diff --git a/docs/javadocs/allclasses-frame.html b/docs/javadocs/allclasses-frame.html index 7d615fb8..ad3d3df5 100644 --- a/docs/javadocs/allclasses-frame.html +++ b/docs/javadocs/allclasses-frame.html @@ -2,7 +2,7 @@ - + All Classes @@ -32,33 +32,20 @@

All Classes

  • OrientationType
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  • Range
    • -
  • readTester
  • RefinementType
  • RestrictionType
    • -
  • SBOLAbstractTests
  • SBOLDocument
    • -
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  • SBOLFactory
    • -
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  • SBOLReader
    • -
  • SBOLReaderTest
    • -
  • SBOLTestSuite
    • -
  • SBOLTestUtils
    • -
  • SBOLTestUtils.Terms
    • -
  • SBOLTestUtils.Terms.moduleRoles
    • -
  • SBOLTestUtils.Terms.sequenceTypes
  • SBOLValidate
  • SBOLValidationException
  • SBOLWriter
    • -
  • SBOLWriterTest
  • Sequence
  • SequenceAnnotation
  • SequenceConstraint
  • SequenceOntology
  • SystemsBiologyOntology
  • TopLevel
    • -
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    • -
  • writeTester
    • diff --git a/docs/javadocs/allclasses-noframe.html b/docs/javadocs/allclasses-noframe.html index 4783183f..eefb0970 100644 --- a/docs/javadocs/allclasses-noframe.html +++ b/docs/javadocs/allclasses-noframe.html @@ -2,7 +2,7 @@ - + All Classes @@ -32,33 +32,20 @@

    All Classes

  • OrientationType
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    • -
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  • SBOLFactory
    • -
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  • SBOLReader
    • -
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    • -
  • SBOLTestSuite
    • -
  • SBOLTestUtils
    • -
  • SBOLTestUtils.Terms
    • -
  • SBOLTestUtils.Terms.moduleRoles
    • -
  • SBOLTestUtils.Terms.sequenceTypes
  • SBOLValidate
  • SBOLValidationException
  • SBOLWriter
    • -
  • SBOLWriterTest
  • Sequence
  • SequenceAnnotation
  • SequenceConstraint
  • SequenceOntology
  • SystemsBiologyOntology
  • TopLevel
    • -
  • URIcomplianceTest
    • -
  • writeTester
    • diff --git a/docs/javadocs/constant-values.html b/docs/javadocs/constant-values.html index fcbe4f8c..b541f3a9 100644 --- a/docs/javadocs/constant-values.html +++ b/docs/javadocs/constant-values.html @@ -2,7 +2,7 @@ - + Constant Field Values @@ -27,7 +27,7 @@
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    • @@ -191,7 +191,7 @@

    org.sbolstandard.*

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    • @@ -75,7 +75,7 @@

    Contents

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    • diff --git a/docs/javadocs/help-doc.html b/docs/javadocs/help-doc.html index a33724bd..f693bd15 100644 --- a/docs/javadocs/help-doc.html +++ b/docs/javadocs/help-doc.html @@ -2,7 +2,7 @@ - + API Help @@ -27,7 +27,7 @@
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    • @@ -176,7 +176,7 @@

    Constant Field Values

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    • diff --git a/docs/javadocs/index-files/index-1.html b/docs/javadocs/index-files/index-1.html index 8f8a9cfc..51e8f44e 100644 --- a/docs/javadocs/index-files/index-1.html +++ b/docs/javadocs/index-files/index-1.html @@ -2,7 +2,7 @@ - + A-Index @@ -27,7 +27,7 @@
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    • @@ -146,8 +146,6 @@

    A

    Adds a namespace QName to a SBOL document
    -
    addPRSequence(SBOLDocument, ComponentDefinition, String) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    addRange(String, int, int) - Method in class org.sbolstandard.core2.SequenceAnnotation
    Creates a Range instance with the given arguments and then adds to this SequenceAnnotation object's @@ -170,8 +168,6 @@

