/Node.html new file mode 100644 index 00000000..cd1e567b --- /dev/null +++ b/docs/edu/ucsd/sbrg/eco/Node.html @@ -0,0 +1,309 @@ + + + + +Node (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
        + +
        +
        + +
        +
        Package edu.ucsd.sbrg.eco
        +

        Class Node

        +
        +
        java.lang.Object +
        edu.ucsd.sbrg.eco.Node
        +
        +
        +
        +
        public class Node +extends Object
        +
        +
        + +
        +
        +
          + +
        • +
          +

          Constructor Details

          +
            +
          • +
            +

            Node

            +
            public Node(org.biojava.nbio.ontology.Term term)
            +
            +
            • +
          +
          +
          • + +
        • +
          +

          Method Details

          +
            +
          • +
            +

            addChild

            +
            public void addChild(Node child)
            +
            +
            • +
          • +
            +

            addChild

            +
            public void addChild(org.biojava.nbio.ontology.Term child)
            +
            +
            • +
          • +
            +

            addParent

            +
            public void addParent(Node parent)
            +
            +
            • +
          • +
            +

            addParent

            +
            public void addParent(org.biojava.nbio.ontology.Term parent)
            +
            +
            • +
          • +
            +

            linkNodes

            +
            public static void linkNodes(Node parent, + Node child)
            +
            +
            • +
          • +
            +

            setChildren

            +
            public void setChildren(List<Node> children)
            +
            +
            • +
          • +
            +

            setParents

            +
            public void setParents(List<Node> parents)
            +
            +
            • +
          • +
            +

            setTerm

            +
            public void setTerm(org.biojava.nbio.ontology.Term term)
            +
            +
            • +
          • +
            +

            getChildren

            +
            public List<Node> getChildren()
            +
            +
            • +
          • +
            +

            getParents

            +
            public List<Node> getParents()
            +
            +
            • +
          • +
            +

            findTerm

            +
            public Node findTerm(org.biojava.nbio.ontology.Term term)
            +
            Returns the Node containing the specified Term or null, if not present
            +
            +
            • +
          • +
            +

            findParent

            +
            public Node findParent(Node node, + org.biojava.nbio.ontology.Term term)
            +
            +
            • +
          • +
            +

            findChild

            +
            public Node findChild(Node node, + org.biojava.nbio.ontology.Term term)
            +
            +
            • +
          • +
            +

            getTerm

            +
            public org.biojava.nbio.ontology.Term getTerm()
            +
            +
            • +
          • +
            +

            equals

            +
            public boolean equals(Object o)
            +
            +
            Overrides:
            +
            equals in class Object
            +
            +
            +
            • +
          • +
            +

            hashCode

            +
            public int hashCode()
            +
            +
            Overrides:
            +
            hashCode in class Object
            +
            +
            +
            • +
          +
          +
          • +
        +
        + +
        +
        +
        + + diff --git a/docs/edu/ucsd/sbrg/eco/package-summary.html b/docs/edu/ucsd/sbrg/eco/package-summary.html index 7f596623..806af423 100644 --- a/docs/edu/ucsd/sbrg/eco/package-summary.html +++ b/docs/edu/ucsd/sbrg/eco/package-summary.html @@ -80,7 +80,7 @@

        Package edu.ucsd.sbrg.ecoDescription

    • DAG
     
    -
    ECOparser
    +
    Node
     
    • diff --git a/docs/edu/ucsd/sbrg/eco/package-tree.html b/docs/edu/ucsd/sbrg/eco/package-tree.html index 7227c464..a999544a 100644 --- a/docs/edu/ucsd/sbrg/eco/package-tree.html +++ b/docs/edu/ucsd/sbrg/eco/package-tree.html @@ -59,7 +59,7 @@

    Class Hierarchy

  • java.lang.Object
    • diff --git a/docs/edu/ucsd/sbrg/polishing/PolishingUtils.html b/docs/edu/ucsd/sbrg/fixing/CompartmentFixer.html similarity index 74% rename from docs/edu/ucsd/sbrg/polishing/PolishingUtils.html rename to docs/edu/ucsd/sbrg/fixing/CompartmentFixer.html index de9e1772..eee36024 100644 --- a/docs/edu/ucsd/sbrg/polishing/PolishingUtils.html +++ b/docs/edu/ucsd/sbrg/fixing/CompartmentFixer.html @@ -2,10 +2,10 @@ -PolishingUtils (ModelPolisher 2.1 API) +CompartmentFixer (ModelPolisher 2.1 API) - + @@ -67,16 +67,21 @@
    -
    Package edu.ucsd.sbrg.polishing
    -

    Class PolishingUtils

    +
    Package edu.ucsd.sbrg.fixing
    +

    Class CompartmentFixer

    java.lang.Object -
    edu.ucsd.sbrg.polishing.PolishingUtils
    +
    edu.ucsd.sbrg.fixing.CompartmentFixer
    +
    +
    All Implemented Interfaces:
    +
    IFixSBases<org.sbml.jsbml.Compartment>
    +
    -
    public class PolishingUtils -extends Object
    +
    public class CompartmentFixer +extends Object +implements IFixSBases<org.sbml.jsbml.Compartment>
    @@ -98,24 +103,25 @@

    Constructor Summary

    Method Summary

    -
    +
    Modifier and Type
    Method
    Description
    -
    static String
    -
    polishName(String name)
    -
    -
    Processes and polishes a given identifier name by applying a series of string transformations - to make it more readable or compliant with certain standards.
    -
    +
    void
    +
    fix(org.sbml.jsbml.Compartment compartment, + int index)
    +
     

    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.fixing.IFixSBases

    +fix
    @@ -129,8 +135,8 @@

    Constructor Details

    • -

      PolishingUtils

      -
      public PolishingUtils()
      +

      CompartmentFixer

      +
      public CompartmentFixer()
    @@ -142,16 +148,13 @@

    PolishingUtils

    Method Details

    • -
      -

      polishName

      -
      public static String polishName(String name)
      -
      Processes and polishes a given identifier name by applying a series of string transformations - to make it more readable or compliant with certain standards.
      +
      +

      fix

      +
      public void fix(org.sbml.jsbml.Compartment compartment, + int index)
      -
      Parameters:
      -
      name - The original identifier name to be polished.
      -
      Returns:
      -
      The polished version of the identifier name.
      +
      Specified by:
      +
      fix in interface IFixSBases<org.sbml.jsbml.Compartment>
      • diff --git a/docs/edu/ucsd/sbrg/fixing/IFixSBases.html b/docs/edu/ucsd/sbrg/fixing/IFixSBases.html new file mode 100644 index 00000000..44efc1de --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/IFixSBases.html @@ -0,0 +1,138 @@ + + + + +IFixSBases (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing
      +

      Interface IFixSBases<SBMLElement extends org.sbml.jsbml.SBase>

      +
      +
      +
      +
      All Known Implementing Classes:
      +
      CompartmentFixer, ListOfObjectivesFixer, ModelFixer, ReactionFixer, SBMLFixer, SpeciesFixer
      +
      +
      +
      public interface IFixSBases<SBMLElement extends org.sbml.jsbml.SBase>
      +
      +
      +
        + +
      • +
        +

        Method Summary

        +
        +
        +
        +
        +
        Modifier and Type
        +
        Method
        +
        Description
        +
        default void
        +
        fix(List<SBMLElement> elements)
        +
         
        +
        void
        +
        fix(SBMLElement element, + int index)
        +
         
        +
        +
        +
        +
        +
        • +
      +
      +
      +
        + +
      • +
        +

        Method Details

        + +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/IFixSpeciesReferences.html b/docs/edu/ucsd/sbrg/fixing/IFixSpeciesReferences.html new file mode 100644 index 00000000..ef59a2f0 --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/IFixSpeciesReferences.html @@ -0,0 +1,136 @@ + + + + +IFixSpeciesReferences (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing
      +

      Interface IFixSpeciesReferences

      +
      +
      +
      +
      All Known Implementing Classes:
      +
      SpeciesReferenceFixer
      +
      +
      +
      public interface IFixSpeciesReferences
      +
      +
      +
        + +
      • +
        +

        Method Summary

        +
        +
        +
        +
        +
        Modifier and Type
        +
        Method
        +
        Description
        +
        default void
        +
        fix(List<org.sbml.jsbml.SpeciesReference> elements)
        +
         
        +
        void
        +
        fix(org.sbml.jsbml.SpeciesReference element)
        +
         
        +
        +
        +
        +
        +
        • +
      +
      +
      +
        + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          fix

          +
          default void fix(List<org.sbml.jsbml.SpeciesReference> elements)
          +
          +
          • +
        • +
          +

          fix

          +
          void fix(org.sbml.jsbml.SpeciesReference element)
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/ModelFixer.html b/docs/edu/ucsd/sbrg/fixing/ModelFixer.html new file mode 100644 index 00000000..64c552ab --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/ModelFixer.html @@ -0,0 +1,171 @@ + + + + +ModelFixer (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing
      +

      Class ModelFixer

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.fixing.ModelFixer
      +
      +
      +
      +
      All Implemented Interfaces:
      +
      IFixSBases<org.sbml.jsbml.Model>
      +
      +
      +
      public class ModelFixer +extends Object +implements IFixSBases<org.sbml.jsbml.Model>
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          ModelFixer

          +
          public ModelFixer()
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          fix

          +
          public void fix(org.sbml.jsbml.Model model, + int index)
          +
          +
          Specified by:
          +
          fix in interface IFixSBases<org.sbml.jsbml.Model>
          +
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/ReactionFixer.html b/docs/edu/ucsd/sbrg/fixing/ReactionFixer.html new file mode 100644 index 00000000..c6360397 --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/ReactionFixer.html @@ -0,0 +1,171 @@ + + + + +ReactionFixer (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing
      +

      Class ReactionFixer

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.fixing.ReactionFixer
      +
      +
      +
      +
      All Implemented Interfaces:
      +
      IFixSBases<org.sbml.jsbml.Reaction>
      +
      +
      +
      public class ReactionFixer +extends Object +implements IFixSBases<org.sbml.jsbml.Reaction>
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          ReactionFixer

          +
          public ReactionFixer()
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          fix

          +
          public void fix(org.sbml.jsbml.Reaction reaction, + int index)
          +
          +
          Specified by:
          +
          fix in interface IFixSBases<org.sbml.jsbml.Reaction>
          +
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/SBMLFixer.html b/docs/edu/ucsd/sbrg/fixing/SBMLFixer.html new file mode 100644 index 00000000..97c3b50b --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/SBMLFixer.html @@ -0,0 +1,171 @@ + + + + +SBMLFixer (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing
      +

      Class SBMLFixer

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.fixing.SBMLFixer
      +
      +
      +
      +
      All Implemented Interfaces:
      +
      IFixSBases<org.sbml.jsbml.SBMLDocument>
      +
      +
      +
      public class SBMLFixer +extends Object +implements IFixSBases<org.sbml.jsbml.SBMLDocument>
      +
      +
      +
        + +
      • +
        +

        Constructor Summary

        +
        Constructors
        +
        +
        Constructor
        +
        Description
        +
        SBMLFixer()
        +
         
        +
        +
        +
        • + +
      • +
        +

        Method Summary

        +
        +
        +
        +
        +
        Modifier and Type
        +
        Method
        +
        Description
        +
        void
        +
        fix(org.sbml.jsbml.SBMLDocument sbmlDocument, + int index)
        +
         
        +
        +
        +
        +
        +

        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.fixing.IFixSBases

        +fix
        +
        +
        • +
      +
      +
      +
        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          SBMLFixer

          +
          public SBMLFixer()
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          fix

          +
          public void fix(org.sbml.jsbml.SBMLDocument sbmlDocument, + int index)
          +
          +
          Specified by:
          +
          fix in interface IFixSBases<org.sbml.jsbml.SBMLDocument>
          +
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/SpeciesFixer.html b/docs/edu/ucsd/sbrg/fixing/SpeciesFixer.html new file mode 100644 index 00000000..b81b8a3e --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/SpeciesFixer.html @@ -0,0 +1,171 @@ + + + + +SpeciesFixer (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing
      +

      Class SpeciesFixer

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.fixing.SpeciesFixer
      +
      +
      +
      +
      All Implemented Interfaces:
      +
      IFixSBases<org.sbml.jsbml.Species>
      +
      +
      +
      public class SpeciesFixer +extends Object +implements IFixSBases<org.sbml.jsbml.Species>
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          SpeciesFixer

          +
          public SpeciesFixer()
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          fix

          +
          public void fix(org.sbml.jsbml.Species species, + int index)
          +
          +
          Specified by:
          +
          fix in interface IFixSBases<org.sbml.jsbml.Species>
          +
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/SpeciesReferenceFixer.html b/docs/edu/ucsd/sbrg/fixing/SpeciesReferenceFixer.html new file mode 100644 index 00000000..7854d878 --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/SpeciesReferenceFixer.html @@ -0,0 +1,169 @@ + + + + +SpeciesReferenceFixer (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing
      +

      Class SpeciesReferenceFixer

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.fixing.SpeciesReferenceFixer
      +
      +
      +
      +
      All Implemented Interfaces:
      +
      IFixSpeciesReferences
      +
      +
      +
      public class SpeciesReferenceFixer +extends Object +implements IFixSpeciesReferences
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          SpeciesReferenceFixer

          +
          public SpeciesReferenceFixer()
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          fix

          +
          public void fix(org.sbml.jsbml.SpeciesReference sr)
          +
          +
          Specified by:
          +
          fix in interface IFixSpeciesReferences
          +
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/ext/fbc/ListOfObjectivesFixer.html b/docs/edu/ucsd/sbrg/fixing/ext/fbc/ListOfObjectivesFixer.html new file mode 100644 index 00000000..39b33077 --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/ext/fbc/ListOfObjectivesFixer.html @@ -0,0 +1,173 @@ + + + + +ListOfObjectivesFixer (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing.ext.fbc
      +

      Class ListOfObjectivesFixer

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.fixing.ext.fbc.ListOfObjectivesFixer
      +
      +
      +
      +
      All Implemented Interfaces:
      +
      IFixSBases<org.sbml.jsbml.ext.fbc.ListOfObjectives>
      +
      +
      +
      public class ListOfObjectivesFixer +extends Object +implements IFixSBases<org.sbml.jsbml.ext.fbc.ListOfObjectives>
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          ListOfObjectivesFixer

          +
          public ListOfObjectivesFixer(PolishingParameters polishingParameters, + org.sbml.jsbml.ext.fbc.FBCModelPlugin modelPlug)
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          fix

          +
          public void fix(org.sbml.jsbml.ext.fbc.ListOfObjectives objectives, + int index)
          +
          +
          Specified by:
          +
          fix in interface IFixSBases<org.sbml.jsbml.ext.fbc.ListOfObjectives>
          +
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/ext/fbc/ObjectiveFixer.html b/docs/edu/ucsd/sbrg/fixing/ext/fbc/ObjectiveFixer.html new file mode 100644 index 00000000..2e93258e --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/ext/fbc/ObjectiveFixer.html @@ -0,0 +1,165 @@ + + + + +ObjectiveFixer (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing.ext.fbc
      +

      Class ObjectiveFixer

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.fixing.ext.fbc.ObjectiveFixer
      +
      +
      +
      +
      public class ObjectiveFixer +extends Object
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          ObjectiveFixer

          +
          public ObjectiveFixer()
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          fixObjective

          +
          public static void fixObjective(String modelDescriptor, + org.sbml.jsbml.ListOf<org.sbml.jsbml.Reaction> listOfReactions, + org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlug, + List<Double> fluxCoefficients, + List<String> fluxObjectives)
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/ext/fbc/package-summary.html b/docs/edu/ucsd/sbrg/fixing/ext/fbc/package-summary.html new file mode 100644 index 00000000..8685ce67 --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/ext/fbc/package-summary.html @@ -0,0 +1,83 @@ + + + + +edu.ucsd.sbrg.fixing.ext.fbc (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      +
      +

      Package edu.ucsd.sbrg.fixing.ext.fbc

      +
      +
      +
      package edu.ucsd.sbrg.fixing.ext.fbc
      +
      + +
      +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/ext/fbc/package-tree.html b/docs/edu/ucsd/sbrg/fixing/ext/fbc/package-tree.html new file mode 100644 index 00000000..d55031c7 --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/ext/fbc/package-tree.html @@ -0,0 +1,71 @@ + + + + +edu.ucsd.sbrg.fixing.ext.fbc Class Hierarchy (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      +
      +

      Hierarchy For Package edu.ucsd.sbrg.fixing.ext.fbc

      +Package Hierarchies: + +
      +
      +

      Class Hierarchy

      + +
      +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/ext/groups/GroupsFixer.html b/docs/edu/ucsd/sbrg/fixing/ext/groups/GroupsFixer.html new file mode 100644 index 00000000..0a099f2e --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/ext/groups/GroupsFixer.html @@ -0,0 +1,160 @@ + + + + +GroupsFixer (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.fixing.ext.groups
      +

      Class GroupsFixer

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.fixing.ext.groups.GroupsFixer
      +
      +
      +
      +
      public class GroupsFixer +extends Object
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          GroupsFixer

          +
          public GroupsFixer()
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          fixGroups

          +
          public static void fixGroups(org.sbml.jsbml.Model model)
          +
          Set group kind where required
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/ext/groups/package-summary.html b/docs/edu/ucsd/sbrg/fixing/ext/groups/package-summary.html new file mode 100644 index 00000000..af7852ac --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/ext/groups/package-summary.html @@ -0,0 +1,81 @@ + + + + +edu.ucsd.sbrg.fixing.ext.groups (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      +
      +

      Package edu.ucsd.sbrg.fixing.ext.groups

      +
      +
      +
      package edu.ucsd.sbrg.fixing.ext.groups
      +
      +
        +
      • +
        +
        Classes
        +
        +
        Class
        +
        Description
        +
        GroupsFixer
        +
         
        +
        +
        +
        • +
      +
      +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/ext/groups/package-tree.html b/docs/edu/ucsd/sbrg/fixing/ext/groups/package-tree.html new file mode 100644 index 00000000..a94f0d72 --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/ext/groups/package-tree.html @@ -0,0 +1,70 @@ + + + + +edu.ucsd.sbrg.fixing.ext.groups Class Hierarchy (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      +
      +

      Hierarchy For Package edu.ucsd.sbrg.fixing.ext.groups

      +Package Hierarchies: + +
      +
      +

      Class Hierarchy

      + +
      +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/package-summary.html b/docs/edu/ucsd/sbrg/fixing/package-summary.html new file mode 100644 index 00000000..362db366 --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/package-summary.html @@ -0,0 +1,112 @@ + + + + +edu.ucsd.sbrg.fixing (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      +
      +

      Package edu.ucsd.sbrg.fixing

      +
      +
      +
      package edu.ucsd.sbrg.fixing
      +
      + +
      +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/fixing/package-tree.html b/docs/edu/ucsd/sbrg/fixing/package-tree.html new file mode 100644 index 00000000..087b4c47 --- /dev/null +++ b/docs/edu/ucsd/sbrg/fixing/package-tree.html @@ -0,0 +1,82 @@ + + + + +edu.ucsd.sbrg.fixing Class Hierarchy (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      +
      +

      Hierarchy For Package edu.ucsd.sbrg.fixing

      +Package Hierarchies: + +
      +
      +

      Class Hierarchy

      + +
      +
      +

      Interface Hierarchy

      + +
      +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/io/IReadModelsFromFile.html b/docs/edu/ucsd/sbrg/io/IReadModelsFromFile.html new file mode 100644 index 00000000..9093d517 --- /dev/null +++ b/docs/edu/ucsd/sbrg/io/IReadModelsFromFile.html @@ -0,0 +1,132 @@ + + + + +IReadModelsFromFile (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.io
      +

      Interface IReadModelsFromFile

      +
      +
      +
      +
      All Known Implementing Classes:
      +
      ModelReader
      +
      +
      +
      public interface IReadModelsFromFile
      +
      +
      +
        + +
      • +
        +

        Method Summary

        +
        +
        +
        +
        +
        Modifier and Type
        +
        Method
        +
        Description
        +
        org.sbml.jsbml.SBMLDocument
        +
        read(File input)
        +
         
        +
        +
        +
        +
        +
        • +
      +
      +
      + +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/io/IWriteModels.html b/docs/edu/ucsd/sbrg/io/IWriteModels.html new file mode 100644 index 00000000..d715bc37 --- /dev/null +++ b/docs/edu/ucsd/sbrg/io/IWriteModels.html @@ -0,0 +1,132 @@ + + + + +IWriteModels (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.io
      +

      Interface IWriteModels

      +
      +
      +
      +
      All Known Implementing Classes:
      +
      ModelWriter
      +
      +
      +
      public interface IWriteModels
      +
      +
      +
        + +
      • +
        +

        Method Summary

        +
        +
        +
        +
        +
        Modifier and Type
        +
        Method
        +
        Description
        +
        InputStream
        +
        write(org.sbml.jsbml.SBMLDocument doc)
        +
         
        +
        +
        +
        +
        +
        • +
      +
      +
      + +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/io/IWriteModelsToFile.html b/docs/edu/ucsd/sbrg/io/IWriteModelsToFile.html new file mode 100644 index 00000000..02d18508 --- /dev/null +++ b/docs/edu/ucsd/sbrg/io/IWriteModelsToFile.html @@ -0,0 +1,134 @@ + + + + +IWriteModelsToFile (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.io
      +

      Interface IWriteModelsToFile

      +
      +
      +
      +
      All Known Implementing Classes:
      +
      ModelWriter
      +
      +
      +
      public interface IWriteModelsToFile
      +
      +
      +
        + +
      • +
        +

        Method Summary

        +
        +
        +
        +
        +
        Modifier and Type
        +
        Method
        +
        Description
        +
        File
        +
        write(org.sbml.jsbml.SBMLDocument doc, + File output)
        +
         
        +
        +
        +
        +
        +
        • +
      +
      +
      + +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/io/ModelReader.html b/docs/edu/ucsd/sbrg/io/ModelReader.html index 623ad32e..b2cd400a 100644 --- a/docs/edu/ucsd/sbrg/io/ModelReader.html +++ b/docs/edu/ucsd/sbrg/io/ModelReader.html @@ -74,9 +74,14 @@

      Class ModelReader

      edu.ucsd.sbrg.io.ModelReader
      +
      +
      All Implemented Interfaces:
      +
      IReadModelsFromFile
      +
      public class ModelReader -extends Object
      +extends Object +implements IReadModelsFromFile
      diff --git a/docs/edu/ucsd/sbrg/io/parsers/json/JSONConverter.html b/docs/edu/ucsd/sbrg/io/parsers/json/JSONConverter.html index a7fd9194..6b75236d 100644 --- a/docs/edu/ucsd/sbrg/io/parsers/json/JSONConverter.html +++ b/docs/edu/ucsd/sbrg/io/parsers/json/JSONConverter.html @@ -104,44 +104,32 @@

      Method Summary

      Modifier and Type
      Method
      Description
      -
      static Root
      -
      convertDocument(org.sbml.jsbml.SBMLDocument doc)
      -
       
      -
      static Gene
      -
      convertGene(org.sbml.jsbml.ext.fbc.GeneProduct g)
      -
       
      -
      static List<Gene>
      -
      convertGenes(org.sbml.jsbml.Model model)
      +
      static Gene
      +
      convertGene(org.sbml.jsbml.ext.fbc.GeneProduct g)
       
      -
      static Metabolite
      -
      convertMetabolite(org.sbml.jsbml.Species species)
      +
      static List<Gene>
      +
      convertGenes(org.sbml.jsbml.Model model)
       
      -
      static List<Metabolite>
      -
      convertMetabolites(org.sbml.jsbml.Model model)
      +
      static Metabolite
      +
      convertMetabolite(org.sbml.jsbml.Species species)
       
      -
      static Root
      -
      convertModel(org.sbml.jsbml.Model model)
      +
      static List<Metabolite>
      +
      convertMetabolites(org.sbml.jsbml.Model model)
       
      -
      static Reaction
      -
      convertReaction(org.sbml.jsbml.Reaction r)
      -
       
      -
      static List<Reaction>
      -
      convertReactions(org.sbml.jsbml.Model model)
      -
       
      -
      static String
      -
      getJSONDocument(org.sbml.jsbml.SBMLDocument doc)
      +
      static Root
      +
      convertModel(org.sbml.jsbml.Model model)
       
      -
      static String
      -
      getJSONGene(org.sbml.jsbml.ext.fbc.GeneProduct g)
      +
      static Reaction
      +
      convertReaction(org.sbml.jsbml.Reaction r)
       
      -
      static String
      -
      getJSONMetabolite(org.sbml.jsbml.Species species)
      +
      static List<Reaction>
      +
      convertReactions(org.sbml.jsbml.Model model)
       
      static String
      -
      getJSONModel(org.sbml.jsbml.Model model)
      +
      getJSONDocument(org.sbml.jsbml.SBMLDocument doc)
       
      static String
      -
      getJSONReaction(org.sbml.jsbml.Reaction r)
      +
      getJSONModel(org.sbml.jsbml.Model model)
       
      @@ -175,81 +163,106 @@

      JSONConverter

      Method Details

      • -
        -

        convertDocument

        -
        public static Root convertDocument(org.sbml.jsbml.SBMLDocument doc)
        -
        -
        • -

      • convertModel

        -
        public static Root convertModel(org.sbml.jsbml.Model model)
        +
        public static Root convertModel(org.sbml.jsbml.Model model) + throws XMLStreamException
        +
        +
        Throws:
        +
        XMLStreamException
        +

      • convertGenes

        -
        public static List<Gene> convertGenes(org.sbml.jsbml.Model model)
        +
        public static List<Gene> convertGenes(org.sbml.jsbml.Model model) + throws XMLStreamException
        +
        +
        Throws:
        +
        XMLStreamException
        +

      • convertGene

        -
        public static Gene convertGene(org.sbml.jsbml.ext.fbc.GeneProduct g)
        +
        public static Gene convertGene(org.sbml.jsbml.ext.fbc.GeneProduct g) + throws XMLStreamException
        +
        +
        Throws:
        +
        XMLStreamException
        +

      • convertMetabolites

        -
        public static List<Metabolite> convertMetabolites(org.sbml.jsbml.Model model)
        +
        public static List<Metabolite> convertMetabolites(org.sbml.jsbml.Model model) + throws XMLStreamException
        +
        +
        Throws:
        +
        XMLStreamException
        +

      • convertMetabolite

        -
        public static Metabolite convertMetabolite(org.sbml.jsbml.Species species)
        +
        public static Metabolite convertMetabolite(org.sbml.jsbml.Species species) + throws XMLStreamException
        +
        +
        Throws:
        +
        XMLStreamException
        +

      • convertReactions

        -
        public static List<Reaction> convertReactions(org.sbml.jsbml.Model model)
        +
        public static List<Reaction> convertReactions(org.sbml.jsbml.Model model) + throws XMLStreamException
        +
        +
        Throws:
        +
        XMLStreamException
        +

      • convertReaction

        -
        public static Reaction convertReaction(org.sbml.jsbml.Reaction r)
        +
        public static Reaction convertReaction(org.sbml.jsbml.Reaction r) + throws XMLStreamException
        +
        +
        Throws:
        +
        XMLStreamException
        +

      • getJSONDocument

        -
        public static String getJSONDocument(org.sbml.jsbml.SBMLDocument doc)
        -
        -
        • -
      • -
        -

        getJSONGene

        -
        public static String getJSONGene(org.sbml.jsbml.ext.fbc.GeneProduct g)
        -
        -
        • -
      • -
        -

        getJSONMetabolite

        -
        public static String getJSONMetabolite(org.sbml.jsbml.Species species)
        -
        -
        • -
      • -
        -

        getJSONReaction

        -
        public static String getJSONReaction(org.sbml.jsbml.Reaction r)
        +
        public static String getJSONDocument(org.sbml.jsbml.SBMLDocument doc) + throws com.fasterxml.jackson.core.JsonProcessingException, +XMLStreamException
        +
        +
        Throws:
        +
        com.fasterxml.jackson.core.JsonProcessingException
        +
        XMLStreamException
        +

      • getJSONModel

        -
        public static String getJSONModel(org.sbml.jsbml.Model model)
        +
        public static String getJSONModel(org.sbml.jsbml.Model model) + throws com.fasterxml.jackson.core.JsonProcessingException, +XMLStreamException
        +
        +
        Throws:
        +
        com.fasterxml.jackson.core.JsonProcessingException
        +
        XMLStreamException
        +
      diff --git a/docs/edu/ucsd/sbrg/package-summary.html b/docs/edu/ucsd/sbrg/package-summary.html index d843c4d9..b4b0117b 100644 --- a/docs/edu/ucsd/sbrg/package-summary.html +++ b/docs/edu/ucsd/sbrg/package-summary.html @@ -15,11 +15,7 @@ -
      -
      -

      Interface Hierarchy

      - -
      -
      -

      Enum Class Hierarchy

      - diff --git a/docs/edu/ucsd/sbrg/parameters/CommandLineParameters.html b/docs/edu/ucsd/sbrg/parameters/CommandLineParameters.html index 1703c74e..bf135460 100644 --- a/docs/edu/ucsd/sbrg/parameters/CommandLineParameters.html +++ b/docs/edu/ucsd/sbrg/parameters/CommandLineParameters.html @@ -89,7 +89,7 @@

