diff --git a/README.md b/README.md index 96f0e964..529baf36 100755 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ In a Maven project that utilizes the libSBOLj library, add a dependency in the M org.sbolstandard libSBOLj - 2.0.0 + 2.1.0 ``` @@ -28,34 +28,26 @@ libSBOLj comes with a command-line interface (CLI) that can be used to validate ```libSBOLj--withDependencies.jar``` to validate and convert files as follows. ``` -java -jar libSBOLj--withDependencies.jar +java -jar libSBOLj--withDependencies.jar -l ``` -If validation is successful, the program will print the contents of the SBOL document. You can also output the result to a file. +If validation/conversion is successful, the program will print the contents of the input file in the specified language (SBOL1, SBOL2, GenBank, and FASTA). You can also output the result to a file. ``` -java -jar libSBOLj--withDependencies.jar -o +java -jar libSBOLj--withDependencies.jar -l -o ``` -If validation fails with an error, there will be a message printed about the validation error. In addition to checking all required validation rules, it will also check if the URIs are compliant and whether the SBOL document is complete (i.e., all referenced objects are contained within the file). These validation checks can be turned off with the -n and -i flags, respectively. It is also possible to turn-on best practices checking using the -b flag. +One can also provide a URI using the -s flag for a TopLevel object, and only that object and all its dependencies will be output. -If the input file is an SBOL 1.1 file, then it will convert the file into an SBOL 2.0 file. This conversion should be provided a default URI prefix. It can also be provided a default version, if desired. Finally, the -t flag will insert the type of top level objects into the URI during conversion, if desired. +If validation fails with an error, there will be a message printed about the validation error. The -f flag can be used to indicate that validation should continue after the first error, while the -d flag will provide a detailed error trace on a validation error. -``` -java -jar libSBOLj--withDependencies.jar -o -p -v -``` +In addition to checking all required validation rules, it will also check if the URIs are compliant and whether the SBOL document is complete (i.e., all referenced objects are contained within the file). These validation checks can be turned off with the -n and -i flags, respectively. It is also possible to turn-on best practices checking using the -b flag. -The command line interface can also convert GenBank files into SBOL 2.0 files using the command below: +When the input file is being converted into SBOL 2.0, the conversion should be provided a default URI prefix. It can also be provided a default version, if desired. Finally, the -t flag will insert the type of top level objects into the URI during conversion, if desired. ``` -java -jar libSBOLj--withDependencies.jar -g -o -p -v -``` - -It can convert a specifed top-level ComponentDefinition within an SBOL 2.0 file into a GenBank file using the following command: -``` -java -jar libSBOLj--withDependencies.jar -c -o +java -jar libSBOLj--withDependencies.jar -o -p -v ``` -Note that if no top-level ComponentDefinition is specified, that it will attempt to find a root ComponentDefinition. If it finds a single root, it will convert that, otherwise it will give an error message. Finally, it can be used to compare the equality of the contents of two SBOL files using the command below: ``` diff --git a/docs/javadocs/allclasses-frame.html b/docs/javadocs/allclasses-frame.html index 3ba00ae3..4376cf40 100644 --- a/docs/javadocs/allclasses-frame.html +++ b/docs/javadocs/allclasses-frame.html @@ -2,16 +2,53 @@ - + All Classes - +

All Classes

diff --git a/docs/javadocs/allclasses-noframe.html b/docs/javadocs/allclasses-noframe.html index 4e5a9dc9..a3a60fe7 100644 --- a/docs/javadocs/allclasses-noframe.html +++ b/docs/javadocs/allclasses-noframe.html @@ -2,16 +2,53 @@ - + All Classes - +

All Classes

diff --git a/docs/javadocs/constant-values.html b/docs/javadocs/constant-values.html index 080137c9..9450340c 100644 --- a/docs/javadocs/constant-values.html +++ b/docs/javadocs/constant-values.html @@ -2,9 +2,9 @@ - + Constant Field Values - + @@ -64,6 +64,150 @@

Constant Field Values

Contents

+ +
+
+ + +

org.sbolstandard.*

+
diff --git a/docs/javadocs/deprecated-list.html b/docs/javadocs/deprecated-list.html index 96ab17fa..22c0cdd7 100644 --- a/docs/javadocs/deprecated-list.html +++ b/docs/javadocs/deprecated-list.html @@ -2,9 +2,9 @@ - + Deprecated List - + diff --git a/docs/javadocs/help-doc.html b/docs/javadocs/help-doc.html index 1075fa2c..42fc879b 100644 --- a/docs/javadocs/help-doc.html +++ b/docs/javadocs/help-doc.html @@ -2,9 +2,9 @@ - + API Help - + diff --git a/docs/javadocs/index-files/index-1.html b/docs/javadocs/index-files/index-1.html index 4fe22758..be6edfb4 100644 --- a/docs/javadocs/index-files/index-1.html +++ b/docs/javadocs/index-files/index-1.html @@ -2,9 +2,9 @@ - + A-Index - + @@ -61,11 +61,65 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X 

A

+
ABSOLUTE_INHIBITION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Control that precludes the execution of a process + (SBO:0000407).
+
+
ABSOLUTE_STIMULATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Control that always triggers the controlled process + (SBO:0000411).
+
+
AccessType - Enum in org.sbolstandard.core2
+
+
Represents all access types for a ComponentInstance object.
+
+
ACETYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Addition of an acetyl group (-COCH3) to a chemical entity + (SBO:0000215).
+
+
ACID_BASE_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Chemical reaction where a proton is given by a compound, the acid, to another one, the + base (Brønsted-Lowry definition) (SBO:0000208).
+
+
addCut(String, int) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Creates a Cut instance with the given arguments and then adds to this SequenceAnnotation instance's + list of locations.
+
+
addCut(String, int, OrientationType) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Creates a Cut instance with the given arguments and then adds to this SequenceAnnotation instance's + list of locations.
+
+
addGenericLocation(String) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Creates a GenericLocation instance with the given arguments, + and then adds to this SequenceAnnotation instance's list of locations.
+
+
addGenericLocation(String, OrientationType) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Creates a GenericLocation instance with the given arguments and then adds to this SequenceAnnotation instance's + list of locations.
+
+
ADDITION_OF_A_CHEMICAL_GROUP - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Covalent reaction that results in the addition of a chemical group on a molecule + (SBO:0000210).
+
+
addMember(URI) - Method in class org.sbolstandard.core2.Collection
+
+
Adds the given member URI to this Collection instance's + set of reference member URIs.
+
addModel(Model) - Method in class org.sbolstandard.core2.ModuleDefinition
Adds the URI of the given model to this module definition's @@ -85,12 +139,122 @@

A

Adds the given model URI to this module definition's set of model URIs.
+
addNamespace(URI, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Adds the given namespace URI and its prefix to this SBOL document.
+
+
addNamespace(QName) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Adds the given namespace QName to this SBOL document.
+
+
addNamespace(URI, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Adds a namespace URI and its prefix to a SBOL document
+
+
addNamespace(QName) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Adds a namespace QName to a SBOL document
+
+
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 instance's + list of locations.
+
+
addRange(String, int, int, OrientationType) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Creates a Range instance with the given arguments and then adds to this SequenceAnnotation instance's + list of locations.
+
+
addRole(URI) - Method in class org.sbolstandard.core2.Component
+
+
Adds the given role URI to this component's set of role URIs.
+
+
addRole(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Adds the given role URI to this component definition's set of role URIs.
+
addRole(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
Adds the given role URI to this module definition's set of role URIs.
+
addRole(URI) - Method in class org.sbolstandard.core2.Participation
+
+
Adds the given role to this participation's set of roles.
+
+
addRole(URI) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Adds the given role URI to this sequence annotation's set of role URIs.
+
+
addSequence(Sequence) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Adds the URI of the given Sequence instance to this component definition's + set of sequence URIs.
+
+
addSequence(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Adds the given sequence URI to this component definition's set of sequence URIs.
+
+
addSequence(String, String) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Constructs a compliant sequence URI with the given display ID and version, and then adds this URI + to this component definition's set of sequence URIs.
+
+
addSequence(String) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Constructs a compliant sequence URI using the given sequence display ID, and then adds this URI to + this component definition's set of sequence URIs.
+
+
addType(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Adds the given type URI to this component definition's set of type URIs.
+
+
addType(URI) - Method in class org.sbolstandard.core2.Interaction
+
+
Adds the given type URI to this interaction's set of type URIs.
+
+
ALLOSTERIC_CONTROL - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Regulation of the influence of a reaction participant by binding an effector to a + binding site of the participant different of the site of the participant conveying the + influence + (SBO:0000239).
+
+
AND - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
All the preceding events or participating entities are necessary to perform the control + (SBO:0000173).
+
+
Annotation - Class in org.sbolstandard.core2
+
+
Represents the SBOL Annotation data model.
+
+
Annotation(QName, String) - Constructor for class org.sbolstandard.core2.Annotation
+
+
Constructs an annotation using the given qName and the string type literal.
+
+
Annotation(QName, int) - Constructor for class org.sbolstandard.core2.Annotation
+
+
Constructs an annotation using the given qName and the integer type literal.
+
+
Annotation(QName, double) - Constructor for class org.sbolstandard.core2.Annotation
+
+
Constructs an annotation using the given qName and the double type literal.
+
+
Annotation(QName, boolean) - Constructor for class org.sbolstandard.core2.Annotation
+
+
Constructs an annotation using the given qName and the boolean type literal.
+
+
Annotation(QName, URI) - Constructor for class org.sbolstandard.core2.Annotation
+
+
Constructs an annotation using the given qName and the URI type literal.
+
+
Annotation(QName, QName, URI, List<Annotation>) - Constructor for class org.sbolstandard.core2.Annotation
+
+
Constructs a nested annotation using the given qName, nested qName, + nested URI, and list of annotations.
+
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
diff --git a/docs/javadocs/index-files/index-10.html b/docs/javadocs/index-files/index-10.html index 37917dec..e2b5d226 100644 --- a/docs/javadocs/index-files/index-10.html +++ b/docs/javadocs/index-files/index-10.html @@ -2,15 +2,15 @@ - -T-Index - + +J-Index + @@ -36,7 +36,7 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X  -