    A

    Adds the given role URI to this Participation's set of role URIs.
    -
    addSeq_CD() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    addSequence(Sequence) - Method in class org.sbolstandard.core2.ComponentDefinition
    Adds the URI of the given Sequence instance to this ComponentDefinition object's @@ -192,12 +188,6 @@

    A

    Adds the URI of the given Sequence instance to this ComponentDefinition object's set of reference Sequence URIs.
    -
    addSequence(SBOLDocument, ComponentDefinition, String, URI, String) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    -
    addSubComponents(SBOLDocument, ComponentDefinition, ComponentDefinition...) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    -
    addSubComponents(SBOLDocument, ComponentDefinition, List<ComponentDefinition>) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    addType(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
    Adds the given type URI to this ComponentDefinition's set of reference type URIs.
    @@ -206,8 +196,6 @@

    A

    Adds the given type URI to this Interaction's set of reference type URIs.
    -
    addType_CD() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    ALLOSTERIC_CONTROL - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    Regulation of the influence of a reaction participant by binding an effector to a @@ -215,8 +203,6 @@

    A

    influence (SBO:0000239).
    -
    aminoacids - Static variable in class org.sbolstandard.core2.SBOLTestUtils.Terms.sequenceTypes
    -
     
    AND - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    All the preceding events or participating entities are necessary to perform the control @@ -249,8 +235,6 @@

    A

    Constructs a nested Annotation instance using the given qName, nestedQName, nestedURI, and a list of annotations to include.
    -
    atoms - Static variable in class org.sbolstandard.core2.SBOLTestUtils.Terms.sequenceTypes
    -
     
    A B C D E F G H I J L M N O P R S T U V W X  @@ -263,7 +247,7 @@

    A

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    • diff --git a/docs/javadocs/index-files/index-10.html b/docs/javadocs/index-files/index-10.html index 6dc2112a..d53f2fa2 100644 --- a/docs/javadocs/index-files/index-10.html +++ b/docs/javadocs/index-files/index-10.html @@ -2,7 +2,7 @@ - + J-Index @@ -27,7 +27,7 @@
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    • @@ -80,7 +80,7 @@

    J

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    • diff --git a/docs/javadocs/index-files/index-11.html b/docs/javadocs/index-files/index-11.html index fd2f55bb..14e6b1d6 100644 --- a/docs/javadocs/index-files/index-11.html +++ b/docs/javadocs/index-files/index-11.html @@ -2,7 +2,7 @@ - + L-Index @@ -27,7 +27,7 @@
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    • @@ -96,7 +96,7 @@

    L

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    • diff --git a/docs/javadocs/index-files/index-12.html b/docs/javadocs/index-files/index-12.html index 9da2e161..13649356 100644 --- a/docs/javadocs/index-files/index-12.html +++ b/docs/javadocs/index-files/index-12.html @@ -2,7 +2,7 @@ - + M-Index @@ -27,7 +27,7 @@
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    • @@ -66,16 +66,10 @@

    M

    -
    main(String[]) - Static method in class org.sbolstandard.core2.readTester
    -
     
    main(String[]) - Static method in class org.sbolstandard.core2.SBOLValidate
    Command line method for reading an input file and producing an output file.
    -
    main(String[]) - Static method in class org.sbolstandard.core2.writeTester
    -
    -
    Top level types
    -
    MapsTo - Class in org.sbolstandard.core2
     
    METHYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    @@ -139,7 +133,7 @@

    M

  • Package
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    • diff --git a/docs/javadocs/index-files/index-13.html b/docs/javadocs/index-files/index-13.html index cd897f0a..d7c51c0a 100644 --- a/docs/javadocs/index-files/index-13.html +++ b/docs/javadocs/index-files/index-13.html @@ -2,7 +2,7 @@ - + N-Index @@ -27,7 +27,7 @@
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    • @@ -118,8 +118,6 @@

