From 4e237f2b4f6aa77e384c2e07f3999810c8bc033e Mon Sep 17 00:00:00 2001 From: Dario Date: Sat, 27 Jul 2024 00:03:33 +0200 Subject: [PATCH] updated javadocs --- docs/allclasses-index.html | 122 +++++----- docs/constant-values.html | 16 ++ .../ucsd/sbrg/ModelPolisherCLILauncher.html | 2 +- ...l => ModelPolisherOptions.OutputType.html} | 48 ++-- docs/edu/ucsd/sbrg/ModelPolisherOptions.html | 76 +++--- docs/edu/ucsd/sbrg/ModelValidator.html | 28 +-- .../ucsd/sbrg/ModelValidatorException.html | 192 +++++++++++++++ .../sbrg/annotation/AbstractAnnotator.html | 39 ++- .../sbrg/annotation/AnnotationException.html | 169 +++++++++++++ .../annotation/adb/ADBReactionsAnnotator.html | 12 +- .../sbrg/annotation/adb/ADBSBMLAnnotator.html | 7 +- .../annotation/adb/ADBSpeciesAnnotator.html | 12 +- .../annotation/adb/AbstractADBAnnotator.html | 14 +- .../bigg/AbstractBiGGAnnotator.html | 7 +- .../bigg/BiGGAnnotationException.html | 196 +++++++++++++++ .../annotation/bigg/BiGGAnnotationUtils.html | 144 ----------- .../annotation/bigg/BiGGCVTermAnnotator.html | 7 +- .../bigg/BiGGCompartmentsAnnotator.html | 12 +- .../bigg/BiGGDocumentNotesProcessor.html | 9 +- .../annotation/bigg/BiGGModelAnnotator.html | 7 +- .../bigg/BiGGPublicationsAnnotator.html | 7 +- .../bigg/BiGGReactionsAnnotator.html | 32 ++- .../annotation/bigg/BiGGSBMLAnnotator.html | 9 +- .../annotation/bigg/BiGGSpeciesAnnotator.html | 22 +- .../annotation/bigg/fbc/BiGGFBCAnnotator.html | 7 +- .../bigg/fbc/BiGGGeneProductAnnotator.html | 27 ++- .../sbrg/annotation/bigg/package-summary.html | 8 +- .../sbrg/annotation/bigg/package-tree.html | 14 +- .../ucsd/sbrg/annotation/package-summary.html | 10 +- .../ucsd/sbrg/annotation/package-tree.html | 9 + docs/edu/ucsd/sbrg/db/adb/AnnotateDB.html | 5 +- docs/edu/ucsd/sbrg/db/bigg/BiGGDB.html | 150 +++++++++--- docs/edu/ucsd/sbrg/io/CombineArchive.html | 78 +++++- .../sbrg/io/DeleteOnCloseFileInputStream.html | 214 ++++++++++++++++ docs/edu/ucsd/sbrg/io/ModelReader.html | 6 +- .../ModelReaderException.html} | 145 ++++------- docs/edu/ucsd/sbrg/io/ModelWriter.html | 40 +-- .../ucsd/sbrg/io/ModelWriterException.html | 228 ++++++++++++++++++ docs/edu/ucsd/sbrg/io/package-summary.html | 28 ++- docs/edu/ucsd/sbrg/io/package-tree.html | 19 ++ docs/edu/ucsd/sbrg/package-summary.html | 12 +- docs/edu/ucsd/sbrg/package-tree.html | 11 +- .../parameters/CommandLineParameters.html | 44 +++- docs/edu/ucsd/sbrg/parameters/Parameters.html | 29 ++- .../ucsd/sbrg/parameters/package-summary.html | 12 +- .../ucsd/sbrg/parameters/package-tree.html | 1 - .../ucsd/sbrg/polishing/AbstractPolisher.html | 45 ++-- .../sbrg/polishing/AnnotationPolisher.html | 2 +- .../sbrg/polishing/CompartmentPolisher.html | 2 +- .../ucsd/sbrg/polishing/ModelPolisher.html | 2 +- .../sbrg/polishing/ParametersPolisher.html | 2 +- .../sbrg/polishing/ReactionsPolisher.html | 2 +- .../edu/ucsd/sbrg/polishing/SBMLPolisher.html | 2 +- .../ucsd/sbrg/polishing/SpeciesPolisher.html | 2 +- .../edu/ucsd/sbrg/polishing/UnitPolisher.html | 2 +- .../ucsd/sbrg/polishing/fbc/FBCPolisher.html | 2 +- .../polishing/fbc/FluxObjectivesPolisher.html | 2 +- .../polishing/fbc/GeneProductsPolisher.html | 2 +- .../ucsd/sbrg/reporting/ProgressUpdate.html | 22 +- docs/edu/ucsd/sbrg/reporting/ReportType.html | 10 +- docs/index-all.html | 137 +++++++---- docs/member-search-index.js | 2 +- docs/overview-tree.html | 29 ++- docs/serialized-form.html | 111 +++++++++ docs/type-search-index.js | 2 +- 65 files changed, 2023 insertions(+), 643 deletions(-) rename docs/edu/ucsd/sbrg/{ModelPolisherOptions.Compression.html => ModelPolisherOptions.OutputType.html} (86%) create mode 100644 docs/edu/ucsd/sbrg/ModelValidatorException.html create mode 100644 docs/edu/ucsd/sbrg/annotation/AnnotationException.html create mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationException.html delete mode 100644 docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationUtils.html create mode 100644 docs/edu/ucsd/sbrg/io/DeleteOnCloseFileInputStream.html rename docs/edu/ucsd/sbrg/{parameters/OutputParameters.html => io/ModelReaderException.html} (55%) create mode 100644 docs/edu/ucsd/sbrg/io/ModelWriterException.html diff --git a/docs/allclasses-index.html b/docs/allclasses-index.html index aa2cacfb..f3ea6ad7 100644 --- a/docs/allclasses-index.html +++ b/docs/allclasses-index.html @@ -50,7 +50,7 @@

All Classes and Interfaces

-
+
Class
@@ -85,91 +85,95 @@

All Classes and Interfaces<
This interface provides options for connecting to the ADB database.
-
AnnotationParameters
-
 
-
AnnotationPolisher
+
AnnotationException
+
 
+
AnnotationParameters
 
-
AnnotationsSorter
+
AnnotationPolisher
 
+
AnnotationsSorter
+
 
+
BiGGAnnotationException
+
 
BiGGAnnotationParameters
 
-
BiGGAnnotationUtils
-
 
-
BiGGCompartmentsAnnotator
-
+
BiGGCompartmentsAnnotator
+
This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
-
BiGGCVTermAnnotator<T>
-
+
BiGGCVTermAnnotator<T>
+
Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
-
BiGGDB
-
+
BiGGDB
+
This class provides a connection to the BiGG database.
-
BiGGDBContract
-
 
-
BiGGDBContract.Constants
+
BiGGDBContract
 
-
BiGGDBContract.Constants.Column
+
BiGGDBContract.Constants
 
-
BiGGDBContract.Constants.Table
-
 
-
BiGGDBOptions
-
 
-
BiGGDocumentNotesProcessor
+
BiGGDBContract.Constants.Column
 
-
BiGGFBCAnnotator
+
BiGGDBContract.Constants.Table
 
-
BiGGGeneProductAnnotator
-
+
BiGGDBOptions
+
 
+
BiGGDocumentNotesProcessor
+
 
+
BiGGFBCAnnotator
+
 
+
BiGGGeneProductAnnotator
+
Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
-
BiGGGeneProductReferencesAnnotator
-
 
-
BiGGId
-
+
BiGGGeneProductReferencesAnnotator
+
 
+
BiGGId
+
Represents a BiGG identifier used to uniquely identify various biological entities such as reactions, metabolites, and genes within the BiGG database.
-
BiGGModelAnnotator
-
+
BiGGModelAnnotator
+
This class is responsible for annotating an SBML Model with relevant metadata and references.
-
BiGGNotesParameters
-
 