      Field Summary

      Modifier and Type
      Field
      Description
      -
      protected ModelPolisherOptions.OutputType
      +
      protected ModelPolisherOptions.OutputType
      outputType
       
      protected boolean
      @@ -131,7 +131,7 @@

      Method Summary

      File
      output()
       
      -
      ModelPolisherOptions.OutputType
      +
      ModelPolisherOptions.OutputType
      outputType()
       
      PolishingParameters
      @@ -169,7 +169,7 @@

      sbmlValidation

    • outputType

      -
      protected ModelPolisherOptions.OutputType outputType
      +
      protected ModelPolisherOptions.OutputType outputType
    @@ -220,7 +220,7 @@

    SBMLValidation

  • outputType

    -
    public ModelPolisherOptions.OutputType outputType()
    +
    public ModelPolisherOptions.OutputType outputType()
  • diff --git a/docs/edu/ucsd/sbrg/ModelPolisherOptions.OutputType.html b/docs/edu/ucsd/sbrg/parameters/ModelPolisherOptions.OutputType.html similarity index 87% rename from docs/edu/ucsd/sbrg/ModelPolisherOptions.OutputType.html rename to docs/edu/ucsd/sbrg/parameters/ModelPolisherOptions.OutputType.html index 2dc8bbd2..04f2d132 100644 --- a/docs/edu/ucsd/sbrg/ModelPolisherOptions.OutputType.html +++ b/docs/edu/ucsd/sbrg/parameters/ModelPolisherOptions.OutputType.html @@ -5,21 +5,21 @@ ModelPolisherOptions.OutputType (ModelPolisher 2.1 API) - + - - - - - - + + + + + +
  • -
    Classes
    +
    +
    Class
    Description
    @@ -92,6 +97,10 @@

    Package edu.ucsd.sbrg
     
    FluxObjectivesPolishingParameters
     
    +
    ModelPolisherOptions
    +
     
    +
    ModelPolisherOptions.OutputType
    +
     
    Parameters
     
    ParametersParser
    @@ -104,6 +113,7 @@

    Package edu.ucsd.sbrg
     

    +
    • diff --git a/docs/edu/ucsd/sbrg/parameters/package-tree.html b/docs/edu/ucsd/sbrg/parameters/package-tree.html index d63a8f24..e86c3b3a 100644 --- a/docs/edu/ucsd/sbrg/parameters/package-tree.html +++ b/docs/edu/ucsd/sbrg/parameters/package-tree.html @@ -74,6 +74,30 @@

    Class Hierarchy

    +
    +

    Interface Hierarchy

    + +
    +
    +

    Enum Class Hierarchy

    + +
    diff --git a/docs/edu/ucsd/sbrg/polishing/AbstractPolisher.html b/docs/edu/ucsd/sbrg/polishing/AbstractPolisher.html index b8245c3b..a3d2bb69 100644 --- a/docs/edu/ucsd/sbrg/polishing/AbstractPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/AbstractPolisher.html @@ -68,19 +68,24 @@
    Package edu.ucsd.sbrg.polishing
    -

    Class AbstractPolisher<SBMLElement>

    +

    Class AbstractPolisher

    java.lang.Object -
    edu.ucsd.sbrg.polishing.AbstractPolisher<SBMLElement>
    +
    edu.ucsd.sbrg.polishing.AbstractPolisher
    +
    All Implemented Interfaces:
    +
    IReportStatus
    +
    +
    Direct Known Subclasses:
    -
    AnnotationPolisher, CompartmentPolisher, FBCPolisher, FluxObjectivesPolisher, GeneProductsPolisher, ModelPolisher, ParametersPolisher, ReactionsPolisher, SBMLPolisher, SpeciesPolisher, UnitPolisher
    +
    AnnotationPolisher, CompartmentPolisher, FBCPolisher, FBCReactionPolisher, GeneProductsPolisher, ModelPolisher, ObjectivesPolisher, ParametersPolisher, ReactionsPolisher, SBMLPolisher, SpeciesPolisher, UnitPolisher
    -
    public abstract class AbstractPolisher<SBMLElement> -extends Object
    +
    public abstract class AbstractPolisher +extends Object +implements IReportStatus
    diff --git a/docs/edu/ucsd/sbrg/polishing/IPolishAnnotations.html b/docs/edu/ucsd/sbrg/polishing/IPolishAnnotations.html new file mode 100644 index 00000000..a2823b50 --- /dev/null +++ b/docs/edu/ucsd/sbrg/polishing/IPolishAnnotations.html @@ -0,0 +1,127 @@ + + + + +IPolishAnnotations (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.polishing
    +

    Interface IPolishAnnotations

    +
    +
    +
    +
    All Known Implementing Classes:
    +
    AnnotationPolisher
    +
    +
    +
    public interface IPolishAnnotations
    +
    +
    +
      + +
    • +
      +

      Method Summary

      +
      +
      +
      +
      +
      Modifier and Type
      +
      Method
      +
      Description
      +
      void
      +
      polish(org.sbml.jsbml.Annotation annotation)
      +
       
      +
      +
      +
      +
      +
      • +
    +
    +
    +
      + +
    • +
      +

      Method Details

      +
        +
      • +
        +

        polish

        +
        void polish(org.sbml.jsbml.Annotation annotation)
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/polishing/IPolishSBaseAttributes.html b/docs/edu/ucsd/sbrg/polishing/IPolishSBaseAttributes.html new file mode 100644 index 00000000..22192a04 --- /dev/null +++ b/docs/edu/ucsd/sbrg/polishing/IPolishSBaseAttributes.html @@ -0,0 +1,136 @@ + + + + +IPolishSBaseAttributes (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.polishing
    +

    Interface IPolishSBaseAttributes

    +
    +
    +
    +
    All Known Implementing Classes:
    +
    NamePolisher
    +
    +
    +
    public interface IPolishSBaseAttributes
    +
    +
    +
      + +
    • +
      +

      Method Summary

      +
      +
      +
      +
      +
      Modifier and Type
      +
      Method
      +
      Description
      +
      default void
      +
      polish(List<org.sbml.jsbml.SBase> elementsToPolish)
      +
       
      +
      void
      +
      polish(org.sbml.jsbml.SBase elementToPolish)
      +
       
      +
      +
      +
      +
      +
      • +
    +
    +
    +
      + +
    • +
      +

      Method Details

      +
        +
      • +
        +

        polish

        +
        default void polish(List<org.sbml.jsbml.SBase> elementsToPolish)
        +
        +
        • +
      • +
        +

        polish

        +
        void polish(org.sbml.jsbml.SBase elementToPolish)
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/polishing/IPolishSBases.html b/docs/edu/ucsd/sbrg/polishing/IPolishSBases.html new file mode 100644 index 00000000..e3a4d2c1 --- /dev/null +++ b/docs/edu/ucsd/sbrg/polishing/IPolishSBases.html @@ -0,0 +1,136 @@ + + + + +IPolishSBases (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.polishing
    +

    Interface IPolishSBases<SBMLElement extends org.sbml.jsbml.SBase>

    +
    +
    +
    +
    All Known Implementing Classes:
    +
    CompartmentPolisher, FBCPolisher, FBCReactionPolisher, GeneProductsPolisher, ModelPolisher, ObjectivesPolisher, ParametersPolisher, ReactionsPolisher, SBMLPolisher, SpeciesPolisher, UnitPolisher
    +
    +
    +
    public interface IPolishSBases<SBMLElement extends org.sbml.jsbml.SBase>
    +
    +
    +
      + +
    • +
      +

      Method Summary

      +
      +
      +
      +
      +
      Modifier and Type
      +
      Method
      +
      Description
      +
      default void
      +
      polish(List<SBMLElement> elementsToPolish)
      +
       
      +
      void
      +
      polish(SBMLElement elementToPolish)
      +
       
      +
      +
      +
      +
      +
      • +
    +
    +
    +
      + +
    • +
      +

      Method Details

      +
        +
      • +
        +

        polish

        +
        default void polish(List<SBMLElement> elementsToPolish)
        +
        +
        • +
      • +
        +

        polish

        +
        void polish(SBMLElement elementToPolish)
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/polishing/IPolishSpeciesReferences.html b/docs/edu/ucsd/sbrg/polishing/IPolishSpeciesReferences.html new file mode 100644 index 00000000..5ea9e054 --- /dev/null +++ b/docs/edu/ucsd/sbrg/polishing/IPolishSpeciesReferences.html @@ -0,0 +1,136 @@ + + + + +IPolishSpeciesReferences (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.polishing
    +

    Interface IPolishSpeciesReferences

    +
    +
    +
    +
    All Known Implementing Classes:
    +
    SpeciesReferencesPolisher
    +
    +
    +
    public interface IPolishSpeciesReferences
    +
    +
    +
      + +
    • +
      +

      Method Summary

      +
      +
      +
      +
      +
      Modifier and Type
      +
      Method
      +
      Description
      +
      default void
      +
      polish(List<org.sbml.jsbml.SpeciesReference> elementsToPolish)
      +
       
      +
      void
      +
      polish(org.sbml.jsbml.SpeciesReference elementToPolish)
      +
       
      +
      +
      +
      +
      +
      • +
    +
    +
    +
      + +
    • +
      +

      Method Details

      +
        +
      • +
        +

        polish

        +
        default void polish(List<org.sbml.jsbml.SpeciesReference> elementsToPolish)
        +
        +
        • +
      • +
        +

        polish

        +
        void polish(org.sbml.jsbml.SpeciesReference elementToPolish)
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/polishing/ModelPolisher.html b/docs/edu/ucsd/sbrg/polishing/ModelPolisher.html index f97594f9..90c55f27 100644 --- a/docs/edu/ucsd/sbrg/polishing/ModelPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/ModelPolisher.html @@ -71,14 +71,19 @@

    Class ModelPolisher

    java.lang.Object -
    edu.ucsd.sbrg.polishing.AbstractPolisher<org.sbml.jsbml.Model> +
    edu.ucsd.sbrg.polishing.AbstractPolisher
    edu.ucsd.sbrg.polishing.ModelPolisher
    +
    +
    All Implemented Interfaces:
    +
    IPolishSBases<org.sbml.jsbml.Model>, IReportStatus
    +
    public class ModelPolisher -extends AbstractPolisher<org.sbml.jsbml.Model>
    +extends AbstractPolisher +implements IPolishSBases<org.sbml.jsbml.Model>
    This class provides functionality to polish an SBML (Systems Biology Markup Language) document. Polishing involves enhancing the document with additional annotations, setting appropriate SBO (Systems Biology Ontology) terms, and ensuring the document adheres to certain standards and conventions useful for computational models in systems biology. @@ -141,10 +146,13 @@

    Method Summary

    Methods inherited from class edu.ucsd.sbrg.polishing.AbstractPolisher

    -diffReport, equals, getObservers, hashCode, polish, statusReport
    +equals, getObservers, hashCode, statusReport

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    +
    +

    Methods inherited from interface edu.ucsd.sbrg.polishing.IPolishSBases

    +polish
    @@ -190,7 +198,7 @@

    polish

    the polishing process.
    Specified by:
    -
    polish in class AbstractPolisher<org.sbml.jsbml.Model>
    +
    polish in interface IPolishSBases<org.sbml.jsbml.Model>
    Parameters:
    model - The SBML Model to be polished.
    @@ -202,7 +210,7 @@

    toString

    public String toString()
    Overrides:
    -
    toString in class AbstractPolisher<org.sbml.jsbml.Model>
    +
    toString in class AbstractPolisher
    diff --git a/docs/edu/ucsd/sbrg/polishing/NamePolisher.html b/docs/edu/ucsd/sbrg/polishing/NamePolisher.html new file mode 100644 index 00000000..9d10212a --- /dev/null +++ b/docs/edu/ucsd/sbrg/polishing/NamePolisher.html @@ -0,0 +1,178 @@ + + + + +NamePolisher (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.polishing
    +

    Class NamePolisher

    +
    +
    java.lang.Object +
    edu.ucsd.sbrg.polishing.NamePolisher
    +
    +
    +
    +
    All Implemented Interfaces:
    +
    IPolishSBaseAttributes
    +
    +
    +
    public class NamePolisher +extends Object +implements IPolishSBaseAttributes
    +
    +
    + +
    +
    +
      + +
    • +
      +

      Constructor Details

      +
        +
      • +
        +

        NamePolisher

        +
        public NamePolisher()
        +
        +
        • +
      +
      +
      • + +
    • +
      +

      Method Details

      + +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/polishing/ParametersPolisher.html b/docs/edu/ucsd/sbrg/polishing/ParametersPolisher.html index 43802866..755cd63f 100644 --- a/docs/edu/ucsd/sbrg/polishing/ParametersPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/ParametersPolisher.html @@ -71,14 +71,19 @@

    Class ParametersPolisher

    java.lang.Object -
    edu.ucsd.sbrg.polishing.AbstractPolisher<org.sbml.jsbml.Parameter> +
    edu.ucsd.sbrg.polishing.AbstractPolisher
    edu.ucsd.sbrg.polishing.ParametersPolisher
    +
    +
    All Implemented Interfaces:
    +
    IPolishSBases<org.sbml.jsbml.Parameter>, IReportStatus
    +
    public class ParametersPolisher -extends AbstractPolisher<org.sbml.jsbml.Parameter>
    +extends AbstractPolisher +implements IPolishSBases<org.sbml.jsbml.Parameter>
      @@ -119,20 +124,16 @@

      Method Summary

      Description
      void
      polish(List<org.sbml.jsbml.Parameter> modelParameters)
      -
      -
      Iterates over all parameters in the model and polishes each one.
      -
      +
       
      void
      polish(org.sbml.jsbml.Parameter p)
      -
      -
      Polishes the name of a parameter if it is not already set.
      -
      +
       

      Methods inherited from class edu.ucsd.sbrg.polishing.AbstractPolisher

      -diffReport, equals, getObservers, hashCode, statusReport, toString
      +equals, getObservers, hashCode, statusReport, toString

      Methods inherited from class java.lang.Object

      clone, finalize, getClass, notify, notifyAll, wait, wait, wait
      @@ -167,11 +168,9 @@

      Method Details

      polish

      public void polish(List<org.sbml.jsbml.Parameter> modelParameters)
      -
      Iterates over all parameters in the model and polishes each one. - Displays progress for each parameter polished.
      -
      Overrides:
      -
      polish in class AbstractPolisher<org.sbml.jsbml.Parameter>
      +
      Specified by:
      +
      polish in interface IPolishSBases<org.sbml.jsbml.Parameter>
      @@ -179,15 +178,9 @@

      polish

      polish

      public void polish(org.sbml.jsbml.Parameter p)
      -
      Polishes the name of a parameter if it is not already set. - This method checks if the parameter has an ID but no name. - If the condition is true, it sets the parameter's name to a polished version of its ID. - The polishing is done using the PolishingUtils.polishName(String) method.
      Specified by:
      -
      polish in class AbstractPolisher<org.sbml.jsbml.Parameter>
      -
      Parameters:
      -
      p - The parameter to be polished.
      +
      polish in interface IPolishSBases<org.sbml.jsbml.Parameter>
      diff --git a/docs/edu/ucsd/sbrg/polishing/ReactionsPolisher.html b/docs/edu/ucsd/sbrg/polishing/ReactionsPolisher.html index 7bf0c8f2..3ae9f004 100644 --- a/docs/edu/ucsd/sbrg/polishing/ReactionsPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/ReactionsPolisher.html @@ -71,14 +71,19 @@

      Class ReactionsPolisher

      java.lang.Object -
      edu.ucsd.sbrg.polishing.AbstractPolisher<org.sbml.jsbml.Reaction> +
      edu.ucsd.sbrg.polishing.AbstractPolisher
      edu.ucsd.sbrg.polishing.ReactionsPolisher
      +
      +
      All Implemented Interfaces:
      +
      IPolishSBases<org.sbml.jsbml.Reaction>, IReportStatus
      +
      public class ReactionsPolisher -extends AbstractPolisher<org.sbml.jsbml.Reaction>
      +extends AbstractPolisher +implements IPolishSBases<org.sbml.jsbml.Reaction>
      This class provides methods to polish and validate SBML reactions according to specific rules and patterns. It includes functionality to: - Check and set SBO terms based on reaction ID patterns. @@ -134,26 +139,19 @@

      Method Summary

      Description
      void
      polish(List<org.sbml.jsbml.Reaction> reactions)
      -
      -
      Polishes all reactions in the given SBML model.
      -
      +
       
      void
      polish(org.sbml.jsbml.Reaction reaction)
      Polishes the reaction by applying various checks and modifications to ensure it conforms to the expected standards and conventions.
      -
      void
      -
      setFluxBoundSBOTerm(org.sbml.jsbml.Parameter bound)
      -
      -
      Polishes the SBO term of a flux bound parameter based on its ID.
      -

      Methods inherited from class edu.ucsd.sbrg.polishing.AbstractPolisher

      -diffReport, equals, getObservers, hashCode, statusReport, toString
      +equals, getObservers, hashCode, statusReport, toString

      Methods inherited from class java.lang.Object

      clone, finalize, getClass, notify, notifyAll, wait, wait, wait
      @@ -197,12 +195,9 @@

      Method Details

      polish

      public void polish(List<org.sbml.jsbml.Reaction> reactions)
      -
      Polishes all reactions in the given SBML model. This method iterates through each reaction, - updates the progress display, and applies polishing operations defined in the ReactionPolishing class. - It also aggregates a strictness flag that indicates if all reactions conform to strict FBC (Flux Balance Constraints) standards.
      -
      Overrides:
      -
      polish in class AbstractPolisher<org.sbml.jsbml.Reaction>
      +
      Specified by:
      +
      polish in interface IPolishSBases<org.sbml.jsbml.Reaction>
      @@ -215,20 +210,7 @@

      polish

      and ensuring proper setup of reactants and products.
      Specified by:
      -
      polish in class AbstractPolisher<org.sbml.jsbml.Reaction>
      -
      -
    - -
  • -
    -

    setFluxBoundSBOTerm

    -
    public void setFluxBoundSBOTerm(org.sbml.jsbml.Parameter bound)
    -
    Polishes the SBO term of a flux bound parameter based on its ID. - If the parameter's ID matches the default flux bound pattern, it sets the SBO term to 626. - Otherwise, it sets the SBO term to 625.
    -
    -
    Parameters:
    -
    bound - The parameter representing a flux bound.
    +
    polish in interface IPolishSBases<org.sbml.jsbml.Reaction>
    • diff --git a/docs/edu/ucsd/sbrg/polishing/SBMLPolisher.html b/docs/edu/ucsd/sbrg/polishing/SBMLPolisher.html index 1218f718..5d9b3bec 100644 --- a/docs/edu/ucsd/sbrg/polishing/SBMLPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/SBMLPolisher.html @@ -71,14 +71,19 @@

    Class SBMLPolisher

    java.lang.Object -
    edu.ucsd.sbrg.polishing.AbstractPolisher<org.sbml.jsbml.SBMLDocument> +
    edu.ucsd.sbrg.polishing.AbstractPolisher
    edu.ucsd.sbrg.polishing.SBMLPolisher
    +
    +
    All Implemented Interfaces:
    +
    IPolishSBases<org.sbml.jsbml.SBMLDocument>, IReportStatus
    +
    public class SBMLPolisher -extends AbstractPolisher<org.sbml.jsbml.SBMLDocument>
    +extends AbstractPolisher +implements IPolishSBases<org.sbml.jsbml.SBMLDocument>
    @@ -181,7 +189,7 @@

    polish

    marks the progress as finished if applicable, and processes any linked resources.
    Specified by:
    -
    polish in class AbstractPolisher<org.sbml.jsbml.SBMLDocument>
    +
    polish in interface IPolishSBases<org.sbml.jsbml.SBMLDocument>
    Parameters:
    doc - The SBMLDocument containing the model to be polished.
    diff --git a/docs/edu/ucsd/sbrg/polishing/SpeciesPolisher.html b/docs/edu/ucsd/sbrg/polishing/SpeciesPolisher.html index c793d5ae..799b8310 100644 --- a/docs/edu/ucsd/sbrg/polishing/SpeciesPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/SpeciesPolisher.html @@ -71,17 +71,19 @@

    Class SpeciesPolisher

    java.lang.Object -
    edu.ucsd.sbrg.polishing.AbstractPolisher<org.sbml.jsbml.Species> +
    edu.ucsd.sbrg.polishing.AbstractPolisher
    edu.ucsd.sbrg.polishing.SpeciesPolisher
    +
    +
    All Implemented Interfaces:
    +
    IPolishSBases<org.sbml.jsbml.Species>, IReportStatus
    +
    public class SpeciesPolisher -extends AbstractPolisher<org.sbml.jsbml.Species>
    -
    This class is responsible for polishing Species objects in an SBML model to ensure they conform to - specific standards and completeness. It handles the annotation processing, ID validation, boundary condition settings, - and default attribute assignments for species within the model.
    +extends AbstractPolisher +implements IPolishSBases<org.sbml.jsbml.Species>
      @@ -124,26 +126,17 @@

      Method Summary

      Method
      Description
      void
      -
      checkCompartment(org.sbml.jsbml.Species species)
      -
      -
      Checks and sets the compartment for a given species.
      -
      +
      polish(List<org.sbml.jsbml.Species> species)
      +
       
      void
      -
      polish(List<org.sbml.jsbml.Species> species)
      -
      -
      Polishes the list of species in the given SBML model.
      -
      -
      void
      -
      polish(org.sbml.jsbml.Species species)
      -
      -
      Polishes the properties of a Species to ensure compliance with standards and completeness.
      -
      +
      polish(org.sbml.jsbml.Species species)
      +
       

      Methods inherited from class edu.ucsd.sbrg.polishing.AbstractPolisher

      -diffReport, equals, getObservers, hashCode, statusReport, toString
      +equals, getObservers, hashCode, statusReport, toString

      Methods inherited from class java.lang.Object

      clone, finalize, getClass, notify, notifyAll, wait, wait, wait
      @@ -185,12 +178,9 @@

      Method Details

      polish

      public void polish(List<org.sbml.jsbml.Species> species)
      -
      Polishes the list of species in the given SBML model. This method iterates through each species, - applies polishing operations, and collects species that need to be removed based on the polishing results. - Removal is based on criteria defined in the SpeciesPolishing class.
      -
      Overrides:
      -
      polish in class AbstractPolisher<org.sbml.jsbml.Species>
      +
      Specified by:
      +
      polish in interface IPolishSBases<org.sbml.jsbml.Species>
      @@ -198,25 +188,9 @@

      polish

      polish

      public void polish(org.sbml.jsbml.Species species)
      -
      Polishes the properties of a Species to ensure compliance with standards and completeness. - This method processes annotations, checks for missing IDs, sets boundary conditions, and ensures - that mandatory attributes are set to default values.
      Specified by:
      -
      polish in class AbstractPolisher<org.sbml.jsbml.Species>
      -
      -
      - -
    • -
      -

      checkCompartment

      -
      public void checkCompartment(org.sbml.jsbml.Species species)
      -
      Checks and sets the compartment for a given species. If the species does not have a compartment set, - it attempts to set it using the BiGG ID compartment code. If the compartment is still not set or found, - it logs a warning and creates a new compartment.
      -
      -
      Parameters:
      -
      species - The species whose compartment needs to be checked or set.
      +
      polish in interface IPolishSBases<org.sbml.jsbml.Species>
      • diff --git a/docs/edu/ucsd/sbrg/polishing/SpeciesReferencesPolisher.html b/docs/edu/ucsd/sbrg/polishing/SpeciesReferencesPolisher.html new file mode 100644 index 00000000..592660d0 --- /dev/null +++ b/docs/edu/ucsd/sbrg/polishing/SpeciesReferencesPolisher.html @@ -0,0 +1,169 @@ + + + + +SpeciesReferencesPolisher (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.polishing
      +

      Class SpeciesReferencesPolisher

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.polishing.SpeciesReferencesPolisher
      +
      +
      +
      +
      All Implemented Interfaces:
      +
      IPolishSpeciesReferences
      +
      +
      +
      public class SpeciesReferencesPolisher +extends Object +implements IPolishSpeciesReferences
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Constructor Details

        +
          +
        • +
          +

          SpeciesReferencesPolisher

          +
          public SpeciesReferencesPolisher(Integer defaultSBOterm)
          +
          +
          • +
        +
        +
        • + +
      • +
        +

        Method Details

        + +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/polishing/UnitPolisher.html b/docs/edu/ucsd/sbrg/polishing/UnitPolisher.html index ae8b3d23..78aefa56 100644 --- a/docs/edu/ucsd/sbrg/polishing/UnitPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/UnitPolisher.html @@ -71,14 +71,19 @@

      Class UnitPolisher

      java.lang.Object -
      edu.ucsd.sbrg.polishing.AbstractPolisher<org.sbml.jsbml.Model> +
      edu.ucsd.sbrg.polishing.AbstractPolisher
      edu.ucsd.sbrg.polishing.UnitPolisher
      +
      +
      All Implemented Interfaces:
      +
      IPolishSBases<org.sbml.jsbml.Model>, IReportStatus
      +
      public class UnitPolisher -extends AbstractPolisher<org.sbml.jsbml.Model>
      +extends AbstractPolisher +implements IPolishSBases<org.sbml.jsbml.Model>
      This class is responsible for ensuring that all necessary UnitDefinitions and Units are correctly defined and present in the SBML model. It handles the creation and verification of units used in the model, particularly focusing on the units related to growth, substance, time, and volume. @@ -180,10 +185,13 @@

      Method Summary

      Methods inherited from class edu.ucsd.sbrg.polishing.AbstractPolisher

      -diffReport, equals, getObservers, hashCode, polish, statusReport, toString
      +equals, getObservers, hashCode, statusReport, toString

      Methods inherited from class java.lang.Object

      clone, finalize, getClass, notify, notifyAll, wait, wait, wait
      +
      +

      Methods inherited from interface edu.ucsd.sbrg.polishing.IPolishSBases

      +polish
    @@ -323,7 +331,7 @@

    polish

    extent and substance units if they are not already set.
    Specified by:
    -
    polish in class AbstractPolisher<org.sbml.jsbml.Model>
    +
    polish in interface IPolishSBases<org.sbml.jsbml.Model>
    diff --git a/docs/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.html b/docs/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.html index 2bd3deb7..2f86c5ef 100644 --- a/docs/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.html @@ -71,14 +71,19 @@

    Class FBCPolisher

    java.lang.Object -
    edu.ucsd.sbrg.polishing.AbstractPolisher<org.sbml.jsbml.Model> +
    edu.ucsd.sbrg.polishing.AbstractPolisher
    edu.ucsd.sbrg.polishing.fbc.FBCPolisher
    +
    +
    All Implemented Interfaces:
    +
    IPolishSBases<org.sbml.jsbml.Model>, IReportStatus
    +
    public class FBCPolisher -extends AbstractPolisher<org.sbml.jsbml.Model>
    +extends AbstractPolisher +implements IPolishSBases<org.sbml.jsbml.Model>
    @@ -141,9 +150,10 @@

    Methods inherited from cl

    Constructor Details

    • -
      +

      FBCPolisher

      public FBCPolisher(PolishingParameters parameters, + SBOParameters sboParameters, Registry registry, List<ProgressObserver> observers)
      @@ -162,7 +172,7 @@

      polish

      public void polish(org.sbml.jsbml.Model model)
      Specified by:
      -
      polish in class AbstractPolisher<org.sbml.jsbml.Model>
      +
      polish in interface IPolishSBases<org.sbml.jsbml.Model>
      • diff --git a/docs/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisher.html b/docs/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisher.html new file mode 100644 index 00000000..ed63fc40 --- /dev/null +++ b/docs/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisher.html @@ -0,0 +1,233 @@ + + + + +FBCReactionPolisher (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.polishing.fbc
      +

      Class FBCReactionPolisher

      +
      +
      java.lang.Object +
      edu.ucsd.sbrg.polishing.AbstractPolisher +
      edu.ucsd.sbrg.polishing.fbc.FBCReactionPolisher
      +
      +
      +
      +
      +
      All Implemented Interfaces:
      +
      IPolishSBases<org.sbml.jsbml.Reaction>, IReportStatus
      +
      +
      +
      public class FBCReactionPolisher +extends AbstractPolisher +implements IPolishSBases<org.sbml.jsbml.Reaction>
      +
      +
      + +
      +
      +
        + +
      • +
        +

        Constructor Details

        + +
        +
        • + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          polish