T

+

J

-
toString() - Method in class org.sbolstandard.core2.ModuleDefinition
-
 
+
JSON - Static variable in class org.sbolstandard.core2.SBOLDocument
+
+
Constant representing JSON file format
+
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
@@ -89,7 +91,7 @@

T

  • Frames
    • diff --git a/docs/javadocs/index-files/index-11.html b/docs/javadocs/index-files/index-11.html index add91474..c4ebb4c0 100644 --- a/docs/javadocs/index-files/index-11.html +++ b/docs/javadocs/index-files/index-11.html @@ -2,9 +2,9 @@ - + K-Index - + diff --git a/docs/javadocs/index-files/index-12.html b/docs/javadocs/index-files/index-12.html index 341e8056..36e15804 100644 --- a/docs/javadocs/index-files/index-12.html +++ b/docs/javadocs/index-files/index-12.html @@ -2,9 +2,9 @@ - + L-Index - + diff --git a/docs/javadocs/index-files/index-13.html b/docs/javadocs/index-files/index-13.html index 932fc3ff..cf1d12b4 100644 --- a/docs/javadocs/index-files/index-13.html +++ b/docs/javadocs/index-files/index-13.html @@ -2,9 +2,9 @@ - + M-Index - + diff --git a/docs/javadocs/index-files/index-14.html b/docs/javadocs/index-files/index-14.html index c94e9f29..350544e0 100644 --- a/docs/javadocs/index-files/index-14.html +++ b/docs/javadocs/index-files/index-14.html @@ -2,9 +2,9 @@ - + N-Index - + diff --git a/docs/javadocs/index-files/index-15.html b/docs/javadocs/index-files/index-15.html index f6527db7..2ea98c24 100644 --- a/docs/javadocs/index-files/index-15.html +++ b/docs/javadocs/index-files/index-15.html @@ -2,9 +2,9 @@ - + O-Index - + diff --git a/docs/javadocs/index-files/index-16.html b/docs/javadocs/index-files/index-16.html index d5592b54..cdd720fd 100644 --- a/docs/javadocs/index-files/index-16.html +++ b/docs/javadocs/index-files/index-16.html @@ -2,9 +2,9 @@ - + P-Index - + diff --git a/docs/javadocs/index-files/index-17.html b/docs/javadocs/index-files/index-17.html index 26641d74..8121188d 100644 --- a/docs/javadocs/index-files/index-17.html +++ b/docs/javadocs/index-files/index-17.html @@ -2,9 +2,9 @@ - + R-Index - + diff --git a/docs/javadocs/index-files/index-18.html b/docs/javadocs/index-files/index-18.html index 739bb057..df6ccc39 100644 --- a/docs/javadocs/index-files/index-18.html +++ b/docs/javadocs/index-files/index-18.html @@ -2,9 +2,9 @@ - + S-Index - + diff --git a/docs/javadocs/index-files/index-19.html b/docs/javadocs/index-files/index-19.html index f62d8297..14e01908 100644 --- a/docs/javadocs/index-files/index-19.html +++ b/docs/javadocs/index-files/index-19.html @@ -2,9 +2,9 @@ - + T-Index - + diff --git a/docs/javadocs/index-files/index-2.html b/docs/javadocs/index-files/index-2.html index aea3bee7..6a553baa 100644 --- a/docs/javadocs/index-files/index-2.html +++ b/docs/javadocs/index-files/index-2.html @@ -2,15 +2,15 @@ - -C-Index - + +B-Index + @@ -61,81 +61,47 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X  -

C

+

B

-
clearFunctionalComponents() - Method in class org.sbolstandard.core2.ModuleDefinition
+
BINDING_ACTIVATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Removes all entries of this module definition's list of functional components.
+
An essential activator that affects the apparent value of the Michaelis constant(s) + (SBO:0000535).
-
clearInteractions() - Method in class org.sbolstandard.core2.ModuleDefinition
+
BIOCHEMICAL_OR_TRANSPORT_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Removes all entries of this module definition's list of interactions.
+
An event involving one or more physical entities that modifies the structure, location + or free energy of at least one of the participants (SBO:0000167).
-
clearModels() - Method in class org.sbolstandard.core2.ModuleDefinition
+
BIOCHEMICAL_REACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Removes all entries of this module definition's set of model URIs.
+
An event involving one or more chemical entities that modifies the electrochemical + structure of at least one of the participants.
-
clearModules() - Method in class org.sbolstandard.core2.ModuleDefinition
+
BIOLOGICAL_ACTIVITY - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Removes all entries of this module definition's list of modules.
+
The potential action that a biological entity has on other entities (SBO:0000412).
-
clearRoles() - Method in class org.sbolstandard.core2.ModuleDefinition
+
BIOLOGICAL_EFFECT_OF_A_PERTURBATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Removes all entries of this module definition's set of role URIs.
+
Biochemical networks can be affected by external influences (SBO:0000357).
-
containsModel(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
BIOPAX - Static variable in class org.sbolstandard.core2.EDAMOntology
-
Checks if the given model URI is included in this module definition's set of reference model URIs.
+
BioPAX is an exchange format for pathway data, with its data model defined in OWL + (BIOPAX).
-
containsRole(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
BOOLEAN_LOGICAL_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Checks if the given role URI is included in this module definition's set of role URIs.
-
-
createFunctionalComponent(String, AccessType, String, String, DirectionType) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Creates a child functional component for this module definition with the given arguments, - and then adds to this module definition's list of functional components.
-
-
createFunctionalComponent(String, AccessType, String, DirectionType) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Creates a child functional component for this module definition with the given arguments, - and then adds to this module definition's list of functional components.
-
-
createFunctionalComponent(String, AccessType, URI, DirectionType) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Creates a child functional component for this module definition with the given arguments, and then adds to this - module definition's list of functional components.
-
-
createInteraction(String, Set<URI>) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Creates a child interaction for this module definition with - the given arguments, and then adds to this module definition's list of interactions.
-
-
createInteraction(String, URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Creates a child interaction for this module definition with - the given arguments, and then adds to this module definition's list of interactions.
-
-
createModule(String, String, String) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Creates a child module for this module definition with the - given arguments, and then adds to this module definition's list of modules.
-
-
createModule(String, String) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Creates a child module for this module definition with the - given arguments, and then adds to this module definition's list of modules.
-
-
createModule(String, URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Creates a child module for this module definition with the - given arguments, and then adds to this module definition's list of modules.
+
Equationally defined algebraic framework usually interpreted as a two-valued logic using the basic + Boolean operations (conjunction, disjunction and negation), together with the constants '0' and '1' + denoting false and true values, respectively (SBO:0000547).
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
diff --git a/docs/javadocs/index-files/index-20.html b/docs/javadocs/index-files/index-20.html index 6b14c80d..983a653a 100644 --- a/docs/javadocs/index-files/index-20.html +++ b/docs/javadocs/index-files/index-20.html @@ -2,9 +2,9 @@ - + U-Index - + diff --git a/docs/javadocs/index-files/index-21.html b/docs/javadocs/index-files/index-21.html index 79901905..9c14ae82 100644 --- a/docs/javadocs/index-files/index-21.html +++ b/docs/javadocs/index-files/index-21.html @@ -2,9 +2,9 @@ - + V-Index - + diff --git a/docs/javadocs/index-files/index-3.html b/docs/javadocs/index-files/index-3.html index 0f6e3888..87875d8d 100644 --- a/docs/javadocs/index-files/index-3.html +++ b/docs/javadocs/index-files/index-3.html @@ -2,15 +2,15 @@ - -E-Index - + +C-Index + @@ -61,15 +61,757 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X  -