-
BiGGPublicationsAnnotator
+
BiGGNotesParameters
 
-
BiGGReactionsAnnotator
-
+
BiGGPublicationsAnnotator
+
 
+
BiGGReactionsAnnotator
+
This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
-
BiGGSBMLAnnotator
-
+
BiGGSBMLAnnotator
+
This class is responsible for annotating SBML models using data from the BiGG database.
-
BiGGSpeciesAnnotator
-
+
BiGGSpeciesAnnotator
+
This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
-
COBRAUtils
-
 
-
CombineArchive
-
+
COBRAUtils
+
 
+
CombineArchive
+
The CombineArchive class provides functionality to create a COMBINE archive from an SBML document.
-
CommandLineParameters
-
 
-
CompartmentPolisher
-
+
CommandLineParameters
+
 
+
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
 
ECOparser
 
@@ -239,17 +243,21 @@

All Classes and Interfaces<

ModelPolisherOptions
 
-
ModelPolisherOptions.Compression
+
ModelPolisherOptions.OutputType
 
ModelReader
 
-
ModelValidator
-
 
+
ModelReaderException
+
 
+
ModelValidator
+
 
+
ModelValidatorException
+
 
ModelWriter
 
-
Namespace
-
 
-
OutputParameters
+
ModelWriterException
+
 
+
Namespace
 
Parameters
 
diff --git a/docs/constant-values.html b/docs/constant-values.html index c5bac169..be8352a9 100644 --- a/docs/constant-values.html +++ b/docs/constant-values.html @@ -123,6 +123,22 @@

edu.ucsd.*

+
@@ -177,13 +182,25 @@

Method Details

  • annotate

    -
    public void annotate(List<SBMLElement> elementsToAnnotate)
    +
    public void annotate(List<SBMLElement> elementsToAnnotate) + throws SQLException
    +
    +
    Throws:
    +
    SQLException
    +

  • annotate

    -
    public abstract void annotate(SBMLElement elementToAnnotate)
    +
    public abstract void annotate(SBMLElement elementToAnnotate) + throws SQLException, +AnnotationException
    +
    +
    Throws:
    +
    SQLException
    +
    AnnotationException
    +
  • @@ -194,6 +211,14 @@

    statusReport

  • +
    +

    diffReport

    +
    protected void diffReport(String elementType, + Object element1, + Object element2)
    +
    +
    • +

  • getObservers

    public List<ProgressObserver> getObservers()
    diff --git a/docs/edu/ucsd/sbrg/annotation/AnnotationException.html b/docs/edu/ucsd/sbrg/annotation/AnnotationException.html new file mode 100644 index 00000000..461e9670 --- /dev/null +++ b/docs/edu/ucsd/sbrg/annotation/AnnotationException.html @@ -0,0 +1,169 @@ + + + + +AnnotationException (ModelPolisher 2.1 API) + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.annotation
    +

    Class AnnotationException

    +
    +
    java.lang.Object +
    java.lang.Throwable +
    java.lang.Exception +
    edu.ucsd.sbrg.annotation.AnnotationException
    +
    +
    +
    +
    +
    +
    All Implemented Interfaces:
    +
    Serializable
    +
    +
    +
    Direct Known Subclasses:
    +
    BiGGAnnotationException
    +
    +
    +
    public class AnnotationException +extends Exception
    +
    +
    See Also:
    +
    + +
    +
    +
    +
    + +
    +
    +
      + +
    • +
      +

      Constructor Details

      +
        +
      • +
        +

        AnnotationException

        +
        public AnnotationException(String msg, + Exception e)
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/annotation/adb/ADBReactionsAnnotator.html b/docs/edu/ucsd/sbrg/annotation/adb/ADBReactionsAnnotator.html index 4027a1ca..ed0cd436 100644 --- a/docs/edu/ucsd/sbrg/annotation/adb/ADBReactionsAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/ADBReactionsAnnotator.html @@ -146,7 +146,7 @@

    addBQB_IS_AnnotationsFromADB

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

    -getObservers, statusReport
    +diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -179,20 +179,26 @@

    Method Details

  • annotate

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

  • annotate

    -
    public void annotate(org.sbml.jsbml.Reaction reaction)
    +
    public void annotate(org.sbml.jsbml.Reaction reaction) + throws SQLException
    Specified by:
    annotate in class AbstractADBAnnotator<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 572f15b9..60582b6f 100644 --- a/docs/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.html @@ -143,7 +143,7 @@

    addBQB_IS_AnnotationsFromADB

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

    -annotate, getObservers, statusReport
    +annotate, diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -176,10 +176,13 @@

    Method Details

  • annotate

    -
    public void annotate(org.sbml.jsbml.SBMLDocument doc)
    +
    public void annotate(org.sbml.jsbml.SBMLDocument doc) + throws SQLException
    Specified by:
    annotate in class AbstractADBAnnotator<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 7455543a..48dc8618 100644 --- a/docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/ADBSpeciesAnnotator.html @@ -146,7 +146,7 @@

    addBQB_IS_AnnotationsFromADB

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

    -getObservers, statusReport
    +diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -179,20 +179,26 @@

    Method Details

  • annotate

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

  • annotate

    -
    public void annotate(org.sbml.jsbml.Species species)
    +
    public void annotate(org.sbml.jsbml.Species species) + throws SQLException
    Specified by:
    annotate in class AbstractADBAnnotator<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 4afd394b..dcecc904 100644 --- a/docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/adb/AbstractADBAnnotator.html @@ -156,7 +156,7 @@

    Method Summary

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

    -annotate, getObservers, statusReport
    +annotate, diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -209,10 +209,13 @@

    Method Details

  • annotate

    -
    public abstract void annotate(SBMLElement element)
    +
    public abstract void annotate(SBMLElement element) + throws SQLException
    Specified by:
    annotate in class AbstractAnnotator<SBMLElement>
    +
    Throws:
    +
    SQLException
    • @@ -221,7 +224,12 @@

    annotate

    addBQB_IS_AnnotationsFromADB

    protected void addBQB_IS_AnnotationsFromADB(org.sbml.jsbml.Annotation annotation, String type, - BiGGId biggId)
    + BiGGId biggId) + throws SQLException
    +
    +
    Throws:
    +
    SQLException
    +
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html index 4bbaf8be..96cf8eb5 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/AbstractBiGGAnnotator.html @@ -163,7 +163,7 @@

    Method Summary

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

    -annotate, annotate, getObservers, statusReport
    +annotate, annotate, diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -233,7 +233,8 @@

    Method Details

    getBiGGIdFromResources

    public Optional<BiGGId> getBiGGIdFromResources(List<String> resources, - String type)
    + String type) + throws SQLException
    Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase. This method processes annotations for biological entities such as Species, Reaction, or GeneProduct. Each entity's annotations are provided as a list of URIs, which are then parsed to retrieve the BiGG ID.
    @@ -245,6 +246,8 @@

    getBiGGIdFromResources

    BiGGDBContract.Constants.TYPE_GENE_PRODUCT.
    Returns:
    An containing the BiGG ID if it could be successfully retrieved, otherwise Optional.empty().
    +
    Throws:
    +
    SQLException
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationException.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationException.html new file mode 100644 index 00000000..3081f32d --- /dev/null +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationException.html @@ -0,0 +1,196 @@ + + + + +BiGGAnnotationException (ModelPolisher 2.1 API) + + + + + + + + + + + + + +
    + +
    +
    + +
    +
    Package edu.ucsd.sbrg.annotation.bigg
    +