          +
          public void polish(List<org.sbml.jsbml.Reaction> reactions)
          +
          +
          Specified by:
          +
          polish in interface IPolishSBases<org.sbml.jsbml.Reaction>
          +
          +
          +
          • +
        • +
          +

          polish

          +
          public void polish(org.sbml.jsbml.Reaction reaction)
          +
          +
          Specified by:
          +
          polish in interface IPolishSBases<org.sbml.jsbml.Reaction>
          +
          +
          +
          • +
        • +
          +

          setFluxBoundSBOTerm

          +
          public void setFluxBoundSBOTerm(org.sbml.jsbml.Parameter bound)
          +
          Polishes the SBO term of a flux bound parameter based on its ID. + If the parameter's ID matches the default flux bound pattern, it sets the SBO term to 626. + Otherwise, it sets the SBO term to 625.
          +
          +
          Parameters:
          +
          bound - The parameter representing a flux bound.
          +
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/polishing/GeneProductAssociationsProcessor.html b/docs/edu/ucsd/sbrg/polishing/fbc/GeneProductAssociationsProcessor.html similarity index 91% rename from docs/edu/ucsd/sbrg/polishing/GeneProductAssociationsProcessor.html rename to docs/edu/ucsd/sbrg/polishing/fbc/GeneProductAssociationsProcessor.html index eda12f6b..e01d12fa 100644 --- a/docs/edu/ucsd/sbrg/polishing/GeneProductAssociationsProcessor.html +++ b/docs/edu/ucsd/sbrg/polishing/fbc/GeneProductAssociationsProcessor.html @@ -5,21 +5,21 @@ GeneProductAssociationsProcessor (ModelPolisher 2.1 API) - + - - - - - - + + + + + +
    @@ -152,16 +155,16 @@

    Constructor Details

    • -

      FluxObjectivesPolisher

      -
      public FluxObjectivesPolisher(org.sbml.jsbml.ext.fbc.FBCModelPlugin modelPlug, +

      ObjectivesPolisher

      +
      public ObjectivesPolisher(org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlugin, PolishingParameters parameters, Registry registry)
    • -

      FluxObjectivesPolisher

      -
      public FluxObjectivesPolisher(org.sbml.jsbml.ext.fbc.FBCModelPlugin modelPlug, +

      ObjectivesPolisher

      +
      public ObjectivesPolisher(org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlugin, PolishingParameters parameters, Registry registry, List<ProgressObserver> observers)
      @@ -176,27 +179,12 @@

      FluxObjectivesPolisher

      Method Details

      -

      Enum Class Hierarchy

      +

      Interface Hierarchy

      diff --git a/docs/edu/ucsd/sbrg/reporting/IReportDiffs.html b/docs/edu/ucsd/sbrg/reporting/IReportDiffs.html new file mode 100644 index 00000000..29db4593 --- /dev/null +++ b/docs/edu/ucsd/sbrg/reporting/IReportDiffs.html @@ -0,0 +1,131 @@ + + + + +IReportDiffs (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.reporting
      +

      Interface IReportDiffs

      +
      +
      +
      +
      All Known Implementing Classes:
      +
      AbstractAnnotator, AbstractBiGGAnnotator, BiGGCompartmentsAnnotator, BiGGCVTermAnnotator, BiGGFBCAnnotator, BiGGGeneProductAnnotator, BiGGModelAnnotator, BiGGPublicationsAnnotator, BiGGReactionsAnnotator, BiGGSBMLAnnotator, BiGGSpeciesAnnotator
      +
      +
      +
      public interface IReportDiffs
      +
      +
      +
        + +
      • +
        +

        Method Summary

        +
        +
        +
        +
        +
        Modifier and Type
        +
        Method
        +
        Description
        +
        void
        +
        diffReport(String elementType, + Object element1, + Object element2)
        +
         
        +
        +
        +
        +
        +
        • +
      +
      +
      +
        + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          diffReport

          +
          void diffReport(String elementType, + Object element1, + Object element2)
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/reporting/IReportStatus.html b/docs/edu/ucsd/sbrg/reporting/IReportStatus.html new file mode 100644 index 00000000..733964cf --- /dev/null +++ b/docs/edu/ucsd/sbrg/reporting/IReportStatus.html @@ -0,0 +1,129 @@ + + + + +IReportStatus (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      + +
      +
      Package edu.ucsd.sbrg.reporting
      +

      Interface IReportStatus

      +
      +
      +
      +
      All Known Implementing Classes:
      +
      AbstractAnnotator, AbstractBiGGAnnotator, AbstractPolisher, AnnotationPolisher, BiGGCompartmentsAnnotator, BiGGCVTermAnnotator, BiGGFBCAnnotator, BiGGGeneProductAnnotator, BiGGModelAnnotator, BiGGPublicationsAnnotator, BiGGReactionsAnnotator, BiGGSBMLAnnotator, BiGGSpeciesAnnotator, CompartmentPolisher, FBCPolisher, FBCReactionPolisher, GeneProductsPolisher, ModelPolisher, ObjectivesPolisher, ParametersPolisher, ReactionsPolisher, SBMLPolisher, SpeciesPolisher, UnitPolisher
      +
      +
      +
      public interface IReportStatus
      +
      +
      +
        + +
      • +
        +

        Method Summary

        +
        +
        +
        +
        +
        Modifier and Type
        +
        Method
        +
        Description
        +
        void
        +
        statusReport(String text, + Object element)
        +
         
        +
        +
        +
        +
        +
        • +
      +
      +
      +
        + +
      • +
        +

        Method Details

        +
          +
        • +
          +

          statusReport

          +
          void statusReport(String text, + Object element)
          +
          +
          • +
        +
        +
        • +
      +
      + +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/reporting/package-summary.html b/docs/edu/ucsd/sbrg/reporting/package-summary.html index db3f3a87..2a7fde2e 100644 --- a/docs/edu/ucsd/sbrg/reporting/package-summary.html +++ b/docs/edu/ucsd/sbrg/reporting/package-summary.html @@ -83,6 +83,10 @@

      Package edu.ucsd.sbrg.
      Class
      Description
      +
      IReportDiffs
      +
       
      +
      IReportStatus
      +
       
      PolisherProgressBar
       
      ProgressFinalization
      diff --git a/docs/edu/ucsd/sbrg/reporting/package-tree.html b/docs/edu/ucsd/sbrg/reporting/package-tree.html index 2e764740..f7d8b6a0 100644 --- a/docs/edu/ucsd/sbrg/reporting/package-tree.html +++ b/docs/edu/ucsd/sbrg/reporting/package-tree.html @@ -73,6 +73,8 @@

      Class Hierarchy

      Interface Hierarchy

      diff --git a/docs/edu/ucsd/sbrg/resolver/Registry.html b/docs/edu/ucsd/sbrg/resolver/Registry.html index cf35f454..e7aa7eff 100644 --- a/docs/edu/ucsd/sbrg/resolver/Registry.html +++ b/docs/edu/ucsd/sbrg/resolver/Registry.html @@ -91,20 +91,20 @@

      Method Summary

      Modifier and Type
      Method
      Description
      -
      Optional<RegistryURI>
      -
      findRegistryUrlForOtherUrl(String url)
      +
      String
      +
      getNamespaceForPrefix(String prefix)
       
      String
      -
      getNamespaceForPrefix(String prefix)
      +
      getPatternByNamespaceName(String namespaceName)
       
      String
      -
      getPatternByNamespaceName(String namespaceName)
      +
      getPrefixByNamespaceName(String namespaceName)
       
      -
      String
      -
      getPrefixByNamespaceName(String namespaceName)
      +
      boolean
      +
      isValid(String url)
       
      -
      boolean
      -
      isValid(String url)
      +
      Optional<RegistryURI>
      +
      resolveBackwards(String url)
       
      boolean
      validRegistryUrlPrefix(RegistryURI uri)
      @@ -142,9 +142,9 @@

      getPatternByNamespaceName

    • -
      -

      findRegistryUrlForOtherUrl

      -
      Optional<RegistryURI> findRegistryUrlForOtherUrl(String url)
      +
      +

      resolveBackwards

      +
      Optional<RegistryURI> resolveBackwards(String url)
    • diff --git a/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrg.html b/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrg.html index e4ccf5aa..d1108f9f 100644 --- a/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrg.html +++ b/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrg.html @@ -115,27 +115,27 @@

      Method Summary

      Modifier and Type
      Method
      Description
      -
      Optional<RegistryURI>
      -
      findRegistryUrlForOtherUrl(String url)
      -
      -
      Checks and processes a given resource URL to ensure it conforms to expected formats and corrections.
      -
      -
      static IdentifiersOrgURI
      -
      fixIdentifiersOrgUri(IdentifiersOrgURI uri)
      -
       
      -
      String
      -
      getNamespaceForPrefix(String prefix)
      -
       
      +
      static IdentifiersOrgURI
      +
      fixIdentifiersOrgUri(IdentifiersOrgURI uri)
      +
       
      String
      -
      getPatternByNamespaceName(String namespaceName)
      +
      getNamespaceForPrefix(String prefix)
       
      String
      -
      getPrefixByNamespaceName(String namespaceName)
      +
      getPatternByNamespaceName(String namespaceName)
       
      -
      boolean
      -
      isValid(String url)
      +
      String
      +
      getPrefixByNamespaceName(String namespaceName)
       
      boolean
      +
      isValid(String url)
      +
       
      +
      Optional<RegistryURI>
      +
      resolveBackwards(String url)
      +
      +
      Checks and processes a given resource URL to ensure it conforms to expected formats and corrections.
      +
      +
      boolean
      validRegistryUrlPrefix(RegistryURI uri)
      Existing models on BiGG and Biomodels use some namespaces that were removed from identifiers.org.
      @@ -202,15 +202,15 @@

      getPatternByNamespaceName

    • -
      -

      findRegistryUrlForOtherUrl

      -
      public Optional<RegistryURI> findRegistryUrlForOtherUrl(String url)
      +
      +

      resolveBackwards

      +
      public Optional<RegistryURI> resolveBackwards(String url)
      Checks and processes a given resource URL to ensure it conforms to expected formats and corrections. This method handles specific cases such as URLs containing "omim", "ncbigi", and "reactome". It also processes general identifiers.org URLs and other alternative formats.
      Specified by:
      -
      findRegistryUrlForOtherUrl in interface Registry
      +
      resolveBackwards in interface Registry
      Parameters:
      url - The URL to be checked and potentially modified.
      Returns:
      diff --git a/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURI.html b/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURI.html index 08ba3653..87d6d044 100644 --- a/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURI.html +++ b/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURI.html @@ -134,7 +134,7 @@

      Method Summary

      Method
      Description
      int
      -
      compareTo(@NotNull IdentifiersOrgURI uri)
      +
      compareTo(IdentifiersOrgURI uri)
       
      boolean
      equals(Object o)
      @@ -291,8 +291,7 @@

      hashCode

    • compareTo

      -
      public int compareTo(@NotNull - @NotNull IdentifiersOrgURI uri)
      +
      public int compareTo(IdentifiersOrgURI uri)
      Specified by:
      compareTo in interface Comparable<IdentifiersOrgURI>
      diff --git a/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURIUtils.html b/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURIUtils.html index 2e6393a4..c4ca29e1 100644 --- a/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURIUtils.html +++ b/docs/edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURIUtils.html @@ -104,10 +104,10 @@

      Method Summary

      Modifier and Type
      Method
      Description
      -
      static @NotNull String
      +
      static String
      addJavaRegexCaptureGroup(String pattern)
       
      -
      static @NotNull String
      +
      static String
      removeHttpProtocolFromUrl(String query)
       
      static String
      @@ -150,15 +150,13 @@

      Method Details

    • addJavaRegexCaptureGroup

      -
      @NotNull -public static @NotNull String addJavaRegexCaptureGroup(String pattern)
      +
      public static String addJavaRegexCaptureGroup(String pattern)

    • removeHttpProtocolFromUrl

      -
      @NotNull -public static @NotNull String removeHttpProtocolFromUrl(String query)
      +
      public static String removeHttpProtocolFromUrl(String query)
    • diff --git a/docs/edu/ucsd/sbrg/polishing/ReactionNamePatterns.html b/docs/edu/ucsd/sbrg/util/ReactionNamePatterns.html similarity index 89% rename from docs/edu/ucsd/sbrg/polishing/ReactionNamePatterns.html rename to docs/edu/ucsd/sbrg/util/ReactionNamePatterns.html index 3da1a789..85c524b9 100644 --- a/docs/edu/ucsd/sbrg/polishing/ReactionNamePatterns.html +++ b/docs/edu/ucsd/sbrg/util/ReactionNamePatterns.html @@ -5,7 +5,7 @@ ReactionNamePatterns (ModelPolisher 2.1 API) - + @@ -67,22 +67,22 @@
      -
      Package edu.ucsd.sbrg.polishing
      +
      Package edu.ucsd.sbrg.util

      Enum Class ReactionNamePatterns

      java.lang.Object -
      java.lang.Enum<ReactionNamePatterns> -
      edu.ucsd.sbrg.polishing.ReactionNamePatterns
      +
      java.lang.Enum<ReactionNamePatterns> +
      edu.ucsd.sbrg.util.ReactionNamePatterns
      All Implemented Interfaces:
      -
      Serializable, Comparable<ReactionNamePatterns>, Constable
      +
      Serializable, Comparable<ReactionNamePatterns>, Constable
      public enum ReactionNamePatterns -extends Enum<ReactionNamePatterns>
      +extends Enum<ReactionNamePatterns>
      Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings. Each enum constant represents a specific type of reaction and is associated with a regex pattern that matches reaction IDs corresponding to that type.
      @@ -153,12 +153,12 @@

      Method Summary

      Retrieves the compiled Pattern object for this enum constant.
      -
      static ReactionNamePatterns
      +
      static ReactionNamePatterns
      valueOf(String name)
      Returns the enum constant of this class with the specified name.
      -
      static ReactionNamePatterns[]
      +
      static ReactionNamePatterns[]
      values()
      Returns an array containing the constants of this enum class, in @@ -187,49 +187,49 @@

      Enum Constant Details

    • ATP_MAINTENANCE

      -
      public static final ReactionNamePatterns ATP_MAINTENANCE
      +
      public static final ReactionNamePatterns ATP_MAINTENANCE
      Pattern for ATP maintenance reactions, which are typically denoted by IDs containing 'ATPM' in any case.

    • BIOMASS_CASE_INSENSITIVE

      -
      public static final ReactionNamePatterns BIOMASS_CASE_INSENSITIVE
      +
      public static final ReactionNamePatterns BIOMASS_CASE_INSENSITIVE
      Case-insensitive pattern for biomass reactions, matching IDs that include the word 'biomass' in any case.

    • BIOMASS_CASE_SENSITIVE

      -
      public static final ReactionNamePatterns BIOMASS_CASE_SENSITIVE
      +
      public static final ReactionNamePatterns BIOMASS_CASE_SENSITIVE
      Case-sensitive pattern for biomass reactions, matching IDs that specifically contain 'BIOMASS'.

    • DEFAULT_FLUX_BOUND

      -
      public static final ReactionNamePatterns DEFAULT_FLUX_BOUND
      +
      public static final ReactionNamePatterns DEFAULT_FLUX_BOUND
      Pattern for default flux bound reactions, matching IDs that typically start with a prefix followed by 'default_'.

    • DEMAND_REACTION

      -
      public static final ReactionNamePatterns DEMAND_REACTION
      +
      public static final ReactionNamePatterns DEMAND_REACTION
      Pattern for demand reactions, identified by IDs starting with 'DM_'.

    • EXCHANGE_REACTION

      -
      public static final ReactionNamePatterns EXCHANGE_REACTION
      +
      public static final ReactionNamePatterns EXCHANGE_REACTION
      Pattern for exchange reactions, identified by IDs starting with 'EX_'.

    • SINK_REACTION

      -
      public static final ReactionNamePatterns SINK_REACTION
      +
      public static final ReactionNamePatterns SINK_REACTION
      Pattern for sink reactions, which are reactions that remove metabolites from the system, identified by IDs starting with 'SK_' or 'SINK_'.
      • @@ -244,7 +244,7 @@

      Method Details

    • values

      -
      public static ReactionNamePatterns[] values()
      +
      public static ReactionNamePatterns[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      @@ -256,7 +256,7 @@

      values

    • valueOf

      -
      public static ReactionNamePatterns valueOf(String name)
      +
      public static ReactionNamePatterns valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are diff --git a/docs/edu/ucsd/sbrg/util/SBMLFix.html b/docs/edu/ucsd/sbrg/util/SBMLFix.html deleted file mode 100644 index e35d0433..00000000 --- a/docs/edu/ucsd/sbrg/util/SBMLFix.html +++ /dev/null @@ -1,267 +0,0 @@ - - - - -SBMLFix (ModelPolisher 2.1 API) - - - - - - - - - - - - - - -
      - -
      -
      - -
      -
      Package edu.ucsd.sbrg.util
      -

      Class SBMLFix

      -
      -
      java.lang.Object -
      edu.ucsd.sbrg.util.SBMLFix
      -
      -
      -
      -
      public class SBMLFix -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 Summary

        -
        Constructors
        -
        -
        Constructor
        -
        Description
        -
        SBMLFix()
        -
         
        -
        -
        -
        • - -
      • -
        -

        Method Summary

        -
        -
        -
        -
        -
        Modifier and Type
        -
        Method
        -
        Description
        -
        static void
        -
        batchProcess(File input, - File output)
        -
         
        -
        static void
        -
        fixGroups(org.sbml.jsbml.Model model)
        -
        -
        Set group kind where required
        -
        -
        static void
        -
        fixObjective(String modelDescriptor, - org.sbml.jsbml.ListOf<org.sbml.jsbml.Reaction> listOfReactions, - org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlug)
        -
         
        -
        static void
        -
        fixObjective(String modelDescriptor, - org.sbml.jsbml.ListOf<org.sbml.jsbml.Reaction> listOfReactions, - org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlug, - List<Double> fluxCoefficients, - List<String> fluxObjectives)
        -
         
        -
        static void
        -
        fixObjective(String modelDescriptor, - org.sbml.jsbml.Model model)
        -
        -
        Check for missing objective function.
        -
        -
        static void
        -
        fixSBML(File in, - File out)
        -
         
        -
        static void
        -
        main(String[] args)
        -
         
        -
        -
        -
        -
        -

        Methods inherited from class java.lang.Object

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

        Constructor Details

        -
          -
        • -
          -

          SBMLFix

          -
          public SBMLFix()
          -
          -
          • -
        -
        -
        • - -
      • -
        -

        Method Details

        -
          -
        • -
          -

          batchProcess

          -
          public static void batchProcess(File input, - File output)
          -
          -
          • -
        • -
          -

          fixGroups

          -
          public static void fixGroups(org.sbml.jsbml.Model model)
          -
          Set group kind where required
          -
          -
          • -
        • -
          -

          fixObjective

          -
          public static void fixObjective(String modelDescriptor, - org.sbml.jsbml.Model model)
          -
          Check for missing objective function.
          -
          -
          Parameters:
          -
          modelDescriptor - this can be the path to the model file or some name that describes - this model.
          -
          -
          -
          • -
        • -
          -

          fixObjective

          -
          public static void fixObjective(String modelDescriptor, - org.sbml.jsbml.ListOf<org.sbml.jsbml.Reaction> listOfReactions, - org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlug)
          -
          -
          Parameters:
          -
          modelDescriptor - some descriptive String for the model, e.g., its id, the path to the - file, or any other meaningful information for users.
          -
          -
          -
          • -
        • -
          -

          fixObjective

          -
          public static void fixObjective(String modelDescriptor, - org.sbml.jsbml.ListOf<org.sbml.jsbml.Reaction> listOfReactions, - org.sbml.jsbml.ext.fbc.FBCModelPlugin fbcPlug, - List<Double> fluxCoefficients, - List<String> fluxObjectives)
          -
          -
          • -
        • -
          -

          fixSBML

          -
          public static void fixSBML(File in, - File out) - throws XMLStreamException, -IOException
          -
          -
          Throws:
          -
          XMLStreamException
          -
          IOException
          -
          -
          -
          • -
        • -
          -

          main

          -
          public static void main(String[] args)
          -
          -
          • -
        -
        -
        • -
      -
      - -
      -
      -
      - - diff --git a/docs/edu/ucsd/sbrg/util/GPRParser.html b/docs/edu/ucsd/sbrg/util/ext/fbc/GPRParser.html similarity index 95% rename from docs/edu/ucsd/sbrg/util/GPRParser.html rename to docs/edu/ucsd/sbrg/util/ext/fbc/GPRParser.html index 25bfb54e..8d2f9593 100644 --- a/docs/edu/ucsd/sbrg/util/GPRParser.html +++ b/docs/edu/ucsd/sbrg/util/ext/fbc/GPRParser.html @@ -5,21 +5,21 @@ GPRParser (ModelPolisher 2.1 API) - + - - - - - - + + + + + +
      • @@ -172,8 +172,8 @@

      Constructor Details

      • -

        SBMLUtils

        -
        public SBMLUtils()
        +

        GroupsUtils

        +
        public GroupsUtils()
      diff --git a/docs/edu/ucsd/sbrg/util/ext/groups/package-summary.html b/docs/edu/ucsd/sbrg/util/ext/groups/package-summary.html new file mode 100644 index 00000000..f565bee9 --- /dev/null +++ b/docs/edu/ucsd/sbrg/util/ext/groups/package-summary.html @@ -0,0 +1,83 @@ + + + + +edu.ucsd.sbrg.util.ext.groups (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      +
      +

      Package edu.ucsd.sbrg.util.ext.groups

      +
      +
      +
      package edu.ucsd.sbrg.util.ext.groups
      +
      +
        +
      • +
        +
        Classes
        +
        +
        Class
        +
        Description
        +
        GroupsUtils
        +
        +
        A collection of helpful functions for dealing with SBML data structures.
        +
        +
        +
        +
        • +
      +
      +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/util/ext/groups/package-tree.html b/docs/edu/ucsd/sbrg/util/ext/groups/package-tree.html new file mode 100644 index 00000000..961436a4 --- /dev/null +++ b/docs/edu/ucsd/sbrg/util/ext/groups/package-tree.html @@ -0,0 +1,70 @@ + + + + +edu.ucsd.sbrg.util.ext.groups Class Hierarchy (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
      + +
      +
      +
      +

      Hierarchy For Package edu.ucsd.sbrg.util.ext.groups

      +Package Hierarchies: + +
      +
      +

      Class Hierarchy

      + +
      +
      +
      +
      + + diff --git a/docs/edu/ucsd/sbrg/util/package-summary.html b/docs/edu/ucsd/sbrg/util/package-summary.html index 46e27f82..133b2d29 100644 --- a/docs/edu/ucsd/sbrg/util/package-summary.html +++ b/docs/edu/ucsd/sbrg/util/package-summary.html @@ -74,22 +74,13 @@

      Package edu.ucsd.sbrg.util<

    • -
      Classes
      +
      Enum Classes
      Class
      Description
      -
      GPRParser
      -
      -
      The GPRParser class provides methods to parse gene product associations (GPRs) from gene reaction rules - and integrate them into SBML models using JSBML.
      -
      -
      SBMLFix
      -
      -
      This is a stand-alone bug-fix program.
      -
      -
      SBMLUtils
      -
      -
      A collection of helpful functions for dealing with SBML data structures.
      +
      ReactionNamePatterns
      +
      +
      Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
      diff --git a/docs/edu/ucsd/sbrg/util/package-tree.html b/docs/edu/ucsd/sbrg/util/package-tree.html index 3068bb31..53f630b7 100644 --- a/docs/edu/ucsd/sbrg/util/package-tree.html +++ b/docs/edu/ucsd/sbrg/util/package-tree.html @@ -54,13 +54,15 @@

      Hierarchy For Package edu.ucsd.sbrg.util

    -

    Class Hierarchy

    +

    Enum Class Hierarchy

    diff --git a/docs/edu/ucsd/sbrg/ModelValidator.html b/docs/edu/ucsd/sbrg/validation/ModelValidator.html similarity index 82% rename from docs/edu/ucsd/sbrg/ModelValidator.html rename to docs/edu/ucsd/sbrg/validation/ModelValidator.html index 22a6725f..10ff04b5 100644 --- a/docs/edu/ucsd/sbrg/ModelValidator.html +++ b/docs/edu/ucsd/sbrg/validation/ModelValidator.html @@ -5,21 +5,21 @@ ModelValidator (ModelPolisher 2.1 API) - + - - - - - - + + + + + +
    diff --git a/docs/edu/ucsd/sbrg/validation/package-summary.html b/docs/edu/ucsd/sbrg/validation/package-summary.html new file mode 100644 index 00000000..25008a5a --- /dev/null +++ b/docs/edu/ucsd/sbrg/validation/package-summary.html @@ -0,0 +1,100 @@ + + + + +edu.ucsd.sbrg.validation (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
    + +
    +
    +
    +

    Package edu.ucsd.sbrg.validation

    +
    +
    +
    package edu.ucsd.sbrg.validation
    +
    + +
    +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/validation/package-tree.html b/docs/edu/ucsd/sbrg/validation/package-tree.html new file mode 100644 index 00000000..f98dcdea --- /dev/null +++ b/docs/edu/ucsd/sbrg/validation/package-tree.html @@ -0,0 +1,79 @@ + + + + +edu.ucsd.sbrg.validation Class Hierarchy (ModelPolisher 2.1 API) + + + + + + + + + + + + + + +
    + +
    +
    +
    +

    Hierarchy For Package edu.ucsd.sbrg.validation

    +Package Hierarchies: + +
    +
    +

    Class Hierarchy

    + +
    +
    +
    +
    + + diff --git a/docs/element-list b/docs/element-list index 05f0b608..6e80cf0a 100644 --- a/docs/element-list +++ b/docs/element-list @@ -7,6 +7,9 @@ edu.ucsd.sbrg.db edu.ucsd.sbrg.db.adb edu.ucsd.sbrg.db.bigg edu.ucsd.sbrg.eco +edu.ucsd.sbrg.fixing +edu.ucsd.sbrg.fixing.ext.fbc +edu.ucsd.sbrg.fixing.ext.groups edu.ucsd.sbrg.io edu.ucsd.sbrg.io.parsers.cobra edu.ucsd.sbrg.io.parsers.json @@ -19,3 +22,6 @@ edu.ucsd.sbrg.resolver edu.ucsd.sbrg.resolver.identifiersorg edu.ucsd.sbrg.resolver.identifiersorg.mapping edu.ucsd.sbrg.util +edu.ucsd.sbrg.util.ext.fbc +edu.ucsd.sbrg.util.ext.groups +edu.ucsd.sbrg.validation diff --git a/docs/index-all.html b/docs/index-all.html index a7de3111..1985e909 100644 --- a/docs/index-all.html +++ b/docs/index-all.html @@ -49,7 +49,7 @@

    Index

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

    A

    A - Enum constant in enum class edu.ucsd.sbrg.io.parsers.cobra.ModelField
    @@ -58,23 +58,23 @@

    A

    0 or g(μ) ⋅ A ⋅ v + B ⋅ v = 0 with g(μ) being some continuous nonlinear function of μ; -
    AbstractADBAnnotator<SBMLElement> - Class in edu.ucsd.sbrg.annotation.adb
    +
    AbstractADBAnnotator - Class in edu.ucsd.sbrg.annotation.adb
     
    AbstractADBAnnotator(AnnotateDB, ADBAnnotationParameters) - Constructor for class edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator
     
    -
    AbstractAnnotator<SBMLElement> - Class in edu.ucsd.sbrg.annotation
    +
    AbstractAnnotator - Class in edu.ucsd.sbrg.annotation
     
    AbstractAnnotator() - Constructor for class edu.ucsd.sbrg.annotation.AbstractAnnotator
     
    AbstractAnnotator(List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.annotation.AbstractAnnotator
     
    -
    AbstractBiGGAnnotator<SBMLElement> - Class in edu.ucsd.sbrg.annotation.bigg
    +
    AbstractBiGGAnnotator - Class in edu.ucsd.sbrg.annotation.bigg
     
    AbstractBiGGAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator
     
    AbstractBiGGAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator
     
    -
    AbstractPolisher<SBMLElement> - Class in edu.ucsd.sbrg.polishing
    +
    AbstractPolisher - Class in edu.ucsd.sbrg.polishing
     
    AbstractPolisher(PolishingParameters, Registry) - Constructor for class edu.ucsd.sbrg.polishing.AbstractPolisher
     
    @@ -106,10 +106,15 @@

    A

     
    add(String, String) - Method in class edu.ucsd.sbrg.io.parsers.json.mapping.Compartments
     
    -
    ADD_ADB_ANNOTATIONS - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    ADD_ADB_ANNOTATIONS - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    If set to true, annotations will be added to species and reactions from AnnotateDB also.
    +
    ADD_GENERIC_TERMS - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    +
    +
    Set this option to true if generic top-level annotations, such as 'process' + should not be applied.
    +
    addADBAnnotations - Variable in class edu.ucsd.sbrg.parameters.ADBAnnotationParameters
     
    addADBAnnotations() - Method in class edu.ucsd.sbrg.parameters.ADBAnnotationParameters
    @@ -122,10 +127,20 @@

    A

    addBQB_IS_AnnotationsFromADB(Annotation, String, BiGGId) - Method in class edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator
     
    +
    addChild(Node) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    +
    addChild(Term) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    addCopyrightToSplashScreen() - Method in class edu.ucsd.sbrg.ModelPolisherCLILauncher
     
    +
    addGenericTerms() - Method in class edu.ucsd.sbrg.parameters.SBOParameters
    +
     
    addJavaRegexCaptureGroup(String) - Static method in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrgURIUtils
     
    +
    addParent(Node) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    +
    addParent(Term) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    addResource(String, CVTerm, String) - Method in class edu.ucsd.sbrg.io.parsers.cobra.ReactionParser
    Tries to update a resource according to pre-defined rules.
    @@ -150,7 +165,7 @@