E

+

C

-
equals(Object) - Method in class org.sbolstandard.core2.ModuleDefinition
+
CATALYSIS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Modification of the velocity of a reaction by lowering the energy of the transition state + (SBO:0000172).
+
+
CATALYST - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Substance that accelerates the velocity of a chemical reaction without itself being + consumed or transformed (SBO:0000013).
+
+
CATALYTIC_ACTIVATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
An essential activator that affects the apparent value of the catalytic constant + (SBO:0000534).
+
+
CDS - Static variable in class org.sbolstandard.core2.SequenceOntology
+
+
A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon + (SO:0000316).
+
+
CELLML - Static variable in class org.sbolstandard.core2.EDAMOntology
+
+
CellML, the format for mathematical models of biological and other networks + (CELLML).
+
+
CIS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Positional relationship between entities on the same strand (e.g.
+
+
clear() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
This clears the internal SBOLDocument used by the factory.
+
+
clearAnnotations() - Method in class org.sbolstandard.core2.Identified
+
+
Removes all entries of this instance's list of annotations.
+
+
clearCollections() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Removes all entries in the list of collections owned by this SBOL document.
+
+
clearCollections() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Removes all entries in the list of Collection instances + owned by this SBOLDocument object.
+
+
clearComponentDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Removes all entries in the list of component definitions owned by this SBOL document.
+
+
clearComponentDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Removes all entries in the list of ComponentDefinition instances + owned by this SBOLDocument object.
+
+
clearComponents() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Removes all entries of this component definition's list of components.
+
+
clearErrors() - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Sets the error list that is used to store SBOL validation exceptions + during reading to empty.
+
+
clearErrors() - Static method in class org.sbolstandard.core2.SBOLValidate
+
+
Empties the error list used to store SBOL validation exceptions.
+
+
clearErrors() - Static method in class org.sbolstandard.core2.SBOLWriter
+
+
Sets the error list that is used to store SBOL conversion exceptions + during reading to empty.
+
+
clearFunctionalComponents() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Removes all entries of this module definition's list of functional components.
+
+
clearGenericTopLevels() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Removes all entries in the list of generic top-levels + owned by this SBOL document.
+
+
clearGenericTopLevels() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Removes all entries in the list of GenericTopLevel instances + owned by this SBOLDocument object.
+
+
clearInteractions() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Removes all entries of this module definition's list of interactions.
+
+
clearMapsTos() - Method in class org.sbolstandard.core2.Component
+
+
Removes all entries the list of mapsTos.
+
+
clearMapsTos() - Method in class org.sbolstandard.core2.FunctionalComponent
+
+
Removes all entries of this object's list of + mapsTos.
+
+
clearMapsTos() - Method in class org.sbolstandard.core2.Module
+
+
Removes all entries of this module's list of mapsTos.
+
+
clearMembers() - Method in class org.sbolstandard.core2.Collection
+
+
Removes all entries of this Collection instance's set of reference + member URIs.
+
+
clearModels() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Removes all entries of this module definition's set of model URIs.
+
+
clearModels() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Removes all entries in the list of models owned by this SBOL document.
+
+
clearModels() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Removes all entries in the list of Model instances + owned by this SBOLDocument object.
+
+
clearModuleDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Removes all entries in the list of module definitions owned by this SBOL document.
+
+
clearModuleDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Removes all entries in the list of ModuleDefinition instances + owned by this SBOLDocument object.
+
+
clearModules() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Removes all entries of this module definition's list of modules.
+
+
clearNamespaces() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Removes all non-required namespaces from this SBOL document.
+
+
clearNamespaces() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Removes all non-required namespaces from the SBOL document.
+
+
clearParticipations() - Method in class org.sbolstandard.core2.Interaction
+
+
Removes all entries of this interaction list of sequence annotations.
+
+
clearRoles() - Method in class org.sbolstandard.core2.Component
+
+
Removes all entries of this component's set of role URIs.
+
+
clearRoles() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Removes all entries of this component definition's set of role URIs.
+
+
clearRoles() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Removes all entries of this module definition's set of role URIs.
+
+
clearRoles() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Removes all entries of this sequence annotation's set of role URIs.
+
+
clearSequenceAnnotations() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Removes all entries of this component definition's list of sequence annotations.
+
+
clearSequenceConstraints() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Removes all entries of this component definition's list of sequence constraints.
+
+
clearSequences() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Removes all entries of this component definition's set of reference + sequence URIs.
+
+
clearSequences() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Removes all entries in the list of sequences owned by this SBOL document.
+
+
clearSequences() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Removes all entries in the list of Sequence instances + owned by this SBOLDocument object.
+
+
CLEAVAGE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Rupture of a covalent bond resulting in the conversion of one physical entity into + several physical entities + (SBO:0000178).
+
+
Collection - Class in org.sbolstandard.core2
+
+
Represents the SBOL Collection data model.
+
+
COLLECTION - Static variable in class org.sbolstandard.core2.TopLevel
+
+
The abbreviation for the Collection type in URI
+
+
compareDocuments(String, SBOLDocument, String, SBOLDocument) - Static method in class org.sbolstandard.core2.SBOLValidate
+
+
Compare the given two SBOLDocument objects and outputs the "standard" error output stream (System.err).
+
+
compareTo(Location) - Method in class org.sbolstandard.core2.Cut
 
+
compareTo(Location) - Method in class org.sbolstandard.core2.GenericLocation
+
 
+
compareTo(Location) - Method in class org.sbolstandard.core2.Range
+
 
+
compareTo(SequenceAnnotation) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
 
