CVTerm (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.CVTerm

```
public class CVTerm
extends java.lang.Object
```
Representation of MIRIAM-compliant controlled vocabulary annotation.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

The SBML Level 2 and Level 3 specifications define a simple format for annotating models when (a) referring to controlled vocabulary terms and database identifiers that define and describe biological and biochemical entities, and (b) describing the creator of a model and the model's modification history. This SBML format is a concrete syntax that conforms to the guidelines of MIRIAM ('Minimum Information Requested in the Annotation of biochemical Models', Nature Biotechnology, vol. 23, no. 12, Dec. 2005). The format uses a subset of W3C RDF (Resource Description Format). In order to help application developers work with annotations in this format, libSBML provides several helper classes that provide higher-level interfaces to the data elements these classes include CVTerm, ModelCreator, ModelHistory, RDFAnnotationParser, and Date.

Components of an SBML annotation

The SBML annotation format consists of RDF-based content placed inside an <annotation> element attached to an SBML component such as Species, Compartment, etc. The following template illustrates the different parts of SBML annotations in XML form:
```
 <SBML_ELEMENT +++ metaid="meta id" +++>
   +++
   <annotation>
     +++
     <rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
              xmlns:dc='http://purl.org/dc/elements/1.1/'
              xmlns:dcterm='http://purl.org/dc/terms/'
              xmlns:vcard='http://www.w3.org/2001/vcard-rdf/3.0#'
              xmlns:bqbiol='http://biomodels.net/biology-qualifiers/'
              xmlns:bqmodel='http://biomodels.net/model-qualifiers/' >
       <rdf:Description rdf:about="#meta id">
         HISTORY
         <RELATION_ELEMENT>
           <rdf:Bag>
             <rdf:li rdf:resource="URI" />
             ...
           </rdf:Bag>
         </RELATION_ELEMENT>
         ...
       </rdf:Description>
       +++
     </rdf:RDF>
     +++
   </annotation>
   +++
 </SBML_ELEMENT>
 
```
In the template above, the placeholder SBML_ELEMENT stands for the XML tag name of an SBML model component (e.g., model, reaction, etc.) and the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, the symbol +++ is a placeholder for either no content or valid XML content that is not defined by this annotation scheme, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element. The optional content HISTORY is a creation and modification history in libSBML, this is stored using ModelHistory objects.
The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace 'http://biomodels.net/model-qualifiers' (for model qualifiers) or 'http://biomodels.net/biology-qualifiers' (for biological qualifier). Note that these namespace URIs are only labels, and not actual Web locations, which means you cannot visit an address such as 'http://biomodels.net/model-qualifiers' in your browser or try to have your application access it. @if Refer instead to the enumerations #ModelQualifierType_t and #BiolQualifierType_t for a list of the available relationship elements that can be used for RELATION_ELEMENT.@endif
The URI is a required data value that uniquely identifies a resource and data within that resource to which the annotation refers. Again, being URIs, these do not refer to physical Web locations nevertheless, applications will often want a means of finding the resource to which a given URI refers. Providing the facilities for this task is the purpose of MIRIAM Resources, described in detail online at http://biomodels.net/miriam) and also in the paper 'MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology', BMC Systems Biology, 58(1), 2007.
The relation-resource pairs above are the 'controlled vocabulary' terms that which CVTerm is designed to store and manipulate. The next section describes these parts in more detail. For more information about SBML annotations in general, please refer to Section 6 in the SBML Level 2 (Versions 2&ndash4) or Level 3 specification documents.

The parts of a CVTerm

Annotations that refer to controlled vocabularies are managed in libSBML using CVTerm objects. A set of RDF-based annotations attached to a given SBML <annotation> element are read by RDFAnnotationParser and converted into a list of these CVTerm objects. Each CVTerm object instance stores the following components of an annotation:
- The qualifier, which can be a BioModels.net 'biological qualifier', a BioModels.net 'model qualifier', or an unknown qualifier (as far as the CVTerm class is concerned). Qualifiers are used in MIRIAM to indicate the nature of the relationship between the object being annotated and the resource. In CVTerm, the qualifiers can be manipulated using the methods CVTerm.getQualifierType(), CVTerm.setQualifierType(int type), and related methods.
- The resource, represented by a URI (which, we must remind developers, is not the same as a URL). In the CVTerm class, the resource component can be manipulated using the methods CVTerm.addResource(String resource) and CVTerm.removeResource(String resource).
Note that a CVTerm contains a single qualifier, but possibly more than one resource. This corresponds to the possibility of an annotation that points to multiple resources, all of which are qualified by the same BioModels.net qualifier. The CVTerm object class supports this by supporting a list of resources.
Detailed explanations of the qualifiers defined by BioModels.net can be found at http://biomodels.net/qualifiers.