    A

    Delegates annotation processing for all chemical species contained in the Model.
    -
    annotate(List<SBMLElement>) - Method in class edu.ucsd.sbrg.annotation.AbstractAnnotator
    +
    annotate(List<SBMLElement>) - Method in interface edu.ucsd.sbrg.annotation.IAnnotateSBases
     
    annotate(Compartment) - Method in class edu.ucsd.sbrg.annotation.bigg.BiGGCompartmentsAnnotator
    @@ -187,11 +202,9 @@

    A

    This method annotates a species with various details fetched from the BiGG Knowledgebase.
    -
    annotate(SBMLElement) - Method in class edu.ucsd.sbrg.annotation.AbstractAnnotator
    +
    annotate(SBMLElement) - Method in interface edu.ucsd.sbrg.annotation.IAnnotateSBases
     
    -
    annotate(SBMLElement) - Method in class edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator
    -
     
    -
    ANNOTATE_WITH_BIGG - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    ANNOTATE_WITH_BIGG - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    If set to true, the model will be annotated with data from BiGG Models database.
    @@ -244,17 +257,13 @@

    A

     
    AnnotationsSorter() - Constructor for class edu.ucsd.sbrg.annotation.AnnotationsSorter
     
    -
    appendAttribute(StringBuilder, String, String) - Static method in class edu.ucsd.sbrg.XHTMLBuilder
    -
     
    -
    appendAttribute(StringBuilder, Map.Entry<String, String>) - Static method in class edu.ucsd.sbrg.XHTMLBuilder
    -
     
    archiveFile() - Method in exception edu.ucsd.sbrg.io.ModelWriterException
     
    asString(Array) - Static method in class edu.ucsd.sbrg.io.parsers.cobra.COBRAUtils
     
    asString(Array, String, int) - Static method in class edu.ucsd.sbrg.io.parsers.cobra.COBRAUtils
     
    -
    ATP_MAINTENANCE - Enum constant in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    ATP_MAINTENANCE - Enum constant in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Pattern for ATP maintenance reactions, which are typically denoted by IDs containing 'ATPM' in any case.
    @@ -276,8 +285,6 @@

    B

    0 or g(μ) ⋅ A ⋅ v + B ⋅ v = 0 with g(μ) being some continuous nonlinear function of μ; -
    batchProcess(File, File) - Static method in class edu.ucsd.sbrg.util.SBMLFix
    -
     
    bigg - Variable in class edu.ucsd.sbrg.annotation.bigg.AbstractBiGGAnnotator
     
    BIGG_GENE_ID_PATTERN - Static variable in class edu.ucsd.sbrg.annotation.bigg.fbc.BiGGGeneProductAnnotator
    @@ -310,7 +317,7 @@

    B

     
    BiGGCompartmentsAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.annotation.bigg.BiGGCompartmentsAnnotator
     
    -
    BiGGCVTermAnnotator<T extends org.sbml.jsbml.AbstractSBase> - Class in edu.ucsd.sbrg.annotation.bigg
    +
    BiGGCVTermAnnotator<T extends org.sbml.jsbml.SBase> - Class in edu.ucsd.sbrg.annotation.bigg
    Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
    @@ -411,11 +418,11 @@

    B

     
    BiGGSpeciesAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.annotation.bigg.BiGGSpeciesAnnotator
     
    -
    BIOMASS_CASE_INSENSITIVE - Enum constant in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    BIOMASS_CASE_INSENSITIVE - Enum constant in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Case-insensitive pattern for biomass reactions, matching IDs that include the word 'biomass' in any case.
    -
    BIOMASS_CASE_SENSITIVE - Enum constant in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    BIOMASS_CASE_SENSITIVE - Enum constant in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Case-sensitive pattern for biomass reactions, matching IDs that specifically contain 'BIOMASS'.
    @@ -427,17 +434,13 @@

    C

    The objective function vector for max(c' ⋅ v) for corresponding reactions.
    -
    CHECK_MASS_BALANCE - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    CHECK_MASS_BALANCE - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    When set to true, the mass balance of each reaction will be checked where possible.
    CHECK_MASS_BALANCE - Static variable in class edu.ucsd.sbrg.parameters.ReactionPolishingParameters
     
    -
    checkCompartment(Species) - Method in class edu.ucsd.sbrg.polishing.SpeciesPolisher
    -
    -
    Checks and sets the compartment for a given species.
    -
    checkCreateOutDir(File) - Static method in class edu.ucsd.sbrg.io.SBMLFileUtils
    Creates output directory or output parent directory, if necessary
    @@ -471,7 +474,7 @@

    C

     
    Column() - Constructor for class edu.ucsd.sbrg.db.bigg.BiGGDBContract.Constants.Column
     
    -
    COMBINE - Enum constant in enum class edu.ucsd.sbrg.ModelPolisherOptions.OutputType
    +
    COMBINE - Enum constant in enum class edu.ucsd.sbrg.parameters.ModelPolisherOptions.OutputType
     
    COMBINE_SPECIFICATION - Static variable in class edu.ucsd.sbrg.io.CombineArchive
     
    @@ -493,6 +496,10 @@

    C

    compareTo(IdentifiersOrgURI) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrgURI
     
    +
    CompartmentFixer - Class in edu.ucsd.sbrg.fixing
    +
     
    +
    CompartmentFixer() - Constructor for class edu.ucsd.sbrg.fixing.CompartmentFixer
    +
     
    compartmentId - Variable in class edu.ucsd.sbrg.db.bigg.BiGGDB.ForeignReaction
     
    compartmentName - Variable in class edu.ucsd.sbrg.db.bigg.BiGGDB.ForeignReaction
    @@ -516,12 +523,10 @@

    C

     
    Constants() - Constructor for class edu.ucsd.sbrg.db.bigg.BiGGDBContract.Constants
     
    -
    convertAssociationsToFBCV2(Reaction, boolean) - Method in class edu.ucsd.sbrg.polishing.GeneProductAssociationsProcessor
    +
    convertAssociationsToFBCV2(Reaction, boolean) - Method in class edu.ucsd.sbrg.polishing.fbc.GeneProductAssociationsProcessor
    Converts gene product associations from a given reaction to the FBC v2 format.
    -
    convertDocument(SBMLDocument) - Static method in class edu.ucsd.sbrg.io.parsers.json.JSONConverter
    -
     
    convertGene(GeneProduct) - Static method in class edu.ucsd.sbrg.io.parsers.json.JSONConverter
     
    convertGenes(Model) - Static method in class edu.ucsd.sbrg.io.parsers.json.JSONConverter
    @@ -536,39 +541,31 @@

    C

     
    convertReactions(Model) - Static method in class edu.ucsd.sbrg.io.parsers.json.JSONConverter
     
    -
    convertToAssociation(ASTNode, String, Model, boolean) - Static method in class edu.ucsd.sbrg.util.GPRParser
    +
    convertToAssociation(ASTNode, String, Model, boolean) - Static method in class edu.ucsd.sbrg.util.ext.fbc.GPRParser
    Converts an ASTNode representing a gene product association into an Association object.
    createGeneId(String) - Static method in class edu.ucsd.sbrg.db.bigg.BiGGId
    -
    Creates a BiGG ID for a gene using the default correction behavior.
    -
    -
    createGeneId(String, boolean) - Static method in class edu.ucsd.sbrg.db.bigg.BiGGId
    -
    Creates a BiGG ID for a gene, with an option to correct the ID to conform to BiGG standards.
    -
    createGPR(String, String, Model) - Static method in class edu.ucsd.sbrg.util.GPRParser
    +
    createGPR(String, String, Model) - Static method in class edu.ucsd.sbrg.util.ext.fbc.GPRParser
    Creates a GeneProductRef instance for a given identifier within a specific reaction context in the model.
    createMetaboliteId(String) - Static method in class edu.ucsd.sbrg.db.bigg.BiGGId
    -
    Creates a BiGG ID for a metabolite with default correction behavior.
    -
    -
    createMetaboliteId(String, boolean) - Static method in class edu.ucsd.sbrg.db.bigg.BiGGId
    -
    Creates a BiGG ID for a metabolite based on the provided string identifier.
    createReactionId(String) - Static method in class edu.ucsd.sbrg.db.bigg.BiGGId
    Creates a BiGG ID for a reaction based on the provided string identifier.
    -
    createReactionId(String, boolean, boolean) - Static method in class edu.ucsd.sbrg.db.bigg.BiGGId
    +
    createReactionId(String, boolean) - Static method in class edu.ucsd.sbrg.db.bigg.BiGGId
    Creates a BiGG ID for a reaction based on the provided string identifier.
    -
    createSubsystemLink(Reaction, Member) - Static method in class edu.ucsd.sbrg.util.SBMLUtils
    +
    createSubsystemLink(Reaction, Member) - Static method in class edu.ucsd.sbrg.util.ext.groups.GroupsUtils
    Establishes a link between a reaction and a subsystem member by setting the member's reference to the reaction.
    @@ -601,6 +598,8 @@

    D

    DAG - Class in edu.ucsd.sbrg.eco
     
    +
    DAG(Term) - Constructor for class edu.ucsd.sbrg.eco.DAG
    +
     
    data() - Method in exception edu.ucsd.sbrg.annotation.bigg.BiGGAnnotationException
     
    DATA - Enum constant in enum class edu.ucsd.sbrg.reporting.ReportType
    @@ -625,7 +624,7 @@

    D

     
    DBParameters(String, String, String, Integer, String) - Constructor for class edu.ucsd.sbrg.parameters.DBParameters
     
    -
    DEFAULT_FLUX_BOUND - Enum constant in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    DEFAULT_FLUX_BOUND - Enum constant in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Pattern for default flux bound reactions, matching IDs that typically start with a prefix followed by 'default_'.
    @@ -635,7 +634,7 @@

    D

     
    DeleteOnCloseFileInputStream(String) - Constructor for class edu.ucsd.sbrg.io.DeleteOnCloseFileInputStream
     
    -
    DEMAND_REACTION - Enum constant in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    DEMAND_REACTION - Enum constant in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Pattern for demand reactions, identified by IDs starting with 'DM_'.
    @@ -645,7 +644,7 @@

    D

    diffReport(String, Object, Object) - Method in class edu.ucsd.sbrg.annotation.AbstractAnnotator
     
    -
    diffReport(String, Object, Object) - Method in class edu.ucsd.sbrg.polishing.AbstractPolisher
    +
    diffReport(String, Object, Object) - Method in interface edu.ucsd.sbrg.reporting.IReportDiffs
     
    disabled - Enum constant in enum class edu.ucsd.sbrg.io.parsers.cobra.ModelField
    @@ -653,12 +652,12 @@

    D

    doc() - Method in exception edu.ucsd.sbrg.io.ModelWriterException
     
    -
    DOCUMENT_NOTES_FILE - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    DOCUMENT_NOTES_FILE - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    This XHTML file defines alternative document notes and makes them exchangeable.
    -
    DOCUMENT_TITLE_PATTERN - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    DOCUMENT_TITLE_PATTERN - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    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 @@ -679,9 +678,9 @@

    E

    The Enzyme Commission codes for the reactions.
    -
    ECOparser - Class in edu.ucsd.sbrg.eco
    +
    ECOParserCLILauncher - Class in edu.ucsd.sbrg
     
    -
    ECOparser() - Constructor for class edu.ucsd.sbrg.eco.ECOparser
    +
    ECOParserCLILauncher() - Constructor for class edu.ucsd.sbrg.ECOParserCLILauncher
     
    edu.ucsd.sbrg - package edu.ucsd.sbrg
     
    @@ -701,6 +700,12 @@

    E

     
    edu.ucsd.sbrg.eco - package edu.ucsd.sbrg.eco
     
    +
    edu.ucsd.sbrg.fixing - package edu.ucsd.sbrg.fixing
    +
     
    +
    edu.ucsd.sbrg.fixing.ext.fbc - package edu.ucsd.sbrg.fixing.ext.fbc
    +
     
    +
    edu.ucsd.sbrg.fixing.ext.groups - package edu.ucsd.sbrg.fixing.ext.groups
    +
     
    edu.ucsd.sbrg.io - package edu.ucsd.sbrg.io
     
    edu.ucsd.sbrg.io.parsers.cobra - package edu.ucsd.sbrg.io.parsers.cobra
    @@ -725,12 +730,20 @@

    E

     
    edu.ucsd.sbrg.util - package edu.ucsd.sbrg.util
     
    +
    edu.ucsd.sbrg.util.ext.fbc - package edu.ucsd.sbrg.util.ext.fbc
    +
     
    +
    edu.ucsd.sbrg.util.ext.groups - package edu.ucsd.sbrg.util.ext.groups
    +
     
    +
    edu.ucsd.sbrg.validation - package edu.ucsd.sbrg.validation
    +
     
    equals(Object) - Method in class edu.ucsd.sbrg.db.bigg.BiGGId
     
    equals(Object) - Method in record class edu.ucsd.sbrg.db.bigg.Publication
    Indicates whether some other object is "equal to" this one.
    +
    equals(Object) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    equals(Object) - Method in class edu.ucsd.sbrg.polishing.AbstractPolisher
     
    equals(Object) - Method in record class edu.ucsd.sbrg.reporting.ProgressFinalization
    @@ -747,7 +760,7 @@

    E

    equals(Object) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrgURI
     
    -
    EXCHANGE_REACTION - Enum constant in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    EXCHANGE_REACTION - Enum constant in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Pattern for exchange reactions, identified by IDs starting with 'EX_'.
    @@ -762,7 +775,13 @@

    F

    FBCPolisher - Class in edu.ucsd.sbrg.polishing.fbc
     
    -
    FBCPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.polishing.fbc.FBCPolisher
    +
    FBCPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.polishing.fbc.FBCPolisher
    +
     
    +
    FBCReactionPolisher - Class in edu.ucsd.sbrg.polishing.fbc
    +
     
    +
    FBCReactionPolisher(FBCModelPlugin, PolishingParameters, SBOParameters, Registry) - Constructor for class edu.ucsd.sbrg.polishing.fbc.FBCReactionPolisher
    +
     
    +
    FBCReactionPolisher(FBCModelPlugin, PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.polishing.fbc.FBCReactionPolisher
     
    findBiGGId(GeneProduct) - Method in class edu.ucsd.sbrg.annotation.bigg.fbc.BiGGGeneProductAnnotator
    @@ -782,40 +801,56 @@

    F

    Abstract method to check the validity of a BiGG ID.
    -
    findRegistryUrlForOtherUrl(String) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrg
    +
    findChild(Node, Term) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    +
    findParent(Node, Term) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    +
    findTerm(Term) - Method in class edu.ucsd.sbrg.eco.Node
    -
    Checks and processes a given resource URL to ensure it conforms to expected formats and corrections.
    +
    Returns the Node containing the specified Term or null, if not present
    -
    findRegistryUrlForOtherUrl(String) - Method in interface edu.ucsd.sbrg.resolver.Registry
    -
     
    finish(ProgressFinalization) - Method in class edu.ucsd.sbrg.reporting.PolisherProgressBar
     
    finish(ProgressFinalization) - Method in interface edu.ucsd.sbrg.reporting.ProgressObserver
     
    -
    fixGroups(Model) - Static method in class edu.ucsd.sbrg.util.SBMLFix
    -
    -
    Set group kind where required
    -
    -
    fixIdentifiersOrgUri(IdentifiersOrgURI) - Static method in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrg
    +
    fix(List<SpeciesReference>) - Method in interface edu.ucsd.sbrg.fixing.IFixSpeciesReferences
    +
     
    +
    fix(List<SBMLElement>) - Method in interface edu.ucsd.sbrg.fixing.IFixSBases
    +
     
    +
    fix(Compartment, int) - Method in class edu.ucsd.sbrg.fixing.CompartmentFixer
    +
     
    +
    fix(ListOfObjectives, int) - Method in class edu.ucsd.sbrg.fixing.ext.fbc.ListOfObjectivesFixer
    +
     
    +
    fix(Model, int) - Method in class edu.ucsd.sbrg.fixing.ModelFixer
    +
     
    +
    fix(Reaction, int) - Method in class edu.ucsd.sbrg.fixing.ReactionFixer
    +
     
    +
    fix(SBMLDocument, int) - Method in class edu.ucsd.sbrg.fixing.SBMLFixer
     
    -
    fixObjective(String, ListOf<Reaction>, FBCModelPlugin) - Static method in class edu.ucsd.sbrg.util.SBMLFix
    +
    fix(Species, int) - Method in class edu.ucsd.sbrg.fixing.SpeciesFixer
     
    -
    fixObjective(String, ListOf<Reaction>, FBCModelPlugin, List<Double>, List<String>) - Static method in class edu.ucsd.sbrg.util.SBMLFix
    +
    fix(SpeciesReference) - Method in interface edu.ucsd.sbrg.fixing.IFixSpeciesReferences
     
    -
    fixObjective(String, Model) - Static method in class edu.ucsd.sbrg.util.SBMLFix
    +
    fix(SpeciesReference) - Method in class edu.ucsd.sbrg.fixing.SpeciesReferenceFixer
    +
     
    +
    fix(SBMLElement, int) - Method in interface edu.ucsd.sbrg.fixing.IFixSBases
    +
     
    +
    fixGroups(Model) - Static method in class edu.ucsd.sbrg.fixing.ext.groups.GroupsFixer
    -
    Check for missing objective function.
    +
    Set group kind where required
    -
    fixSBML(File, File) - Static method in class edu.ucsd.sbrg.util.SBMLFix
    +
    fixIdentifiersOrgUri(IdentifiersOrgURI) - Static method in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrg
     
    -
    FLUX_COEFFICIENTS - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    fixObjective(String, ListOf<Reaction>, FBCModelPlugin, List<Double>, List<String>) - Static method in class edu.ucsd.sbrg.fixing.ext.fbc.ObjectiveFixer
     
    FLUX_COEFFICIENTS - Static variable in class edu.ucsd.sbrg.parameters.FluxObjectivesPolishingParameters
     
    -
    FLUX_OBJECTIVES - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    FLUX_COEFFICIENTS - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
     
    FLUX_OBJECTIVES - Static variable in class edu.ucsd.sbrg.parameters.FluxObjectivesPolishingParameters
     
    +
    FLUX_OBJECTIVES - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    +
     
    fluxCoefficients - Variable in class edu.ucsd.sbrg.parameters.FluxObjectivesPolishingParameters
     
    fluxCoefficients() - Method in class edu.ucsd.sbrg.parameters.FluxObjectivesPolishingParameters
    @@ -829,12 +864,6 @@

    F

     
    fluxObjectives() - Method in class edu.ucsd.sbrg.parameters.FluxObjectivesPolishingParameters
     
    -
    FluxObjectivesPolisher - Class in edu.ucsd.sbrg.polishing.fbc
    -
     
    -
    FluxObjectivesPolisher(FBCModelPlugin, PolishingParameters, Registry) - Constructor for class edu.ucsd.sbrg.polishing.fbc.FluxObjectivesPolisher
    -
     
    -
    FluxObjectivesPolisher(FBCModelPlugin, PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.polishing.fbc.FluxObjectivesPolisher
    -
     
    fluxObjectivesPolishingParameters() - Method in class edu.ucsd.sbrg.parameters.PolishingParameters
     
    FluxObjectivesPolishingParameters - Class in edu.ucsd.sbrg.parameters
    @@ -868,14 +897,12 @@

    G

     
    GeneParser(FBCModelPlugin, int) - Constructor for class edu.ucsd.sbrg.io.parsers.cobra.GeneParser
     
    -
    GeneProductAssociationsProcessor - Class in edu.ucsd.sbrg.polishing
    +
    GeneProductAssociationsProcessor - Class in edu.ucsd.sbrg.polishing.fbc
     
    -
    GeneProductAssociationsProcessor() - Constructor for class edu.ucsd.sbrg.polishing.GeneProductAssociationsProcessor
    +
    GeneProductAssociationsProcessor() - Constructor for class edu.ucsd.sbrg.polishing.fbc.GeneProductAssociationsProcessor
     
    GeneProductsPolisher - Class in edu.ucsd.sbrg.polishing.fbc
    -
    -
    This class is responsible for polishing GeneProduct instances by processing their annotations and adjusting their identifiers and names.
    -
    +
     
    GeneProductsPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.polishing.fbc.GeneProductsPolisher
     
    genes - Enum constant in enum class edu.ucsd.sbrg.io.parsers.cobra.ModelField
    @@ -949,6 +976,8 @@

    G

    Retrieves the unique chemical formula for a given component within a specific compartment.
    +
    getChildren() - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    getCitation(boolean) - Method in class edu.ucsd.sbrg.ModelPolisherCLILauncher
     
    getCmdLineOptions() - Method in class edu.ucsd.sbrg.ModelPolisherCLILauncher
    @@ -971,7 +1000,7 @@

    G

    Retrieves the type of the component associated with the given BiGG ID from the database.
    -
    getConfidenceScoreForTerm(String) - Static method in class edu.ucsd.sbrg.eco.ECOparser
    +
    getConfidenceScoreForTerm(String) - Static method in class edu.ucsd.sbrg.ECOParserCLILauncher
     
    getConnection() - Method in class edu.ucsd.sbrg.db.PostgresConnectionPool
     
    @@ -998,11 +1027,11 @@

    G

     
    getDescription() - Method in class edu.ucsd.sbrg.resolver.identifiersorg.mapping.Resource
     
    -
    getECOTermFromScore(int) - Static method in class edu.ucsd.sbrg.eco.ECOparser
    +
    getECOTermFromScore(int) - Static method in class edu.ucsd.sbrg.ECOParserCLILauncher
     
    getErrorMessage() - Method in class edu.ucsd.sbrg.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
     
    -
    getFileExtension() - Method in enum class edu.ucsd.sbrg.ModelPolisherOptions.OutputType
    +
    getFileExtension() - Method in enum class edu.ucsd.sbrg.parameters.ModelPolisherOptions.OutputType
     
    getFileType(File) - Static method in class edu.ucsd.sbrg.io.SBMLFileUtils
    @@ -1058,14 +1087,8 @@

    G

     
    getJSONDocument(SBMLDocument) - Static method in class edu.ucsd.sbrg.io.parsers.json.JSONConverter
     
    -
    getJSONGene(GeneProduct) - Static method in class edu.ucsd.sbrg.io.parsers.json.JSONConverter
    -
     
    -
    getJSONMetabolite(Species) - Static method in class edu.ucsd.sbrg.io.parsers.json.JSONConverter
    -
     
    getJSONModel(Model) - Static method in class edu.ucsd.sbrg.io.parsers.json.JSONConverter
     
    -
    getJSONReaction(Reaction) - Static method in class edu.ucsd.sbrg.io.parsers.json.JSONConverter
    -
     
    getLabel(GeneProduct, BiGGId) - Method in class edu.ucsd.sbrg.annotation.bigg.fbc.BiGGGeneProductAnnotator
    Retrieves the label for a gene product based on the provided BiGGId.
    @@ -1135,12 +1158,14 @@

    G

    Fix output file name to contain xml extension
    -
    getPattern() - Method in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    getParents() - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    +
    getPattern() - Method in class edu.ucsd.sbrg.resolver.identifiersorg.mapping.Namespace
    +
     
    +
    getPattern() - Method in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Retrieves the compiled Pattern object for this enum constant.
    -
    getPattern() - Method in class edu.ucsd.sbrg.resolver.identifiersorg.mapping.Namespace
    -
     
    getPatternByNamespaceName(String) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrg
     
    getPatternByNamespaceName(String) - Method in interface edu.ucsd.sbrg.resolver.Registry
    @@ -1185,7 +1210,7 @@

    G

    Retrieves a set of resource URLs for a given BiGG ID, optionally filtering to include only those containing 'identifiers.org'.
    -
    getResourceURL(String) - Static method in class edu.ucsd.sbrg.eco.ECOparser
    +
    getResourceURL(String) - Static method in class edu.ucsd.sbrg.ECOParserCLILauncher
     
    getRoot() - Method in class edu.ucsd.sbrg.eco.DAG
     
    @@ -1209,6 +1234,8 @@

    G

    Retrieves the taxonomic identifier (taxon ID) for a given model based on its abbreviation.
    +
    getTerm() - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    getTissueCode() - Method in class edu.ucsd.sbrg.db.bigg.BiGGId
     
    getUpperBound() - Method in class edu.ucsd.sbrg.io.parsers.json.mapping.Reaction
    @@ -1231,18 +1258,28 @@

    G

     
    getYearWhenProjectWasStarted() - Method in class edu.ucsd.sbrg.ModelPolisherCLILauncher
     
    -
    GPRParser - Class in edu.ucsd.sbrg.util
    +
    GPRParser - Class in edu.ucsd.sbrg.util.ext.fbc
    The GPRParser class provides methods to parse gene product associations (GPRs) from gene reaction rules and integrate them into SBML models using JSBML.
    -
    GPRParser() - Constructor for class edu.ucsd.sbrg.util.GPRParser
    +
    GPRParser() - Constructor for class edu.ucsd.sbrg.util.ext.fbc.GPRParser
     
    groupAndSortAnnotations(SBase) - Method in class edu.ucsd.sbrg.annotation.AnnotationsSorter
    Recursively goes through all annotations in the given SBase and alphabetically sort annotations after grouping them by CVTerm.Qualifier.
    +
    GroupsFixer - Class in edu.ucsd.sbrg.fixing.ext.groups
    +
     
    +
    GroupsFixer() - Constructor for class edu.ucsd.sbrg.fixing.ext.groups.GroupsFixer
    +
     
    +
    GroupsUtils - Class in edu.ucsd.sbrg.util.ext.groups
    +
    +
    A collection of helpful functions for dealing with SBML data structures.
    +
    +
    GroupsUtils() - Constructor for class edu.ucsd.sbrg.util.ext.groups.GroupsUtils
    +
     
    GROWTH_UNIT_ID - Static variable in class edu.ucsd.sbrg.polishing.UnitPolisher
     
    GROWTH_UNIT_NAME - Static variable in class edu.ucsd.sbrg.polishing.UnitPolisher
    @@ -1260,6 +1297,8 @@

    H

    Returns a hash code value for this object.
    +
    hashCode() - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    hashCode() - Method in class edu.ucsd.sbrg.polishing.AbstractPolisher
     
    hashCode() - Method in record class edu.ucsd.sbrg.reporting.ProgressFinalization
    @@ -1285,6 +1324,8 @@

    H

    I

    +
    IAnnotateSBases<SBMLElement extends org.sbml.jsbml.SBase> - Interface in edu.ucsd.sbrg.annotation
    +
     
    IDENTIFIERS_ORG_ID_PATTERN - Static variable in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrgURI
     
    IdentifiersOrg - Class in edu.ucsd.sbrg.resolver.identifiersorg
    @@ -1314,7 +1355,11 @@

    I

     
    IdentifiersOrgURIUtils() - Constructor for class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrgURIUtils
     
    -
    INCLUDE_ANY_URI - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    IFixSBases<SBMLElement extends org.sbml.jsbml.SBase> - Interface in edu.ucsd.sbrg.fixing
    +
     
    +
    IFixSpeciesReferences - Interface in edu.ucsd.sbrg.fixing
    +
     
    +
    INCLUDE_ANY_URI - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    This switch allows users to specify if also those database cross-links should be extracted from BiGG Models database for which currently no entry @@ -1346,7 +1391,7 @@

    I

     
    initialize(ProgressInitialization) - Method in interface edu.ucsd.sbrg.reporting.ProgressObserver
     
    -
    input() - Method in exception edu.ucsd.sbrg.io.ModelReaderException
    +
    input() - Method in class edu.ucsd.sbrg.io.ModelReaderException
     
    input() - Method in class edu.ucsd.sbrg.parameters.CommandLineParameters
     
    @@ -1360,6 +1405,22 @@

    I

     
    IOOptions - Interface in edu.ucsd.sbrg.io
     
    +
    IPolishAnnotations - Interface in edu.ucsd.sbrg.polishing
    +
     
    +
    IPolishSBaseAttributes - Interface in edu.ucsd.sbrg.polishing
    +
     
    +
    IPolishSBases<SBMLElement extends org.sbml.jsbml.SBase> - Interface in edu.ucsd.sbrg.polishing
    +
     
    +
    IPolishSpeciesReferences - Interface in edu.ucsd.sbrg.polishing
    +
     
    +
    IProcessNotes - Interface in edu.ucsd.sbrg.annotation
    +
     
    +
    IReadModelsFromFile - Interface in edu.ucsd.sbrg.io
    +
     
    +
    IReportDiffs - Interface in edu.ucsd.sbrg.reporting
    +
     
    +
    IReportStatus - Interface in edu.ucsd.sbrg.reporting
    +
     
    isBoundSet(Parameter) - Method in class edu.ucsd.sbrg.polishing.fbc.StrictnessPredicate
     
    isCompartment(String) - Method in class edu.ucsd.sbrg.db.bigg.BiGGDB
    @@ -1405,10 +1466,14 @@

    I

     
    isValid(String) - Method in interface edu.ucsd.sbrg.resolver.Registry
     
    +
    IWriteModels - Interface in edu.ucsd.sbrg.io
    +
     
    +
    IWriteModelsToFile - Interface in edu.ucsd.sbrg.io
    +
     

    J

    -
    JSON - Enum constant in enum class edu.ucsd.sbrg.ModelPolisherOptions.OutputType
    +
    JSON - Enum constant in enum class edu.ucsd.sbrg.parameters.ModelPolisherOptions.OutputType
     