    N

    The preceding event or participating entity cannot participate to the control (SBO:0000238).
    -
    nucleotides - Static variable in class org.sbolstandard.core2.SBOLTestUtils.Terms.sequenceTypes
    -
     
    A B C D E F G H I J L M N O P R S T U V W X  @@ -132,7 +130,7 @@

    N

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    • diff --git a/docs/javadocs/index-files/index-14.html b/docs/javadocs/index-files/index-14.html index a4750b77..93efb89c 100644 --- a/docs/javadocs/index-files/index-14.html +++ b/docs/javadocs/index-files/index-14.html @@ -2,7 +2,7 @@ - + O-Index @@ -27,7 +27,7 @@
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    • @@ -108,7 +108,7 @@

    O

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    • diff --git a/docs/javadocs/index-files/index-15.html b/docs/javadocs/index-files/index-15.html index d4ae147e..ccf4c879 100644 --- a/docs/javadocs/index-files/index-15.html +++ b/docs/javadocs/index-files/index-15.html @@ -2,7 +2,7 @@ - + P-Index @@ -27,7 +27,7 @@
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    • @@ -73,8 +73,6 @@

    P

    Participation - Class in org.sbolstandard.core2
     
    -
    path - Static variable in class org.sbolstandard.core2.readTester
    -
     
    PETRI_NET_TRANSITION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    A process that can modify the state of petri net 'places' @@ -99,8 +97,6 @@

    P

    Substance that increases the probability of a chemical reaction without itself being consumed or transformed by the reaction (SBO:0000021).
    -
    pr - Static variable in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    PRENYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    Addition of a prenyl group (generic sense) to a chemical entity @@ -163,7 +159,7 @@

    P

  • Package
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    • diff --git a/docs/javadocs/index-files/index-16.html b/docs/javadocs/index-files/index-16.html index 47381a93..e4fc5c34 100644 --- a/docs/javadocs/index-files/index-16.html +++ b/docs/javadocs/index-files/index-16.html @@ -2,7 +2,7 @@ - + R-Index @@ -27,7 +27,7 @@
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    • @@ -102,10 +102,6 @@

    R

    Takes in a given RDF InputStream and converts the file to an SBOLDocument.
    -
    readTester - Class in org.sbolstandard.core2
    -
     
    -
    readTester() - Constructor for class org.sbolstandard.core2.readTester
    -
     
    REDOX_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    Chemical process in which atoms have their oxidation number (oxidation state) changed @@ -222,10 +218,6 @@

    R

    Removes the given role reference from the set of role references.
    -
    removeRole_CD() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    removeSeq_CD() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    removeSequence(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
    Removes the given Sequence reference from the set of Sequence references.
    @@ -252,8 +244,6 @@

    R

    Removes the given type reference from the set of type references.
    -
    removeType_CD() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    RESTRICTION_ENZYME_RECOGNITION_SITE - Static variable in class org.sbolstandard.core2.SequenceOntology
    Represents a region of a DNA molecule which is a nucleotide region (usually a palindrome) that is recognized by a @@ -271,14 +261,6 @@

    R

    A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid (RNA).
    -
    runTest(String, SBOLDocument, String) - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    runTest(String, SBOLDocument, String) - Method in class org.sbolstandard.core2.SBOLGenerateFile
    -
     
    -
    runTest(String, SBOLDocument, String) - Method in class org.sbolstandard.core2.SBOLReaderTest
    -
     
    -
    runTest(String, SBOLDocument, String) - Method in class org.sbolstandard.core2.SBOLWriterTest
    -
     
    A B C D E F G H I J L M N O P R S T U V W X  @@ -291,7 +273,7 @@

    R

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    • diff --git a/docs/javadocs/index-files/index-17.html b/docs/javadocs/index-files/index-17.html index 07822334..656c8888 100644 --- a/docs/javadocs/index-files/index-17.html +++ b/docs/javadocs/index-files/index-17.html @@ -2,7 +2,7 @@ - + S-Index @@ -27,7 +27,7 @@
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    • @@ -72,12 +72,6 @@