Constructor Summary

Constructors
Constructor and Description
`CVTerm()` Creates an empty `CVTerm`, optionally with the given qualifier `type`.
`CVTerm(CVTerm orig)` Copy constructor creates a copy of a `CVTerm` object.
`CVTerm(int type)` Creates an empty `CVTerm`, optionally with the given qualifier `type`.
`CVTerm(XMLNode node)` Creates a new `CVTerm` from the given `XMLNode`.

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`addResource(java.lang.String resource)` Adds a resource reference to this `CVTerm` object.
`CVTerm`	`cloneObject()` Creates and returns a deep copy of this `CVTerm` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`boolean`	`equals(java.lang.Object sb)` Equality comparison method for CVTerm.
`int`	`getBiologicalQualifierType()` Returns the biological qualifier type of this `CVTerm` object.
`int`	`getModelQualifierType()` Returns the model qualifier type of this `CVTerm` object.
`long`	`getNumResources()` Returns the number of resources for this `CVTerm` object.
`int`	`getQualifierType()` Returns the qualifier type of this `CVTerm` object.
`XMLAttributes`	`getResources()` Returns the resource references for this `CVTerm` object.
`java.lang.String`	`getResourceURI(long n)` Returns the value of the nth resource for this `CVTerm` object.
`int`	`hashCode()` Returns a hashcode for this CVTerm object.
`boolean`	`hasRequiredAttributes()` Predicate returning `true` if all the required elements for this `CVTerm` object have been set.
`int`	`removeResource(java.lang.String resource)` Removes a resource URI from the set of resources stored in this `CVTerm` object.
`int`	`setBiologicalQualifierType(int type)` Sets the biology qualifier type of this `CVTerm` object.
`int`	`setBiologicalQualifierType(java.lang.String qualifier)` Sets the biology qualifier type code of this `CVTerm` object.
`int`	`setModelQualifierType(int type)` Sets the model qualifier type of this `CVTerm` object.
`int`	`setModelQualifierType(java.lang.String qualifier)` Sets the model qualifier type code value of this `CVTerm` object.
`int`	`setQualifierType(int type)` Sets the qualifier code of this `CVTerm` object.

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CVTerm
```
public CVTerm()
```
    Creates an empty CVTerm, optionally with the given qualifier type.
    
    The SBML Level 2 and Level 3 specifications define a simple format for annotating models when (a) referring to controlled vocabulary terms and database identifiers that define and describe biological and other entities, and (b) describing the creator of a model and the model's modification history. The annotation content is stored in <annotation> elements attached to individual SBML elements. The format for storing the content inside SBML <annotation> elements is a subset of W3C RDF (Resource Description Format) expressed in XML. The CVTerm class provides a programming interface for working directly with controlled vocabulary term ('CV term') objects without having to deal directly with the XML form. When libSBML reads in an SBML model containing RDF annotations, it parses those annotations into a list of CVTerm objects, and when writing a model, it parses the CVTerm objects back into the appropriate SBML <annotation> structure.
    This method creates an empty CVTerm object. The possible qualifier types usable as values of type are MODEL_QUALIFIER and BIOLOGICAL_QUALIFIER. If an explicit value for type is not given, this method defaults to using UNKNOWN_QUALIFIER. The qualifier type can be set later using the CVTerm.setQualifierType(int type) method.
    Different BioModels.net qualifier elements encode different types of relationships. Please refer to the SBML specification or the BioModels.net qualifiers web page for an explanation of the meaning of these different qualifiers.
    
    Parameters:
    type - a qualifier type
    
    Documentation note:
    The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
  - CVTerm
```
public CVTerm(CVTerm orig)
```
    Copy constructor creates a copy of a CVTerm object.
    