    JSON_FILE - Enum constant in enum class edu.ucsd.sbrg.io.SBMLFileUtils.FileType
     
    @@ -1427,24 +1492,28 @@

    L

    Lower reaction flux bounds for corresponding reactions
    +
    linkNodes(Node, Node) - Static method in class edu.ucsd.sbrg.eco.Node
    +
     
    +
    ListOfObjectivesFixer - Class in edu.ucsd.sbrg.fixing.ext.fbc
    +
     
    +
    ListOfObjectivesFixer(PolishingParameters, FBCModelPlugin) - Constructor for class edu.ucsd.sbrg.fixing.ext.fbc.ListOfObjectivesFixer
    +
     
    Location - Class in edu.ucsd.sbrg.resolver.identifiersorg.mapping
     
    Location() - Constructor for class edu.ucsd.sbrg.resolver.identifiersorg.mapping.Location
     
    -
    logException(Exception) - Static method in class edu.ucsd.sbrg.io.parsers.cobra.COBRAUtils
    -
     

    M

    -
    main(String[]) - Static method in class edu.ucsd.sbrg.eco.ECOparser
    +
    main(String[]) - Static method in class edu.ucsd.sbrg.ECOParserCLILauncher
     
    main(String[]) - Static method in class edu.ucsd.sbrg.ModelPolisherCLILauncher
    Entry point
    -
    main(String...) - Static method in class edu.ucsd.sbrg.SBMLValidator
    +
    main(String[]) - Static method in class edu.ucsd.sbrg.SBMLFixerCLILauncher
     
    -
    main(String[]) - Static method in class edu.ucsd.sbrg.util.SBMLFix
    +
    main(String...) - Static method in class edu.ucsd.sbrg.SBMLValidatorCLILauncher
     
    MAT_FILE - Enum constant in enum class edu.ucsd.sbrg.io.SBMLFileUtils.FileType
     
    @@ -1457,10 +1526,8 @@

    M

    Bundle for ModelPolisher logger messages
    MESSAGES - Static variable in class edu.ucsd.sbrg.io.parsers.cobra.SpeciesParser
    -
    -
    Bundle for ModelPolisher logger messages
    -
    -
    MESSAGES - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
     
    +
    MESSAGES - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    Bundle for ModelPolisher logger messages
    @@ -1512,7 +1579,7 @@

    M

    Optional: if present, it must have same dimension as ModelField.mets.
    -
    MODEL_NOTES_FILE - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    MODEL_NOTES_FILE - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    This XHTML file defines alternative model notes and makes them exchangeable.
    @@ -1523,6 +1590,10 @@

    M

    Supplementary Material.
    +
    ModelFixer - Class in edu.ucsd.sbrg.fixing
    +
     
    +
    ModelFixer() - Constructor for class edu.ucsd.sbrg.fixing.ModelFixer
    +
     
    modelNotesFile - Variable in class edu.ucsd.sbrg.parameters.BiGGNotesParameters
     
    modelNotesFile() - Method in class edu.ucsd.sbrg.parameters.BiGGNotesParameters
    @@ -1544,29 +1615,31 @@

    M

    Initializes super class with Commandline arguments, which are converted into AppConf and passed to ModelPolisherCLILauncher.commandLineMode(AppConf), which runs the rest of the program
    -
    ModelPolisherOptions - Interface in edu.ucsd.sbrg
    +
    ModelPolisherOptions - Interface in edu.ucsd.sbrg.parameters
     
    -
    ModelPolisherOptions.OutputType - Enum Class in edu.ucsd.sbrg
    +
    ModelPolisherOptions.OutputType - Enum Class in edu.ucsd.sbrg.parameters
     
    ModelReader - Class in edu.ucsd.sbrg.io
     
    ModelReader(SBOParameters, Registry) - Constructor for class edu.ucsd.sbrg.io.ModelReader
     
    -
    ModelReaderException - Exception in edu.ucsd.sbrg.io
    +
    ModelReaderException - Class in edu.ucsd.sbrg.io
    +
     
    +
    ModelReaderException(String, File) - Constructor for class edu.ucsd.sbrg.io.ModelReaderException
     
    -
    ModelReaderException(String, Exception, File) - Constructor for exception edu.ucsd.sbrg.io.ModelReaderException
    +
    ModelReaderException(String, Exception, File) - Constructor for class edu.ucsd.sbrg.io.ModelReaderException
     
    -
    ModelValidator - Class in edu.ucsd.sbrg
    +
    ModelValidator - Class in edu.ucsd.sbrg.validation
     
    -
    ModelValidator() - Constructor for class edu.ucsd.sbrg.ModelValidator
    +
    ModelValidator() - Constructor for class edu.ucsd.sbrg.validation.ModelValidator
     
    -
    ModelValidatorException - Exception in edu.ucsd.sbrg
    +
    ModelValidatorException - Exception in edu.ucsd.sbrg.validation
     
    -
    ModelValidatorException(Exception, File) - Constructor for exception edu.ucsd.sbrg.ModelValidatorException
    +
    ModelValidatorException(Exception, File) - Constructor for exception edu.ucsd.sbrg.validation.ModelValidatorException
     
    ModelWriter - Class in edu.ucsd.sbrg.io
     
    -
    ModelWriter(ModelPolisherOptions.OutputType) - Constructor for class edu.ucsd.sbrg.io.ModelWriter
    +
    ModelWriter(ModelPolisherOptions.OutputType) - Constructor for class edu.ucsd.sbrg.io.ModelWriter
     
    ModelWriterException - Exception in edu.ucsd.sbrg.io
     
    @@ -1581,15 +1654,23 @@

    N

    Can be part of the ModelField.description.
    +
    NamePolisher - Class in edu.ucsd.sbrg.polishing
    +
     
    +
    NamePolisher() - Constructor for class edu.ucsd.sbrg.polishing.NamePolisher
    +
     
    Namespace - Class in edu.ucsd.sbrg.resolver.identifiersorg.mapping
     
    Namespace() - Constructor for class edu.ucsd.sbrg.resolver.identifiersorg.mapping.Namespace
     
    -
    NO_MODEL_NOTES - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    NO_MODEL_NOTES - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    If set to true, no web content will be inserted in the SBML container nor into the model within the SBML file.
    +
    Node - Class in edu.ucsd.sbrg.eco
    +
     
    +
    Node(Term) - Constructor for class edu.ucsd.sbrg.eco.Node
    +
     
    nodeAdded(TreeNode) - Method in class edu.ucsd.sbrg.io.UpdateListener
    Handles the event when a new node is added to the TreeNode structure.
    @@ -1613,14 +1694,17 @@

    O

    Returns the value of the obj record component.
    -
    OMIT_GENERIC_TERMS - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    -
    -
    Set this option to true if generic top-level annotations, such as 'process' - should not be applied.
    -
    -
    omitGenericTerms - Variable in class edu.ucsd.sbrg.parameters.SBOParameters
    +
    ObjectiveFixer - Class in edu.ucsd.sbrg.fixing.ext.fbc
    +
     
    +
    ObjectiveFixer() - Constructor for class edu.ucsd.sbrg.fixing.ext.fbc.ObjectiveFixer
    +
     
    +
    ObjectivesPolisher - Class in edu.ucsd.sbrg.polishing.fbc
    +
     
    +
    ObjectivesPolisher(FBCModelPlugin, PolishingParameters, Registry) - Constructor for class edu.ucsd.sbrg.polishing.fbc.ObjectivesPolisher
     
    -
    omitGenericTerms() - Method in class edu.ucsd.sbrg.parameters.SBOParameters
    +
    ObjectivesPolisher(FBCModelPlugin, PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.polishing.fbc.ObjectivesPolisher
    +
     
    +
    omitGenericTerms - Variable in class edu.ucsd.sbrg.parameters.SBOParameters
     
    organism - Enum constant in enum class edu.ucsd.sbrg.io.parsers.cobra.ModelField
    @@ -1638,16 +1722,16 @@

    O

    The path to the file into which the output should be written.
    -
    OUTPUT_COMBINE - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    OUTPUT_COMBINE - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    Produce output as a single COMBINE Archive.
    -
    OUTPUT_TYPE - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    OUTPUT_TYPE - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    Decides whether or not the output file should directly be compressed and if so, which archive type should be used.
    -
    outputFile() - Method in exception edu.ucsd.sbrg.ModelValidatorException
    +
    outputFile() - Method in exception edu.ucsd.sbrg.validation.ModelValidatorException
     
    outputType - Variable in class edu.ucsd.sbrg.parameters.CommandLineParameters
     
    @@ -1660,8 +1744,6 @@

    O

    P

    -
    p(String) - Static method in class edu.ucsd.sbrg.XHTMLBuilder
    -
     
    parameters - Variable in class edu.ucsd.sbrg.annotation.adb.AbstractADBAnnotator
     
    Parameters - Class in edu.ucsd.sbrg.parameters
    @@ -1697,7 +1779,7 @@

    P

     
    parseCompartments(ModelBuilder, Map<String, String>) - Method in class edu.ucsd.sbrg.io.parsers.json.JSONParser
     
    -
    parseECO() - Static method in class edu.ucsd.sbrg.eco.ECOparser
    +
    parseECO() - Static method in class edu.ucsd.sbrg.ECOParserCLILauncher
     
    parseGene(Model, Gene, String) - Method in class edu.ucsd.sbrg.io.parsers.json.JSONParser
     
    @@ -1705,7 +1787,7 @@

    P

    Parses gene reaction rules for a given reaction based on the BiGG database identifier.
    -
    parseGPR(Reaction, String, boolean) - Static method in class edu.ucsd.sbrg.util.GPRParser
    +
    parseGPR(Reaction, String, boolean) - Static method in class edu.ucsd.sbrg.util.ext.fbc.GPRParser
    Parses the gene product association (GPR) from a gene reaction rule string and associates it with a given reaction.
    @@ -1721,44 +1803,42 @@

    P

     
    PASSWD - Static variable in interface edu.ucsd.sbrg.db.bigg.BiGGDBOptions
     
    +
    polish(String) - Method in class edu.ucsd.sbrg.polishing.NamePolisher
    +
     
    polish(List<Compartment>) - Method in class edu.ucsd.sbrg.polishing.CompartmentPolisher
    Polishes all compartments in the given SBML model.
    polish(List<GeneProduct>) - Method in class edu.ucsd.sbrg.polishing.fbc.GeneProductsPolisher
     
    -
    polish(List<Objective>) - Method in class edu.ucsd.sbrg.polishing.fbc.FluxObjectivesPolisher
    -
    -
    Polishes the list of objectives in the given FBC model plugin.
    -
    polish(List<Parameter>) - Method in class edu.ucsd.sbrg.polishing.ParametersPolisher
    -
    -
    Iterates over all parameters in the model and polishes each one.
    -
    +
     
    +
    polish(List<Reaction>) - Method in class edu.ucsd.sbrg.polishing.fbc.FBCReactionPolisher
    +
     
    polish(List<Reaction>) - Method in class edu.ucsd.sbrg.polishing.ReactionsPolisher
    -
    -
    Polishes all reactions in the given SBML model.
    -
    +
     
    +
    polish(List<SBase>) - Method in interface edu.ucsd.sbrg.polishing.IPolishSBaseAttributes
    +
     
    polish(List<Species>) - Method in class edu.ucsd.sbrg.polishing.SpeciesPolisher
    -
    -
    Polishes the list of species in the given SBML model.
    -
    -
    polish(List<SBMLElement>) - Method in class edu.ucsd.sbrg.polishing.AbstractPolisher
    +
     
    +
    polish(List<SpeciesReference>) - Method in interface edu.ucsd.sbrg.polishing.IPolishSpeciesReferences
    +
     
    +
    polish(List<SBMLElement>) - Method in interface edu.ucsd.sbrg.polishing.IPolishSBases
     
    polish(Annotation) - Method in class edu.ucsd.sbrg.polishing.AnnotationPolisher
    Processes the annotations of an SBML entity to potentially correct identifiers and/or retrieve additional identifiers.org URLs.
    +
    polish(Annotation) - Method in interface edu.ucsd.sbrg.polishing.IPolishAnnotations
    +
     
    polish(Compartment) - Method in class edu.ucsd.sbrg.polishing.CompartmentPolisher
    Polishes the properties of a compartment to ensure compliance with standards and completeness.
    polish(GeneProduct) - Method in class edu.ucsd.sbrg.polishing.fbc.GeneProductsPolisher
    -
    -
    Polishes the GeneProduct by processing its annotations, setting its ID and name based on certain conditions.
    -
    -
    polish(Objective) - Method in class edu.ucsd.sbrg.polishing.fbc.FluxObjectivesPolisher
    +
     
    +
    polish(Objective) - Method in class edu.ucsd.sbrg.polishing.fbc.ObjectivesPolisher
     
    polish(Model) - Method in class edu.ucsd.sbrg.polishing.fbc.FBCPolisher
     
    @@ -1772,23 +1852,29 @@

    P

    Ensures that all necessary UnitDefinitions and Units are present in the model.
    polish(Parameter) - Method in class edu.ucsd.sbrg.polishing.ParametersPolisher
    -
    -
    Polishes the name of a parameter if it is not already set.
    -
    +
     
    +
    polish(Reaction) - Method in class edu.ucsd.sbrg.polishing.fbc.FBCReactionPolisher
    +
     
    polish(Reaction) - Method in class edu.ucsd.sbrg.polishing.ReactionsPolisher
    Polishes the reaction by applying various checks and modifications to ensure it conforms to the expected standards and conventions.
    +
    polish(SBase) - Method in interface edu.ucsd.sbrg.polishing.IPolishSBaseAttributes
    +
     
    +
    polish(SBase) - Method in class edu.ucsd.sbrg.polishing.NamePolisher
    +
     
    polish(SBMLDocument) - Method in class edu.ucsd.sbrg.polishing.SBMLPolisher
    This method serves as the entry point from the ModelPolisher class to polish an SBML document.
    polish(Species) - Method in class edu.ucsd.sbrg.polishing.SpeciesPolisher
    -
    -
    Polishes the properties of a Species to ensure compliance with standards and completeness.
    -
    -
    polish(SBMLElement) - Method in class edu.ucsd.sbrg.polishing.AbstractPolisher
    +
     
    +
    polish(SpeciesReference) - Method in interface edu.ucsd.sbrg.polishing.IPolishSpeciesReferences
    +
     
    +
    polish(SpeciesReference) - Method in class edu.ucsd.sbrg.polishing.SpeciesReferencesPolisher
    +
     
    +
    polish(SBMLElement) - Method in interface edu.ucsd.sbrg.polishing.IPolishSBases
     
    PolisherProgressBar - Class in edu.ucsd.sbrg.reporting
     
    @@ -1808,15 +1894,6 @@

    P

     
    PolishingParameters(ReactionPolishingParameters, FluxObjectivesPolishingParameters) - Constructor for class edu.ucsd.sbrg.parameters.PolishingParameters
     
    -
    PolishingUtils - Class in edu.ucsd.sbrg.polishing
    -
     
    -
    PolishingUtils() - Constructor for class edu.ucsd.sbrg.polishing.PolishingUtils
    -
     
    -
    polishName(String) - Static method in class edu.ucsd.sbrg.polishing.PolishingUtils
    -
    -
    Processes and polishes a given identifier name by applying a series of string transformations - to make it more readable or compliant with certain standards.
    -
    port() - Method in class edu.ucsd.sbrg.parameters.DBParameters
     
    PORT - Static variable in interface edu.ucsd.sbrg.db.adb.AnnotateDBOptions
    @@ -1876,6 +1953,10 @@

    R

     
    Reaction() - Constructor for class edu.ucsd.sbrg.io.parsers.json.mapping.Reaction
     
    +
    ReactionFixer - Class in edu.ucsd.sbrg.fixing
    +
     
    +
    ReactionFixer() - Constructor for class edu.ucsd.sbrg.fixing.ReactionFixer
    +
     
    reactionHasValidBounds(Reaction) - Method in class edu.ucsd.sbrg.polishing.fbc.StrictnessPredicate
    1) Each Reaction in a Model must define values for the attributes 'lowerFluxBound' and 'upperFluxBound', @@ -1883,7 +1964,7 @@

    R

    reactionId - Variable in class edu.ucsd.sbrg.db.bigg.BiGGDB.ForeignReaction
     
    -
    ReactionNamePatterns - Enum Class in edu.ucsd.sbrg.polishing
    +
    ReactionNamePatterns - Enum Class in edu.ucsd.sbrg.util
    Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
    @@ -1913,6 +1994,8 @@

    R

     
    ReactionsPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.polishing.ReactionsPolisher
     
    +
    read(File) - Method in interface edu.ucsd.sbrg.io.IReadModelsFromFile
    +
     
    read(File) - Method in class edu.ucsd.sbrg.io.ModelReader
     
    REF_SEQ_ACCESSION_NUMBER_PATTERN - Static variable in class edu.ucsd.sbrg.annotation.bigg.BiGGModelAnnotator
    @@ -1945,6 +2028,12 @@

    R

    ReportType - Enum Class in edu.ucsd.sbrg.reporting
     
    +
    resolveBackwards(String) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrg
    +
    +
    Checks and processes a given resource URL to ensure it conforms to expected formats and corrections.
    +
    +
    resolveBackwards(String) - Method in interface edu.ucsd.sbrg.resolver.Registry
    +
     
    Resource - Class in edu.ucsd.sbrg.resolver.identifiersorg.mapping
     
    Resource() - Constructor for class edu.ucsd.sbrg.resolver.identifiersorg.mapping.Resource
    @@ -2021,11 +2110,11 @@

    S

    Stoichiometric matrix in sparse format.
    -
    SBML - Enum constant in enum class edu.ucsd.sbrg.ModelPolisherOptions.OutputType
    +
    SBML - Enum constant in enum class edu.ucsd.sbrg.parameters.ModelPolisherOptions.OutputType
     
    SBML_FILE - Enum constant in enum class edu.ucsd.sbrg.io.SBMLFileUtils.FileType
     
    -
    SBML_VALIDATION - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    SBML_VALIDATION - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    If true, the created SBML file will be validated through the online validator service at http://sbml.org.
    @@ -2038,11 +2127,15 @@

    S

    Possible FileTypes of input file
    -
    SBMLFix - Class in edu.ucsd.sbrg.util
    +
    SBMLFixer - Class in edu.ucsd.sbrg.fixing
    +
     
    +
    SBMLFixer() - Constructor for class edu.ucsd.sbrg.fixing.SBMLFixer
    +
     
    +
    SBMLFixerCLILauncher - Class in edu.ucsd.sbrg
    This is a stand-alone bug-fix program.
    -
    SBMLFix() - Constructor for class edu.ucsd.sbrg.util.SBMLFix
    +
    SBMLFixerCLILauncher() - Constructor for class edu.ucsd.sbrg.SBMLFixerCLILauncher
     
    SBMLPolisher - Class in edu.ucsd.sbrg.polishing
     
    @@ -2050,12 +2143,6 @@

    S

     
    SBMLPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.polishing.SBMLPolisher
     
    -
    SBMLUtils - Class in edu.ucsd.sbrg.util
    -
    -
    A collection of helpful functions for dealing with SBML data structures.
    -
    -
    SBMLUtils() - Constructor for class edu.ucsd.sbrg.util.SBMLUtils
    -
     
    sbmlValidation - Variable in class edu.ucsd.sbrg.parameters.CommandLineParameters
     
    sbmlValidation - Variable in class edu.ucsd.sbrg.parameters.Parameters
    @@ -2064,9 +2151,9 @@

    S

     
    SBMLValidation() - Method in class edu.ucsd.sbrg.parameters.CommandLineParameters
     
    -
    SBMLValidator - Class in edu.ucsd.sbrg
    +
    SBMLValidatorCLILauncher - Class in edu.ucsd.sbrg
     
    -
    SBMLValidator() - Constructor for class edu.ucsd.sbrg.SBMLValidator
    +
    SBMLValidatorCLILauncher() - Constructor for class edu.ucsd.sbrg.SBMLValidatorCLILauncher
     
    sboParameters() - Method in class edu.ucsd.sbrg.parameters.CommandLineParameters
     
    @@ -2104,6 +2191,8 @@

    S

     
    setCharge(int) - Method in class edu.ucsd.sbrg.io.parsers.json.mapping.Metabolite
     
    +
    setChildren(List<Node>) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    setCompartment(String) - Method in class edu.ucsd.sbrg.io.parsers.json.mapping.Metabolite
     
    setCompartmentCode(String) - Method in class edu.ucsd.sbrg.db.bigg.BiGGId
    @@ -2137,7 +2226,7 @@

    S

     
    setErrorMessage(String) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
     
    -
    setFluxBoundSBOTerm(Parameter) - Method in class edu.ucsd.sbrg.polishing.ReactionsPolisher
    +
    setFluxBoundSBOTerm(Parameter) - Method in class edu.ucsd.sbrg.polishing.fbc.FBCReactionPolisher
    Polishes the SBO term of a flux bound parameter based on its ID.
    @@ -2221,6 +2310,8 @@

    S

     
    setOfficial(boolean) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.mapping.Resource
     
    +
    setParents(List<Node>) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    setPattern(String) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.mapping.Namespace
     
    setPayload(Map<String, List<Namespace>>) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
    @@ -2257,6 +2348,8 @@

    S

    setSubsystem(String) - Method in class edu.ucsd.sbrg.io.parsers.json.mapping.Reaction
     
    +
    setTerm(Term) - Method in class edu.ucsd.sbrg.eco.Node
    +
     
    setTissueCode(String) - Method in class edu.ucsd.sbrg.db.bigg.BiGGId
    One or two characters in length, and contain only upper case letters and @@ -2272,29 +2365,40 @@

    S

    Executes a SQL query with a single parameter and returns the result as an Optional.
    -
    SINK_REACTION - Enum constant in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    SINK_REACTION - Enum constant in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Pattern for sink reactions, which are reactions that remove metabolites from the system, identified by IDs starting with 'SK_' or 'SINK_'.
    +
    SpeciesFixer - Class in edu.ucsd.sbrg.fixing
    +
     
    +
    SpeciesFixer() - Constructor for class edu.ucsd.sbrg.fixing.SpeciesFixer
    +
     
    SpeciesParser - Class in edu.ucsd.sbrg.io.parsers.cobra
     
    SpeciesParser(Model, int, Registry) - Constructor for class edu.ucsd.sbrg.io.parsers.cobra.SpeciesParser
     
    SpeciesPolisher - Class in edu.ucsd.sbrg.polishing
    -
    -
    This class is responsible for polishing Species objects in an SBML model to ensure they conform to - specific standards and completeness.
    -
    +
     
    SpeciesPolisher(PolishingParameters, Registry) - Constructor for class edu.ucsd.sbrg.polishing.SpeciesPolisher
     
    SpeciesPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class edu.ucsd.sbrg.polishing.SpeciesPolisher
     
    +
    SpeciesReferenceFixer - Class in edu.ucsd.sbrg.fixing
    +
     
    +
    SpeciesReferenceFixer() - Constructor for class edu.ucsd.sbrg.fixing.SpeciesReferenceFixer
    +
     
    +
    SpeciesReferencesPolisher - Class in edu.ucsd.sbrg.polishing
    +
     
    +
    SpeciesReferencesPolisher(Integer) - Constructor for class edu.ucsd.sbrg.polishing.SpeciesReferencesPolisher
    +
     
    STATUS - Enum constant in enum class edu.ucsd.sbrg.reporting.ReportType
     
    statusReport(String, Object) - Method in class edu.ucsd.sbrg.annotation.AbstractAnnotator
     
    statusReport(String, Object) - Method in class edu.ucsd.sbrg.polishing.AbstractPolisher
     
    +
    statusReport(String, Object) - Method in interface edu.ucsd.sbrg.reporting.IReportStatus
    +
     
    strictnessOfSpeciesReferences(ListOf<SpeciesReference>) - Method in class edu.ucsd.sbrg.polishing.fbc.StrictnessPredicate
    3) SpeciesReference objects in Reaction objects must have their 'stoichiometry' attribute set to a double value @@ -2306,11 +2410,11 @@

    S

    StrictnessPredicate() - Constructor for class edu.ucsd.sbrg.polishing.fbc.StrictnessPredicate
     
    -
    stringify(Association) - Static method in class edu.ucsd.sbrg.util.GPRParser
    +
    stringify(Association) - Static method in class edu.ucsd.sbrg.util.ext.fbc.GPRParser
    Converts an Association object into a human-readable string representation.
    -
    SUBSYSTEM_LINK - Static variable in class edu.ucsd.sbrg.util.SBMLUtils
    +
    SUBSYSTEM_LINK - Static variable in class edu.ucsd.sbrg.util.ext.groups.GroupsUtils
    Key to link from Reaction directly to Members referencing that reaction.
    @@ -2322,8 +2426,6 @@

    S

    T

    -
    table(Object[], Object[][], String, Map<String, String>) - Static method in class edu.ucsd.sbrg.XHTMLBuilder
    -
     
    Table() - Constructor for class edu.ucsd.sbrg.db.adb.AnnotateDBContract.Constants.Table
     
    Table() - Constructor for class edu.ucsd.sbrg.db.bigg.BiGGDBContract.Constants.Table
    @@ -2424,7 +2526,9 @@

    U

    V

    -
    validate(File) - Method in class edu.ucsd.sbrg.ModelValidator
    +
    validate(File) - Method in class edu.ucsd.sbrg.validation.ModelValidator
    +
     
    +
    validate(SBMLDocument) - Method in class edu.ucsd.sbrg.validation.ModelValidator
     
    validRegistryUrlPrefix(RegistryURI) - Method in class edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrg
    @@ -2440,15 +2544,15 @@

    V

    Returns the enum constant of this class with the specified name.
    -
    valueOf(String) - Static method in enum class edu.ucsd.sbrg.ModelPolisherOptions.OutputType
    +
    valueOf(String) - Static method in enum class edu.ucsd.sbrg.parameters.ModelPolisherOptions.OutputType
    Returns the enum constant of this class with the specified name.
    -
    valueOf(String) - Static method in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    valueOf(String) - Static method in enum class edu.ucsd.sbrg.reporting.ReportType
    Returns the enum constant of this class with the specified name.
    -
    valueOf(String) - Static method in enum class edu.ucsd.sbrg.reporting.ReportType
    +
    valueOf(String) - Static method in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Returns the enum constant of this class with the specified name.
    @@ -2462,17 +2566,17 @@

    V

    Returns an array containing the constants of this enum class, in the order they are declared.
    -
    values() - Static method in enum class edu.ucsd.sbrg.ModelPolisherOptions.OutputType
    +
    values() - Static method in enum class edu.ucsd.sbrg.parameters.ModelPolisherOptions.OutputType
    Returns an array containing the constants of this enum class, in the order they are declared.
    -
    values() - Static method in enum class edu.ucsd.sbrg.polishing.ReactionNamePatterns
    +
    values() - Static method in enum class edu.ucsd.sbrg.reporting.ReportType
    Returns an array containing the constants of this enum class, in the order they are declared.
    -
    values() - Static method in enum class edu.ucsd.sbrg.reporting.ReportType
    +
    values() - Static method in enum class edu.ucsd.sbrg.util.ReactionNamePatterns
    Returns an array containing the constants of this enum class, in the order they are declared.
    @@ -2482,21 +2586,20 @@

    W

    write() - Method in class edu.ucsd.sbrg.io.CombineArchive
     
    +
    write(SBMLDocument) - Method in interface edu.ucsd.sbrg.io.IWriteModels
    +
     
    write(SBMLDocument) - Method in class edu.ucsd.sbrg.io.ModelWriter
     
    +
    write(SBMLDocument, File) - Method in interface edu.ucsd.sbrg.io.IWriteModelsToFile
    +
     
    write(SBMLDocument, File) - Method in class edu.ucsd.sbrg.io.ModelWriter
     
    -
    WRITE_JSON - Static variable in interface edu.ucsd.sbrg.ModelPolisherOptions
    +
    WRITE_JSON - Static variable in interface edu.ucsd.sbrg.parameters.ModelPolisherOptions
    TODO
    -

    X

    -
    -
    XHTMLBuilder - Class in edu.ucsd.sbrg
    -
     
    -
    -A B C D E F G H I J L M N O P R S T U V W X 
    All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form +A B C D E F G H I J L M N O P R S T U V W 
    All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form diff --git a/docs/index.html b/docs/index.html index f4151e3a..53b97901 100644 --- a/docs/index.html +++ b/docs/index.html @@ -72,29 +72,41 @@

    ModelPolisher 2.1 API

     
    edu.ucsd.sbrg.eco
     
    -
    edu.ucsd.sbrg.io
    +
    edu.ucsd.sbrg.fixing
     
    -
    edu.ucsd.sbrg.io.parsers.cobra
    +
    edu.ucsd.sbrg.fixing.ext.fbc
     
    -
    edu.ucsd.sbrg.io.parsers.json
    +
    edu.ucsd.sbrg.fixing.ext.groups
     
    -
    edu.ucsd.sbrg.io.parsers.json.mapping
    +
    edu.ucsd.sbrg.io
     
    -
    edu.ucsd.sbrg.parameters
    +
    edu.ucsd.sbrg.io.parsers.cobra
     
    -
    edu.ucsd.sbrg.polishing
    +
    edu.ucsd.sbrg.io.parsers.json
     
    -
    edu.ucsd.sbrg.polishing.fbc
    +
    edu.ucsd.sbrg.io.parsers.json.mapping
     