+
COMPETITIVE_INHIBITOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Substance that decreases the probability of a chemical reaction, without itself being + consumed or transformed by the reaction, by stericaly hindering the interaction between + reactants + (SBO:0000206).
+
+
COMPLEX - Static variable in class org.sbolstandard.core2.ComponentDefinition
+
+
A physical entity whose structure is comprised of other physical entities bound to each other covalently or non-covalently, + at least one of which is a macromolecule (e.g.
+
+
Component - Class in org.sbolstandard.core2
+
+
Represents the SBOL Component data model.
+
+
COMPONENT_DEFINITION - Static variable in class org.sbolstandard.core2.TopLevel
+
+
The abbreviation for the ComponentDefinition type in URI
+
+
ComponentDefinition - Class in org.sbolstandard.core2
+
+
Represents the SBOL ComponentDefinition data model.
+
+
ComponentInstance - Class in org.sbolstandard.core2
+
+
Represents the SBOL ComponentInstance data model.
+
+
COMPOSITE_BIOCHEMICAL_PROCESS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Process that involves the participation of chemical or biological entities and is + composed of several elementary steps or reactions + (SBO:0000205).
+
+
CONFORMATIONAL_TRANSITION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Biochemical reaction that does not result in the modification of covalent bonds of + reactants, but rather modifies the conformation of some reactants, that is the relative + position of their atoms in space (SBO:0000181).
+
+
CONSUMPTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Decrease in amount of a material or conceptual entity + (SBO:0000394).
+
+
CONTAINMENT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
An entity that is a subset of another entity or object + (SBO:0000469).
+
+
containsMember(URI) - Method in class org.sbolstandard.core2.Collection
+
+
Checks if the given URI is included in this Collection + instance's set of member URIs.
+
+
containsModel(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Checks if the given model URI is included in this module definition's set of reference model URIs.
+
+
containsRole(URI) - Method in class org.sbolstandard.core2.Component
+
+
Checks if the given role URI is included in this component's set of role URIs.
+
+
containsRole(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Checks if the given role URI is included in this component definition's set of role URIs.
+
+
containsRole(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Checks if the given role URI is included in this module definition's set of role URIs.
+
+
containsRole(URI) - Method in class org.sbolstandard.core2.Participation
+
+
Checks if the given role is included in this participation's set of roles.
+
+
containsRole(URI) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Checks if the given role URI is included in this sequence annotation's set of role URIs.
+
+
containsSequence(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Checks if the given sequence URI is included in this component definition's + set of sequence URIs.
+
+
containsType(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Checks if the given type URI is included in this component definition's + set of type URIs.
+
+
containsType(URI) - Method in class org.sbolstandard.core2.Interaction
+
+
Checks if the given type URI is included in this interaction's set of type URIs.
+
+
CONTINUOUS_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Modelling approach where the quantities of participants are considered continuous, + and represented by real values (SBO:0000062).
+
+
CONTROL - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Modification of the execution of an event or a process + (SBO:0000168).
+
+
CONVERSION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Biochemical reaction that results in the modification of some covalent bonds (SBO:0000182).
+
+
createAnnotation(QName, String) - Method in class org.sbolstandard.core2.Identified
+
+
Creates an annotation using the given arguments, + then adds to this instance's list of annotations.
+
+
createAnnotation(QName, double) - Method in class org.sbolstandard.core2.Identified
+
+
Creates an annotation using the given arguments, + then adds to this instance's list of annotations.
+
+
createAnnotation(QName, int) - Method in class org.sbolstandard.core2.Identified
+
+
Creates an annotation using the given arguments, + then adds to this instance's list of annotations.
+
+
createAnnotation(QName, boolean) - Method in class org.sbolstandard.core2.Identified
+
+
Creates an annotation using the given arguments, and + then adds to the list of annotaions.
+
+
createAnnotation(QName, URI) - Method in class org.sbolstandard.core2.Identified
+
+
Creates an annotation using the given arguments, + then adds to this instance's list of annotations.
+
+
createAnnotation(QName, QName, URI, List<Annotation>) - Method in class org.sbolstandard.core2.Identified
+
+
Creates an annotation with nested annotations using the given arguments, and then adds to this instance's list of annotations.
+
+
createCollection(String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a collection first, and then adds to this SBOL document's list of collections.
+
+
createCollection(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a collection first, and then adds to this SBOL document's list of collections.
+
+
createCollection(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a collection first, and then adds to this SBOL document's list of collections.
+
+
createCollection(String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a Collection instance with this SBOLDocument object's defaultURIprefix, + the given displayId argument, and an empty version string, and then + adds it to this SBOLDocument object's list of Collection instances.
+
+
createCollection(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a Collection instance with this SBOLDocument object's defaultURIprefix and + the given arguments, and then adds it to this SBOLDocument object's list of Collection instances.
+
+
createCollection(String, String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a Collection instance with the given arguments, and then adds it to this SBOLDocument + object's list of Collection instances.
+
+
createComponent(String, AccessType, String, String) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child component for this component definition with the given arguments, + and then adds it to this component definition's list of components.
+
+
createComponent(String, AccessType, String) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child component for this component definition with the given arguments, + and then adds it to this component definition's list of components.
+
+
createComponent(String, AccessType, URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child component for this component definition with the given arguments, + and then adds to this component definition's list of components.
+
+
createComponentDefinition(String, Set<URI>) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a component definition, and then adds it to this SBOL document's list of component definitions.
+
+
createComponentDefinition(String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a component definition, and then adds it to this SBOL document's list of component definitions.
+
+
createComponentDefinition(String, String, Set<URI>) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a component definition, and then adds it to this SBOL document's list of component definitions.
+
+
createComponentDefinition(String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a component definition, and then adds it to this SBOL document's list of component definitions.
+
+
createComponentDefinition(String, String, String, Set<URI>) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a component definition, and then adds it to this SBOL document's list of component definitions.
+
+
createComponentDefinition(String, String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a component definition, and then adds it to this SBOL document's list of component definitions.
+
+
createComponentDefinition(String, Set<URI>) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a ComponentDefinition instance with this SBOLDocument object's defaultURIprefix, + the given arguments, and empty version string, and then + adds it to this SBOLDocument object's list of ComponentDefinition instances.
+
+
createComponentDefinition(String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a ComponentDefinition instance with this SBOLDocument object's defaultURIprefix, + the given arguments, and empty version string, and then + adds it to this SBOLDocument object's list of ComponentDefinition instances.
+
+
createComponentDefinition(String, String, Set<URI>) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a ComponentDefinition instance with this SBOLDocument object's defaultURIprefix + and the given arguments, and then adds it to this SBOLDocument object's list of ComponentDefinition instances.
+
+
createComponentDefinition(String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a ComponentDefinition instance with this SBOLDocument object's defaultURIprefix + and the given arguments, and then adds it to this SBOLDocument object's list of ComponentDefinition instances.
+
+
createComponentDefinition(String, String, String, Set<URI>) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a ComponentDefinition instance with the given arguments, and then adds it to this SBOLDocument + object's list of ComponentDefinition instances.
+
+
createComponentDefinition(String, String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a ComponentDefinition instance with the given arguments, and then adds it to this SBOLDocument + object's list of ComponentDefinition instances.
+
+
createCopy(TopLevel) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates an identical copy of the given top-level, and then adds the created top-level to the corresponding + list of top-levels in this SBOL document.
+
+
createCopy(TopLevel, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a copy of the given top-level with the given display ID, and then adds the created top-level to the corresponding + list of top-levels in this SBOL document.
+
+
createCopy(TopLevel, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a copy of the given top-level with the given display ID and version, + and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
+
+
createCopy(TopLevel, String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a copy of the given top-level with the given URI prefix, display ID and version, + and then adds the created top-level to the corresponding list of top-levels in this SBOL document.
+
+
createCopy(TopLevel) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates an identical copy of the given TopLevel instance.
+
+
createCopy(TopLevel, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a copy of the given TopLevel instance with this SBOLDocument object's defaultURIprefix + the given arguments, and an empty version string, and then adds it to the + corresponding top-level list owned by this SBOLDocument object.
+
+
createCopy(TopLevel, String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a copy of the given TopLevel instance with this SBOLDocument object's defaultURIprefix + and the given arguments, and then adds it to the + corresponding top-level list owned by this SBOLDocument object.
+
+
createCopy(TopLevel, String, String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a copy of the given TopLevel instance with the given arguments, and then adds it to + the corresponding top-level list owned by this SBOLDocument object.
+
+
createFunctionalComponent(String, AccessType, String, String, DirectionType) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Creates a child functional component for this module definition with the given arguments, + and then adds to this module definition's list of functional components.
+
+
createFunctionalComponent(String, AccessType, String, DirectionType) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Creates a child functional component for this module definition with the given arguments, + and then adds to this module definition's list of functional components.
+
+
createFunctionalComponent(String, AccessType, URI, DirectionType) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Creates a child functional component for this module definition with the given arguments, and then adds to this + module definition's list of functional components.
+
+
createGenericTopLevel(String, QName) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a generic top-level, and then adds it to this SBOL document's list of generic top-levels.
+
+
createGenericTopLevel(String, String, QName) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a generic top-level, and then adds it to this SBOL document's list of generic top-levels.
+
+
createGenericTopLevel(String, String, String, QName) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a generic top-level, and then adds it to this SBOL document's list of generic top-levels.
+
+
createGenericTopLevel(String, QName) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a GenericTopLevel instance with this SBOLDocument object's defaultURIprefix, + the given arguments, and an empty version string, and then + adds it to this SBOLDocument object's list of GenericTopLevel instances.
+
+
createGenericTopLevel(String, String, QName) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a GenericTopLevel instance with this SBOLDocument object's defaultURIprefix + and the given arguments, and then adds it to this SBOLDocument object's list of GenericTopLevel instances.
+
+
createGenericTopLevel(String, String, String, QName) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a GenericTopLevel instance with the given arguments, and then adds it to this SBOLDocument + object's list of GenericTopLevel instances.
+
+
createInteraction(String, Set<URI>) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Creates a child interaction for this module definition with + the given arguments, and then adds to this module definition's list of interactions.
+
+
createInteraction(String, URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Creates a child interaction for this module definition with + the given arguments, and then adds to this module definition's list of interactions.
+
+
createMapsTo(String, RefinementType, String, String) - Method in class org.sbolstandard.core2.Component
+
+
Creates a child mapsTo for this component with the given arguments, and then adds it to its list of mapsTos.
+
+
createMapsTo(String, RefinementType, URI, URI) - Method in class org.sbolstandard.core2.Component
+
+
Creates a child mapsTo for this component with the given arguments, + and then adds it to its list of mapsTos.
+
+
createMapsTo(String, RefinementType, String, String) - Method in class org.sbolstandard.core2.FunctionalComponent
+
+
Creates a child MapsTo instance for this module with the given arguments, and then adds to this module's list of mapsTos.
+
+
createMapsTo(String, RefinementType, URI, URI) - Method in class org.sbolstandard.core2.FunctionalComponent
+
+
Creates a child mapsTo for this functional component with the given arguments, + and then adds it to this functional compoennt's list of mapsTos.
+
+
createMapsTo(String, RefinementType, String, String) - Method in class org.sbolstandard.core2.Module
+
+
Creates a child mapsTo for this module with the given arguments, and then adds it to its list of mapsTos.
+
+
createMapsTo(String, RefinementType, URI, URI) - Method in class org.sbolstandard.core2.Module
+
+
Creates a child mapsTo for this module with the given arguments, and then adds it to its list of mapsTos.
+
+
createModel(String, URI, URI, URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a model, and then adds it to this SBOL document's list of models.
+
+
createModel(String, String, URI, URI, URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a model, and then adds it to this SBOL document's list of models.
+
+
createModel(String, String, String, URI, URI, URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a model, and then adds it to this SBOL document's list of models.
+
+
createModel(String, URI, URI, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a Model instance with this SBOLDocument object's defaultURIprefix, + the given arguments, and an empty version string, and then + adds it to this SBOLDocument object's list of Model instances.
+
+
createModel(String, String, URI, URI, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a Model instance with this SBOLDocument object's defaultURIprefix + and the given arguments, and then adds it to this SBOLDocument object's list of Model instances.
+
+
createModel(String, String, String, URI, URI, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a Model instance with the given arguments, and then adds it to this SBOLDocument + object's list of Model instances.
+
+
createModule(String, String, String) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Creates a child module for this module definition with the + given arguments, and then adds to this module definition's list of modules.
+
+
createModule(String, String) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Creates a child module for this module definition with the + given arguments, and then adds to this module definition's list of modules.
+
+
createModule(String, URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Creates a child module for this module definition with the + given arguments, and then adds to this module definition's list of modules.
+
+
createModuleDefinition(String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a module definition, and then adds it to this SBOL document's list of module definitions.
+
+
createModuleDefinition(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a module definition, and then adds it to this SBOL document's list of module definitions.
+
+
createModuleDefinition(String, String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a module definition, and then adds it to this SBOL document's list of module definitions.
+
+
createModuleDefinition(String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a ModuleDefinition instance with this SBOLDocument object's defaultURIprefix, + the given arguments, and an empty version string, and then + adds it to this SBOLDocument object's list of ModuleDefinition instances.
+
+
createModuleDefinition(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a ModuleDefinition instance with this SBOLDocument object's defaultURIprefix + and the given arguments, and then adds it to this SBOLDocument object's list of ModuleDefinition instances.
+
+
createModuleDefinition(String, String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a ModuleDefinition instance with the given arguments, and then adds it to this SBOLDocument + object's list of ModuleDefinition instances.
+
+
createParticipation(String, String, URI) - Method in class org.sbolstandard.core2.Interaction
+
+
Creates a child participation for this interaction with the given arguments, + and then adds to this interaction's list of participations.
+
+
createParticipation(String, String, Set<URI>) - Method in class org.sbolstandard.core2.Interaction
+
+
Creates a child participation for this interaction with the given arguments, and then adds to this interaction's + list of participations.
+
+
createParticipation(String, URI, URI) - Method in class org.sbolstandard.core2.Interaction
+
+
Creates a child participation for this interaction with the given arguments, and then adds to its list of participations.
+
+
createParticipation(String, URI, Set<URI>) - Method in class org.sbolstandard.core2.Interaction
+
+
Creates a child participation for this interaction with the given arguments, + and then adds to this interaction's list of participations.
+
+
createRecursiveCopy(TopLevel) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates an identical copy of the given TopLevel instance and all its dependencies and returns them in + a new SBOLDocument.
+
+
createRecursiveCopy(TopLevel) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates an identical copy of the given TopLevel instance and all its dependencies and returns them in + a new SBOLDocument.
+
+
createSequence(String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a Sequence instance with this SBOL document's defaultURIprefix, + the given arguments, and an empty version string, and then + adds it to this SBOL document's list of Sequence instances.
+
+
createSequence(String, String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a Sequence instance with this SBOL document's defaultURIprefix + and the given arguments, and then adds it to this SBOL document's list of Sequence instances.
+
+
createSequence(String, String, String, String, URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a Sequence instance with the given arguments, and then adds it to this SBOLDocument + object's list of Sequence instances.
+
+
createSequence(String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a Sequence instance with this SBOLDocument object's defaultURIprefix, + the given arguments, and an empty version string, and then + adds it to this SBOLDocument object's list of Sequence instances.
+
+
createSequence(String, String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a Sequence instance with this SBOLDocument object's defaultURIprefix + and the given arguments, and then adds it to this SBOLDocument object's list of Sequence instances.
+
+
createSequence(String, String, String, String, URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a Sequence instance with the given arguments, and then adds it to this SBOLDocument + object's list of Sequence instances.
+
+
createSequenceAnnotation(String, String) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child sequence annotation for this component definition with the given arguments, + and then adds to this component definition's list of sequence annotations.
+
+
createSequenceAnnotation(String, String, OrientationType) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child sequence annotation for this component definition with the given arguments, + and then adds to this component definition's list of sequence annotations.
+
+
createSequenceAnnotation(String, String, int) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child sequence annotation for this component definition with the given arguments, + and then adds to its list of sequence annotations.
+
+
createSequenceAnnotation(String, String, int, OrientationType) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child sequence annotation for this component definition with the given arguments, + and then adds to its list of sequence annotations.
+
+
createSequenceAnnotation(String, String, int, int) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child sequence annotation for this component definition with the given arguments, and then adds to this ComponentDefinition's + list of sequence annotations.
+
+
createSequenceAnnotation(String, String, int, int, OrientationType) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child sequence annotation for this ComponentDefinition + instance with the given arguments, and then adds to this ComponentDefinition's + list of sequence annotations.
+
+
createSequenceConstraint(String, RestrictionType, String, String) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child sequence constraint for this component definition with the given arguments, + and then adds to this component definition's list of sequence constraints.
+
+
createSequenceConstraint(String, RestrictionType, URI, URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Creates a child sequence constraint for this component definition + with the given arguments, and then adds to this component definition's + list of sequence constraints.
+
+
Cut - Class in org.sbolstandard.core2
+
+
Represents the Cut extension of the SBOL Location class.
+
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
diff --git a/docs/javadocs/index-files/index-4.html b/docs/javadocs/index-files/index-4.html index 50a84068..a6f85d19 100644 --- a/docs/javadocs/index-files/index-4.html +++ b/docs/javadocs/index-files/index-4.html @@ -2,15 +2,15 @@ - -G-Index - + +D-Index + @@ -61,66 +61,72 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X  -