    Class BiGGAnnotationException

    +
    +
    java.lang.Object +
    java.lang.Throwable +
    java.lang.Exception +
    edu.ucsd.sbrg.annotation.AnnotationException +
    edu.ucsd.sbrg.annotation.bigg.BiGGAnnotationException
    +
    +
    +
    +
    +
    +
    +
    All Implemented Interfaces:
    +
    Serializable
    +
    +
    +
    public class BiGGAnnotationException +extends AnnotationException
    +
    +
    See Also:
    +
    + +
    +
    +
    +
    + +
    +
    +
      + +
    • +
      +

      Constructor Details

      +
        +
      • +
        +

        BiGGAnnotationException

        +
        public BiGGAnnotationException(String msg, + Exception e, + Object o)
        +
        +
        • +
      +
      +
      • + +
    • +
      +

      Method Details

      +
        +
      • +
        +

        data

        +
        public Object data()
        +
        +
        • +
      +
      +
      • +
    +
    + +
    +
    +
    + + diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationUtils.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationUtils.html deleted file mode 100644 index c4bbb83d..00000000 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGAnnotationUtils.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - -BiGGAnnotationUtils (ModelPolisher 2.1 API) - - - - - - - - - - - - - -
    - -
    -
    - -
    -
    Package edu.ucsd.sbrg.annotation.bigg
    -

    Class BiGGAnnotationUtils

    -
    -
    java.lang.Object -
    edu.ucsd.sbrg.annotation.bigg.BiGGAnnotationUtils
    -
    -
    -
    -
    public class BiGGAnnotationUtils -extends Object
    -
    -
    - -
    -
    -
      - -
    • -
      -

      Constructor Details

      -
        -
      • -
        -

        BiGGAnnotationUtils

        -
        public BiGGAnnotationUtils()
        -
        -
        • -
      -
      -
      • -
    -
    - -
    -
    -
    - - diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCVTermAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCVTermAnnotator.html index 748e3fbf..2bdb02a0 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCVTermAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCVTermAnnotator.html @@ -159,7 +159,7 @@

    getBiGGIdFromResources

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

    -annotate, annotate, getObservers, statusReport
    +annotate, annotate, diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -202,12 +202,15 @@

    Method Details

  • findBiGGId

    -
    protected abstract Optional<BiGGId> findBiGGId(T element)
    +
    protected abstract Optional<BiGGId> findBiGGId(T element) + throws SQLException
    Abstract method to check the validity of a BiGG ID. Implementations should return an Optional containing the BiGG ID if it is valid, or an empty Optional if not.
    Returns:
    Optional containing the valid BiGG ID or empty if the ID is invalid.
    +
    Throws:
    +
    SQLException
    • diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCompartmentsAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCompartmentsAnnotator.html index b97c5af3..33612007 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCompartmentsAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGCompartmentsAnnotator.html @@ -157,7 +157,7 @@

    getBiGGIdFromResources

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

    -getObservers, statusReport
    +diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -200,23 +200,29 @@

    Method Details

  • annotate

    -
    public void annotate(List<org.sbml.jsbml.Compartment> compartments)
    +
    public void annotate(List<org.sbml.jsbml.Compartment> compartments) + throws SQLException
    Overrides:
    annotate in class AbstractAnnotator<org.sbml.jsbml.Compartment>
    +
    Throws:
    +
    SQLException

  • annotate

    -
    public void annotate(org.sbml.jsbml.Compartment compartment)
    +
    public void annotate(org.sbml.jsbml.Compartment compartment) + throws SQLException
    Annotates the compartment with BiGG and SBO terms. If the compartment's name is not set or is set to "default", it updates the name based on the BiGG database. This method only processes compartments that are recognized within the BiGG Knowledgebase.
    Specified by:
    annotate in class AbstractAnnotator<org.sbml.jsbml.Compartment>
    +
    Throws:
    +
    SQLException
    • diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGDocumentNotesProcessor.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGDocumentNotesProcessor.html index fad63794..ada8102a 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGDocumentNotesProcessor.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGDocumentNotesProcessor.html @@ -157,7 +157,14 @@

    Method Details

  • processNotes

    -
    public void processNotes(org.sbml.jsbml.SBMLDocument doc)
    +
    public void processNotes(org.sbml.jsbml.SBMLDocument doc) + throws BiGGAnnotationException, +SQLException
    +
    +
    Throws:
    +
    BiGGAnnotationException
    +
    SQLException
    +
    • diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html index 513f4435..d929adbf 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html @@ -168,7 +168,7 @@

    getBiGGIdFromResources

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

    -annotate, getObservers, statusReport
    +annotate, diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -247,7 +247,8 @@

    Method Details

  • annotate

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

    @@ -258,6 +259,8 @@

    annotate

    Specified by:
    annotate in class AbstractAnnotator<org.sbml.jsbml.Model>
    +
    Throws:
    +
    SQLException
    • diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGPublicationsAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGPublicationsAnnotator.html index eca80796..7a5e10ef 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGPublicationsAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGPublicationsAnnotator.html @@ -145,7 +145,7 @@

    getBiGGIdFromResources

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

    -annotate, getObservers, statusReport
    +annotate, diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -180,10 +180,13 @@

    Method Details

  • annotate

    -
    public void annotate(org.sbml.jsbml.Model model)
    +
    public void annotate(org.sbml.jsbml.Model model) + throws SQLException
    Specified by:
    annotate in class AbstractAnnotator<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 6cee28bb..3d94cc4f 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGReactionsAnnotator.html @@ -189,7 +189,7 @@

    getBiGGIdFromResources

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

    -getObservers, statusReport
    +diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -234,20 +234,24 @@

    Method Details

  • annotate

    -
    public void annotate(List<org.sbml.jsbml.Reaction> reactions)
    +
    public void annotate(List<org.sbml.jsbml.Reaction> reactions) + throws SQLException
    Delegates the annotation process for each reaction in the given SBML model. 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>
    +
    Throws:
    +
    SQLException

  • annotate

    -
    public void annotate(org.sbml.jsbml.Reaction reaction)
    +
    public void annotate(org.sbml.jsbml.Reaction reaction) + throws SQLException
    Annotates a reaction by setting its name, SBO term, and additional annotations. It also processes gene reaction rules and subsystem information associated with the reaction. This method retrieves a BiGG ID for the reaction, either from the reaction's ID directly or through associated annotations. If a valid BiGG ID is found, it proceeds with the @@ -255,13 +259,16 @@

    annotate

    Specified by:
    annotate in class AbstractAnnotator<org.sbml.jsbml.Reaction>
    +
    Throws:
    +
    SQLException

  • findBiGGId

    -
    public Optional<BiGGId> findBiGGId(org.sbml.jsbml.Reaction reaction)
    +
    public Optional<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 @@ -273,6 +280,8 @@

    findBiGGId

    findBiGGId in class BiGGCVTermAnnotator<org.sbml.jsbml.Reaction>
    Returns:
    An Optional containing the BiGG ID if found or created successfully, otherwise Optional.empty()
    +
    Throws:
    +
    SQLException
    • @@ -280,12 +289,15 @@

    findBiGGId

    setName

    public void setName(org.sbml.jsbml.Reaction reaction, - BiGGId biggId)
    + 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.
    Parameters:
    biggId - The BiGGId object containing the abbreviation used to fetch and potentially update the reaction's name.
    +
    Throws:
    +
    SQLException
    @@ -293,7 +305,8 @@

    setName

    setSBOTerm

    public void setSBOTerm(org.sbml.jsbml.Reaction reaction, - BiGGId biggId)
    + BiGGId biggId) + throws SQLException
    Sets the SBO term for a reaction based on the given BiGGId. If the reaction does not already have an SBO term set, it determines the appropriate SBO term based on whether the reaction is a pseudoreaction or a generic process. Pseudoreactions are assigned @@ -302,6 +315,8 @@

    setSBOTerm

    Parameters:
    biggId - The BiGGId object containing the abbreviation used to check if the reaction is a pseudoreaction.
    +
    Throws:
    +
    SQLException
    @@ -309,7 +324,8 @@

    setSBOTerm

    parseGeneReactionRules

    public void parseGeneReactionRules(org.sbml.jsbml.Reaction reaction, - BiGGId biggId)
    + BiGGId biggId) + throws SQLException
    Parses gene reaction rules for a given reaction based on the BiGG database identifier. This method retrieves gene reaction rules associated with the reaction's abbreviation from the BiGG database and applies gene-protein-reaction (GPR) parsing to the reaction. @@ -317,6 +333,8 @@

    parseGeneReactionRules

    Parameters:
    biggId - The BiGG database identifier for the reaction, used to fetch and parse gene reaction rules.
    +
    Throws:
    +
    SQLException
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.html index cfa58b76..d50c00de 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSBMLAnnotator.html @@ -155,7 +155,7 @@

    getBiGGIdFromResources

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

    -annotate, getObservers, statusReport
    +annotate, diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -200,7 +200,9 @@