    Parameters:
    orig - the CVTerm instance to copy.
    
    Throws:
    
    SBMLConstructorException - Thrown if the argument orig is null.
  - CVTerm
```
public CVTerm(int type)
```
    Creates an empty CVTerm, optionally with the given qualifier type.
    
    The SBML Level 2 and Level 3 specifications define a simple format for annotating models when (a) referring to controlled vocabulary terms and database identifiers that define and describe biological and other entities, and (b) describing the creator of a model and the model's modification history. The annotation content is stored in <annotation> elements attached to individual SBML elements. The format for storing the content inside SBML <annotation> elements is a subset of W3C RDF (Resource Description Format) expressed in XML. The CVTerm class provides a programming interface for working directly with controlled vocabulary term ('CV term') objects without having to deal directly with the XML form. When libSBML reads in an SBML model containing RDF annotations, it parses those annotations into a list of CVTerm objects, and when writing a model, it parses the CVTerm objects back into the appropriate SBML <annotation> structure.
    This method creates an empty CVTerm object. The possible qualifier types usable as values of type are MODEL_QUALIFIER and BIOLOGICAL_QUALIFIER. If an explicit value for type is not given, this method defaults to using UNKNOWN_QUALIFIER. The qualifier type can be set later using the CVTerm.setQualifierType(int type) method.
    Different BioModels.net qualifier elements encode different types of relationships. Please refer to the SBML specification or the BioModels.net qualifiers web page for an explanation of the meaning of these different qualifiers.
    
    Parameters:
    type - a qualifier type
    
    Documentation note:
    The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
  - CVTerm
```
public CVTerm(XMLNode node)
```
    Creates a new CVTerm from the given XMLNode.
    
    The SBML Level 2 and Level 3 specifications define a simple format for annotating models when (a) referring to controlled vocabulary terms and database identifiers that define and describe biological and other entities, and (b) describing the creator of a model and the model's modification history. The annotation content is stored in <annotation> elements attached to individual SBML elements. The format for storing the content inside SBML <annotation> elements is a subset of W3C RDF (Resource Description Format) expressed in XML. The CVTerm class provides a programming interface for working directly with controlled vocabulary term ('CV term') objects without having to deal directly with the XML form. When libSBML reads in an SBML model containing RDF annotations, it parses those annotations into a list of CVTerm objects, and when writing a model, it parses the CVTerm objects back into the appropriate SBML <annotation> structure.
    This method creates a CVTerm object from the given XMLNode object node. XMLNode is libSBML's representation of a node in an XML tree of elements, and each such element can be placed in a namespace. This constructor looks for the element to be in the XML namespaces 'http://biomodels.net/model-qualifiers' (for model qualifiers) and 'http://biomodels.net/biology-qualifiers' (for biological qualifier), and if they are, creates CVTerm objects for the result.
    
    Parameters:
    node - an XMLNode representing a CVTerm.
    "Note:"
    
    This method assumes that the given XMLNode object node is of the correct structural form.
- Method Detail
  - addResource
```
public int addResource(java.lang.String resource)
```
    Adds a resource reference to this CVTerm object.
    
    The SBML Level 2 and Level 3 specifications define a simple format for annotating models when (a) referring to controlled vocabulary terms and database identifiers that define and describe biological and other entities, and (b) describing the creator of a model and the model's modification history. The annotation content is stored in <annotation> elements attached to individual SBML elements. The format for storing the content inside SBML <annotation> elements is a subset of W3C RDF (Resource Description Format) expressed in XML. The CVTerm class provides a programming interface for working directly with controlled vocabulary term ('CV term') objects without having to deal directly with the XML form. When libSBML reads in an SBML model containing RDF annotations, it parses those annotations into a list of CVTerm objects, and when writing a model, it parses the CVTerm objects back into the appropriate SBML <annotation> structure.
    The specific RDF element used in this SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element containing one or more <rdf:li> elements. Each such element refers to a data item in an external resource the resource and data item are together identified uniquely using a URI. The following template illustrates the structure:
```
   <rdf:Description rdf:about="#meta id">
     HISTORY
     <RELATION_ELEMENT>
       <rdf:Bag>
         <rdf:li rdf:resource="resource URI" />
         ...
       </rdf:Bag>
     </RELATION_ELEMENT>
     ...
   </rdf:Description>
   
```
    In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element. The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace 'http://biomodels.net/model-qualifiers' (for model qualifiers) or 'http://biomodels.net/biology-qualifiers' (for biological qualifier).
    The resource URI is a required data value that uniquely identifies a resource and data within that resource to which the annotation refers. The present method allows callers to add a reference to a resource URI with the same relationship to the enclosing SBML object. (In other words, the argument to this method is a resource URI as shown in the XML fragment above.) Resources are stored in this CVTerm object within an XMLAttributes object.
    The relationship of this CVTerm to the enclosing SBML object can be determined using the CVTerm methods such as getModelQualifierType() and getBiologicalQualifierType().
    Parameters:
    resource - a string representing the URI of the resource and data item being referenced e.g., 'http://www.geneontology.org/#GO:0005892'.
    