G

+

D

-
getFunctionalComponent(String) - Method in class org.sbolstandard.core2.ModuleDefinition
+
DEAMINATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the functional component matching the given display ID from - this module definition's list of functional components.
+
Removal of an amine group from a molecule, often under the addition of water + (SBO:0000401).
-
getFunctionalComponent(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
DECARBONYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the functional component matching the given functional component identity URI from this - module definition's list of functional components.
+
Removal of a carbonyl group (-C-O-) from a molecule, usually as carbon monoxide + (SBO:0000400).
-
getFunctionalComponents() - Method in class org.sbolstandard.core2.ModuleDefinition
+
DECARBOXYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of functional components owned by this - module definition.
+
A process in which a carboxyl group (COOH) is removed from a molecule as carbon dioxide + (SBO:0000399).
-
getInteraction(String) - Method in class org.sbolstandard.core2.ModuleDefinition
+
DEGRADATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the interaction matching the given interaction's identity URI from the - list of interactions.
+
Complete disappearance of a physical entity + (SBO:0000179).
-
getInteraction(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
DEPHOSPHORYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the instance matching the given Interaction URI from the list of - Interaction instances.
+
Removal of a phosphate group (-H2PO4) from a chemical entity + (SBO:0000330).
-
getInteractions() - Method in class org.sbolstandard.core2.ModuleDefinition
+
DEPROTONATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of interactions owned by this module definition.
+
Removal of a proton (hydrogen ion H+) from a chemical entity (SBO:0000213).
-
getModels() - Method in class org.sbolstandard.core2.ModuleDefinition
+
DirectionType - Enum in org.sbolstandard.core2
-
Returns the set of models referenced by this module definition.
+
Represents all direction types for a FunctionalComponent object.
-
getModelURIs() - Method in class org.sbolstandard.core2.ModuleDefinition
+
DISCRETE_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of model URIs referenced by this module definition.
+
Modelling approach where the quantities of participants are considered discrete, and represented by + integer values (SBO:0000063).
-
getModule(String) - Method in class org.sbolstandard.core2.ModuleDefinition
+
DISSOCIATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the module matching the given display ID from the list of modules.
+
Transformation of a non-covalent complex that results in the formation of several + independent biochemical entities + (SBO:0000180).
-
getModule(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
DNA - Static variable in class org.sbolstandard.core2.ComponentDefinition
-
Returns the module matching the given identity URI from the list of modules.
+
A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid + (DNA).
-
getModules() - Method in class org.sbolstandard.core2.ModuleDefinition
+
DNA_REPLICATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of modules owned by this module definition.
+
Process in which a DNA duplex is transformed into two identical DNA duplexes + (SBO:0000204).
-
getRoles() - Method in class org.sbolstandard.core2.ModuleDefinition
+
DUAL_ACTIVITY_MODIFIER - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Returns the set of role URIs owned by this module definition.
+
A modifier that can exhibit either inhibitory or stimulatory effects on a process + depending on the context in which it occurs (SBO:0000595).
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
diff --git a/docs/javadocs/index-files/index-5.html b/docs/javadocs/index-files/index-5.html index cd71ee16..5f1fe61e 100644 --- a/docs/javadocs/index-files/index-5.html +++ b/docs/javadocs/index-files/index-5.html @@ -2,15 +2,15 @@ - -H-Index - + +E-Index + @@ -61,15 +61,99 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X  -

H

+

E

-
hashCode() - Method in class org.sbolstandard.core2.ModuleDefinition
+
EDAMOntology - Class in org.sbolstandard.core2
+
+
This class provides methods for accessing EMBRACE Data and Methods (EDAM) terms + and querying about their relationships.
+
+
EDAMOntology() - Constructor for class org.sbolstandard.core2.EDAMOntology
+
+
Construct an EDAM ontology object and read the OBO definition file, if necessary.
+
+
EFFECTOR - Static variable in class org.sbolstandard.core2.ComponentDefinition
+
+
A small molecule which increases (activator) or decreases (inhibitor) the activity of an + (allosteric) enzyme by binding to the enzyme at the regulatory site + (which is different from the substrate-binding catalytic site) (Effector).
+
+
ENCAPSULATING_PROCESS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
An aggregation of interactions and entities into a single process + (SBO:0000395).
+
+
ENGINEERED_GENE - Static variable in class org.sbolstandard.core2.SequenceOntology
+
+
A gene that is engineered (SO:0000280).
+
+
ENGINEERED_REGION - Static variable in class org.sbolstandard.core2.SequenceOntology
+
+
A region that is engineered (SO:0000804).
+
+
ENZYMATIC_CATALYST - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
A substance that accelerates the velocity of a chemical reaction without itself being + consumed or transformed, by lowering the free energy of the transition state (SBO:0000460).
+
+
equals(Object) - Method in class org.sbolstandard.core2.Annotation
 
+
equals(Object) - Method in class org.sbolstandard.core2.Collection
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.Component
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.ComponentDefinition
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.ComponentInstance
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.Cut
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.FunctionalComponent
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.GenericLocation
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.GenericTopLevel
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.Identified
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.Interaction
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.MapsTo
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.Model
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.Module
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.ModuleDefinition
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.Range
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.SBOLDocument
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.SBOLFactory
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.Sequence
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
 
+
equals(Object) - Method in class org.sbolstandard.core2.SequenceConstraint
+
 
+
EQUIVALENCE - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Term to signify those material or conceptual entities that are identical in some respect + within a frame of reference + (SBO:0000392).
+
+
ESSENTIAL_ACTIVATOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
A substance that is absolutely required for occurrence and stimulation of a reaction + (SBO:0000461).
+
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
diff --git a/docs/javadocs/index-files/index-6.html b/docs/javadocs/index-files/index-6.html index 8e9687ee..413059b7 100644 --- a/docs/javadocs/index-files/index-6.html +++ b/docs/javadocs/index-files/index-6.html @@ -2,15 +2,15 @@ - -M-Index - + +F-Index + @@ -61,17 +61,47 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X  -

M

+

F

-
ModuleDefinition - Class in org.sbolstandard.core2
+
FARNESYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Represents the SBOL ModuleDefinition data model.
+
Addition of a farnesyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) + to a chemical entity + (SBO:0000222).
+
+
FASTAformat - Static variable in class org.sbolstandard.core2.SBOLDocument
+
+
Constant representing FASTA file format
+
+
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 + protein (SO:0000204).
+
+
FLUX_BALANCE_FRAMEWORK - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Modelling approach, typically used for metabolic models, where the flow of metabolites (flux) + through a network can be calculated (SBO:0000624).
+
+
FORMAT - Static variable in class org.sbolstandard.core2.EDAMOntology
+
+
A defined way or layout of representing and structuring data in a computer file, blob, + string, message, or elsewhere.
+
+
FUNCTIONAL_COMPARTMENT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Logical or physical subset of the event space that contains pools, that is sets of participants + considered identical when it comes to the event they are involved into (SBO:0000289).
+
+
FunctionalComponent - Class in org.sbolstandard.core2
+
+
Represents the SBOL FunctionalComponent data model.
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
diff --git a/docs/javadocs/index-files/index-7.html b/docs/javadocs/index-files/index-7.html index 3a3843d8..87d1e12d 100644 --- a/docs/javadocs/index-files/index-7.html +++ b/docs/javadocs/index-files/index-7.html @@ -2,15 +2,15 @@ - -O-Index - + +G-Index + @@ -61,15 +61,924 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X  -