    S

    processes such as for example metabolism, cell signaling, and gene regulation (SBML). -
    sbo - Static variable in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    -
    SBOLAbstractTests - Class in org.sbolstandard.core2
    -
     
    -
    SBOLAbstractTests() - Constructor for class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    SBOLDocument - Class in org.sbolstandard.core2
     
    SBOLDocument() - Constructor for class org.sbolstandard.core2.SBOLDocument
    @@ -86,46 +80,12 @@

    S

    and then adds the following namespaces: Sbol2Terms.sbol2, Sbol1Terms.rdf, Sbol2Terms.dc, and Sbol2Terms.prov. -
    SBOLDocumentTest - Class in org.sbolstandard.core2
    -
     
    -
    SBOLDocumentTest() - Constructor for class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    SBOLFactory - Class in org.sbolstandard.core2
     
    -
    SBOLGenerateFile - Class in org.sbolstandard.core2
    -
     
    -
    SBOLGenerateFile() - Constructor for class org.sbolstandard.core2.SBOLGenerateFile
    -
     
    SBOLReader - Class in org.sbolstandard.core2
     
    SBOLReader() - Constructor for class org.sbolstandard.core2.SBOLReader
     
    -
    SBOLReaderTest - Class in org.sbolstandard.core2
    -
     
    -
    SBOLReaderTest() - Constructor for class org.sbolstandard.core2.SBOLReaderTest
    -
     
    -
    SBOLTestSuite - Class in org.sbolstandard.core2
    -
    -
    Runs all specified Test Classes.
    -
    -
    SBOLTestSuite() - Constructor for class org.sbolstandard.core2.SBOLTestSuite
    -
     
    -
    SBOLTestUtils - Class in org.sbolstandard.core2
    -
    -
    Construction of TopLevel objects along with any of its' sub-parts.
    -
    -
    SBOLTestUtils.Terms - Class in org.sbolstandard.core2
    -
     
    -
    SBOLTestUtils.Terms() - Constructor for class org.sbolstandard.core2.SBOLTestUtils.Terms
    -
     
    -
    SBOLTestUtils.Terms.moduleRoles - Class in org.sbolstandard.core2
    -
     
    -
    SBOLTestUtils.Terms.moduleRoles() - Constructor for class org.sbolstandard.core2.SBOLTestUtils.Terms.moduleRoles
    -
     
    -
    SBOLTestUtils.Terms.sequenceTypes - Class in org.sbolstandard.core2
    -
     
    -
    SBOLTestUtils.Terms.sequenceTypes() - Constructor for class org.sbolstandard.core2.SBOLTestUtils.Terms.sequenceTypes
    -
     
    SBOLValidate - Class in org.sbolstandard.core2
     
    SBOLValidate() - Constructor for class org.sbolstandard.core2.SBOLValidate
    @@ -140,10 +100,6 @@

    S

     
    SBOLWriter() - Constructor for class org.sbolstandard.core2.SBOLWriter
     
    -
    SBOLWriterTest - Class in org.sbolstandard.core2
    -
     
    -
    SBOLWriterTest() - Constructor for class org.sbolstandard.core2.SBOLWriterTest
    -
     
    Sequence - Class in org.sbolstandard.core2
     
    SEQUENCE - Static variable in class org.sbolstandard.core2.TopLevel
    @@ -185,8 +141,6 @@

    S

    Sets the flag to the given createDefaults to determine if default component instances should be created when not present.
    -
    setDefaultNameSpace(SBOLDocument, String) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    setDefaultURIprefix(String) - Method in class org.sbolstandard.core2.SBOLDocument
    Sets the default URI prefix to the given defaultURIprefix.
    @@ -369,8 +323,6 @@