    -
    edu.ucsd.sbrg.reporting
    +
    edu.ucsd.sbrg.parameters
     
    -
    edu.ucsd.sbrg.resolver
    +
    edu.ucsd.sbrg.polishing
     
    -
    edu.ucsd.sbrg.resolver.identifiersorg
    +
    edu.ucsd.sbrg.polishing.fbc
     
    -
    edu.ucsd.sbrg.resolver.identifiersorg.mapping
    +
    edu.ucsd.sbrg.reporting
     
    -
    edu.ucsd.sbrg.util
    +
    edu.ucsd.sbrg.resolver
    +
     
    +
    edu.ucsd.sbrg.resolver.identifiersorg
    +
     
    +
    edu.ucsd.sbrg.resolver.identifiersorg.mapping
    +
     
    +
    edu.ucsd.sbrg.util
    +
     
    +
    edu.ucsd.sbrg.util.ext.fbc
    +
     
    +
    edu.ucsd.sbrg.util.ext.groups
    +
     
    +
    edu.ucsd.sbrg.validation
     
    diff --git a/docs/member-search-index.js b/docs/member-search-index.js index bb3b78d1..912e896c 100644 --- a/docs/member-search-index.js +++ b/docs/member-search-index.js @@ -1 +1 @@ -memberSearchIndex = [{"p":"edu.ucsd.sbrg.io.parsers.cobra","c":"ModelField","l":"A"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"AbstractADBAnnotator","l":"AbstractADBAnnotator(AnnotateDB, ADBAnnotationParameters)","u":"%3Cinit%3E(edu.ucsd.sbrg.db.adb.AnnotateDB,edu.ucsd.sbrg.parameters.ADBAnnotationParameters)"},{"p":"edu.ucsd.sbrg.annotation","c":"AbstractAnnotator","l":"AbstractAnnotator()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.annotation","c":"AbstractAnnotator","l":"AbstractAnnotator(List)","u":"%3Cinit%3E(java.util.List)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"AbstractBiGGAnnotator","l":"AbstractBiGGAnnotator(BiGGDB, BiGGAnnotationParameters, Registry)","u":"%3Cinit%3E(edu.ucsd.sbrg.db.bigg.BiGGDB,edu.ucsd.sbrg.parameters.BiGGAnnotationParameters,edu.ucsd.sbrg.resolver.Registry)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"AbstractBiGGAnnotator","l":"AbstractBiGGAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List)","u":"%3Cinit%3E(edu.ucsd.sbrg.db.bigg.BiGGDB,edu.ucsd.sbrg.parameters.BiGGAnnotationParameters,edu.ucsd.sbrg.resolver.Registry,java.util.List)"},{"p":"edu.ucsd.sbrg.polishing","c":"AbstractPolisher","l":"AbstractPolisher(PolishingParameters, Registry)","u":"%3Cinit%3E(edu.ucsd.sbrg.parameters.PolishingParameters,edu.ucsd.sbrg.resolver.Registry)"},{"p":"edu.ucsd.sbrg.polishing","c":"AbstractPolisher","l":"AbstractPolisher(PolishingParameters, Registry, List)","u":"%3Cinit%3E(edu.ucsd.sbrg.parameters.PolishingParameters,edu.ucsd.sbrg.resolver.Registry,java.util.List)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"AbstractADBAnnotator","l":"adb"},{"p":"edu.ucsd.sbrg.parameters","c":"AnnotationParameters","l":"adbAnnotationParameters()"},{"p":"edu.ucsd.sbrg.parameters","c":"ADBAnnotationParameters","l":"ADBAnnotationParameters()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.parameters","c":"ADBAnnotationParameters","l":"ADBAnnotationParameters(SBProperties)","u":"%3Cinit%3E(de.zbit.util.prefs.SBProperties)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"ADBReactionsAnnotator","l":"ADBReactionsAnnotator(AnnotateDB, ADBAnnotationParameters)","u":"%3Cinit%3E(edu.ucsd.sbrg.db.adb.AnnotateDB,edu.ucsd.sbrg.parameters.ADBAnnotationParameters)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"ADBSBMLAnnotator","l":"ADBSBMLAnnotator(AnnotateDB, ADBAnnotationParameters)","u":"%3Cinit%3E(edu.ucsd.sbrg.db.adb.AnnotateDB,edu.ucsd.sbrg.parameters.ADBAnnotationParameters)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"ADBSpeciesAnnotator","l":"ADBSpeciesAnnotator(AnnotateDB, ADBAnnotationParameters)","u":"%3Cinit%3E(edu.ucsd.sbrg.db.adb.AnnotateDB,edu.ucsd.sbrg.parameters.ADBAnnotationParameters)"},{"p":"edu.ucsd.sbrg","c":"ModelPolisherOptions","l":"ADD_ADB_ANNOTATIONS"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Metabolites","l":"add(String, double)","u":"add(java.lang.String,double)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Compartments","l":"add(String, String)","u":"add(java.lang.String,java.lang.String)"},{"p":"edu.ucsd.sbrg.parameters","c":"ADBAnnotationParameters","l":"addADBAnnotations"},{"p":"edu.ucsd.sbrg.parameters","c":"ADBAnnotationParameters","l":"addADBAnnotations()"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Compartments","l":"addAll(Map)","u":"addAll(java.util.Map)"},{"p":"edu.ucsd.sbrg.annotation.bigg.fbc","c":"BiGGGeneProductAnnotator","l":"addAnnotations(GeneProduct, BiGGId)","u":"addAnnotations(org.sbml.jsbml.ext.fbc.GeneProduct,edu.ucsd.sbrg.db.bigg.BiGGId)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"AbstractADBAnnotator","l":"addBQB_IS_AnnotationsFromADB(Annotation, String, BiGGId)","u":"addBQB_IS_AnnotationsFromADB(org.sbml.jsbml.Annotation,java.lang.String,edu.ucsd.sbrg.db.bigg.BiGGId)"},{"p":"edu.ucsd.sbrg","c":"ModelPolisherCLILauncher","l":"addCopyrightToSplashScreen()"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg","c":"IdentifiersOrgURIUtils","l":"addJavaRegexCaptureGroup(String)","u":"addJavaRegexCaptureGroup(java.lang.String)"},{"p":"edu.ucsd.sbrg.io.parsers.cobra","c":"ReactionParser","l":"addResource(String, CVTerm, String)","u":"addResource(java.lang.String,org.sbml.jsbml.CVTerm,java.lang.String)"},{"p":"edu.ucsd.sbrg","c":"ModelPolisherCLILauncher","l":"addVersionNumberToSplashScreen()"},{"p":"edu.ucsd.sbrg","c":"ModelPolisherOptions","l":"ANNOTATE_WITH_BIGG"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGCompartmentsAnnotator","l":"annotate(Compartment)","u":"annotate(org.sbml.jsbml.Compartment)"},{"p":"edu.ucsd.sbrg.annotation.bigg.fbc","c":"BiGGGeneProductAnnotator","l":"annotate(GeneProduct)","u":"annotate(org.sbml.jsbml.ext.fbc.GeneProduct)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGCompartmentsAnnotator","l":"annotate(List)","u":"annotate(java.util.List)"},{"p":"edu.ucsd.sbrg.annotation.bigg.fbc","c":"BiGGGeneProductAnnotator","l":"annotate(List)","u":"annotate(java.util.List)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"ADBReactionsAnnotator","l":"annotate(List)","u":"annotate(java.util.List)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGReactionsAnnotator","l":"annotate(List)","u":"annotate(java.util.List)"},{"p":"edu.ucsd.sbrg.annotation","c":"AbstractAnnotator","l":"annotate(List)","u":"annotate(java.util.List)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"ADBSpeciesAnnotator","l":"annotate(List)","u":"annotate(java.util.List)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGSpeciesAnnotator","l":"annotate(List)","u":"annotate(java.util.List)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGModelAnnotator","l":"annotate(Model)","u":"annotate(org.sbml.jsbml.Model)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGPublicationsAnnotator","l":"annotate(Model)","u":"annotate(org.sbml.jsbml.Model)"},{"p":"edu.ucsd.sbrg.annotation.bigg.fbc","c":"BiGGFBCAnnotator","l":"annotate(Model)","u":"annotate(org.sbml.jsbml.Model)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"ADBReactionsAnnotator","l":"annotate(Reaction)","u":"annotate(org.sbml.jsbml.Reaction)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGReactionsAnnotator","l":"annotate(Reaction)","u":"annotate(org.sbml.jsbml.Reaction)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"ADBSBMLAnnotator","l":"annotate(SBMLDocument)","u":"annotate(org.sbml.jsbml.SBMLDocument)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGSBMLAnnotator","l":"annotate(SBMLDocument)","u":"annotate(org.sbml.jsbml.SBMLDocument)"},{"p":"edu.ucsd.sbrg.annotation","c":"AbstractAnnotator","l":"annotate(SBMLElement)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"AbstractADBAnnotator","l":"annotate(SBMLElement)"},{"p":"edu.ucsd.sbrg.annotation.adb","c":"ADBSpeciesAnnotator","l":"annotate(Species)","u":"annotate(org.sbml.jsbml.Species)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGSpeciesAnnotator","l":"annotate(Species)","u":"annotate(org.sbml.jsbml.Species)"},{"p":"edu.ucsd.sbrg.db.adb","c":"AnnotateDB","l":"AnnotateDB(DBParameters)","u":"%3Cinit%3E(edu.ucsd.sbrg.parameters.DBParameters)"},{"p":"edu.ucsd.sbrg.db.adb","c":"AnnotateDB","l":"AnnotateDB(String, Integer, String, String, String)","u":"%3Cinit%3E(java.lang.String,java.lang.Integer,java.lang.String,java.lang.String,java.lang.String)"},{"p":"edu.ucsd.sbrg.db.adb","c":"AnnotateDBContract","l":"AnnotateDBContract()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.parameters","c":"BiGGAnnotationParameters","l":"annotateWithBiGG"},{"p":"edu.ucsd.sbrg.parameters","c":"BiGGAnnotationParameters","l":"annotateWithBiGG()"},{"p":"edu.ucsd.sbrg.parameters","c":"Parameters","l":"annotation()"},{"p":"edu.ucsd.sbrg.annotation","c":"AnnotationException","l":"AnnotationException(String, Exception)","u":"%3Cinit%3E(java.lang.String,java.lang.Exception)"},{"p":"edu.ucsd.sbrg.parameters","c":"CommandLineParameters","l":"annotationParameters()"},{"p":"edu.ucsd.sbrg.parameters","c":"AnnotationParameters","l":"AnnotationParameters()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.parameters","c":"AnnotationParameters","l":"AnnotationParameters(SBProperties)","u":"%3Cinit%3E(de.zbit.util.prefs.SBProperties)"},{"p":"edu.ucsd.sbrg.polishing","c":"AnnotationPolisher","l":"AnnotationPolisher(PolishingParameters, Registry)","u":"%3Cinit%3E(edu.ucsd.sbrg.parameters.PolishingParameters,edu.ucsd.sbrg.resolver.Registry)"},{"p":"edu.ucsd.sbrg.polishing","c":"AnnotationPolisher","l":"AnnotationPolisher(PolishingParameters, Registry, 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BiGGId)","u":"setName(org.sbml.jsbml.Species,edu.ucsd.sbrg.db.bigg.BiGGId)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Gene","l":"setName(String)","u":"setName(java.lang.String)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Metabolite","l":"setName(String)","u":"setName(java.lang.String)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Reaction","l":"setName(String)","u":"setName(java.lang.String)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Root","l":"setName(String)","u":"setName(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Institution","l":"setName(String)","u":"setName(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Namespace","l":"setName(String)","u":"setName(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Resource","l":"setName(String)","u":"setName(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Namespace","l":"setNamespaceEmbeddedInLui(boolean)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Gene","l":"setNotes(Object)","u":"setNotes(java.lang.Object)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Metabolite","l":"setNotes(Object)","u":"setNotes(java.lang.Object)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Reaction","l":"setNotes(Object)","u":"setNotes(java.lang.Object)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Root","l":"setNotes(Object)","u":"setNotes(java.lang.Object)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Reaction","l":"setObjectiveCoefficient(double)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Resource","l":"setOfficial(boolean)"},{"p":"edu.ucsd.sbrg.eco","c":"Node","l":"setParents(List)","u":"setParents(java.util.List)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Namespace","l":"setPattern(String)","u":"setPattern(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"RawIdentifiersOrgRegistry","l":"setPayload(Map>)","u":"setPayload(java.util.Map)"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGId","l":"setPrefix(String)","u":"setPrefix(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Namespace","l":"setPrefix(String)","u":"setPrefix(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Resource","l":"setProviderCode(String)","u":"setProviderCode(java.lang.String)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Root","l":"setReactions(List)","u":"setReactions(java.util.List)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Resource","l":"setResourceHomeUrl(String)","u":"setResourceHomeUrl(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Namespace","l":"setResources(List)","u":"setResources(java.util.List)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Institution","l":"setRorId(String)","u":"setRorId(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Namespace","l":"setSampleId(String)","u":"setSampleId(java.lang.String)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Resource","l":"setSampleId(String)","u":"setSampleId(java.lang.String)"},{"p":"edu.ucsd.sbrg.annotation.bigg","c":"BiGGReactionsAnnotator","l":"setSBOTerm(Reaction, BiGGId)","u":"setSBOTerm(org.sbml.jsbml.Reaction,edu.ucsd.sbrg.db.bigg.BiGGId)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Reaction","l":"setSubsystem(String)","u":"setSubsystem(java.lang.String)"},{"p":"edu.ucsd.sbrg.eco","c":"Node","l":"setTerm(Term)","u":"setTerm(org.biojava.nbio.ontology.Term)"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGId","l":"setTissueCode(String)","u":"setTissueCode(java.lang.String)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Reaction","l":"setUpperBound(double)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg.mapping","c":"Resource","l":"setUrlPattern(String)","u":"setUrlPattern(java.lang.String)"},{"p":"edu.ucsd.sbrg.io.parsers.json.mapping","c":"Root","l":"setVersion(int)"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGDB","l":"singleParamStatement(String, String)","u":"singleParamStatement(java.lang.String,java.lang.String)"},{"p":"edu.ucsd.sbrg.util","c":"ReactionNamePatterns","l":"SINK_REACTION"},{"p":"edu.ucsd.sbrg.fixing","c":"SpeciesFixer","l":"SpeciesFixer()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.io.parsers.cobra","c":"SpeciesParser","l":"SpeciesParser(Model, int, Registry)","u":"%3Cinit%3E(org.sbml.jsbml.Model,int,edu.ucsd.sbrg.resolver.Registry)"},{"p":"edu.ucsd.sbrg.polishing","c":"SpeciesPolisher","l":"SpeciesPolisher(PolishingParameters, Registry)","u":"%3Cinit%3E(edu.ucsd.sbrg.parameters.PolishingParameters,edu.ucsd.sbrg.resolver.Registry)"},{"p":"edu.ucsd.sbrg.polishing","c":"SpeciesPolisher","l":"SpeciesPolisher(PolishingParameters, Registry, List)","u":"%3Cinit%3E(edu.ucsd.sbrg.parameters.PolishingParameters,edu.ucsd.sbrg.resolver.Registry,java.util.List)"},{"p":"edu.ucsd.sbrg.fixing","c":"SpeciesReferenceFixer","l":"SpeciesReferenceFixer()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.polishing","c":"SpeciesReferencesPolisher","l":"SpeciesReferencesPolisher(Integer)","u":"%3Cinit%3E(java.lang.Integer)"},{"p":"edu.ucsd.sbrg.reporting","c":"ReportType","l":"STATUS"},{"p":"edu.ucsd.sbrg.annotation","c":"AbstractAnnotator","l":"statusReport(String, Object)","u":"statusReport(java.lang.String,java.lang.Object)"},{"p":"edu.ucsd.sbrg.polishing","c":"AbstractPolisher","l":"statusReport(String, Object)","u":"statusReport(java.lang.String,java.lang.Object)"},{"p":"edu.ucsd.sbrg.reporting","c":"IReportStatus","l":"statusReport(String, Object)","u":"statusReport(java.lang.String,java.lang.Object)"},{"p":"edu.ucsd.sbrg.polishing.fbc","c":"StrictnessPredicate","l":"strictnessOfSpeciesReferences(ListOf)","u":"strictnessOfSpeciesReferences(org.sbml.jsbml.ListOf)"},{"p":"edu.ucsd.sbrg.polishing.fbc","c":"StrictnessPredicate","l":"StrictnessPredicate()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.util.ext.fbc","c":"GPRParser","l":"stringify(Association)","u":"stringify(org.sbml.jsbml.ext.fbc.Association)"},{"p":"edu.ucsd.sbrg.util.ext.groups","c":"GroupsUtils","l":"SUBSYSTEM_LINK"},{"p":"edu.ucsd.sbrg.io.parsers.cobra","c":"ModelField","l":"subSystems"},{"p":"edu.ucsd.sbrg.db.adb","c":"AnnotateDBContract.Constants.Table","l":"Table()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGDBContract.Constants.Table","l":"Table()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.polishing.fbc","c":"StrictnessPredicate","l":"test(Model)","u":"test(org.sbml.jsbml.Model)"},{"p":"edu.ucsd.sbrg.reporting","c":"ProgressUpdate","l":"text()"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGId","l":"toBiGGId()"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGId","l":"toBiGGId(String, String, String, String)","u":"toBiGGId(java.lang.String,java.lang.String,java.lang.String,java.lang.String)"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGId","l":"toString()"},{"p":"edu.ucsd.sbrg.db.bigg","c":"Publication","l":"toString()"},{"p":"edu.ucsd.sbrg.eco","c":"DAG","l":"toString()"},{"p":"edu.ucsd.sbrg.polishing","c":"AbstractPolisher","l":"toString()"},{"p":"edu.ucsd.sbrg.polishing","c":"ModelPolisher","l":"toString()"},{"p":"edu.ucsd.sbrg.reporting","c":"ProgressFinalization","l":"toString()"},{"p":"edu.ucsd.sbrg.reporting","c":"ProgressInitialization","l":"toString()"},{"p":"edu.ucsd.sbrg.reporting","c":"ProgressUpdate","l":"toString()"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg","c":"IdentifiersOrgURI","l":"toString()"},{"p":"edu.ucsd.sbrg.reporting","c":"ProgressInitialization","l":"totalCalls()"},{"p":"edu.ucsd.sbrg.eco","c":"DAG","l":"traverse(Node, int, StringBuilder)","u":"traverse(edu.ucsd.sbrg.eco.Node,int,java.lang.StringBuilder)"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGDBContract.Constants","l":"TYPE_GENE_PRODUCT"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGDBContract.Constants","l":"TYPE_REACTION"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGDBContract.Constants","l":"TYPE_SPECIES"},{"p":"edu.ucsd.sbrg.io.parsers.cobra","c":"ModelField","l":"ub"},{"p":"edu.ucsd.sbrg.polishing","c":"UnitPolisher","l":"UnitPolisher(PolishingParameters, Registry)","u":"%3Cinit%3E(edu.ucsd.sbrg.parameters.PolishingParameters,edu.ucsd.sbrg.resolver.Registry)"},{"p":"edu.ucsd.sbrg.polishing","c":"UnitPolisher","l":"UnitPolisher(PolishingParameters, Registry, List)","u":"%3Cinit%3E(edu.ucsd.sbrg.parameters.PolishingParameters,edu.ucsd.sbrg.resolver.Registry,java.util.List)"},{"p":"edu.ucsd.sbrg.io","c":"SBMLFileUtils.FileType","l":"UNKNOWN"},{"p":"edu.ucsd.sbrg.annotation.bigg.fbc","c":"BiGGGeneProductReferencesAnnotator","l":"update(GeneProduct)","u":"update(org.sbml.jsbml.ext.fbc.GeneProduct)"},{"p":"edu.ucsd.sbrg.reporting","c":"PolisherProgressBar","l":"update(ProgressUpdate)","u":"update(edu.ucsd.sbrg.reporting.ProgressUpdate)"},{"p":"edu.ucsd.sbrg.reporting","c":"ProgressObserver","l":"update(ProgressUpdate)","u":"update(edu.ucsd.sbrg.reporting.ProgressUpdate)"},{"p":"edu.ucsd.sbrg.io","c":"UpdateListener","l":"UpdateListener()","u":"%3Cinit%3E()"},{"p":"edu.ucsd.sbrg.db.adb","c":"AnnotateDBOptions","l":"USER"},{"p":"edu.ucsd.sbrg.db.bigg","c":"BiGGDBOptions","l":"USER"},{"p":"edu.ucsd.sbrg.parameters","c":"DBParameters","l":"user()"},{"p":"edu.ucsd.sbrg.validation","c":"ModelValidator","l":"validate(File)","u":"validate(java.io.File)"},{"p":"edu.ucsd.sbrg.validation","c":"ModelValidator","l":"validate(SBMLDocument)","u":"validate(org.sbml.jsbml.SBMLDocument)"},{"p":"edu.ucsd.sbrg.resolver.identifiersorg","c":"IdentifiersOrg","l":"validRegistryUrlPrefix(RegistryURI)","u":"validRegistryUrlPrefix(edu.ucsd.sbrg.resolver.RegistryURI)"},{"p":"edu.ucsd.sbrg.resolver","c":"Registry","l":"validRegistryUrlPrefix(RegistryURI)","u":"validRegistryUrlPrefix(edu.ucsd.sbrg.resolver.RegistryURI)"},{"p":"edu.ucsd.sbrg.io.parsers.cobra","c":"ModelField","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"edu.ucsd.sbrg.io","c":"SBMLFileUtils.FileType","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"edu.ucsd.sbrg.parameters","c":"ModelPolisherOptions.OutputType","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"edu.ucsd.sbrg.reporting","c":"ReportType","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"edu.ucsd.sbrg.util","c":"ReactionNamePatterns","l":"valueOf(String)","u":"valueOf(java.lang.String)"},{"p":"edu.ucsd.sbrg.io.parsers.cobra","c":"ModelField","l":"values()"},{"p":"edu.ucsd.sbrg.io","c":"SBMLFileUtils.FileType","l":"values()"},{"p":"edu.ucsd.sbrg.parameters","c":"ModelPolisherOptions.OutputType","l":"values()"},{"p":"edu.ucsd.sbrg.reporting","c":"ReportType","l":"values()"},{"p":"edu.ucsd.sbrg.util","c":"ReactionNamePatterns","l":"values()"},{"p":"edu.ucsd.sbrg.parameters","c":"ModelPolisherOptions","l":"WRITE_JSON"},{"p":"edu.ucsd.sbrg.io","c":"CombineArchive","l":"write()"},{"p":"edu.ucsd.sbrg.io","c":"IWriteModels","l":"write(SBMLDocument)","u":"write(org.sbml.jsbml.SBMLDocument)"},{"p":"edu.ucsd.sbrg.io","c":"ModelWriter","l":"write(SBMLDocument)","u":"write(org.sbml.jsbml.SBMLDocument)"},{"p":"edu.ucsd.sbrg.io","c":"IWriteModelsToFile","l":"write(SBMLDocument, File)","u":"write(org.sbml.jsbml.SBMLDocument,java.io.File)"},{"p":"edu.ucsd.sbrg.io","c":"ModelWriter","l":"write(SBMLDocument, File)","u":"write(org.sbml.jsbml.SBMLDocument,java.io.File)"}];updateSearchResults(); \ No newline at end of file diff --git a/docs/overview-tree.html b/docs/overview-tree.html index d80ec6db..54d6cd3b 100644 --- a/docs/overview-tree.html +++ b/docs/overview-tree.html @@ -59,6 +59,9 @@

    Hierarchy For All Packages

  • edu.ucsd.sbrg.db.adb,
  • edu.ucsd.sbrg.db.bigg,
  • edu.ucsd.sbrg.eco,
    • +
  • edu.ucsd.sbrg.fixing,
    • +
  • edu.ucsd.sbrg.fixing.ext.fbc,
    • +
  • edu.ucsd.sbrg.fixing.ext.groups,
  • edu.ucsd.sbrg.io,
  • edu.ucsd.sbrg.io.parsers.cobra,
  • edu.ucsd.sbrg.io.parsers.json,
    • @@ -70,7 +73,10 @@

    Hierarchy For All Packages

  • edu.ucsd.sbrg.resolver,
  • edu.ucsd.sbrg.resolver.identifiersorg,
  • edu.ucsd.sbrg.resolver.identifiersorg.mapping,
    • -
  • edu.ucsd.sbrg.util
    • +
  • edu.ucsd.sbrg.util,
    • +
  • edu.ucsd.sbrg.util.ext.fbc,
    • +
  • edu.ucsd.sbrg.util.ext.groups,
    • +
  • edu.ucsd.sbrg.validation
    • @@ -78,46 +84,47 @@

    Class Hierarchy

  • edu.ucsd.sbrg.io.UpdateListener (implements org.sbml.jsbml.util.TreeNodeChangeListener)
    • -
  • edu.ucsd.sbrg.XHTMLBuilder
    • @@ -232,12 +249,25 @@

    Class Hierarchy

    Interface Hierarchy

      +
    • edu.ucsd.sbrg.annotation.IAnnotateSBases<SBMLElement>
      • +
    • edu.ucsd.sbrg.fixing.IFixSBases<SBMLElement>
      • +
    • edu.ucsd.sbrg.fixing.IFixSpeciesReferences
      • +
    • edu.ucsd.sbrg.polishing.IPolishAnnotations
      • +
    • edu.ucsd.sbrg.polishing.IPolishSBaseAttributes
      • +
    • edu.ucsd.sbrg.polishing.IPolishSBases<SBMLElement>
      • +
    • edu.ucsd.sbrg.polishing.IPolishSpeciesReferences
      • +
    • edu.ucsd.sbrg.annotation.IProcessNotes
      • +
    • edu.ucsd.sbrg.io.IReadModelsFromFile
      • +
    • edu.ucsd.sbrg.reporting.IReportDiffs
      • +
    • edu.ucsd.sbrg.reporting.IReportStatus
      • +
    • edu.ucsd.sbrg.io.IWriteModels
      • +
    • edu.ucsd.sbrg.io.IWriteModelsToFile
    • de.zbit.util.prefs.KeyProvider
    • edu.ucsd.sbrg.reporting.ProgressObserver
      • @@ -253,8 +283,8 @@

      Enum Class Hierarchy

    • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable) diff --git a/docs/package-search-index.js b/docs/package-search-index.js index 7091b703..c22dd5fb 100644 --- a/docs/package-search-index.js +++ b/docs/package-search-index.js @@ -1 +1 @@ -packageSearchIndex = [{"l":"All Packages","u":"allpackages-index.html"},{"l":"edu.ucsd.sbrg"},{"l":"edu.ucsd.sbrg.annotation"},{"l":"edu.ucsd.sbrg.annotation.adb"},{"l":"edu.ucsd.sbrg.annotation.bigg"},{"l":"edu.ucsd.sbrg.annotation.bigg.fbc"},{"l":"edu.ucsd.sbrg.db"},{"l":"edu.ucsd.sbrg.db.adb"},{"l":"edu.ucsd.sbrg.db.bigg"},{"l":"edu.ucsd.sbrg.eco"},{"l":"edu.ucsd.sbrg.io"},{"l":"edu.ucsd.sbrg.io.parsers.cobra"},{"l":"edu.ucsd.sbrg.io.parsers.json"},{"l":"edu.ucsd.sbrg.io.parsers.json.mapping"},{"l":"edu.ucsd.sbrg.parameters"},{"l":"edu.ucsd.sbrg.polishing"},{"l":"edu.ucsd.sbrg.polishing.fbc"},{"l":"edu.ucsd.sbrg.reporting"},{"l":"edu.ucsd.sbrg.resolver"},{"l":"edu.ucsd.sbrg.resolver.identifiersorg"},{"l":"edu.ucsd.sbrg.resolver.identifiersorg.mapping"},{"l":"edu.ucsd.sbrg.util"}];updateSearchResults(); \ No newline at end of file +packageSearchIndex = [{"l":"All Packages","u":"allpackages-index.html"},{"l":"edu.ucsd.sbrg"},{"l":"edu.ucsd.sbrg.annotation"},{"l":"edu.ucsd.sbrg.annotation.adb"},{"l":"edu.ucsd.sbrg.annotation.bigg"},{"l":"edu.ucsd.sbrg.annotation.bigg.fbc"},{"l":"edu.ucsd.sbrg.db"},{"l":"edu.ucsd.sbrg.db.adb"},{"l":"edu.ucsd.sbrg.db.bigg"},{"l":"edu.ucsd.sbrg.eco"},{"l":"edu.ucsd.sbrg.fixing"},{"l":"edu.ucsd.sbrg.fixing.ext.fbc"},{"l":"edu.ucsd.sbrg.fixing.ext.groups"},{"l":"edu.ucsd.sbrg.io"},{"l":"edu.ucsd.sbrg.io.parsers.cobra"},{"l":"edu.ucsd.sbrg.io.parsers.json"},{"l":"edu.ucsd.sbrg.io.parsers.json.mapping"},{"l":"edu.ucsd.sbrg.parameters"},{"l":"edu.ucsd.sbrg.polishing"},{"l":"edu.ucsd.sbrg.polishing.fbc"},{"l":"edu.ucsd.sbrg.reporting"},{"l":"edu.ucsd.sbrg.resolver"},{"l":"edu.ucsd.sbrg.resolver.identifiersorg"},{"l":"edu.ucsd.sbrg.resolver.identifiersorg.mapping"},{"l":"edu.ucsd.sbrg.util"},{"l":"edu.ucsd.sbrg.util.ext.fbc"},{"l":"edu.ucsd.sbrg.util.ext.groups"},{"l":"edu.ucsd.sbrg.validation"}];updateSearchResults(); \ No newline at end of file diff --git a/docs/serialized-form.html b/docs/serialized-form.html index 94f0df1b..de033ea4 100644 --- a/docs/serialized-form.html +++ b/docs/serialized-form.html @@ -85,25 +85,6 @@
      registry
    -
  • -
    -