O

+

G

-
org.sbolstandard.core2 - package org.sbolstandard.core2
-
 
+
GENBANK - Static variable in class org.sbolstandard.core2.SBOLDocument
+
+
Constant representing GenBank file format
+
+
GENE - Static variable in class org.sbolstandard.core2.SequenceOntology
+
+
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript.
+
+
GENERIC_TOP_LEVEL - Static variable in class org.sbolstandard.core2.TopLevel
+
+
The abbreviation for the GenericTopLevel type in URI
+
+
GenericLocation - Class in org.sbolstandard.core2
+
+
Represents the GenericLocation extension of the SBOL Location class.
+
+
GenericTopLevel - Class in org.sbolstandard.core2
+
+
Represents the SBOL GenericTopLevel data model.
+
+
GENETIC_ENHANCEMENT - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Genetic enhancement is said to have occurred when the phenotypic effect of an initial + mutation in a gene is made increasingly severe by a subsequent mutation + (SBO:0000501).
+
+
GENETIC_INTERACTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable + by the simple additive effects of the individual gene pertubations alone (SBO:0000343).
+
+
GENETIC_PRODUCTION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
A composite biochemical process through which a gene sequence is fully converted into + mature gene products (SBO:0000589).
+
+
GENETIC_SUPPRESSION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Genetic suppression is said to have occurred when the phenotypic effect of an initial + mutation in a gene is less severe, or entirely negated, by a subsequent mutation + (SBO:0000500).
+
+
GERANYLGERANYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Addition of a geranylgeranyl group + (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) + to a chemical entity + (SBO:0000223).
+
+
getAccess() - Method in class org.sbolstandard.core2.ComponentInstance
+
+
Returns the access property.
+
+
getAnnotation(QName) - Method in class org.sbolstandard.core2.Identified
+
+
Returns the annotation matching the given QName.
+
+
getAnnotations() - Method in class org.sbolstandard.core2.Annotation
+
+
Returns the list of Annotations of the nested value property.
+
+
getAnnotations() - Method in class org.sbolstandard.core2.Identified
+
+
Returns the list of annotations owned by this instance.
+
+
getAt() - Method in class org.sbolstandard.core2.Cut
+
+
Returns the at property of this Cut instance.
+
+
getBooleanValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Returns a Boolean representation of the value property.
+
+
getByWasDerivedFrom(URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Creates a set of TopLevels with derived from the same object + as specified by the wasDerivedFrom parameter.
+
+
getByWasDerivedFrom(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Creates a set of TopLevels with derived from the same object + as specified by the wasDerivedFrom parameter.
+
+
getCollection(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the collection matching the given displayId + and version from this SBOL document's list of + collections.
+
+
getCollection(URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the collection matching the given collectionURI from this + SBOL document's list of collections.
+
+
getCollection(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the Collection instance matching the given displayId + and version from this SBOLDocument object's list of + Collection instances.
+
+
getCollection(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the Collection instance matching the given collectionURI from this + SBOLDocument object's list of Collection instances.
+
+
getCollections() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the set of Collection instances owned by this SBOL document.
+
+
getCollections() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the set of Collection instances owned by this SBOLDocument object.
+
+
getComponent(String) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the component matching the given component's display ID.
+
+
getComponent(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the instance matching the given component's identity URI.
+
+
getComponent() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Returns the Component instance this SequenceAnnotation instance refers to.
+
+
getComponentDefinition(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the component definition matching the given displayId + and version from this SBOL document's list of + component definitions.
+
+
getComponentDefinition(URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the component definition matching the given componentDefinitionURI from this + SBOL document's list of component definitions.
+
+
getComponentDefinition(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the ComponentDefinition instance matching the given displayId + and version from this SBOLDocument object's list of + ComponentDefinition instances.
+
+
getComponentDefinition(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the ComponentDefinition instance matching the given componentDefinitionURI from this + SBOLDocument object's list of ComponentDefinition instances.
+
+
getComponentDefinition() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Get the component definition for the component annotated by this sequence annotation.
+
+
getComponentDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the set of ComponentDefinition instances owned by this SBOL document.
+
+
getComponentDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the set of ComponentDefinition instances owned by this SBOLDocument object.
+
+
getComponents() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the set of components owned by this component definition.
+
+
getComponentURI() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Returns the Component URI that this SequenceAnnotation instance refers to.
+
+
getDefaultSequenceEncoding() - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Sets the default sequence encoding for FASTA conversion.
+
+
getDefaultURIprefix() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the default URI prefix of this SBOL document
+
+
getDefaultURIprefix() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the default URI prefix of this SBOLDocument object
+
+
getDefinition() - Method in class org.sbolstandard.core2.ComponentInstance
+
+
Returns the component definition referenced by this component or functional component.
+
+
getDefinition() - Method in class org.sbolstandard.core2.Module
+
+
Returns the module definition that this module refers to.
+
+
getDefinitionURI() - Method in class org.sbolstandard.core2.ComponentInstance
+
+
Returns the reference component definition URI.
+
+
getDefinitionURI() - Method in class org.sbolstandard.core2.Module
+
+
Returns the module definition URI that this module refers to.
+
+
getDescendantsOf(String) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns a set of child ids that are descendants of a given parent id.
+
+
getDescendantsOf(URI) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns a set of child ids that are descendants of a given parent URI.
+
+
getDescendantsOf(String) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns a set of child ids that are descendants of a given parent id.
+
+
getDescendantsOf(URI) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns a set of child ids that are descendants of a given parent URI.
+
+
getDescendantsOf(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns a set of child ids that are descendants of a given parent id.
+
+
getDescendantsOf(URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns a set of child ids that are descendants of a given parent URI.
+
+
getDescendantURIsOf(String) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns a set of child URIs that are descendants of a given parent id.
+
+
getDescendantURIsOf(URI) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns a set of child URIs that are descendants of a given parent URI.
+
+
getDescendantURIsOf(String) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns a set of child URIs that are descendants of a given parent id.
+
+
getDescendantURIsOf(URI) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns a set of child URIs that are descendants of a given parent URI.
+
+
getDescendantURIsOf(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns a set of child URIs that are descendants of a given parent id.
+
+
getDescendantURIsOf(URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns a set of child URIs that are descendants of a given parent URI.
+
+
getDescription() - Method in class org.sbolstandard.core2.Identified
+
+
Returns the description property of this instance.
+
+
getDirection() - Method in class org.sbolstandard.core2.FunctionalComponent
+
+
Returns the direction property of this functional component.
+
+
getDisplayId() - Method in class org.sbolstandard.core2.Identified
+
+
Returns the display ID of this instance.
+
+
getDocument() - Method in class org.sbolstandard.core2.TopLevel
+
+
Returns the SBOLDocument that was used + to instantiate this TopLevel instance.
+
+
getDoubleValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Returns a Double representation of the value property.
+
+
getElements() - Method in class org.sbolstandard.core2.Sequence
+
+
Returns the elements property of this Sequence object.
+
+
getEncoding() - Method in class org.sbolstandard.core2.Sequence
+
+
Returns the encoding property of this Sequence object.
+
+
getEnd() - Method in class org.sbolstandard.core2.Range
+
+
Returns the end position of this range.
+
+
getErrors() - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Returns the error list that is used to store SBOL validation exceptions.
+
+
getErrors() - Static method in class org.sbolstandard.core2.SBOLValidate
+
+
Returns the error list used to store SBOL validation exceptions.
+
+
getErrors() - Static method in class org.sbolstandard.core2.SBOLWriter
+
+
Returns the error list that is used to store SBOL conversion exceptions.
+
+
getFramework() - Method in class org.sbolstandard.core2.Model
+
+
Returns the URI of the framework property of this Model object.
+
+
getFunctionalComponent(String) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the functional component matching the given display ID from + this module definition's list of functional components.
+
+
getFunctionalComponent(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the functional component matching the given functional component identity URI from this + module definition's list of functional components.
+
+
getFunctionalComponents() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the set of functional components owned by this + module definition.
+
+
getGenericTopLevel(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the GenericTopLevel instance matching the given displayId + and version from this SBOL document's list of + GenericTopLevel instances.
+
+
getGenericTopLevel(URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the GenericTopLevel instance matching the given topLevelURI from this + SBOL document's list of GenericTopLevel instances.
+
+
getGenericTopLevel(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the GenericTopLevel instance matching the given displayId + and version from this SBOLDocument object's list of + GenericTopLevel instances.
+
+
getGenericTopLevel(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the GenericTopLevel instance matching the given topLevelURI from this + SBOLDocument object's list of GenericTopLevel instances.
+
+
getGenericTopLevels() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the set of GenericTopLevel instances owned by this SBOL document.
+
+
getGenericTopLevels() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the set of GenericTopLevel instances owned by this SBOLDocument object.
+
+
getId(URI) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns the extracted ID of the given stanza's URI.
+
+
getId(String) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns the ID field of the stanza whose name field matches the given name.
+
+
getId(URI) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
* Creates a new URI from the Sequence Ontology namespace with the given ID.
+
+
getId(String) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns the ID of the stanza whose name matches the given stanza name.
+
+
getId(URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns the extracted ID of the given term's URI.
+
+
getId(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns the ID field of the stanza whose name matches the given name.
+
+
getIdentity() - Method in class org.sbolstandard.core2.Identified
+
+
Returns the identity URI of this instance.
+
+
getImpliedNucleicAcidSequence() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Return the elements of a nucleic acid sequence implied by the hierarchically included components.
+
+
getIntegerValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Returns an Integer representation of the value property.
+
+
getInteraction(String) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the interaction matching the given interaction's identity URI from the + list of interactions.
+
+
getInteraction(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the instance matching the given Interaction URI from the list of + Interaction instances.
+
+
getInteractions() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the set of interactions owned by this module definition.
+
+
getLanguage() - Method in class org.sbolstandard.core2.Model
+
+
Returns this model's language property.
+
+
getLocal() - Method in class org.sbolstandard.core2.MapsTo
+
+
Returns this mapsTo's local component instance.
+
+
getLocalDefinition() - Method in class org.sbolstandard.core2.MapsTo
+
+
Retrieves referenced component definition by this mapsTo's local component instance.
+
+
getLocalURI() - Method in class org.sbolstandard.core2.MapsTo
+
+
Returns this mapsTo's local component instance's URI.
+
+
getLocation(String) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Returns the Location instance owned by this SequenceAnnotation instance + that matches the given displayId
+
+
getLocation(URI) - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Returns the Location instance owned by this SequenceAnnotation instance + that matches the given location URI.
+
+
getLocations() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Returns the set of Location instances referenced by this SequenceAnnotation instance.
+
+
getMapsTo(String) - Method in class org.sbolstandard.core2.Component
+
+
Returns the mapsTo that matches the given display ID.
+
+
getMapsTo(URI) - Method in class org.sbolstandard.core2.Component
+
+
Returns the mapsTo that matches the given URI.
+
+
getMapsTo(String) - Method in class org.sbolstandard.core2.FunctionalComponent
+
+
Returns the mapsTo that matches the given display ID.
+
+
getMapsTo(URI) - Method in class org.sbolstandard.core2.FunctionalComponent
+
+
Returns the mapsTo that matches the given URI.
+
+
getMapsTo(String) - Method in class org.sbolstandard.core2.Module
+
+
Returns the mapsTo that matches the given display ID.
+
+
getMapsTo(URI) - Method in class org.sbolstandard.core2.Module
+
+
Returns the MapsTo instance owned by this Module object that matches the given displayId
+
+
getMapsTos() - Method in class org.sbolstandard.core2.Component
+
+
Returns the set of mapsTos owned by this instance.
+
+
getMapsTos() - Method in class org.sbolstandard.core2.FunctionalComponent
+
+
Returns the set of mapsTos owned by this object.
+
+
getMapsTos() - Method in class org.sbolstandard.core2.Module
+
+
Returns the set of MapsTo instances referenced by this Module object.
+
+
getMembers() - Method in class org.sbolstandard.core2.Collection
+
+