    S

    widely accepted as a defacto standard for exchange of molecular structures (SMILES).
    -
    so - Static variable in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    SPATIAL_CONTINUOUS_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    Modelling approach where the quantities of participants are considered continuous, and represented @@ -434,7 +386,7 @@

    S

  • Package
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    • diff --git a/docs/javadocs/index-files/index-18.html b/docs/javadocs/index-files/index-18.html index b22c99c4..e1eddaca 100644 --- a/docs/javadocs/index-files/index-18.html +++ b/docs/javadocs/index-files/index-18.html @@ -2,7 +2,7 @@ - + T-Index @@ -27,7 +27,7 @@
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    • @@ -71,236 +71,6 @@

    T

    The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription (SO:0000141).
    -
    test_AnnotationOutput() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_BBa_I0462_File() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_BBa_T9002_File() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    Test_Collection_CopyCreate() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_Collection_remove() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_CollectionOutput() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    Test_ComponentDefinition_CopyCreate() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_ComponentDefinition_remove() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_ComponentDefinitionOutput() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_CreateAndRemoveCollections() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_CreateAndRemoveComponentDefintion() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_CreateAndRemoveGenericTopLevel() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_CreateAndRemoveModel() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_CreateAndRemoveModuleDefintion() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_CutExample() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    Test_GenericTopLevel_CopyCreate() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_GenericTopLevel_remove() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_GenericTopLevelOutput() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    Test_getCollection() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    Test_getModuleDefinition() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_igem1_File() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_igem2_File() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_igem3_File() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_All_File() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Aspergillus_nidulans() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Bacillus_subtilis() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Drosophila_melanogaster() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Escherichia_Coli() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Gramnegative_bacteria() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Insect_Cells() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Kluyveromyces_lactis() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Mammalian_Cells() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Pichia_pastoris() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Plant_Cells() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Saccharomyces_cerevisiae() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Schizosaccharomyces_pombe() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_labhost_Unspecified() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_memberAnnotations() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    Test_Model_CopyCreate() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_Model_remove() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_ModelOutput() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    Test_ModuleDefinition_CreateCopy() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_ModuleDefinition_remove() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_ModuleDefinitionOutput() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_multipleCollections_no_Members() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_multipleGenericTopLevel() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_multipleSquences() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_partial_pIKE_left_cassette() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_partial_pIKE_right_casette() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_partial_pIKE_right_cassette() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_partial_pTAK_left_cassette() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_partial_pTAK_right_cassette() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_pIKE_pTAK_cassettes() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_pIKE_pTAK_cassettes_2() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_pIKE_pTAK_left_right_cassettes() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_pIKE_pTAK_toggle_switches() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_removeModuleDefinition() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_SBOLDocumentOutput() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    Test_Sequence_CopyCreate_Create() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_Sequence_remove() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_SequenceConstraintOutput() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_SequenceEquals() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_SequenceOutput() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    Test_setEncoding() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_setTypes() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    -
    test_SimpleComponentDefinitionExample() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_SimpleModuleDefinition() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_single_emptyModuleDefinition() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_singleCollection() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_singleCompDef_withSeq() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_singleComponentDefinition() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_singleFunctionalComponent() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_singleGenericTopLevel() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_singleModel() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_singleSequence() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    test_toggle_File() - Method in class org.sbolstandard.core2.SBOLAbstractTests
    -
     