    Method Details

  • annotate

    -
    public void annotate(org.sbml.jsbml.SBMLDocument doc)
    +
    public void annotate(org.sbml.jsbml.SBMLDocument doc) + throws SQLException, +AnnotationException
    Annotates an SBMLDocument using data from the BiGG Knowledgebase. This method processes various components of the SBML model such as compartments, species, reactions, and gene products by adding relevant annotations from BiGG. It also handles the addition of publications and notes related to the model.
    @@ -209,6 +211,9 @@

    annotate

    annotate in class AbstractAnnotator<org.sbml.jsbml.SBMLDocument>
    Parameters:
    doc - The SBMLDocument that contains the model to be annotated.
    +
    Throws:
    +
    SQLException
    +
    AnnotationException
    • diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSpeciesAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSpeciesAnnotator.html index 91c215e2..2054553a 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSpeciesAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/BiGGSpeciesAnnotator.html @@ -179,7 +179,7 @@

    getBiGGIdFromResources

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

    -getObservers, statusReport
    +diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -224,19 +224,23 @@

    Method Details

  • annotate

    -
    public void annotate(List<org.sbml.jsbml.Species> species)
    +
    public void annotate(List<org.sbml.jsbml.Species> species) + throws SQLException
    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>
    +
    Throws:
    +
    SQLException

  • annotate

    -
    public void annotate(org.sbml.jsbml.Species species)
    +
    public void annotate(org.sbml.jsbml.Species species) + throws SQLException
    This method annotates a species with various details fetched from the BiGG Knowledgebase. It performs the following: 1. Sets the species name based on the BiGGId. If the species does not have a name, it uses the BiGGId as the name. 2. Assigns an SBO (Systems Biology Ontology) term to the species based on the BiGGId. @@ -247,13 +251,16 @@

    annotate

    Specified by:
    annotate in class AbstractAnnotator<org.sbml.jsbml.Species>
    +
    Throws:
    +
    SQLException

  • findBiGGId

    -
    public Optional<BiGGId> findBiGGId(org.sbml.jsbml.Species species)
    +
    public Optional<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.
    @@ -262,6 +269,8 @@

    findBiGGId

    findBiGGId in class BiGGCVTermAnnotator<org.sbml.jsbml.Species>
    Returns:
    An Optional containing the BiGGId if a valid one is found or created, otherwise Optional.empty()
    +
    Throws:
    +
    SQLException
    • @@ -269,13 +278,16 @@

    findBiGGId

    setName

    public void setName(org.sbml.jsbml.Species species, - BiGGId biggId)
    + 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 compartment code. This method relies on the availability of a valid BiGGId for the species.
    Parameters:
    biggId - The BiGGId associated with the species, used to fetch the component name from the BiGG database.
    +
    Throws:
    +
    SQLException
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html b/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html index e48f6ae7..f764e0b0 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGFBCAnnotator.html @@ -145,7 +145,7 @@

    getBiGGIdFromResources

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

    -annotate, getObservers, statusReport
    +annotate, diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -180,10 +180,13 @@

    Method Details

  • annotate

    -
    public void annotate(org.sbml.jsbml.Model model)
    +
    public void annotate(org.sbml.jsbml.Model model) + throws SQLException
    Specified by:
    annotate in class AbstractAnnotator<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 fafe301a..1a3e0bc1 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html @@ -191,7 +191,7 @@

    getBiGGIdFromResources

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

    -getObservers, statusReport
    +diffReport, getObservers, statusReport

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    @@ -249,20 +249,24 @@

    Method Details

  • annotate

    -
    public void annotate(List<org.sbml.jsbml.ext.fbc.GeneProduct> geneProducts)
    +
    public void annotate(List<org.sbml.jsbml.ext.fbc.GeneProduct> geneProducts) + throws SQLException
    This method handles the annotation of gene products in a given SBML model. It checks if the model has the FBC plugin 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>
    +
    Throws:
    +
    SQLException

  • annotate

    -
    public void annotate(org.sbml.jsbml.ext.fbc.GeneProduct geneProduct)
    +
    public void annotate(org.sbml.jsbml.ext.fbc.GeneProduct geneProduct) + throws SQLException
    Annotates a gene product by adding relevant metadata and references. This method first checks the gene product's ID for validity and retrieves a corresponding BiGGId if available. It then attempts to get a label for the gene product. If no label is found, the method returns early. @@ -271,13 +275,16 @@

    annotate

    Specified by:
    annotate in class AbstractAnnotator<org.sbml.jsbml.ext.fbc.GeneProduct>
    +
    Throws:
    +
    SQLException

  • findBiGGId

    -
    public Optional<BiGGId> findBiGGId(org.sbml.jsbml.ext.fbc.GeneProduct geneProduct)
    +
    public Optional<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 @@ -288,6 +295,8 @@

    findBiGGId

    findBiGGId in class BiGGCVTermAnnotator<org.sbml.jsbml.ext.fbc.GeneProduct>
    Returns:
    An Optional<BiGGId> containing the validated or retrieved BiGG ID, or an empty Optional if no valid ID is found.
    +
    Throws:
    +
    SQLException
    • @@ -311,7 +320,8 @@

    getLabel

    setGPLabelName

    public void setGPLabelName(org.sbml.jsbml.ext.fbc.GeneProduct geneProduct, - String label)
    + String label) + throws SQLException
    Updates the label of a gene product and sets its name based on the retrieved gene name from the BiGG database. If the current label is set to "None", it updates the label to the provided one. It then attempts to fetch the gene name corresponding to this label from the BiGG database. If a gene name is found, it checks if the @@ -321,6 +331,8 @@

    setGPLabelName

    Parameters:
    label - The label to set or use for fetching the gene name. This label should correspond to a BiGGId or be derived from AbstractSBase.getId().
    +
    Throws:
    +
    SQLException
    @@ -328,7 +340,8 @@

    setGPLabelName

    addAnnotations

    public void addAnnotations(org.sbml.jsbml.ext.fbc.GeneProduct geneProduct, - BiGGId biggId)
    + BiGGId biggId) + throws SQLException
    Adds annotations to a gene product based on a given BiGGId. This method differentiates between annotations that specify what the gene product 'is' and what it 'is encoded by'. Resources are fetched from the BiGG database using the abbreviation from the provided BiGGId. Each resource URL is checked and @@ -336,6 +349,8 @@

    addAnnotations

    Parameters:
    biggId - The BiGGId associated with the gene product, typically derived from a species ID.
    +
    Throws:
    +
    SQLException
    diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/package-summary.html b/docs/edu/ucsd/sbrg/annotation/bigg/package-summary.html index 4a16575e..fb91445b 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/package-summary.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/package-summary.html @@ -87,14 +87,15 @@

    Package edu.ucsd
  • -
    Classes
    +
    +
    Class
    Description
    AbstractBiGGAnnotator<SBMLElement>
     