    Exception edu.ucsd.sbrg.ModelValidatorException

    -
    class ModelValidatorException extends Exception implements Serializable
    -
      -
    • -
      -

      Serialized Fields

      -
        -
      • -
        outputFile
        -
        File outputFile
        -
        • -
      -
      -
      • -
    -
    -
    • @@ -152,8 +133,8 @@

    Package 
  • -

    Exception edu.ucsd.sbrg.io.ModelReaderException

    -
    class ModelReaderException extends Exception implements Serializable
    +

    Class edu.ucsd.sbrg.io.ModelReaderException

    +
    class ModelReaderException extends Throwable implements Serializable
    • @@ -199,6 +180,32 @@
      output
    • +
  • +
    +

    Package edu.ucsd.sbrg.validation

    + +
    +
    • diff --git a/docs/type-search-index.js b/docs/type-search-index.js index 64f7b042..b97049b1 100644 --- a/docs/type-search-index.js +++ b/docs/type-search-index.js @@ -1 +1 @@ -typeSearchIndex = [{"p":"edu.ucsd.sbrg.annotation.adb","l":"AbstractADBAnnotator"},{"p":"edu.ucsd.sbrg.annotation","l":"AbstractAnnotator"},{"p":"edu.ucsd.sbrg.annotation.bigg","l":"AbstractBiGGAnnotator"},{"p":"edu.ucsd.sbrg.polishing","l":"AbstractPolisher"},{"p":"edu.ucsd.sbrg.parameters","l":"ADBAnnotationParameters"},{"p":"edu.ucsd.sbrg.annotation.adb","l":"ADBReactionsAnnotator"},{"p":"edu.ucsd.sbrg.annotation.adb","l":"ADBSBMLAnnotator"},{"p":"edu.ucsd.sbrg.annotation.adb","l":"ADBSpeciesAnnotator"},{"l":"All Classes and 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\ No newline at end of file diff --git a/src/main/java/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.java b/src/main/java/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.java index 48b92327..a5e140cb 100644 --- a/src/main/java/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.java +++ b/src/main/java/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.java @@ -242,7 +242,7 @@ public void parseGeneReactionRules(Reaction reaction, BiGGId biggId) throws SQLE String abbreviation = biggId.getAbbreviation(); List geneReactionRules = bigg.getGeneReactionRule(abbreviation, reaction.getModel().getId()); for (String geneReactionRule : geneReactionRules) { - GPRParser.parseGPR(reaction, geneReactionRule, sboParameters.addGenericTerms()); + GPRParser.setGeneProductAssociation(reaction, geneReactionRule, sboParameters.addGenericTerms()); } } diff --git a/src/main/java/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.java b/src/main/java/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.java index 4e5c3554..30788089 100644 --- a/src/main/java/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.java +++ b/src/main/java/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.java @@ -8,7 +8,7 @@ import edu.ucsd.sbrg.parameters.BiGGAnnotationParameters; import edu.ucsd.sbrg.parameters.SBOParameters; import edu.ucsd.sbrg.annotation.AnnotationsSorter; -import edu.ucsd.sbrg.annotation.bigg.fbc.BiGGFBCAnnotator; +import edu.ucsd.sbrg.annotation.bigg.ext.fbc.BiGGFBCAnnotator; import edu.ucsd.sbrg.reporting.ProgressObserver; import edu.ucsd.sbrg.resolver.Registry; import org.sbml.jsbml.Model; diff --git a/src/main/java/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.java b/src/main/java/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGFBCAnnotator.java similarity index 97% rename from src/main/java/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.java rename to src/main/java/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGFBCAnnotator.java index 9db7d7c2..76db4305 100644 --- a/src/main/java/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.java +++ b/src/main/java/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGFBCAnnotator.java @@ -1,4 +1,4 @@ -package edu.ucsd.sbrg.annotation.bigg.fbc; +package edu.ucsd.sbrg.annotation.bigg.ext.fbc; import edu.ucsd.sbrg.annotation.IAnnotateSBases; import edu.ucsd.sbrg.parameters.BiGGAnnotationParameters; diff --git a/src/main/java/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.java b/src/main/java/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGGeneProductAnnotator.java similarity index 99% rename from src/main/java/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.java rename to src/main/java/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGGeneProductAnnotator.java index cd44429e..fa308818 100644 --- a/src/main/java/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.java +++ b/src/main/java/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGGeneProductAnnotator.java @@ -1,4 +1,4 @@ -package edu.ucsd.sbrg.annotation.bigg.fbc; +package edu.ucsd.sbrg.annotation.bigg.ext.fbc; import de.zbit.util.ResourceManager; import edu.ucsd.sbrg.annotation.IAnnotateSBases; diff --git a/src/main/java/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductReferencesAnnotator.java b/src/main/java/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGGeneProductReferencesAnnotator.java similarity index 98% rename from src/main/java/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductReferencesAnnotator.java rename to src/main/java/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGGeneProductReferencesAnnotator.java index 325f5565..1b78d9cf 100644 --- a/src/main/java/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductReferencesAnnotator.java +++ b/src/main/java/edu/ucsd/sbrg/annotation/bigg/ext/fbc/BiGGGeneProductReferencesAnnotator.java @@ -1,4 +1,4 @@ -package edu.ucsd.sbrg.annotation.bigg.fbc; +package edu.ucsd.sbrg.annotation.bigg.ext.fbc; import org.sbml.jsbml.ListOf; import org.sbml.jsbml.Reaction; diff --git a/src/main/java/edu/ucsd/sbrg/db/bigg/BiGGId.java b/src/main/java/edu/ucsd/sbrg/db/bigg/BiGGId.java index 6445dbca..22b19150 100644 --- a/src/main/java/edu/ucsd/sbrg/db/bigg/BiGGId.java +++ b/src/main/java/edu/ucsd/sbrg/db/bigg/BiGGId.java @@ -102,13 +102,7 @@ public BiGGId(String prefix, String abbreviation, String compartmentCode, String parseBiGGId(id); } - /** - * Creates a BiGG ID for a metabolite based on the provided string identifier. - * This method handles the correction and standardization of the metabolite ID according to BiGG database standards. - * - * @param id The raw metabolite ID string. - * @return An Optional containing the BiGGId if the ID is non-empty and valid, or an empty Optional otherwise. - */ + public static BiGGId createMetaboliteId(String id) { // Fix the compartment code in the ID id = fixCompartmentCode(id); @@ -139,18 +133,6 @@ public static BiGGId createMetaboliteId(String id) { } - /** - * Creates a BiGG ID for a gene, with an option to correct the ID to conform to BiGG standards. - *

    - * This method first checks if the provided ID is empty, returning an empty Optional if true. - * If the 'correct' parameter is true, the ID is processed to conform to BiGG standards: - * - Leading underscores are removed. - * - The prefix "g_" is replaced with "G_" to standardize the gene ID format. - * - If the ID does not start with "G_", the prefix "G_" is prepended. - * - * @param id The raw gene ID string. - * @return An Optional containing the BiGGId if the ID is non-empty and valid, or an empty Optional otherwise. - */ public static BiGGId createGeneId(String id) { id = makeBiGGConform(id); if (id.startsWith("_")) { @@ -164,14 +146,7 @@ public static BiGGId createGeneId(String id) { return new BiGGId(id); } - /** - * Creates a BiGG ID for a reaction based on the provided string identifier. - * This method handles the prefix stripping and checks if the reaction is a pseudo-reaction. - * Depending on these checks, it delegates to the overloaded createReactionId method with appropriate flags. - * - * @param id The raw reaction ID string. - * @return An Optional containing the BiGGId if the ID is non-empty and valid, or an empty Optional otherwise. - */ + public static BiGGId createReactionId(String id) { String prefixStripped = ""; // Strip the prefix if it starts with 'R_' or 'r_' @@ -250,8 +225,12 @@ private static String makeBiGGConform(String id) { id = "_" + id; } // Replace problematic characters with specific strings - id = id.replaceAll("[-/]", "__").replaceAll("\\.", "__SBML_DOT__").replaceAll("\\(", "_LPAREN_") - .replaceAll("\\)", "_RPAREN_").replaceAll("\\[", "_LBRACKET_").replaceAll("]", "_RBRACKET_"); + id = id.replaceAll("[-/]", "__") + .replaceAll("\\.", "__SBML_DOT__") + .replaceAll("\\(", "_LPAREN_") + .replaceAll("\\)", "_RPAREN_") + .replaceAll("\\[", "_LBRACKET_") + .replaceAll("]", "_RBRACKET_"); // Extract and reformat compartment codes enclosed in parentheses Pattern parenCompartment = Pattern.compile("_LPAREN_(?.*?)_RPAREN_"); Matcher parenMatcher = parenCompartment.matcher(id); @@ -353,13 +332,13 @@ private void parseBiGGId(String id) { */ private void handleNormalId(Matcher matcher) { String prefix = matcher.group("prefix"); - setPrefix(prefix); + this.setPrefix(prefix); String abbreviation = matcher.group("abbreviation"); - setAbbreviation(abbreviation); + this.setAbbreviation(abbreviation); String compartment = matcher.group("compartment"); - setCompartmentCode(compartment); + this.setCompartmentCode(compartment); String tissueCode = matcher.group("tissueCode"); - setTissueCode(tissueCode); + this.setTissueCode(tissueCode); } @@ -380,17 +359,17 @@ private void handleSpecialCases(String id) { id = id.replaceAll("^([Rr]_?)?[Ee][Xx]", "EX"); id = id.replaceAll("^([Rr]_?)?[Dd][Mm]", "DM"); id = id.replaceAll("^([Rr]_?)?[Ss]([Ii][Nn])?[Kk]", "SK"); - setAbbreviation(id); + this.setAbbreviation(id); } else if (biomassMatcher.matches()) { id = id.replaceAll("^([Rr]_?)?[Bb][Ii][Oo][Mm][Aa][Ss][Ss]", "BIOMASS"); - setAbbreviation(id); + this.setAbbreviation(id); } else if (atpmMatcher.matches()) { - setAbbreviation("ATPM"); + this.setAbbreviation("ATPM"); } else if (compartmentMatcher.matches()) { - setAbbreviation(id); + this.setAbbreviation(id); } else { logger.info(format(MESSAGES.getString("BIGGID_CONVERSION_FAIL"), id)); - setAbbreviation(id); + this.setAbbreviation(id); } } diff --git a/src/main/java/edu/ucsd/sbrg/io/parsers/cobra/MatlabParser.java b/src/main/java/edu/ucsd/sbrg/io/parsers/cobra/MatlabParser.java index b8c5998a..674ba119 100644 --- a/src/main/java/edu/ucsd/sbrg/io/parsers/cobra/MatlabParser.java +++ b/src/main/java/edu/ucsd/sbrg/io/parsers/cobra/MatlabParser.java @@ -219,7 +219,7 @@ private void parseGPRs(Model model) { if (model.getReaction(i) == null) { logger.info(format(MESSAGES.getString("CREATE_GPR_FAILED"), i)); } else { - GPRParser.parseGPR(model.getReaction(i), geneReactionRule, sboParameters.addGenericTerms()); + GPRParser.setGeneProductAssociation(model.getReaction(i), geneReactionRule, sboParameters.addGenericTerms()); } } }); diff --git a/src/main/java/edu/ucsd/sbrg/io/parsers/json/JSONParser.java b/src/main/java/edu/ucsd/sbrg/io/parsers/json/JSONParser.java index 64a3f828..5a328436 100644 --- a/src/main/java/edu/ucsd/sbrg/io/parsers/json/JSONParser.java +++ b/src/main/java/edu/ucsd/sbrg/io/parsers/json/JSONParser.java @@ -365,7 +365,7 @@ public void parseReaction(ModelBuilder builder, Reaction reaction, String id) { setReactionStoichiometry(reaction, model, r); String geneReactionRule = reaction.getGeneReactionRule(); if (!geneReactionRule.isEmpty()) { - GPRParser.parseGPR(r, geneReactionRule, false); + GPRParser.setGeneProductAssociation(r, geneReactionRule, false); } createSubsystem(model, reaction, r); setObjectiveCoefficient(reaction, model, r); diff --git a/src/main/java/edu/ucsd/sbrg/polishing/ModelPolisher.java b/src/main/java/edu/ucsd/sbrg/polishing/ModelPolisher.java index b8acbfbe..8aad8cda 100644 --- a/src/main/java/edu/ucsd/sbrg/polishing/ModelPolisher.java +++ b/src/main/java/edu/ucsd/sbrg/polishing/ModelPolisher.java @@ -17,7 +17,7 @@ import de.zbit.util.ResourceManager; import edu.ucsd.sbrg.parameters.PolishingParameters; import edu.ucsd.sbrg.parameters.SBOParameters; -import edu.ucsd.sbrg.polishing.fbc.FBCPolisher; +import edu.ucsd.sbrg.polishing.ext.fbc.FBCPolisher; import edu.ucsd.sbrg.reporting.ProgressObserver; import edu.ucsd.sbrg.resolver.Registry; import org.sbml.jsbml.*; diff --git a/src/main/java/edu/ucsd/sbrg/polishing/ReactionsPolisher.java b/src/main/java/edu/ucsd/sbrg/polishing/ReactionsPolisher.java index 418a4d72..0c79cdcd 100644 --- a/src/main/java/edu/ucsd/sbrg/polishing/ReactionsPolisher.java +++ b/src/main/java/edu/ucsd/sbrg/polishing/ReactionsPolisher.java @@ -1,170 +1,173 @@ -package edu.ucsd.sbrg.polishing; - -import edu.ucsd.sbrg.parameters.PolishingParameters; -import edu.ucsd.sbrg.parameters.SBOParameters; -import edu.ucsd.sbrg.db.bigg.BiGGId; -import edu.ucsd.sbrg.resolver.Registry; -import edu.ucsd.sbrg.reporting.ProgressObserver; -import edu.ucsd.sbrg.util.ReactionNamePatterns; -import org.sbml.jsbml.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; - - -/** - * This class provides methods to polish and validate SBML reactions according to specific rules and patterns. - * It includes functionality to: - * - Check and set SBO terms based on reaction ID patterns. - * - Polish species references and compartments. - * - Validate and set flux bounds and objectives. - * - Convert gene associations from reaction notes to FBCv2 format. - * - Check mass and atom balance of reactions. - *

    - * The class operates on an SBML {@link Reaction} object and modifies it to conform to standards and conventions - * used in systems biology models, particularly those related to flux balance constraints. - */ -public class ReactionsPolisher extends AbstractPolisher implements IPolishSBases { - - private static final Logger logger = LoggerFactory.getLogger(ReactionsPolisher.class); - - private final SBOParameters sboParameters; - - public ReactionsPolisher(PolishingParameters polishingParameters, - SBOParameters sboParameters, - Registry registry) { - super(polishingParameters, registry); - this.sboParameters = sboParameters; - } + package edu.ucsd.sbrg.polishing; - public ReactionsPolisher(PolishingParameters polishingParameters, - SBOParameters sboParameters, - Registry registry, - List observers) { - super(polishingParameters, registry, observers); - this.sboParameters = sboParameters; - } + import edu.ucsd.sbrg.parameters.PolishingParameters; + import edu.ucsd.sbrg.parameters.SBOParameters; + import edu.ucsd.sbrg.db.bigg.BiGGId; + import edu.ucsd.sbrg.resolver.Registry; + import edu.ucsd.sbrg.reporting.ProgressObserver; + import edu.ucsd.sbrg.util.ReactionNamePatterns; + import org.sbml.jsbml.*; + import org.slf4j.Logger; + import org.slf4j.LoggerFactory; - @Override - public void polish(List reactions) { - logger.debug("Polish Reactions"); + import java.util.List; + import java.util.Objects; + import java.util.Optional; + import java.util.stream.Collectors; - for (var reaction : reactions) { - statusReport("Polishing Reactions (5/9) ", reaction); - polish(reaction); - } - } /** - * Polishes the reaction by applying various checks and modifications to ensure it conforms to - * the expected standards and conventions. This includes setting SBO terms, checking compartments, - * and ensuring proper setup of reactants and products. + * This class provides methods to polish and validate SBML reactions according to specific rules and patterns. + * It includes functionality to: + * - Check and set SBO terms based on reaction ID patterns. + * - Polish species references and compartments. + * - Validate and set flux bounds and objectives. + * - Convert gene associations from reaction notes to FBCv2 format. + * - Check mass and atom balance of reactions. + *

    + * The class operates on an SBML {@link Reaction} object and modifies it to conform to standards and conventions + * used in systems biology models, particularly those related to flux balance constraints. */ - @Override - public void polish(Reaction reaction) { - var originalReaction = reaction.clone(); - // Process any external resources linked via annotations in the reaction - new AnnotationPolisher(polishingParameters, registry).polish(reaction.getAnnotation()); + public class ReactionsPolisher extends AbstractPolisher implements IPolishSBases { - setMetaId(reaction); + private static final Logger logger = LoggerFactory.getLogger(ReactionsPolisher.class); - if (sboParameters.addGenericTerms()) { - if (reaction.isSetListOfReactants()) { - new SpeciesReferencesPolisher(SBO.getReactant()).polish(reaction.getListOfReactants()); - } - if (reaction.isSetListOfProducts()) { - new SpeciesReferencesPolisher(SBO.getProduct()).polish(reaction.getListOfProducts()); + private final SBOParameters sboParameters; + + public ReactionsPolisher(PolishingParameters polishingParameters, + SBOParameters sboParameters, + Registry registry) { + super(polishingParameters, registry); + this.sboParameters = sboParameters; + } + + public ReactionsPolisher(PolishingParameters polishingParameters, + SBOParameters sboParameters, + Registry registry, + List observers) { + super(polishingParameters, registry, observers); + this.sboParameters = sboParameters; + } + + @Override + public void polish(List reactions) { + logger.debug("Polish Reactions"); + + for (var reaction : reactions) { + statusReport("Polishing Reactions (5/9) ", reaction); + polish(reaction); } } - setCompartmentFromReactionParticipants(reaction); + /** + * Polishes the reaction by applying various checks and modifications to ensure it conforms to + * the expected standards and conventions. This includes setting SBO terms, checking compartments, + * and ensuring proper setup of reactants and products. + */ + @Override + public void polish(Reaction reaction) { + var originalReaction = reaction.clone(); + // Process any external resources linked via annotations in the reaction + new AnnotationPolisher(polishingParameters, registry).polish(reaction.getAnnotation()); + + setMetaId(reaction); + + if (sboParameters.addGenericTerms()) { + if (reaction.isSetListOfReactants()) { + new SpeciesReferencesPolisher(SBO.getReactant()).polish(reaction.getListOfReactants()); + } + if (reaction.isSetListOfProducts()) { + new SpeciesReferencesPolisher(SBO.getProduct()).polish(reaction.getListOfProducts()); + } + } - removeCopySuffix(reaction); + setCompartmentFromReactionParticipants(reaction); - setSBOTerm(reaction); - } + removeCopySuffix(reaction); - private void setMetaId(Reaction reaction) { - if (!reaction.isSetMetaId() && (reaction.getCVTermCount() > 0)) { - reaction.setMetaId(reaction.getId()); + setSBOTerm(reaction); } - } - private void setCompartmentFromReactionParticipants(Reaction reaction) { - if (reaction.getCompartment() == null || reaction.getCompartment().isEmpty()) { - var reactantsCompartment = getCommonCompartmentCode(reaction.getListOfReactants()); - var productsCompartment = getCommonCompartmentCode(reaction.getListOfProducts()); - if (reactantsCompartment.isEmpty() && productsCompartment.isPresent()) { - reaction.setCompartment(productsCompartment.get()); - } - else if (reactantsCompartment.isPresent() && productsCompartment.isEmpty()) { - reaction.setCompartment(reactantsCompartment.get()); + private void setMetaId(Reaction reaction) { + if (!reaction.isSetMetaId() && (reaction.getCVTermCount() > 0)) { + reaction.setMetaId(reaction.getId()); } - else if (reactantsCompartment.isPresent() - && reactantsCompartment.get().equals(productsCompartment.get())) { - reaction.setCompartment(reactantsCompartment.get()); + } + + private void setCompartmentFromReactionParticipants(Reaction reaction) { + if (reaction.getCompartment() == null || reaction.getCompartment().isEmpty()) { + var reactantsCompartment = getCommonCompartmentCode(reaction.getListOfReactants()); + var productsCompartment = getCommonCompartmentCode(reaction.getListOfProducts()); + if (reactantsCompartment.isEmpty() && productsCompartment.isPresent()) { + reaction.setCompartment(productsCompartment.get()); + } + else if (reactantsCompartment.isPresent() && productsCompartment.isEmpty()) { + reaction.setCompartment(reactantsCompartment.get()); + } + else if (reactantsCompartment.isPresent() + && reactantsCompartment.get().equals(productsCompartment.get())) { + reaction.setCompartment(reactantsCompartment.get()); + } } } - } - private Optional getCommonCompartmentCode(ListOf speciesReferences) { - // Attempt to identify a common compartment for all species references - if (null != speciesReferences) { - var modelSpecies = speciesReferences.stream() - .map(SpeciesReference::getSpeciesInstance) - .map(Species::getCompartmentInstance) - .map(Compartment::getId) - .collect(Collectors.toSet()); - return modelSpecies.size() == 1 ? modelSpecies.stream().findFirst() : Optional.empty(); + private Optional getCommonCompartmentCode(ListOf speciesReferences) { + // Attempt to identify a common compartment for all species references + if (null != speciesReferences) { + var modelSpecies = speciesReferences.stream() + .map(SpeciesReference::getSpeciesInstance) + .filter(Objects::nonNull) + .map(Species::getCompartmentInstance) + .filter(Objects::nonNull ) + .map(Compartment::getId) + .collect(Collectors.toSet()); + return modelSpecies.size() == 1 ? modelSpecies.stream().findFirst() : Optional.empty(); + } + return Optional.empty(); } - return Optional.empty(); - } - private void removeCopySuffix(Reaction reaction) { - String rName = reaction.getName(); - if (rName.matches(".*_copy\\d*")) { - rName = rName.substring(0, rName.lastIndexOf('_')); - reaction.setName(rName); + private void removeCopySuffix(Reaction reaction) { + String rName = reaction.getName(); + if (rName.matches(".*_copy\\d*")) { + rName = rName.substring(0, rName.lastIndexOf('_')); + reaction.setName(rName); + } } - } - private void setSBOTerm(Reaction reaction) { - setSBOTermFromPattern(reaction, BiGGId.createReactionId(reaction.getId())); + private void setSBOTerm(Reaction reaction) { + setSBOTermFromPattern(reaction, BiGGId.createReactionId(reaction.getId())); - if (!reaction.isSetSBOTerm()) { - if (reaction.getReactantCount() != 0 && reaction.getProductCount() == 0 && !reaction.isReversible()) { - reaction.setSBOTerm(632); - } - else if (reaction.getReactantCount() == 0 && reaction.getProductCount() != 0 && !reaction.isReversible()) { - reaction.setSBOTerm(628); + if (!reaction.isSetSBOTerm()) { + if (reaction.getReactantCount() != 0 && reaction.getProductCount() == 0 && !reaction.isReversible()) { + reaction.setSBOTerm(632); + } + else if (reaction.getReactantCount() == 0 && reaction.getProductCount() != 0 && !reaction.isReversible()) { + reaction.setSBOTerm(628); + } } } - } - /** - * Sets the Systems Biology Ontology (SBO) term for a reaction based on the abbreviation of its BiGG ID. - * The method matches the abbreviation against predefined patterns to determine the appropriate SBO term. - * - * @param id The BiGGId object containing the abbreviation to be checked. - */ - private void setSBOTermFromPattern(Reaction reaction, BiGGId id) { - String abbrev = id.getAbbreviation(); - if (ReactionNamePatterns.BIOMASS_CASE_INSENSITIVE.getPattern().matcher(abbrev).matches()) { - reaction.setSBOTerm(629); // Set SBO term for biomass production - } else if (ReactionNamePatterns.DEMAND_REACTION.getPattern().matcher(abbrev).matches()) { - reaction.setSBOTerm(628); // Set SBO term for demand reaction - } else if (ReactionNamePatterns.EXCHANGE_REACTION.getPattern().matcher(abbrev).matches()) { - reaction.setSBOTerm(627); // Set SBO term for exchange reaction - } else if (ReactionNamePatterns.ATP_MAINTENANCE.getPattern().matcher(abbrev).matches()) { - reaction.setSBOTerm(630); // Set SBO term for ATP maintenance - } else if (ReactionNamePatterns.SINK_REACTION.getPattern().matcher(abbrev).matches()) { - reaction.setSBOTerm(632); // Set SBO term for sink reaction + /** + * Sets the Systems Biology Ontology (SBO) term for a reaction based on the abbreviation of its BiGG ID. + * The method matches the abbreviation against predefined patterns to determine the appropriate SBO term. + * + * @param id The BiGGId object containing the abbreviation to be checked. + */ + private void setSBOTermFromPattern(Reaction reaction, BiGGId id) { + String abbrev = id.getAbbreviation(); + if (ReactionNamePatterns.BIOMASS_CASE_INSENSITIVE.getPattern().matcher(abbrev).matches()) { + reaction.setSBOTerm(629); // Set SBO term for biomass production + } else if (ReactionNamePatterns.DEMAND_REACTION.getPattern().matcher(abbrev).matches()) { + reaction.setSBOTerm(628); // Set SBO term for demand reaction + } else if (ReactionNamePatterns.EXCHANGE_REACTION.getPattern().matcher(abbrev).matches()) { + reaction.setSBOTerm(627); // Set SBO term for exchange reaction + } else if (ReactionNamePatterns.ATP_MAINTENANCE.getPattern().matcher(abbrev).matches()) { + reaction.setSBOTerm(630); // Set SBO term for ATP maintenance + } else if (ReactionNamePatterns.SINK_REACTION.getPattern().matcher(abbrev).matches()) { + reaction.setSBOTerm(632); // Set SBO term for sink reaction + } } - } -} + } diff --git a/src/main/java/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.java b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/FBCPolisher.java similarity index 98% rename from src/main/java/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.java rename to src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/FBCPolisher.java index 89d47056..7fd9f3bb 100644 --- a/src/main/java/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.java +++ b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/FBCPolisher.java @@ -1,4 +1,4 @@ -package edu.ucsd.sbrg.polishing.fbc; +package edu.ucsd.sbrg.polishing.ext.fbc; import de.zbit.util.ResourceManager; import edu.ucsd.sbrg.parameters.SBOParameters; diff --git a/src/main/java/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisher.java b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/FBCReactionPolisher.java similarity index 91% rename from src/main/java/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisher.java rename to src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/FBCReactionPolisher.java index 6c9ec004..9e52c9a0 100644 --- a/src/main/java/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisher.java +++ b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/FBCReactionPolisher.java @@ -1,4 +1,4 @@ -package edu.ucsd.sbrg.polishing.fbc; +package edu.ucsd.sbrg.polishing.ext.fbc; import edu.ucsd.sbrg.parameters.PolishingParameters; import edu.ucsd.sbrg.parameters.SBOParameters; @@ -33,7 +33,7 @@ public FBCReactionPolisher(FBCModelPlugin fbcPlugin, this.gpaProcessor = new GeneProductAssociationsProcessor(); } - public FBCReactionPolisher(FBCModelPlugin fbcPlugin, + public FBCReactionPolisher(FBCModelPlugin fbcPlugin, PolishingParameters polishingParameters, SBOParameters sboParameters, Registry registry, @@ -67,7 +67,7 @@ private void fluxObjectiveFromLocalParameter(Reaction reaction) { Objective obj = fbcPlugin.getActiveObjectiveInstance(); // Check if a flux objective associated with the reaction already exists - boolean foExists = obj.getListOfFluxObjectives().stream() + boolean foExists = obj.getListOfFluxObjectives().stream() .anyMatch(fo -> fo.getReactionInstance().equals(reaction)); if (foExists) { return; @@ -86,11 +86,7 @@ private void fluxObjectiveFromLocalParameter(Reaction reaction) { } } - /** - * This method extracts gene associations from the notes of a reaction and converts them into - * the FBCv2 GeneProductAssociation format. It specifically looks for notes tagged with "GENE_ASSOCIATION:" - * and processes them to set the gene product association for the reaction if it has not been set already. - */ + private void associationFromNotes(Reaction reaction) { // Obtain the FBC plugin for the reaction to handle FBC-specific features. var reactionPlugin = (FBCReactionPlugin) reaction.getPlugin(FBCConstants.shortLabel); @@ -115,7 +111,7 @@ private void associationFromNotes(Reaction reaction) { String association = splits[1]; if (!association.isEmpty()) { // Parse the gene product association and apply it to the reaction. - GPRParser.parseGPR(reaction, association, sboParameters.addGenericTerms()); + GPRParser.setGeneProductAssociation(reaction, association, sboParameters.addGenericTerms()); } } } @@ -201,7 +197,7 @@ public void setFluxBoundSBOTerm(Parameter bound) { * Retrieves a local parameter from a reaction's kinetic law based on the specified parameter name. * This method specifically looks for parameters that define either the lower or upper flux bounds. * - * @param r The reaction from which the kinetic law and the parameter are to be retrieved. + * @param r The reaction from which the kinetic law and the parameter are to be retrieved. * @param parameterName The name of the parameter to retrieve, expected to be either "LOWER_BOUND" or "UPPER_BOUND". * @return The local parameter if found, or {@code null} if the kinetic law is not defined or the parameter does not exist. */ @@ -219,8 +215,8 @@ private Parameter getBoundFromKineticLawParameters(Reaction r, String parameterN * If the bound value matches a specific threshold, the ID is set to a corresponding default value. * Otherwise, the ID is customized using the reaction's ID combined with the original bound's ID. * - * @param r The {@link Reaction} instance from which the model and parameter are derived. - * @param bound The {@link Parameter} instance representing either a lower or upper bound. + * @param r The {@link Reaction} instance from which the model and parameter are derived. + * @param bound The {@link Parameter} instance representing either a lower or upper bound. * @param boundValue The numeric value of the bound, which determines how the {@link Parameter}'s ID is set. */ private void setBoundId(Reaction r, Parameter bound, double boundValue) { diff --git a/src/main/java/edu/ucsd/sbrg/polishing/fbc/GeneProductAssociationsProcessor.java b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/GeneProductAssociationsProcessor.java similarity index 59% rename from src/main/java/edu/ucsd/sbrg/polishing/fbc/GeneProductAssociationsProcessor.java rename to src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/GeneProductAssociationsProcessor.java index 278f5f2a..e53ad943 100644 --- a/src/main/java/edu/ucsd/sbrg/polishing/fbc/GeneProductAssociationsProcessor.java +++ b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/GeneProductAssociationsProcessor.java @@ -1,4 +1,4 @@ -package edu.ucsd.sbrg.polishing.fbc; +package edu.ucsd.sbrg.polishing.ext.fbc; import de.zbit.util.ResourceManager; import edu.ucsd.sbrg.db.bigg.BiGGId; @@ -19,61 +19,43 @@ public class GeneProductAssociationsProcessor { private static final Logger logger = LoggerFactory.getLogger(GeneProductAssociationsProcessor.class); private static final ResourceBundle MESSAGES = ResourceManager.getBundle("edu.ucsd.sbrg.polisher.Messages"); - /** - * Mapping holding geneAssociations from model annotations - */ - private Map oldGeneAssociations; + private final Map oldGeneAssociations = new HashMap<>(); - /** - * Converts gene product associations from a given reaction to the FBC v2 format. - * This method processes the non-RDF annotations of the reaction's model to update or create - * gene product associations according to the FBC v2 specification. - * - * @param reaction The reaction whose gene product associations are to be converted. - * @param omitGenericTerms A boolean flag indicating whether to omit generic terms (SBO terms) in the association. - */ - public void convertAssociationsToFBCV2(Reaction reaction, boolean omitGenericTerms) { - Model model = reaction.getModel(); - Annotation annotation = model.getAnnotation(); - XMLNode node = annotation.getNonRDFannotation(); - if (node == null) { - return; - } - if (oldGeneAssociations == null) { - oldGeneAssociations = new HashMap<>(); - for (int i = 0; i < node.getChildCount(); i++) { - XMLNode current = node.getChild(i); - if (current.getName().equals("geneAssociation")) { - String reactionId = current.getAttributes().getValue("reaction"); - oldGeneAssociations.put(reactionId, node.getChild(i)); - node.removeChild(i); - } - } - } + public void convertAssociationsToFBCV2(Reaction reaction, boolean addGenericTerms) { + var model = reaction.getModel(); String id = reaction.getId(); XMLNode ga = oldGeneAssociations.getOrDefault(id, null); if (ga != null) { - FBCReactionPlugin plugin = (FBCReactionPlugin) reaction.getPlugin(FBCConstants.shortLabel); - GeneProductAssociation gpa = new GeneProductAssociation(reaction.getLevel(), reaction.getVersion()); - List associations = processAssociation(ga, model, omitGenericTerms); + var reactionPlugin = (FBCReactionPlugin) reaction.getPlugin(FBCConstants.shortLabel); + var gpa = new GeneProductAssociation(reaction.getLevel(), reaction.getVersion()); + List associations = processAssociation(ga, model, addGenericTerms); if (associations.size() == 1) { gpa.setAssociation(associations.get(0)); - plugin.setGeneProductAssociation(gpa); + reactionPlugin.setGeneProductAssociation(gpa); + } + } + } + + // TODO: das war extrahiert aus convertAssociationsToFBCV2 und muss aufgerufen werden noch + private boolean processNonRDFGeneAssociationAnnotations(Model model) { + var annotation = model.getAnnotation(); + XMLNode node = annotation.getNonRDFannotation(); + if (node == null) { + return true; + } + for (int i = 0; i < node.getChildCount(); i++) { + XMLNode current = node.getChild(i); + if (current.getName().equals("geneAssociation")) { + String reactionId = current.getAttributes().getValue("reaction"); + oldGeneAssociations.put(reactionId, node.getChild(i)); + node.removeChild(i); } } + return false; } - /** - * Processes an XMLNode representing a gene product association and converts it into a list of Association objects. - * This method handles the logical operators "and" and "or", as well as gene product references. - * - * @param association The XMLNode representing the gene product association. - * @param model The SBML model to which the association belongs. - * @param omitGenericTerms A boolean flag indicating whether to omit generic terms (SBO terms) in the association. - * @return A list of Association objects representing the processed gene product association. - */ - private List processAssociation(XMLNode association, Model model, boolean omitGenericTerms) { + private List processAssociation(XMLNode association, Model model, boolean addGenericTerms) { int level = model.getLevel(), version = model.getVersion(); List associations = new ArrayList<>(); for (int i = 0; i < association.getChildCount(); i++) { @@ -81,20 +63,20 @@ private List processAssociation(XMLNode association, Model model, b switch (current.getName()) { case "and": And and = new And(level, version); - if (!omitGenericTerms) { + if (addGenericTerms) { and.setSBOTerm(173); // AND } - and.addAllAssociations(processAssociation(current, model, omitGenericTerms)); + and.addAllAssociations(processAssociation(current, model, addGenericTerms)); if (and.isSetListOfAssociations()) { associations.add(and); } break; case "or": Or or = new Or(level, version); - if (!omitGenericTerms) { + if (!addGenericTerms) { or.setSBOTerm(174); // OR } - or.addAllAssociations(processAssociation(current, model, omitGenericTerms)); + or.addAllAssociations(processAssociation(current, model, addGenericTerms)); if (or.isSetListOfAssociations()) { associations.add(or); } diff --git a/src/main/java/edu/ucsd/sbrg/polishing/fbc/GeneProductsPolisher.java b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/GeneProductsPolisher.java similarity index 98% rename from src/main/java/edu/ucsd/sbrg/polishing/fbc/GeneProductsPolisher.java rename to src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/GeneProductsPolisher.java index 192c1657..c821190e 100644 --- a/src/main/java/edu/ucsd/sbrg/polishing/fbc/GeneProductsPolisher.java +++ b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/GeneProductsPolisher.java @@ -1,4 +1,4 @@ -package edu.ucsd.sbrg.polishing.fbc; +package edu.ucsd.sbrg.polishing.ext.fbc; import edu.ucsd.sbrg.polishing.AbstractPolisher; import edu.ucsd.sbrg.polishing.AnnotationPolisher; diff --git a/src/main/java/edu/ucsd/sbrg/polishing/fbc/ObjectivesPolisher.java b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/ObjectivesPolisher.java similarity index 98% rename from src/main/java/edu/ucsd/sbrg/polishing/fbc/ObjectivesPolisher.java rename to src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/ObjectivesPolisher.java index 1a23701d..6683d6a8 100644 --- a/src/main/java/edu/ucsd/sbrg/polishing/fbc/ObjectivesPolisher.java +++ b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/ObjectivesPolisher.java @@ -1,4 +1,4 @@ -package edu.ucsd.sbrg.polishing.fbc; +package edu.ucsd.sbrg.polishing.ext.fbc; import edu.ucsd.sbrg.polishing.AbstractPolisher; import edu.ucsd.sbrg.parameters.PolishingParameters; diff --git a/src/main/java/edu/ucsd/sbrg/polishing/fbc/StrictnessPredicate.java b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/StrictnessPredicate.java similarity index 99% rename from src/main/java/edu/ucsd/sbrg/polishing/fbc/StrictnessPredicate.java rename to src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/StrictnessPredicate.java index 12fefafd..498fd54a 100644 --- a/src/main/java/edu/ucsd/sbrg/polishing/fbc/StrictnessPredicate.java +++ b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/StrictnessPredicate.java @@ -1,4 +1,4 @@ -package edu.ucsd.sbrg.polishing.fbc; +package edu.ucsd.sbrg.polishing.ext.fbc; import org.sbml.jsbml.*; import org.sbml.jsbml.ext.fbc.*; diff --git a/src/main/java/edu/ucsd/sbrg/reporting/DiffListener.java b/src/main/java/edu/ucsd/sbrg/reporting/DiffListener.java new file mode 100644 index 00000000..e9a8b40b --- /dev/null +++ b/src/main/java/edu/ucsd/sbrg/reporting/DiffListener.java @@ -0,0 +1,46 @@ +package edu.ucsd.sbrg.reporting; + +import edu.ucsd.sbrg.io.parsers.json.mapping.Compartments; +import org.sbml.jsbml.SBase; +import org.sbml.jsbml.Species; +import org.sbml.jsbml.util.TreeNodeChangeListener; +import org.sbml.jsbml.util.TreeNodeRemovedEvent; +import org.sbml.jsbml.util.TreeNodeWithChangeSupport; + +import javax.swing.tree.TreeNode; +import java.beans.PropertyChangeEvent; +import java.util.ArrayList; +import java.util.List; + +public class DiffListener implements TreeNodeChangeListener { + + + private final List removedIds; + + public DiffListener() { + removedIds = new ArrayList<>(); + } +{} + @Override + public void nodeAdded(TreeNode node) { + + } + + @Override + public void nodeRemoved(TreeNodeRemovedEvent event) { + if(event.getSource() instanceof SBase) { + removedIds.add(((SBase) event.getSource()).getId()); + } + } + + @Override + public void propertyChange(PropertyChangeEvent propertyChangeEvent) { + if (propertyChangeEvent.getSource().getClass().equals(Species.class)) { + + } else if (propertyChangeEvent.getSource().getClass().equals(Species.class)) { + + } else if (propertyChangeEvent.getSource().getClass().equals(Species.class)) { + + } + } +} diff --git a/src/main/java/edu/ucsd/sbrg/util/ext/fbc/GPRParser.java b/src/main/java/edu/ucsd/sbrg/util/ext/fbc/GPRParser.java index 56a655b4..acc814f1 100644 --- a/src/main/java/edu/ucsd/sbrg/util/ext/fbc/GPRParser.java +++ b/src/main/java/edu/ucsd/sbrg/util/ext/fbc/GPRParser.java @@ -28,84 +28,55 @@ import static java.text.MessageFormat.format; -/** - * The {@code GPRParser} class provides methods to parse gene product associations (GPRs) from gene reaction rules - * and integrate them into SBML models using JSBML. It supports converting textual gene reaction rules into structured - * {@link Association} objects, handling logical operators, and merging associations into existing models. - * It also includes utilities for converting associations to the FBC v2 format and managing gene product references. - * - *