Returns the set instances referenced by this Collection instance's members.
+
+
getMemberURIs() - Method in class org.sbolstandard.core2.Collection
+
+
Returns the set of member URIs referenced by this Collection instance.
+
+
getModel(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the Model instance matching the given displayId + and version from this SBOL document's list of + Model instances.
+
+
getModel(URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the Model instance matching the given modelURI from this + SBOL document's list of Model instances.
+
+
getModel(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the Model instance matching the given displayId + and version from this SBOLDocument object's list of + Model instances.
+
+
getModel(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the Model instance matching the given modelURI from this + SBOLDocument object's list of Model instances.
+
+
getModels() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the set of models referenced by this module definition.
+
+
getModels() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the set of Model instances owned by this SBOL document.
+
+
getModels() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the set of Model instances owned by this SBOLDocument object.
+
+
getModelURIs() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the set of model URIs referenced by this module definition.
+
+
getModule(String) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the module matching the given display ID from the list of modules.
+
+
getModule(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the module matching the given identity URI from the list of modules.
+
+
getModuleDefinition(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the ModuleDefinition instance matching the given displayId + and version from this SBOLDocument object's list of + ModuleDefinition instances.
+
+
getModuleDefinition(URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the ModuleDefinition instance matching the given modelURI from this + SBOLDocument object's list of ModuleDefinition instances.
+
+
getModuleDefinition(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the ModuleDefinition instance matching the given displayId + and version from this SBOLDocument object's list of + ModuleDefinition instances.
+
+
getModuleDefinition(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the ModuleDefinition instance matching the given modelURI from this + SBOLDocument object's list of ModuleDefinition instances.
+
+
getModuleDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the set of ModuleDefinition instances owned by this SBOLDocument object.
+
+
getModuleDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the set of ModuleDefinition instances owned by this SBOLDocument object.
+
+
getModules() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the set of modules owned by this module definition.
+
+
getName(URI) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns the name field of the stanza that matches the ID for the given stanzaURI.
+
+
getName(String) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns the name field of the stanza matching the ID extracted from the given stanzaURI.
+
+
getName() - Method in class org.sbolstandard.core2.Identified
+
+
Returns the name property of this instance.
+
+
getName(URI) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns the name field of the stanza that matches the ID for the given term URI.
+
+
getName(String) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns the name field of the stanza that matches the ID referred by the given stanzaURI.
+
+
getName(URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns the name field of the stanza that matches the ID for the given term URI.
+
+
getName(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns the name field of the stanza that matches the ID referred by the given stanzaURI.
+
+
getNamespace(URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the QName instance matching the given modelURI from this + SBOL document's list of namespace QName instances.
+
+
getNamespace(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the QName instance matching the given modelURI from this + SBOLDocument object's list of namespace QName instances.
+
+
getNamespaces() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the list of namespace bindings owned by this SBOL document.
+
+
getNamespaces() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the list of namespace bindings owned by this SBOLDocument object.
+
+
getNestedIdentity() - Method in class org.sbolstandard.core2.Annotation
+
+
Returns the nested identity URI of the nested Annotation.
+
+
getNestedQName() - Method in class org.sbolstandard.core2.Annotation
+
+
Returns the nested QName of the nested Annotation.
+
+
getNumErrors() - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Returns the number of errors in the error list.
+
+
getNumErrors() - Static method in class org.sbolstandard.core2.SBOLValidate
+
+
Returns the number of errors in the error list.
+
+
getNumErrors() - Static method in class org.sbolstandard.core2.SBOLWriter
+
+
Returns the number of errors in the error list.
+
+
getObject() - Method in class org.sbolstandard.core2.SequenceConstraint
+
+
Returns the object Component instance this SequenceConstraint object refers to.
+
+
getObjectDefinition() - Method in class org.sbolstandard.core2.SequenceConstraint
+
+
Get the component definition for the object of this sequence constraint.
+
+
getObjectURI() - Method in class org.sbolstandard.core2.SequenceConstraint
+
+
Returns the object Component URI that this SequenceConstraint object refers to.
+
+
getOrientation() - Method in class org.sbolstandard.core2.Location
+
+
Returns the orientation property of this location.
+
+
getParticipant() - Method in class org.sbolstandard.core2.Participation
+
+
Returns the functional component this participation refers to.
+
+
getParticipantDefinition() - Method in class org.sbolstandard.core2.Participation
+
+
Returns the component definition referenced by this participation's participant.
+
+
getParticipantURI() - Method in class org.sbolstandard.core2.Participation
+
+
Returns the FunctionalComponent URI that this participation refers to.
+
+
getParticipation(String) - Method in class org.sbolstandard.core2.Interaction
+
+
Returns the participation matching the given display ID from + this interaction's list of participations.
+
+
getParticipation(URI) - Method in class org.sbolstandard.core2.Interaction
+
+
Returns the participation matching the given participation URI from this + interaction's list of participations.
+
+
getParticipations() - Method in class org.sbolstandard.core2.Interaction
+
+
Returns the set of participations owned by this + interaction.
+
+
getPersistentIdentity() - Method in class org.sbolstandard.core2.Identified
+
+
Returns the persistent identity URI of this instance.
+
+
getQName() - Method in class org.sbolstandard.core2.Annotation
+
+
Returns the QName of this Annotation instance.
+
+
getRDFType() - Method in class org.sbolstandard.core2.GenericTopLevel
+
+
Returns the RDF type property of this GenericTopLevel instance.
+
+
getRefinement() - Method in class org.sbolstandard.core2.MapsTo
+
+
Returns the refinement property of this mapsTo.
+
+
getRemote() - Method in class org.sbolstandard.core2.MapsTo
+
+
Returns this mapsTo's remote component instance.
+
+
getRemoteDefinition() - Method in class org.sbolstandard.core2.MapsTo
+
+
Returns the remote component definition referenced by mapsTo.
+
+
getRemoteURI() - Method in class org.sbolstandard.core2.MapsTo
+
+
Returns this mapsTo's remote URI.
+
+
getRestriction() - Method in class org.sbolstandard.core2.SequenceConstraint
+
+
Returns the restriction property of this SequenceConstraint object.
+
+
getRestrictionURI() - Method in class org.sbolstandard.core2.SequenceConstraint
+
+
Returns the restriction property of this SequenceConstraint object.
+
+
getRoleIntegration() - Method in class org.sbolstandard.core2.Component
+
+
Returns the roleIntegration property of this object.
+
+
getRoleIntegration() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Returns the roleIntegration property of this object.
+
+
getRoles() - Method in class org.sbolstandard.core2.Component
+
+
Returns the set of role URIs owned by this component.
+
+
getRoles() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the set of role URIs owned by this component definition.
+
+
getRoles() - Method in class org.sbolstandard.core2.ModuleDefinition
+
+
Returns the set of role URIs owned by this module definition.
+
+
getRoles() - Method in class org.sbolstandard.core2.Participation
+
+
Returns the set of role URIs owned by this participation.
+
+
getRoles() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Returns the set of role URIs owned by this sequence annotation.
+
+
getRootComponentDefinitions() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the set of root ComponentDefinitions.
+
+
getRootComponentDefinitions() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the set of root ComponentDefinitions.
+
+
getSBOLVersion(String) - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Takes in a given RDF filename and returns the SBOL version of the file.
+
+
getSBOLVersion(File) - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Takes in a given RDF File and returns the SBOL version of the file.
+
+
getSBOLVersion(InputStream) - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Takes in a given RDF InputStream and returns the SBOL version of the file.
+
+
getSequence(String, String) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the Sequence instance matching the given displayId + and version from this SBOL document's list of + Sequence instances.
+
+
getSequence(URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the Sequence instance matching the given modelURI from this + SBOL document's list of Sequence instances.
+
+
getSequence(String, String) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the Sequence instance matching the given displayId + and version from this SBOLDocument object's list of + Sequence instances.
+
+
getSequence(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the Sequence instance matching the given modelURI from this + SBOLDocument object's list of Sequence instances.
+
+
getSequenceAnnotation(String) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the sequence annotation matching the given display ID.
+
+
getSequenceAnnotation(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the instance matching the given SequenceAnnotation URI from the + list of sequence annotations.
+
+
getSequenceAnnotation(Component) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the sequence annotation that references to the given component.
+
+
getSequenceAnnotations() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the set of sequence annotations owned by this + component definition.
+
+
getSequenceByEncoding(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the first sequence that matches the given encoding.
+
+
getSequenceConstraint(String) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the sequence constraint matching the given display ID.
+
+
getSequenceConstraint(URI) - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the sequence constraint matching the given URI.
+
+
getSequenceConstraints() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the set of sequence constraints owned by this + component definition.
+
+
getSequences() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the set of sequences referenced by this component definition.
+
+
getSequences() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the set of Sequence instances owned by this SBOL document.
+
+
getSequences() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the set of Sequence instances owned by this SBOLDocument object.
+
+
getSequenceURIs() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the set of sequence URIs referenced by this component definition.
+
+
getSortedComponents() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns a sorted list of components owned by this component definition.
+
+
getSortedLocations() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Returns a sorted list of Locations referenced by this SequenceAnnotation instance.
+
+
getSortedSequenceAnnotations() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns a sorted list of sequence annotations owned by this + component definition.
+
+
getSource() - Method in class org.sbolstandard.core2.Model
+
+
Returns the this model's source property.
+
+
getStart() - Method in class org.sbolstandard.core2.Range
+
+
Returns the start position of this range.
+
+
getStringValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Returns a string representation of the value property.
+
+
getSubject() - Method in class org.sbolstandard.core2.SequenceConstraint
+
+
Returns the subject Component instance this SequenceConstraint object refers to.
+
+
getSubjectDefinition() - Method in class org.sbolstandard.core2.SequenceConstraint
+
+
Get the component definition for the subject of this sequence constraint.
+
+
getSubjectURI() - Method in class org.sbolstandard.core2.SequenceConstraint
+
+
Returns the subject Component URI that this SequenceConstraint object refers to.
+
+
getTopLevel(URI) - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns the top-level instance matching the given topLevelURI from this + SBOL document's lists of top-level instances.
+
+
getTopLevel(URI) - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns the top-level instance matching the given topLevelURI from this + SBOLDocument object's lists of top-level instances.
+
+
getTopLevels() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns a set of all TopLevel objects.
+
+
getTopLevels() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns a set of all TopLevel objects.
+
+
getTypes() - Method in class org.sbolstandard.core2.ComponentDefinition
+
+
Returns the set of type URIs owned by this component definition.
+
+
getTypes() - Method in class org.sbolstandard.core2.Interaction
+
+
Returns the set of type URIs owned by this Interaction object.
+
+
getURIbyId(String) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Creates a new URI from the EDAM Ontology namespace with the given ID.
+
+
getURIbyId(String) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Creates a URI from the Sequence Ontology namespace，i.e.
+
+
getURIbyId(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Creates a new URI from the Systems Biology Ontology namespace, "http://identifiers.org/biomodels.sbo/", with the given ID.
+
+
getURIbyName(String) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns the URI, i.e.
+
+
getURIbyName(String) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns the URI, i.e.
+
+
getURIbyName(String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns the URI, i.e.
+
+
getURIValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Returns a URI representation of the value property.
+
+
getVersion() - Method in class org.sbolstandard.core2.Identified
+
+
Returns this instance's version.
+
+
getWasDerivedFrom() - Method in class org.sbolstandard.core2.Identified
+
+
Returns the wasDerivedFrom property of this instance.
+
+
GLYCOSYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Addition of a saccharide group to a chemical entity + (SBO:0000217).
+
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
diff --git a/docs/javadocs/index-files/index-8.html b/docs/javadocs/index-files/index-8.html index 35a850a5..6ab6ce3b 100644 --- a/docs/javadocs/index-files/index-8.html +++ b/docs/javadocs/index-files/index-8.html @@ -2,15 +2,15 @@ - -R-Index - + +H-Index + @@ -61,34 +61,70 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X  -