    -
    BiGGAnnotationUtils
    -
     
    +
    BiGGAnnotationException
    +
     
    BiGGCompartmentsAnnotator
    This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
    @@ -125,6 +126,7 @@

    Package edu.ucsd

    +
    • diff --git a/docs/edu/ucsd/sbrg/annotation/bigg/package-tree.html b/docs/edu/ucsd/sbrg/annotation/bigg/package-tree.html index 58f0e6e7..017fa212 100644 --- a/docs/edu/ucsd/sbrg/annotation/bigg/package-tree.html +++ b/docs/edu/ucsd/sbrg/annotation/bigg/package-tree.html @@ -76,8 +76,20 @@

    Class Hierarchy

    -
  • edu.ucsd.sbrg.annotation.bigg.BiGGAnnotationUtils
  • edu.ucsd.sbrg.annotation.bigg.BiGGDocumentNotesProcessor
    • +
  • java.lang.Throwable (implements java.io.Serializable) + +
    • diff --git a/docs/edu/ucsd/sbrg/annotation/package-summary.html b/docs/edu/ucsd/sbrg/annotation/package-summary.html index 8fc088ff..137ae785 100644 --- a/docs/edu/ucsd/sbrg/annotation/package-summary.html +++ b/docs/edu/ucsd/sbrg/annotation/package-summary.html @@ -87,14 +87,18 @@

    Package edu.ucsd.sbrg
  • -
    Classes
    +
    +
    Class
    Description
    AbstractAnnotator<SBMLElement>
     
    -
    AnnotationsSorter
    -
     
    +
    AnnotationException
    +
     
    +
    AnnotationsSorter
    +
     
    +
    • diff --git a/docs/edu/ucsd/sbrg/annotation/package-tree.html b/docs/edu/ucsd/sbrg/annotation/package-tree.html index 2226014f..bfe831f8 100644 --- a/docs/edu/ucsd/sbrg/annotation/package-tree.html +++ b/docs/edu/ucsd/sbrg/annotation/package-tree.html @@ -60,6 +60,15 @@

    Class Hierarchy

    diff --git a/docs/edu/ucsd/sbrg/db/adb/AnnotateDB.html b/docs/edu/ucsd/sbrg/db/adb/AnnotateDB.html index 748d861d..62f98c15 100644 --- a/docs/edu/ucsd/sbrg/db/adb/AnnotateDB.html +++ b/docs/edu/ucsd/sbrg/db/adb/AnnotateDB.html @@ -192,7 +192,8 @@

    init

    getAnnotations

    public Set<String> getAnnotations(String type, - String biggId)
    + String biggId) + throws SQLException
    Retrieves a set of annotated URLs based on the type and BiGG ID provided. This method queries the database to find matching annotations and constructs URLs using the retrieved data.
    @@ -203,6 +204,8 @@

    getAnnotations

    Returns:
    A sorted set of URLs that are annotations for the given BiGG ID. If the type is neither metabolite nor reaction, or if an SQL exception occurs, an empty set is returned.
    +
    Throws:
    +
    SQLException
    diff --git a/docs/edu/ucsd/sbrg/db/bigg/BiGGDB.html b/docs/edu/ucsd/sbrg/db/bigg/BiGGDB.html index 611d3a05..9c5e7a5a 100644 --- a/docs/edu/ucsd/sbrg/db/bigg/BiGGDB.html +++ b/docs/edu/ucsd/sbrg/db/bigg/BiGGDB.html @@ -356,7 +356,8 @@

    init

  • getBiGGVersion

    -
    public Optional<Date> getBiGGVersion()
    +
    public Optional<Date> getBiGGVersion() + throws SQLException
    Retrieves the version date of the BiGG database. This method queries the database to fetch the date and time of the last update @@ -365,6 +366,8 @@

    getBiGGVersion

    Returns:
    Optional<Date> The date of the last database update, or an empty Optional if not available.
    +
    Throws:
    +
    SQLException
    • @@ -372,7 +375,8 @@

    getBiGGVersion

    getSubsystems

    public List<String> getSubsystems(String modelBiGGid, - String reactionBiGGid)
    + String reactionBiGGid) + throws SQLException
    Retrieves a list of distinct subsystems associated with a specific model and reaction BiGG IDs. This method executes a SQL query to fetch subsystems from the database where both the model and reaction match the provided BiGG IDs. Only subsystems with a non-zero length are considered.
    @@ -382,13 +386,16 @@

    getSubsystems

    reactionBiGGid - The BiGG ID of the reaction.
    Returns:
    A List of subsystem names as strings. Returns an empty list if no subsystems are found or if an error occurs.
    +
    Throws:
    +
    SQLException

  • getSubsystemsForReaction

    -
    public List<String> getSubsystemsForReaction(String reactionBiGGid)
    +
    public List<String> getSubsystemsForReaction(String reactionBiGGid) + throws SQLException
    Retrieves a list of distinct subsystems associated with a specific reaction BiGG ID. This method executes a SQL query to fetch subsystems from the database where the reaction matches the provided BiGG ID. Only subsystems with a non-zero length are considered.
    @@ -397,6 +404,8 @@

    getSubsystemsForReaction

    reactionBiGGid - The BiGG ID of the reaction for which subsystems are to be retrieved.
    Returns:
    A List of subsystem names as strings. Returns an empty list if no subsystems are found or if an error occurs.
    +
    Throws:
    +
    SQLException
    • @@ -404,7 +413,8 @@

    getSubsystemsForReaction

    getChemicalFormulaByCompartment

    public Optional<String> getChemicalFormulaByCompartment(String componentId, - String compartmentId)
    + String compartmentId) + throws SQLException
    Retrieves the unique chemical formula for a given component within a specific compartment. This method queries the database to find the distinct chemical formula associated with the specified component and compartment IDs. It ensures that the formula is unique for the given parameters. @@ -416,6 +426,8 @@

    getChemicalFormulaByCompartment

    Returns:
    An Optional containing the chemical formula if exactly one unique formula is found, otherwise an empty Optional if none or multiple formulas are found.
    +
    Throws:
    +
    SQLException
    @@ -423,7 +435,8 @@

    getChemicalFormulaByCompartment

    getChemicalFormula

    public Optional<String> getChemicalFormula(String componentId, - String modelId)
    + String modelId) + throws SQLException
    Retrieves the chemical formula for a given component within a specific model in the BiGG database. This method executes a SQL query to find distinct chemical formulas associated with the component and model IDs provided. If exactly one unique formula is found, it is returned. If none or multiple formulas are found, an empty Optional is returned. @@ -434,13 +447,16 @@

    getChemicalFormula

    modelId - The BiGG ID of the model in which the component is present.
    Returns:
    An Optional<String> containing the chemical formula if exactly one is found, otherwise empty.
    +
    Throws:
    +
    SQLException

  • getCompartmentName

    -
    public Optional<String> getCompartmentName(BiGGId biggId)
    +
    public Optional<String> getCompartmentName(BiGGId biggId) + throws SQLException
    Retrieves the name of the compartment associated with the given BiGG ID from the database. This method constructs a SQL query to select the compartment name where the BiGG ID matches and the name is not an empty string.
    @@ -449,6 +465,8 @@

    getCompartmentName

    biggId - The BiGGId object containing the abbreviation of the compartment.
    Returns:
    An Optional<String> containing the name of the compartment if found, otherwise empty.
    +
    Throws:
    +
    SQLException
    • @@ -456,7 +474,8 @@

    getCompartmentName

    singleParamStatement

    public Optional<String> singleParamStatement(String query, - String param)
    + String param) + throws SQLException
    Executes a SQL query with a single parameter and returns the result as an Optional. This method is designed to handle queries that are expected to return a single result. If multiple results are found, a severe log is recorded indicating the issue.
    @@ -466,13 +485,16 @@

    singleParamStatement

    param - The parameter value to be used in the SQL query.
    Returns:
    An Optional<String> containing the result if exactly one result is found, otherwise empty.
    +
    Throws:
    +
    SQLException