    -
    testExtractPersistentId1() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test null<\code> for top-level URI not compliant in extractPersistentId.
    -
    -
    testExtractPersistentId2() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test the extracted persistent ID string for the compliant top-level URI.
    -
    -
    testExtractPersistentId3() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test null<\code> for child URI not compliant in extractPersistentId.
    -
    -
    testExtractPersistentId4() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test the extracted persistent ID string for the compliant child URI.
    -
    -
    testExtractPersistentId5() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test null<\code> for grand child URI not compliant in extractPersistentId.
    -
    -
    testExtractPersistentId6() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test the extracted persistent ID string for the compliant grand child URI.
    -
    -
    testExtractPersistentId7() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test null<\code> for great grand child URI not compliant in extractPersistentId.
    -
    -
    testExtractPersistentId8() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test the extracted persistent ID string for the compliant great grand child URI.
    -
    -
    testExtractURIprefix1() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test null<\code> for grand child URI not compliant in extractPersistentId.
    -
    -
    testExtractVersion1() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test null<\code> for extractVersion for the compliant top-level URI.
    -
    -
    testExtractVersion2() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test null<\code> for extractVersion for the compliant child URI.
    -
    -
    testExtractVersion3() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test null<\code> for extractVersion for the compliant grand child URI.
    -
    -
    testExtractVersion4() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test null<\code> for extractVersion for the compliant great grand child URI.
    -
    -
    testExtractVersion5() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test the extracted version string for extractVersion for the compliant top-level URI.
    -
    -
    testExtractVersion6() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test the extracted version string for extractVersion for the compliant child URI.
    -
    -
    testExtractVersion7() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test the extracted version string for extractVersion for the compliant grand child URI.
    -
    -
    testExtractVersion8() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
    -
    Test the extracted version string for extractVersion for the compliant great grand child URI.
    -
    -
    testIDcase() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
     
    -
    testIsDisplayIdCompliant1() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
     
    -
    testIsDisplayIdCompliant2() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
     
    -
    testIsDisplayIdCompliant3() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
     
    -
    testURLcase() - Method in class org.sbolstandard.core2.URIcomplianceTest
    -
     
    TopLevel - Class in org.sbolstandard.core2
     
    toString() - Method in enum org.sbolstandard.core2.AccessType
    @@ -357,8 +127,6 @@

    T

     
    toString() - Method in class org.sbolstandard.core2.SequenceConstraint
     
    -
    toURI(QName) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    TRANS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    Positional relationship between entities on different sides, or strands @@ -421,7 +189,7 @@

    T

  • Package
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    • diff --git a/docs/javadocs/index-files/index-19.html b/docs/javadocs/index-files/index-19.html index 10715df5..bb61bdbe 100644 --- a/docs/javadocs/index-files/index-19.html +++ b/docs/javadocs/index-files/index-19.html @@ -2,7 +2,7 @@ - + U-Index @@ -27,7 +27,7 @@
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    • @@ -76,8 +76,6 @@

    U

    An equivocal or conjectural process, whose existence is assumed but not proven (SBO:0000396).
    -
    uniprot - Static variable in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    unsetComponent() - Method in class org.sbolstandard.core2.SequenceAnnotation
    Dereference the component URI by setting it to null.
    @@ -102,10 +100,6 @@

    U

    Sets the wasDerivedFrom property to null.
    -
    URIcomplianceTest - Class in org.sbolstandard.core2
    -
     
    -
    URIcomplianceTest() - Constructor for class org.sbolstandard.core2.URIcomplianceTest
    -
     
    A B C D E F G H I J L M N O P R S T U V W X  @@ -118,7 +112,7 @@

    U

  • Package
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    • diff --git a/docs/javadocs/index-files/index-2.html b/docs/javadocs/index-files/index-2.html index 16b554f4..72e83ce9 100644 --- a/docs/javadocs/index-files/index-2.html +++ b/docs/javadocs/index-files/index-2.html @@ -2,7 +2,7 @@ - + B-Index @@ -27,7 +27,7 @@
  • Package
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    • -
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    • @@ -94,8 +94,6 @@

    B

    BioPAX is an exchange format for pathway data, with its data model defined in OWL (BIOPAX).
    -
    biopax - Static variable in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    BOOLEAN_LOGICAL_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    Equationally defined algebraic framework usually interpreted as a two-valued logic using the basic @@ -114,7 +112,7 @@