R

+

H

-
removeFunctionalComponent(FunctionalComponent) - Method in class org.sbolstandard.core2.ModuleDefinition
+
hasAnnotations() - Method in class org.sbolstandard.core2.Identified
-
Removes the given functional component from this module definition's list of - functional components.
+
Test if this instance has any annotations.
-
removeInteraction(Interaction) - Method in class org.sbolstandard.core2.ModuleDefinition
+
hashCode() - Method in class org.sbolstandard.core2.Annotation
+
 
+
hashCode() - Method in class org.sbolstandard.core2.Collection
+
 
+
hashCode() - Method in class org.sbolstandard.core2.Component
+
 
+
hashCode() - Method in class org.sbolstandard.core2.ComponentDefinition
+
 
+
hashCode() - Method in class org.sbolstandard.core2.ComponentInstance
+
 
+
hashCode() - Method in class org.sbolstandard.core2.Cut
+
 
+
hashCode() - Method in class org.sbolstandard.core2.FunctionalComponent
+
 
+
hashCode() - Method in class org.sbolstandard.core2.GenericLocation
+
 
+
hashCode() - Method in class org.sbolstandard.core2.GenericTopLevel
+
 
+
hashCode() - Method in class org.sbolstandard.core2.Identified
+
 
+
hashCode() - Method in class org.sbolstandard.core2.Interaction
+
 
+
hashCode() - Method in class org.sbolstandard.core2.MapsTo
+
 
+
hashCode() - Method in class org.sbolstandard.core2.Model
+
 
+
hashCode() - Method in class org.sbolstandard.core2.Module
+
 
+
hashCode() - Method in class org.sbolstandard.core2.ModuleDefinition
+
 
+
hashCode() - Method in class org.sbolstandard.core2.Range
+
 
+
hashCode() - Method in class org.sbolstandard.core2.SBOLDocument
+
 
+
hashCode() - Method in class org.sbolstandard.core2.SBOLFactory
+
 
+
hashCode() - Method in class org.sbolstandard.core2.Sequence
+
 
+
hashCode() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
 
+
hashCode() - Method in class org.sbolstandard.core2.SequenceConstraint
+
 
+
HYDROLYSIS - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Removes the given interaction from the list of interactions.
+
Decomposition of a compound by reaction with water, where the hydroxyl and H groups are + incorporated into different products + (SBO:0000376).
-
removeModel(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
+
HYDROXYLATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Removes the given model URI from the set of model URIs owned by this module definition.
-
-
removeModule(Module) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Removes the given module from the list of modules.
-
-
removeRole(URI) - Method in class org.sbolstandard.core2.ModuleDefinition
-
-
Removes the given role from the set of roles.
+
Addition of an hydroxyl group (-OH) to a chemical entity + (SBO:0000233).
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
diff --git a/docs/javadocs/index-files/index-9.html b/docs/javadocs/index-files/index-9.html index c3ed6351..7399b805 100644 --- a/docs/javadocs/index-files/index-9.html +++ b/docs/javadocs/index-files/index-9.html @@ -2,15 +2,15 @@ - -S-Index - + +I-Index + @@ -61,23 +61,204 @@
-
A C E G H M O R S T  +
A B C D E F G H I J K L M N O P R S T U V W X  -

S

+

I

-
setModels(Set<URI>) - Method in class org.sbolstandard.core2.ModuleDefinition
+
Identified - Class in org.sbolstandard.core2
-
Clears the existing set of model URIs first, then adds the given - set of the model URIs to this module definition.
+
Represents the SBOL Identified data model.
-
setRoles(Set<URI>) - Method in class org.sbolstandard.core2.ModuleDefinition
+
INHIBITION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
-
Clears the existing set of roles first, and then adds the given - set of the roles this module definition.
+
Negative modulation of the execution of a process + (SBO:0000169).
+
+
INHIBITOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Substance that decreases the probability of a chemical reaction without itself being + consumed or transformed by the reaction + (SBO:0000020).
+
+
INSULATOR - Static variable in class org.sbolstandard.core2.SequenceOntology
+
+
A transcriptional cis regulatory region that, when located between a CM and a gene's promoter, prevents the CRM + from modulating that genes expression (SO:0000627)
+
+
Interaction - Class in org.sbolstandard.core2
+
+
Represents the SBOL Interaction data model.
+
+
INTERACTOR - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Entity participating in a physical or functional interaction + (SBO:0000336).
+
+
IONISATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Ionization is the physical process of converting an atom or molecule into an ion by + changing the difference between the number of protons and electrons + (SBO:0000209).
+
+
isBooleanValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Checks if the annotation has a boolean value property.
+
+
isComplete() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns true if the complete flag for this SBOL document is set.
+
+
isComplete() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns true if the complete flag for this SBOLDocument object is set.
+
+
isCompliant() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns true if all URIs in this SBOL document are compliant.
+
+
isCompliant() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns true if all URIs in this SBOLDocument object are compliant.
+
+
isCompliant() - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Check if document is to be read as being compliant.
+
+
isCreateDefaults() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns true if default component instances should be created when not present.
+
+
isCreateDefaults() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns true if default component instances should be created when not present.
+
+
isDescendantOf(String, String) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
+
+
isDescendantOf(URI, URI) - Method in class org.sbolstandard.core2.EDAMOntology
+
+
Returns true if the stanza with childURI is a descendant of the stanza with parentURI.
+
+
isDescendantOf(String, String) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
+
+
isDescendantOf(URI, URI) - Method in class org.sbolstandard.core2.SequenceOntology
+
+
Returns true if the term with childURI is a descendant of the term with parentURI.
+
+
isDescendantOf(URI, URI) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns true if the term with childURI is a descendant of the term with parentURI.
+
+
isDescendantOf(String, String) - Method in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
+
+
isDoubleValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Checks if the annotation has a double value property.
+
+
isDropObjectsWithDuplicateURIs() - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Check if objects with duplicate URIs should be dropped.
+
+
isIntegerValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Checks if the annotation has an integer value property.
+
+
isKeepGoing() - Static method in class org.sbolstandard.core2.SBOLReader
+
+
Returns the value of the keepGoing flag.
+
+
isKeepGoing() - Static method in class org.sbolstandard.core2.SBOLWriter
+
+
Returns the value of the keepGoing flag.
+
+
isNestedAnnotations() - Method in class org.sbolstandard.core2.Annotation
+
+
Checks if the annotation has a nested value property.
+
+
ISOMERISATION - Static variable in class org.sbolstandard.core2.SystemsBiologyOntology
+
+
A reaction in which the principal reactant and principal product are isomers of each other + (SBO:0000377).
+
+
isSetComponent() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Test if the reference Component instance is set.
+
+
isSetDescription() - Method in class org.sbolstandard.core2.Identified
+
+
Test if the description property is set.
+
+
isSetDisplayId() - Method in class org.sbolstandard.core2.Identified
+
+
Test if the display ID is set.
+
+
isSetName() - Method in class org.sbolstandard.core2.Identified
+
+
Test if the name property is set.
+
+
isSetOrientation() - Method in class org.sbolstandard.core2.Location
+
+
Checks if the orientation property is set.
+
+
isSetPersistentIdentity() - Method in class org.sbolstandard.core2.Identified
+
+
Test if the persistent identity URI is set.
+
+
isSetRoleIntegration() - Method in class org.sbolstandard.core2.Component
+
+
Test if the roleIntegration property is set.
+
+
isSetRoleIntegration() - Method in class org.sbolstandard.core2.SequenceAnnotation
+
+
Test if the roleIntegration property is set.
+
+
isSetVersion() - Method in class org.sbolstandard.core2.Identified
+
+
Test if the version is set.
+
+
isSetWasDerivedFrom() - Method in class org.sbolstandard.core2.Identified
+
+
Test if the wasDerivedFrom property is set.
+
+
isStringValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Checks if the annotation has a string value property.
+
+
isTypesInURIs() - Method in class org.sbolstandard.core2.SBOLDocument
+
+
Returns true if types are to be inserted into top-level URIs.
+
+
isTypesInURIs() - Static method in class org.sbolstandard.core2.SBOLFactory
+
+
Returns true if types are to be inserted into top-level URIs.
+
+
isURIValue() - Method in class org.sbolstandard.core2.Annotation
+
+
Checks if the annotation is a URI value property.
+
+
IUPAC_DNA - Static variable in class org.sbolstandard.core2.Sequence
+
+
Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences + (IUPAC_DNA).
+
+
IUPAC_PROTEIN - Static variable in class org.sbolstandard.core2.Sequence
+
+
Nomenclature and Symbolism for Amino Acids and Peptides + (IUPAC_PROTEIN).
+
+
IUPAC_RNA - Static variable in class org.sbolstandard.core2.Sequence
+
+
Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences + (IUPAC_RNA).
-A C E G H M O R S T 
+A B C D E F G H I J K L M N O P R S T U V W X 
diff --git a/docs/javadocs/index.html b/docs/javadocs/index.html index 2426382a..22f6c6d7 100644 --- a/docs/javadocs/index.html +++ b/docs/javadocs/index.html @@ -2,7 +2,7 @@ - + Generated Documentation (Untitled)