  • getComponentName

    -
    public Optional<String> getComponentName(BiGGId biggId)
    +
    public Optional<String> getComponentName(BiGGId biggId) + throws SQLException
    Retrieves the name of the component associated with the given BiGG ID from the database. This method constructs a SQL query to select the component name where the BiGG ID matches and the name is not an empty string.
    @@ -481,13 +503,16 @@

    getComponentName

    biggId - The BiGGId object containing the abbreviation of the component.
    Returns:
    An Optional<String> containing the name of the component if found, otherwise empty.
    +
    Throws:
    +
    SQLException

  • getComponentType

    -
    public Optional<String> getComponentType(BiGGId biggId)
    +
    public Optional<String> getComponentType(BiGGId biggId) + throws SQLException
    Retrieves the type of the component associated with the given BiGG ID from the database. This method constructs a SQL query to select the component type where the BiGG ID matches and the name field is not an empty string.
    @@ -496,13 +521,16 @@

    getComponentType

    biggId - The BiGGId object containing the abbreviation of the component.
    Returns:
    An Optional<String> containing the type of the component if found, otherwise empty.
    +
    Throws:
    +
    SQLException

  • getGeneIds

    -
    public TreeSet<IdentifiersOrgURI> getGeneIds(String label)
    +
    public TreeSet<IdentifiersOrgURI> getGeneIds(String label) + throws SQLException
    Retrieves all possible MIRIAM-compliant gene identifiers from the database based on a given label. This method queries the database for gene identifiers that match the provided label and are compliant with MIRIAM standards. Non-compliant entries are ignored.
    @@ -511,13 +539,16 @@

    getGeneIds

    label - The label used to query gene identifiers.
    Returns:
    A TreeSet containing unique, sorted MIRIAM-compliant gene identifiers.
    +
    Throws:
    +
    SQLException

  • getGeneName

    -
    public Optional<String> getGeneName(String label)
    +
    public Optional<String> getGeneName(String label) + throws SQLException
    Retrieves the gene name from the database based on a given label. This method constructs a SQL query to fetch the synonym of a gene that matches the given label, ensuring that the gene is associated with a valid data source and genome region, and that the @@ -528,6 +559,8 @@

    getGeneName

    label - The label used to query the gene name, typically a BIGG ID.
    Returns:
    An Optional containing the gene name if found, otherwise an empty Optional.
    +
    Throws:
    +
    SQLException
    • @@ -535,7 +568,8 @@

    getGeneName

    getGeneReactionRule

    public List<String> getGeneReactionRule(String reactionId, - String modelId)
    + String modelId) + throws SQLException
    Retrieves formatted gene reaction rules for a specific reaction and model from the database. This method constructs a SQL query to fetch and format the gene reaction rules associated with the given reaction ID and model ID. The formatting includes replacing logical operators 'or' and 'and' @@ -546,6 +580,8 @@

    getGeneReactionRule

    modelId - The ID of the model associated with the reaction.
    Returns:
    A list of formatted gene reaction rules as strings.
    +
    Throws:
    +
    SQLException
    @@ -554,7 +590,8 @@

    getGeneReactionRule

    getReactionRules

    public List<String> getReactionRules(String query, String reactionId, - String modelId)
    + String modelId) + throws SQLException
    Executes a provided SQL query to retrieve gene reaction rules from the database. This method prepares a statement with the given query, setting the specified reactionId and modelId as parameters. It then executes the query and collects the results into a list of strings.
    @@ -565,13 +602,16 @@

    getReactionRules

    modelId - The ID of the model to be used as the second parameter in the SQL query.
    Returns:
    A list of strings where each string is a gene reaction rule retrieved based on the given IDs.
    +
    Throws:
    +
    SQLException

  • getOrganism

    -
    public Optional<String> getOrganism(String abbreviation)
    +
    public Optional<String> getOrganism(String abbreviation) + throws SQLException
    Retrieves the organism associated with a given BiGG model abbreviation from the database. This method constructs and executes a SQL query that joins the GENOME and MODEL tables to find the organism corresponding to the specified model abbreviation.
    @@ -580,13 +620,16 @@

    getOrganism

    abbreviation - The abbreviation of the model for which the organism is to be retrieved.
    Returns:
    An Optional containing the organism name if found, otherwise an empty Optional.
    +
    Throws:
    +
    SQLException

  • getPublications

    -
    public List<Publication> getPublications(String abbreviation)
    +
    public List<Publication> getPublications(String abbreviation) + throws SQLException
    Retrieves a list of publications associated with a given BiGG model abbreviation from the database. This method constructs and executes a SQL query that joins the PUBLICATION, PUBLICATION_MODEL, and MODEL tables to find the publications related to the specified model abbreviation.
    @@ -595,13 +638,16 @@

    getPublications

    abbreviation - The abbreviation of the model for which the publications are to be retrieved.
    Returns:
    A list of pairs where each pair consists of a publication type and its corresponding ID.
    +
    Throws:
    +
    SQLException

  • getReactionName

    -
    public Optional<String> getReactionName(String abbreviation)
    +
    public Optional<String> getReactionName(String abbreviation) + throws SQLException
    Retrieves the name of a reaction based on its BiGG ID abbreviation, ensuring the name is not empty. This method constructs and executes a SQL query that selects the reaction name from the REACTION table where the BIGG_ID matches the specified abbreviation and the name is not an empty string.
    @@ -610,6 +656,8 @@

    getReactionName

    abbreviation - The abbreviation of the reaction for which the name is to be retrieved.
    Returns:
    An Optional containing the reaction name if found and not empty, otherwise an empty Optional.
    +
    Throws:
    +
    SQLException
    • @@ -618,7 +666,8 @@

    getReactionName

    getResources

    public Set<IdentifiersOrgURI> getResources(BiGGId biggId, boolean includeAnyURI, - boolean isReaction)
    + boolean isReaction) + throws SQLException
    Retrieves a set of resource URLs for a given BiGG ID, optionally filtering to include only those containing 'identifiers.org'. This method constructs and executes a SQL query to fetch URLs from the database based on the type of BiGG ID (reaction or component). It then filters these URLs based on the 'includeAnyURI' parameter.
    @@ -629,13 +678,16 @@

    getResources

    isReaction - If true, the BiGG ID is treated as a reaction; if false, it is treated as a component.
    Returns:
    A sorted set of URLs as strings, potentially filtered by the 'identifiers.org' domain.
    +
    Throws:
    +
    SQLException

  • getTaxonId

    -
    public Optional<Integer> getTaxonId(String abbreviation)
    +
    public Optional<Integer> getTaxonId(String abbreviation) + throws SQLException
    Retrieves the taxonomic identifier (taxon ID) for a given model based on its abbreviation. This method queries the database to find the taxon ID associated with the model's abbreviation. If multiple taxon IDs are found for the same abbreviation, a severe log message is generated.
    @@ -644,13 +696,16 @@

    getTaxonId

    abbreviation - The abbreviation of the model for which the taxon ID is being queried.
    Returns:
    An Optional containing the taxon ID if found; otherwise, an empty Optional.
    +
    Throws:
    +
    SQLException

  • getGenomeAccesion

    -
    public String getGenomeAccesion(String id)
    +
    public String getGenomeAccesion(String id) + throws SQLException
    Retrieves the genome accession for a given model ID from the BiGG database. The accession can be used to construct URLs for accessing genomic data from various sources. The URLs can be formed using the accession ID with the following patterns: @@ -663,13 +718,16 @@

    getGenomeAccesion

    Returns:
    The accession string which can be appended to the base URLs mentioned above. If the query fails or no accession is found, an empty string is returned.
    +
    Throws:
    +
    SQLException