    This class is designed to be used in scenarios where gene reaction rules need to be parsed from various formats - * and integrated into computational models in a structured and standardized form. It provides comprehensive support - * for handling complex logical structures in gene product associations, such as nested AND/OR conditions.

    - * - *

    Utility methods in this class are static, allowing direct invocation without needing an instance of {@code GPRParser}. - * This class heavily relies on the JSBML library to manipulate elements of SBML files, particularly those related to - * the FBC (Flux Balance Constraints) package.

    - */ + public class GPRParser { private static final Logger logger = LoggerFactory.getLogger(GPRParser.class); private static final ResourceBundle MESSAGES = ResourceManager.getBundle("edu.ucsd.sbrg.polisher.Messages"); - /** - * Parses the gene product association (GPR) from a gene reaction rule string and associates it with a given reaction. - * This method first converts the gene reaction rule string into an Association object using a formula parser. - * If the conversion is successful and the Association object is not null, it further processes the association - * by parsing it into the reaction's gene product association. - * - * @param r The reaction to which the gene product association will be linked. - * @param geneReactionRule The gene reaction rule string representing the association of gene products. - * @param omitGenericTerms Flag indicating whether to omit generic terms (e.g., SBO terms) in the association. - */ - public static void parseGPR(Reaction r, String geneReactionRule, boolean omitGenericTerms) { - ASTNode ast = null; + public static void setGeneProductAssociation(Reaction r, String geneReactionRule, boolean addGenericTerms) { try { - ast = ASTNode.parseFormula( + ASTNode ast = ASTNode.parseFormula( geneReactionRule, new CobraFormulaParser(new StringReader(""))); + Association association = convertToAssociation( ast, - r.getId(), r.getModel(), - omitGenericTerms); - parseGPR(r, association, omitGenericTerms); + addGenericTerms); + + var reactionPlugin = (FBCReactionPlugin) r.getPlugin(FBCConstants.shortLabel); + if (!reactionPlugin.isSetGeneProductAssociation()) { + var gpa = new GeneProductAssociation(r.getLevel(), r.getVersion()); + gpa.setAssociation(association); + reactionPlugin.setGeneProductAssociation(gpa); + } else if (!areEqual(association, reactionPlugin.getGeneProductAssociation().getAssociation())) { + mergeAssociation(r, association, reactionPlugin, addGenericTerms); + } } catch (ParseException e) { logger.info(format(MESSAGES.getString("PARSE_GPR_ERROR"), geneReactionRule, Utils.getMessage(e))); } } - /** - * Converts an ASTNode representing a gene product association into an Association object. - * This method handles the logical structure of the gene product association, creating appropriate - * logical operators (AND, OR) based on the ASTNode type. It also manages the inclusion of SBO terms - * if they are not omitted. - * - * @param ast The ASTNode to be converted, representing the logical structure of the gene product association. - * @param reactionId The ID of the reaction associated with this gene product association. - * @param model The SBML model to which the reaction belongs, used to determine the level and version for new elements. - * @param omitGenericTerms A boolean flag indicating whether to omit SBO terms in the resulting Association. - * @return An Association object representing the gene product association, which could be a LogicalOperator or a direct GeneProductRef. - */ - public static Association convertToAssociation(ASTNode ast, String reactionId, Model model, - boolean omitGenericTerms) { + private static Association convertToAssociation(ASTNode ast, Model model, boolean addGenericTerms) { int level = model.getLevel(), version = model.getVersion(); if (ast.isLogical()) { LogicalOperator operator; if (ast.getType() == ASTNode.Type.LOGICAL_AND) { operator = new And(level, version); - if (!omitGenericTerms) { + if (addGenericTerms) { operator.setSBOTerm(173); // AND } } else { operator = new Or(level, version); - if (!omitGenericTerms) { + if (addGenericTerms) { operator.setSBOTerm(174); // OR } } for (ASTNode child : ast.getListOfNodes()) { - Association tmp = convertToAssociation(child, reactionId, model, omitGenericTerms); + Association tmp = convertToAssociation(child, model, addGenericTerms); if (tmp.getClass().equals(operator.getClass())) { // Flatten binary trees to compact representation LogicalOperator lo = (LogicalOperator) tmp; @@ -118,50 +89,30 @@ public static Association convertToAssociation(ASTNode ast, String reactionId, M } return operator; } - return createGPR(ast.toString(), reactionId, model); + return createGPR(ast.toString(), model); } - /** - * Creates a GeneProductRef instance for a given identifier within a specific reaction context in the model. - * This method first checks if the identifier exists in the model, either with or without a "G_" prefix. - * If the identifier does not exist, it attempts to create a new GeneProduct in the model. - * If the identifier exists, it updates the existing GeneProduct's ID. - * - * @param identifier The identifier for the gene product, which may or may not start with "G_". - * @param reactionId The ID of the reaction associated with this gene product. - * @param model The SBML model containing the reaction and potentially the gene product. - * @return A GeneProductRef object linked to the gene product identified or created. - */ - public static GeneProductRef createGPR(String identifier, String reactionId, Model model) { + private static GeneProductRef createGPR(String astString, Model model) { // Determine the SBML document level and version for creating new elements. int level = model.getLevel(), version = model.getVersion(); - GeneProductRef gpr = new GeneProductRef(level, version); + var gpr = new GeneProductRef(level, version); // Normalize the identifier to include "G_" prefix if missing. - String oldId = identifier.startsWith("G_") ? identifier : "G_" + identifier; + String oldId = astString.startsWith("G_") ? astString : "G_" + astString; boolean containsOldId = !model.containsUniqueNamedSBase(oldId); // Attempt to create or find the GeneProduct using a standardized identifier. - var id = BiGGId.createGeneId(identifier).toBiGGId(); + var id = BiGGId.createGeneId(astString).toBiGGId(); if (!model.containsUniqueNamedSBase(id)) { - GeneProduct gp; // Check if the old ID exists, if so, retrieve the GeneProduct, otherwise use the new ID. if (containsOldId) { - gp = (GeneProduct) model.findUniqueNamedSBase(oldId); + var gp = (GeneProduct) model.findUniqueNamedSBase(oldId); + gp.setId(id); } else { - gp = (GeneProduct) model.findUniqueNamedSBase(id); - } - // If the GeneProduct does not exist, create a new one and log a warning. - if (gp == null) { - logger.info(format(MESSAGES.getString("CREATE_MISSING_GPR"), id, reactionId)); - FBCModelPlugin fbcPlug = (FBCModelPlugin) model.getPlugin(FBCConstants.shortLabel); - gp = fbcPlug.createGeneProduct(id); + var fbcPlug = (FBCModelPlugin) model.getPlugin(FBCConstants.shortLabel); + var gp = fbcPlug.createGeneProduct(id); gp.setLabel(id); - } else { - // If the GeneProduct exists, update its ID and log the update. - logger.info(format(MESSAGES.getString("UPDATE_GP_ID"), gp.getId(), id)); - gp.setId(id); } } // Set the GeneProduct reference in the GeneProductRef. @@ -170,47 +121,80 @@ public static GeneProductRef createGPR(String identifier, String reactionId, Mod } - /** - * Parses the Gene Product Representation (GPR) for a given reaction and updates the reaction's gene product association. - * If the reaction does not have an existing gene product association, a new one is created and set. - * If an association already exists and it is not equivalent to the provided association, the associations are merged. - * - * @param r The reaction for which the GPR is being parsed. - * @param association The association to be parsed and potentially merged into the reaction's gene product association. - * @param omitGenericTerms A boolean flag indicating whether generic terms should be omitted during the merging process. - */ - private static void parseGPR(Reaction r, Association association, boolean omitGenericTerms) { - var reactionPlugin = (FBCReactionPlugin) r.getPlugin(FBCConstants.shortLabel); - if (!reactionPlugin.isSetGeneProductAssociation()) { - var gpa = new GeneProductAssociation(r.getLevel(), r.getVersion()); - gpa.setAssociation(association); - reactionPlugin.setGeneProductAssociation(gpa); - } else if (!areEqual(association, reactionPlugin.getGeneProductAssociation().getAssociation())) { - mergeAssociation(r, association, reactionPlugin, omitGenericTerms); + private static void mergeAssociation(Reaction r, + Association association, + FBCReactionPlugin reactionPlugin, + boolean addGenericTerms) { + // get current association to replace + var oldGpa = reactionPlugin.getGeneProductAssociation().getAssociation(); + var gpa = new GeneProductAssociation(r.getLevel(), r.getVersion()); + // link all GPRs fetched with or + LogicalOperator or = new Or(r.getLevel(), r.getVersion()); + if (addGenericTerms) { + or.setSBOTerm(174); // OR + } + if (oldGpa instanceof And) { + or.addAssociation(oldGpa); + or.addAssociation(association); + Set gprs = new HashSet<>(); + for (int i = 0; i < or.getChildCount(); i++) { + Association current = (Association) or.getChildAt(i); + if (current instanceof GeneProductRef) { + String geneProduct = ((GeneProductRef) current).getGeneProduct(); + if (gprs.contains(geneProduct)) { + if (!or.removeAssociation(current)) { + logger.info(format("Failed to unset duplicate GeneProductReference {0} for reaction {1}", + geneProduct, r.getId())); + } + } else { + gprs.add(geneProduct); + } + } + } + gpa.setAssociation(or); + } else if (oldGpa instanceof GeneProductRef) { + if (association instanceof Or) { + or = (Or) association; + } else { + or.addAssociation(association); + } + or.addAssociation(oldGpa); + gpa.setAssociation(or); + } else { // OR + if (association instanceof Or) { + for (int idx = 0; idx < association.getChildCount(); idx++) { + Association child = (Association) association.getChildAt(idx); + ((Or) association).removeAssociation(idx); + ((LogicalOperator) oldGpa).addAssociation(child); + } + } else { + ((LogicalOperator) oldGpa).addAssociation(association); + } + gpa.setAssociation(oldGpa); } + reactionPlugin.setGeneProductAssociation(gpa); } - - private static boolean areEqual(Association gpa1, Association gpa2) { - if (gpa1.isLeaf() && gpa2.isLeaf()) { + private static boolean areEqual(Association association1, Association association2) { + if (association1.isLeaf() && association2.isLeaf()) { return true; - } else if (gpa1 instanceof Or && gpa2 instanceof Or) { - if (((Or) gpa1).getNumChildren() != ((Or) gpa2).getNumChildren()) { + } else if (association1 instanceof Or && association2 instanceof Or) { + if (((Or) association1).getNumChildren() != ((Or) association2).getNumChildren()) { return false; } else { boolean childrenEqual = true; - for (int i = 0; i < ((Or) gpa1).getNumChildren(); i++) { - childrenEqual &= areEqual((Association) gpa1.getChildAt(i), (Association) gpa2.getChildAt(i)); + for (int i = 0; i < ((Or) association1).getNumChildren(); i++) { + childrenEqual &= areEqual((Association) association1.getChildAt(i), (Association) association2.getChildAt(i)); } return childrenEqual; } - } else if (gpa1 instanceof And && gpa2 instanceof And) { - if (((And) gpa1).getNumChildren() != ((And) gpa2).getNumChildren()) { + } else if (association1 instanceof And && association2 instanceof And) { + if (((And) association1).getNumChildren() != ((And) association2).getNumChildren()) { return false; } else { boolean childrenEqual = true; - for (int i = 0; i < ((And) gpa1).getNumChildren(); i++) { - childrenEqual &= areEqual((Association) gpa1.getChildAt(i), (Association) gpa2.getChildAt(i)); + for (int i = 0; i < ((And) association1).getNumChildren(); i++) { + childrenEqual &= areEqual((Association) association1.getChildAt(i), (Association) association2.getChildAt(i)); } return childrenEqual; } @@ -219,14 +203,6 @@ private static boolean areEqual(Association gpa1, Association gpa2) { } - /** - * Converts an Association object into a human-readable string representation. - * This method handles different types of associations including GeneProductRef, And, and Or. - * For And and Or associations, it recursively calls itself to handle nested associations. - * - * @param association The Association object to be converted into a string. - * @return A string representation of the Association object. - */ public static String stringify(Association association) { if (association instanceof GeneProductRef) { // Directly return the gene product identifier for GeneProductRef instances. @@ -255,68 +231,6 @@ public static String stringify(Association association) { } - /** - * Merges a new association into an existing gene product association for a reaction. - * This method handles the merging of associations by considering different types of associations (AND, OR, GeneProductRef). - * It ensures that duplicate gene products are not added and maintains the logical structure of the association. - * - * @param r The reaction for which the gene product association is being merged. - * @param association The new association to merge into the existing gene product association. - * @param plugin The FBCReactionPlugin instance associated with the reaction. - * @param omitGenericTerms Flag indicating whether to omit generic terms in the association. - */ - private static void mergeAssociation(Reaction r, Association association, FBCReactionPlugin plugin, - boolean omitGenericTerms) { - // get current association to replace - Association old_association = plugin.getGeneProductAssociation().getAssociation(); - plugin.getGeneProductAssociation().unsetAssociation(); - GeneProductAssociation gpa = new GeneProductAssociation(r.getLevel(), r.getVersion()); - // link all GPRs fetched with or - LogicalOperator or = new Or(r.getLevel(), r.getVersion()); - if (!omitGenericTerms) { - or.setSBOTerm(174); // OR - } - if (old_association instanceof And) { - or.addAssociation(old_association); - or.addAssociation(association); - Set gprs = new HashSet<>(); - for (int i = 0; i < or.getChildCount(); i++) { - Association current = (Association) or.getChildAt(i); - if (current instanceof GeneProductRef) { - String geneProduct = ((GeneProductRef) current).getGeneProduct(); - if (gprs.contains(geneProduct)) { - if (!or.removeAssociation(current)) { - logger.info(format("Failed to unset duplicate GeneProductReference {0} for reaction {1}", - geneProduct, r.getId())); - } - } else { - gprs.add(geneProduct); - } - } - } - gpa.setAssociation(or); - } else if (old_association instanceof GeneProductRef) { - if (association instanceof Or) { - or = (Or) association; - } else { - or.addAssociation(association); - } - or.addAssociation(old_association); - gpa.setAssociation(or); - } else { // OR - if (association instanceof Or) { - for (int idx = 0; idx < association.getChildCount(); idx++) { - Association child = (Association) association.getChildAt(idx); - ((Or) association).removeAssociation(idx); - ((LogicalOperator) old_association).addAssociation(child); - } - } else { - ((LogicalOperator) old_association).addAssociation(association); - } - gpa.setAssociation(old_association); - } - plugin.setGeneProductAssociation(gpa); - } diff --git a/src/test/java/edu/ucsd/sbrg/polishing/ReactionsPolisherTest.java b/src/test/java/edu/ucsd/sbrg/polishing/ReactionsPolisherTest.java index b122b791..62a30b4a 100644 --- a/src/test/java/edu/ucsd/sbrg/polishing/ReactionsPolisherTest.java +++ b/src/test/java/edu/ucsd/sbrg/polishing/ReactionsPolisherTest.java @@ -2,15 +2,10 @@ import edu.ucsd.sbrg.parameters.PolishingParameters; import edu.ucsd.sbrg.parameters.SBOParameters; -import edu.ucsd.sbrg.polishing.fbc.StrictnessPredicate; +import edu.ucsd.sbrg.polishing.ext.fbc.StrictnessPredicate; import edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrg; import org.junit.jupiter.api.Test; import org.sbml.jsbml.Model; -import org.sbml.jsbml.Species; -import org.sbml.jsbml.SpeciesReference; - -import java.util.Set; -import java.util.stream.Collectors; import static org.junit.jupiter.api.Assertions.*; diff --git a/src/test/java/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisherTest.java b/src/test/java/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisherTest.java index 301c73ed..de1d2370 100644 --- a/src/test/java/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisherTest.java +++ b/src/test/java/edu/ucsd/sbrg/polishing/fbc/FBCReactionPolisherTest.java @@ -2,6 +2,7 @@ import edu.ucsd.sbrg.parameters.PolishingParameters; import edu.ucsd.sbrg.parameters.SBOParameters; +import edu.ucsd.sbrg.polishing.ext.fbc.FBCReactionPolisher; import edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrg; import org.junit.jupiter.api.Test; import org.sbml.jsbml.Model; diff --git a/src/test/java/edu/ucsd/sbrg/polishing/fbc/ObjectivesPolisherTest.java b/src/test/java/edu/ucsd/sbrg/polishing/fbc/ObjectivesPolisherTest.java index d0a30ae7..de33523b 100644 --- a/src/test/java/edu/ucsd/sbrg/polishing/fbc/ObjectivesPolisherTest.java +++ b/src/test/java/edu/ucsd/sbrg/polishing/fbc/ObjectivesPolisherTest.java @@ -2,16 +2,14 @@ import edu.ucsd.sbrg.parameters.FluxObjectivesPolishingParameters; import edu.ucsd.sbrg.parameters.PolishingParameters; +import edu.ucsd.sbrg.polishing.ext.fbc.ObjectivesPolisher; import edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrg; import org.junit.jupiter.api.Test; import org.sbml.jsbml.Model; import org.sbml.jsbml.ext.fbc.FBCConstants; import org.sbml.jsbml.ext.fbc.FBCModelPlugin; -import org.sbml.jsbml.ext.fbc.FluxObjective; import java.util.List; -import java.util.Set; -import java.util.stream.Collectors; import static org.junit.jupiter.api.Assertions.*;