    B

  • Package
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    • diff --git a/docs/javadocs/index-files/index-20.html b/docs/javadocs/index-files/index-20.html index 50431804..e16185aa 100644 --- a/docs/javadocs/index-files/index-20.html +++ b/docs/javadocs/index-files/index-20.html @@ -2,7 +2,7 @@ - + V-Index @@ -27,7 +27,7 @@
  • Package
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    • @@ -119,8 +119,6 @@

    V

    Returns an array containing the constants of this enum type, in the order they are declared.
    -
    vpr - Static variable in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    A B C D E F G H I J L M N O P R S T U V W X  @@ -133,7 +131,7 @@

    V

  • Package
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    • diff --git a/docs/javadocs/index-files/index-21.html b/docs/javadocs/index-files/index-21.html index 9ef7bf73..a62d3943 100644 --- a/docs/javadocs/index-files/index-21.html +++ b/docs/javadocs/index-files/index-21.html @@ -2,7 +2,7 @@ - + W-Index @@ -27,7 +27,7 @@
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    • @@ -100,20 +100,6 @@

    W

    Serializes a given SBOLDocument and outputs the data from the serialization to the given output file name in RDF format
    -
    writeAndRead(SBOLDocument) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    -
    writeJsonFile(SBOLDocument, String) - Static method in class org.sbolstandard.core2.SBOLGenerateFile
    -
     
    -
    writeRdfFile(SBOLDocument, String) - Static method in class org.sbolstandard.core2.SBOLGenerateFile
    -
     
    -
    writeRdfOutputStream(SBOLDocument) - Static method in class org.sbolstandard.core2.writeTester
    -
     
    -
    writeTester - Class in org.sbolstandard.core2
    -
     
    -
    writeTester() - Constructor for class org.sbolstandard.core2.writeTester
    -
     
    -
    writeTurtleFile(SBOLDocument, String) - Static method in class org.sbolstandard.core2.SBOLGenerateFile
    -
     
    A B C D E F G H I J L M N O P R S T U V W X  @@ -126,7 +112,7 @@

    W

  • Package
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    • diff --git a/docs/javadocs/index-files/index-3.html b/docs/javadocs/index-files/index-3.html index 31679c34..38d65e7a 100644 --- a/docs/javadocs/index-files/index-3.html +++ b/docs/javadocs/index-files/index-3.html @@ -2,7 +2,7 @@ - + C-Index @@ -27,7 +27,7 @@
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    • @@ -287,8 +287,6 @@

    C

    Checks if the given role URI is included in this Participation object's set of reference role URIs.
    -
    containsRole_CD() - Method in class org.sbolstandard.core2.SBOLDocumentTest
    -
     
    containsSequence(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
    Checks if the given Sequence URI is included in this ComponentDefinition @@ -318,10 +316,6 @@

    C

    Biochemical reaction that results in the modification of some covalent bonds (SBO:0000182).
    -
    convertRDFTripleStore(String, String) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    -
    convertSBOL1(String, String, String, boolean) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    createAnnotation(QName, String) - Method in class org.sbolstandard.core2.Identified
    Creates an Annotation instance using the given parameters, @@ -368,8 +362,6 @@

    C

    Creates a Collection instance with the given arguments, and then adds it to this SBOLDocument object's list of Collection instances.
    -
    createComponenDefinition(SBOLDocument, QName, String, URI, URI, String) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    createComponent(String, AccessType, String, String) - Method in class org.sbolstandard.core2.ComponentDefinition
    Creates a child Component instance for this ComponentDefinition @@ -485,8 +477,6 @@

    C

    Creates a child Interaction object for this ModuleDefinition object with the given arguments, and then adds to this ModuleDefinition's list of Interaction instances.
    -
    createInverter(SBOLDocument, ModuleDefinition, ComponentDefinition, ComponentDefinition) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    createMapsTo(String, RefinementType, URI, URI) - Method in class org.sbolstandard.core2.Component
    Creates a child MapsTo instance for this object with the given arguments, @@ -644,7 +634,7 @@