  • getAllBiggIds

    -
    public Set<String> getAllBiggIds(String table)
    +
    public Set<String> getAllBiggIds(String table) + throws SQLException
    Retrieves a set of unique BiGG IDs from a specified table in the database. This method queries the database for all unique BiGG IDs in the specified table and returns them as a set. The IDs are ordered by their natural ordering in the database.
    @@ -679,6 +737,8 @@

    getAllBiggIds

    Returns:
    A Set of strings containing unique BiGG IDs from the specified table. If an SQL error occurs, the returned set will be empty.
    +
    Throws:
    +
    SQLException
    • @@ -686,7 +746,8 @@

    getAllBiggIds

    getChargeByCompartment

    public Optional<Integer> getChargeByCompartment(String componentId, - String compartmentId)
    + String compartmentId) + throws SQLException
    Retrieves the charge associated with a specific component in a given compartment when the model ID is unknown. This method executes a SQL query to find a distinct charge value for a component based on its BiGG ID and the compartment's BiGG ID. The method ensures that the charge value is not empty and returns it if it is unique.
    @@ -697,6 +758,8 @@

    getChargeByCompartment

    Returns:
    An Optional containing the charge if it is unique and present; otherwise, an empty Optional. If multiple unique charge values are found, a warning is logged.
    +
    Throws:
    +
    SQLException
    @@ -704,7 +767,8 @@

    getChargeByCompartment

    getCharge

    public Optional<Integer> getCharge(String componentId, - String modelId)
    + String modelId) + throws SQLException
    Retrieves the charge for a given component and model from the database. This method executes a SQL query to select distinct charge values associated with the specified component ID and model ID. It ensures that the charge value is not null.
    @@ -715,13 +779,16 @@

    getCharge

    Returns:
    An Optional containing the charge if exactly one distinct charge is found, otherwise an empty Optional. If multiple distinct charges are found, a warning is logged.
    +
    Throws:
    +
    SQLException

  • isPseudoreaction

    -
    public boolean isPseudoreaction(String reactionId)
    +
    public boolean isPseudoreaction(String reactionId) + throws SQLException
    Determines if a given reaction ID corresponds to a pseudoreaction in the database. A pseudoreaction is typically used to represent non-biochemical data flows such as biomass accumulation, demand reactions, or exchange reactions.
    @@ -730,6 +797,8 @@

    isPseudoreaction

    reactionId - The BiGG ID of the reaction to be checked.
    Returns:
    true if the reaction is a pseudoreaction, false otherwise.
    +
    Throws:
    +
    SQLException
    • @@ -772,31 +841,56 @@

    getBiggIdsForReactionForeignId

  • isCompartment

    -
    public boolean isCompartment(String id)
    +
    public boolean isCompartment(String id) + throws SQLException
    +
    +
    Throws:
    +
    SQLException
    +

  • isDataSource

    -
    public boolean isDataSource(String id)
    +
    public boolean isDataSource(String id) + throws SQLException
    +
    +
    Throws:
    +
    SQLException
    +

  • isMetabolite

    -
    public boolean isMetabolite(String id)
    +
    public boolean isMetabolite(String id) + throws SQLException
    +
    +
    Throws:
    +
    SQLException
    +

  • isModel

    -
    public boolean isModel(String id)
    +
    public boolean isModel(String id) + throws SQLException
    +
    +
    Throws:
    +
    SQLException
    +

  • isReaction

    -
    public boolean isReaction(String id)
    +
    public boolean isReaction(String id) + throws SQLException
    +
    +
    Throws:
    +
    SQLException
    +
    • diff --git a/docs/edu/ucsd/sbrg/io/CombineArchive.html b/docs/edu/ucsd/sbrg/io/CombineArchive.html index d10ce6f5..89e5f00d 100644 --- a/docs/edu/ucsd/sbrg/io/CombineArchive.html +++ b/docs/edu/ucsd/sbrg/io/CombineArchive.html @@ -38,7 +38,7 @@

    Summary:

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

  • Detail:

    @@ -58,13 +58,13 @@ @@ -109,6 +109,24 @@

    Class CombineArchive

    • +
  • +
    +

    outputType

    +
    protected ModelPolisherOptions.OutputType outputType
    +
    +
    • @@ -208,15 +220,21 @@

    input

  • +
    +

    output

    +
    public File output()
    +
    +
    • +

  • SBMLValidation

    public boolean SBMLValidation()
  • -
    -

    outputParameters

    -
    public OutputParameters outputParameters()
    +
    +

    outputType

    +
    public ModelPolisherOptions.OutputType outputType()
  • diff --git a/docs/edu/ucsd/sbrg/parameters/Parameters.html b/docs/edu/ucsd/sbrg/parameters/Parameters.html index c93b7a09..886d2859 100644 --- a/docs/edu/ucsd/sbrg/parameters/Parameters.html +++ b/docs/edu/ucsd/sbrg/parameters/Parameters.html @@ -103,9 +103,12 @@

    Field Summary

    Modifier and Type
    Field
    Description
    -
    protected boolean
    -
    sbmlValidation
    +
    protected ModelPolisherOptions.OutputType
    +
    outputType
     
    +
    protected boolean
    +
    sbmlValidation
    +
     
    • @@ -136,8 +139,8 @@

    Method Summary

    AnnotationParameters
    annotation()
     
    -
    OutputParameters
    -
    output()
    +
    ModelPolisherOptions.OutputType
    +
    outputType()
     
    PolishingParameters
    polishing()
    @@ -171,6 +174,12 @@

    sbmlValidation

    protected boolean sbmlValidation
    +
  • +
    +

    outputType

    +
    protected ModelPolisherOptions.OutputType outputType
    +
    +
    • @@ -212,17 +221,17 @@

    sboTerms

  • -
    -

    output

    -
    public OutputParameters output()
    -
    -
    • -

  • sbmlValidation

    public boolean sbmlValidation()
    • +
  • +
    +

    outputType

    +
    public ModelPolisherOptions.OutputType outputType()
    +
    +
    • diff --git a/docs/edu/ucsd/sbrg/parameters/package-summary.html b/docs/edu/ucsd/sbrg/parameters/package-summary.html index 03c93ead..86854d4a 100644 --- a/docs/edu/ucsd/sbrg/parameters/package-summary.html +++ b/docs/edu/ucsd/sbrg/parameters/package-summary.html @@ -101,18 +101,16 @@

    Package edu.ucsd.sbrg
     
    FluxObjectivesPolishingParameters
     
    -
    OutputParameters
    +
    Parameters
     
    -
    Parameters
    +
    ParametersParser
     
    -
    ParametersParser
    +
    PolishingParameters
     
    -
    PolishingParameters
    +
    ReactionPolishingParameters
     
    -
    ReactionPolishingParameters
    +
    SBOParameters
     
    -
    SBOParameters
    -
     
    diff --git a/docs/edu/ucsd/sbrg/parameters/package-tree.html b/docs/edu/ucsd/sbrg/parameters/package-tree.html index 28e375bf..fa21de37 100644 --- a/docs/edu/ucsd/sbrg/parameters/package-tree.html +++ b/docs/edu/ucsd/sbrg/parameters/package-tree.html @@ -65,7 +65,6 @@

    Class Hierarchy

  • edu.ucsd.sbrg.parameters.CommandLineParameters
  • edu.ucsd.sbrg.parameters.DBParameters
  • edu.ucsd.sbrg.parameters.FluxObjectivesPolishingParameters
    • -
  • edu.ucsd.sbrg.parameters.OutputParameters
  • edu.ucsd.sbrg.parameters.Parameters
  • edu.ucsd.sbrg.parameters.ParametersParser
  • edu.ucsd.sbrg.parameters.PolishingParameters
    • diff --git a/docs/edu/ucsd/sbrg/polishing/AbstractPolisher.html b/docs/edu/ucsd/sbrg/polishing/AbstractPolisher.html index 4e770b73..e5016a9b 100644 --- a/docs/edu/ucsd/sbrg/polishing/AbstractPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/AbstractPolisher.html @@ -145,28 +145,33 @@