    C

  • Package
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    • diff --git a/docs/javadocs/index-files/index-4.html b/docs/javadocs/index-files/index-4.html index b98dc1f3..c9f77fa0 100644 --- a/docs/javadocs/index-files/index-4.html +++ b/docs/javadocs/index-files/index-4.html @@ -2,7 +2,7 @@ - + D-Index @@ -27,7 +27,7 @@
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    • @@ -135,7 +135,7 @@

    D

  • Package
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    • diff --git a/docs/javadocs/index-files/index-5.html b/docs/javadocs/index-files/index-5.html index c58e253c..420ae242 100644 --- a/docs/javadocs/index-files/index-5.html +++ b/docs/javadocs/index-files/index-5.html @@ -2,7 +2,7 @@ - + E-Index @@ -27,7 +27,7 @@
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    • @@ -137,8 +137,6 @@

    E

    A substance that is absolutely required for occurrence and stimulation of a reaction (SBO:0000461).
    -
    example - Static variable in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    A B C D E F G H I J L M N O P R S T U V W X  @@ -151,7 +149,7 @@

    E

  • Package
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    • diff --git a/docs/javadocs/index-files/index-6.html b/docs/javadocs/index-files/index-6.html index 3a600baa..cc1964c1 100644 --- a/docs/javadocs/index-files/index-6.html +++ b/docs/javadocs/index-files/index-6.html @@ -2,7 +2,7 @@ - + F-Index @@ -27,7 +27,7 @@
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    • @@ -72,44 +72,6 @@

    F

    to a chemical entity (SBO:0000222). -
    filenameJson - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameRdf - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameTurtle - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_1 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_10 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_11 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_12 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_13 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_14 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_15 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_16 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_2 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_3 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_4 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_5 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_6 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_7 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_8 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    -
    filenameV1_9 - Static variable in class org.sbolstandard.core2.readTester
    -
     
    FIVE_PRIME_UTR - Static variable in class org.sbolstandard.core2.SequenceOntology
    A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a @@ -141,7 +103,7 @@

    F

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    • diff --git a/docs/javadocs/index-files/index-7.html b/docs/javadocs/index-files/index-7.html index 9014590f..c8df5baf 100644 --- a/docs/javadocs/index-files/index-7.html +++ b/docs/javadocs/index-files/index-7.html @@ -2,7 +2,7 @@ - + G-Index @@ -27,7 +27,7 @@
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    • @@ -486,8 +486,6 @@

    G

    Returns the persistent identity URI of this object.
    -
    getPropertyURI(String) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    getQName() - Method in class org.sbolstandard.core2.Annotation
    Returns the name of the value property.
    @@ -583,8 +581,6 @@

    G

    Returns the set of SequenceConstraint instances owned by this ComponentDefinition object.
    -
    getSequenceLength(SBOLDocument, ComponentDefinition) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    getSequences() - Method in class org.sbolstandard.core2.ComponentDefinition
    Returns the set of Sequence instances referenced by this ComponentDefinition object.
    @@ -597,8 +593,6 @@

    G

    Returns the set of Sequence URIs referenced by this ComponentDefinition's object.
    -
    getSetPropertyURI(String...) - Static method in class org.sbolstandard.core2.SBOLTestUtils
    -
     
    getSource() - Method in class org.sbolstandard.core2.Model
    Returns the URI of the source property of this Model object.
    @@ -665,7 +659,7 @@

    G

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    • @@ -129,7 +129,7 @@

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    • @@ -91,8 +91,6 @@

    I

    Entity participating in a physical or functional interaction (SBO:0000336).
    -
    inverter - Static variable in class org.sbolstandard.core2.SBOLTestUtils.Terms.moduleRoles
    -
     
    IONISATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
    Ionization is the physical process of converting an atom or molecule into an ion by @@ -203,7 +201,7 @@

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