    Method Summary

    Modifier and Type
    Method
    Description
    -
    boolean
    -
    equals(Object o)
    +
    protected void
    +
    diffReport(String elementType, + Object element1, + Object element2)
     
    -
    List<ProgressObserver>
    -
    getObservers()
    +
    boolean
    +
    equals(Object o)
     
    -
    int
    -
    hashCode()
    +
    List<ProgressObserver>
    +
    getObservers()
     
    -
    void
    -
    polish(List<SBMLElement> elementsToPolish)
    +
    int
    +
    hashCode()
     
    -
    abstract void
    -
    polish(SBMLElement elementToPolish)
    -
     
    -
    protected void
    -
    statusReport(String text, +
    void
    +
    polish(List<SBMLElement> elementsToPolish)
    +
     
    +
    abstract void
    +
    polish(SBMLElement elementToPolish)
    +
     
    +
    protected void
    +
    statusReport(String text, Object element)
    -
     
    -
    String
    -
    toString()
     
    +
    String
    +
    toString()
    +
     
    @@ -247,6 +252,14 @@

    statusReport

  • +
    +

    diffReport

    +
    protected void diffReport(String elementType, + Object element1, + Object element2)
    +
    +
    • +

  • getObservers

    public List<ProgressObserver> getObservers()
    diff --git a/docs/edu/ucsd/sbrg/polishing/AnnotationPolisher.html b/docs/edu/ucsd/sbrg/polishing/AnnotationPolisher.html index a63b72ff..750abf67 100644 --- a/docs/edu/ucsd/sbrg/polishing/AnnotationPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/AnnotationPolisher.html @@ -145,7 +145,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/CompartmentPolisher.html b/docs/edu/ucsd/sbrg/polishing/CompartmentPolisher.html index 08f89d54..30cb7bbe 100644 --- a/docs/edu/ucsd/sbrg/polishing/CompartmentPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/CompartmentPolisher.html @@ -149,7 +149,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/ModelPolisher.html b/docs/edu/ucsd/sbrg/polishing/ModelPolisher.html index 921b24d3..d99977b5 100644 --- a/docs/edu/ucsd/sbrg/polishing/ModelPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/ModelPolisher.html @@ -155,7 +155,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/ParametersPolisher.html b/docs/edu/ucsd/sbrg/polishing/ParametersPolisher.html index fde95cc1..d9de2c78 100644 --- a/docs/edu/ucsd/sbrg/polishing/ParametersPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/ParametersPolisher.html @@ -146,7 +146,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/ReactionsPolisher.html b/docs/edu/ucsd/sbrg/polishing/ReactionsPolisher.html index 9d01e21e..84bbf26b 100644 --- a/docs/edu/ucsd/sbrg/polishing/ReactionsPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/ReactionsPolisher.html @@ -167,7 +167,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/SBMLPolisher.html b/docs/edu/ucsd/sbrg/polishing/SBMLPolisher.html index 1b7e903a..dc7c964d 100644 --- a/docs/edu/ucsd/sbrg/polishing/SBMLPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/SBMLPolisher.html @@ -146,7 +146,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/SpeciesPolisher.html b/docs/edu/ucsd/sbrg/polishing/SpeciesPolisher.html index c85c9a62..035efd4c 100644 --- a/docs/edu/ucsd/sbrg/polishing/SpeciesPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/SpeciesPolisher.html @@ -157,7 +157,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/UnitPolisher.html b/docs/edu/ucsd/sbrg/polishing/UnitPolisher.html index be0437fd..e37119ef 100644 --- a/docs/edu/ucsd/sbrg/polishing/UnitPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/UnitPolisher.html @@ -194,7 +194,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.html b/docs/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.html index 48aa37b8..99fc3394 100644 --- a/docs/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/fbc/FBCPolisher.html @@ -139,7 +139,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/fbc/FluxObjectivesPolisher.html b/docs/edu/ucsd/sbrg/polishing/fbc/FluxObjectivesPolisher.html index a10f1363..5575fdc9 100644 --- a/docs/edu/ucsd/sbrg/polishing/fbc/FluxObjectivesPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/fbc/FluxObjectivesPolisher.html @@ -149,7 +149,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/polishing/fbc/GeneProductsPolisher.html b/docs/edu/ucsd/sbrg/polishing/fbc/GeneProductsPolisher.html index ab8af86f..286644cc 100644 --- a/docs/edu/ucsd/sbrg/polishing/fbc/GeneProductsPolisher.html +++ b/docs/edu/ucsd/sbrg/polishing/fbc/GeneProductsPolisher.html @@ -145,7 +145,7 @@

    Method Summary

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

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

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    diff --git a/docs/edu/ucsd/sbrg/reporting/ProgressUpdate.html b/docs/edu/ucsd/sbrg/reporting/ProgressUpdate.html index bec59f56..d49e203e 100644 --- a/docs/edu/ucsd/sbrg/reporting/ProgressUpdate.html +++ b/docs/edu/ucsd/sbrg/reporting/ProgressUpdate.html @@ -91,7 +91,7 @@

    Record Class ProgressUpdat
    -
    public record ProgressUpdate(String text, Object obj, ReportType status) +
    public record ProgressUpdate(String text, Object obj, ReportType reportType) extends Record
    @@ -106,7 +106,7 @@

    Constructor Summary

    Description
    ProgressUpdate(String text, Object obj, - ReportType status)
    + ReportType reportType)
    Creates an instance of a ProgressUpdate record class.
    @@ -140,9 +140,9 @@

    Method Summary

    Returns the value of the obj record component.
    ReportType
    -
    status()
    +
    reportType()
    -
    Returns the value of the status record component.
    +
    Returns the value of the reportType record component.
    String
    text()
    @@ -176,13 +176,13 @@

    Constructor Details

    ProgressUpdate

    public ProgressUpdate(String text, Object obj, - ReportType status)
    + ReportType reportType)
    Creates an instance of a ProgressUpdate record class.
    Parameters:
    text - the value for the text record component
    obj - the value for the obj record component
    -
    status - the value for the status record component
    +
    reportType - the value for the reportType record component

    • @@ -258,13 +258,13 @@

    obj

  • -
    -

    status

    -
    public ReportType status()
    -
    Returns the value of the status record component.
    +
    +

    reportType

    +
    public ReportType reportType()
    +
    Returns the value of the reportType record component.
    Returns:
    -
    the value of the status record component
    +
    the value of the reportType record component
    • diff --git a/docs/edu/ucsd/sbrg/reporting/ReportType.html b/docs/edu/ucsd/sbrg/reporting/ReportType.html index 35394356..910dc62e 100644 --- a/docs/edu/ucsd/sbrg/reporting/ReportType.html +++ b/docs/edu/ucsd/sbrg/reporting/ReportType.html @@ -117,8 +117,10 @@

    Enum Constant Summary

    Enum Constant
    Description
    -
    STATUS
    +
    DATA
     
    +
    STATUS
    +
     
    @@ -165,6 +167,12 @@

    Methods inherited from cl

    Enum Constant Details

    @@ -222,7 +245,7 @@

    Enum Class Hierarchy

  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    • +
  • +
    +

    Exception Class edu.ucsd.sbrg.ModelValidatorException

    +
    class ModelValidatorException extends Exception implements Serializable
    +
      +
    • +
      +

      Serialized Fields

      +
        +
      • +
        outputFile
        +
        File outputFile
        +
        • +
      +
      +
      • +
    +
    +
    • + + + +
  • +
    +

    Package edu.ucsd.sbrg.annotation

    + +
    +
    • +
  • +
    +

    Package edu.ucsd.sbrg.annotation.bigg

    + +
    +
    • +
  • +
    +

    Package edu.ucsd.sbrg.io

    +
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