    Returns:
    integer value indicating success/failure of the call. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    See Also:
    CVTerm.getResources(), CVTerm.removeResource(String resource), CVTerm.getQualifierType(), CVTerm.getModelQualifierType(), CVTerm.getBiologicalQualifierType()
  - cloneObject
```
public CVTerm cloneObject()
```
    Creates and returns a deep copy of this CVTerm object.
    
    Returns:
    a (deep) copy of this CVTerm.
  - delete
```
public void delete()
```
    Explicitly deletes the underlying native object.
    In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the CVTerm.delete() method on the libSBML object.
    This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke CVTerm.delete() themselves.
  - equals
```
public boolean equals(java.lang.Object sb)
```
    Equality comparison method for CVTerm.
    Because the Java methods for libSBML are actually wrappers around code implemented in C++ and C, certain operations will not behave as expected. Equality comparison is one such case. An instance of a libSBML object class is actually a proxy object wrapping the real underlying C/C++ object. The normal == equality operator in Java will only compare the Java proxy objects, not the underlying native object. The result is almost never what you want in practical situations. Unfortunately, Java does not provide a way to override ==.
    The alternative that must be followed is to use the equals() method. The equals method on this class overrides the default java.lang.Object one, and performs an intelligent comparison of instances of objects of this class. The result is an assessment of whether two libSBML Java objects are truly the same underlying native-code objects.
    The use of this method in practice is the same as the use of any other Java equals method. For example, a.equals(b) returns true if a and b are references to the same underlying object.
    
    Overrides:
    
    equals in class java.lang.Object
    
    Parameters:
    sb - a reference to an object to which the current object instance will be compared
    
    Returns:
    true if sb refers to the same underlying native object as this one, false otherwise
  - getBiologicalQualifierType
```
public int getBiologicalQualifierType()
```
    Returns the biological qualifier type of this CVTerm object.
    
    The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
```
 <rdf:Description rdf:about="#meta id">
   HISTORY
   <RELATION_ELEMENT>
     <rdf:Bag>
     <rdf:li rdf:resource="resource URI" />
     ...
     </rdf:Bag>
   </RELATION_ELEMENT>
   ...
 </rdf:Description>
 
```
    In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.
    The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace 'http://biomodels.net/model-qualifiers' (for model qualifiers) or 'http://biomodels.net/biology-qualifiers' (for biological qualifier). Callers will typically use getQualifierType() to find out the type of qualifier relevant to this particular CVTerm object, then if it is a biological qualifier, use the present method to determine the specific qualifier.
    Annotations with biological qualifiers express a relationship between an annotation resource and the biological concept represented by a given object in the model. The diagram below illustrates the relationship in this case:
    
    The set of known biological qualifiers is, at the time of this libSBML release, the following:
    Any other BioModels.net qualifier found in the model is considered unknown by libSBML and reported as BQB_UNKNOWN.
    Returns:
    the biology qualifier type of this object or BQB_UNKNOWN (the default).
  - getModelQualifierType
```
public int getModelQualifierType()
```
    Returns the model qualifier type of this CVTerm object.
    
    The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
```
 <rdf:Description rdf:about="#meta id">
   HISTORY
   <RELATION_ELEMENT>
     <rdf:Bag>
     <rdf:li rdf:resource="resource URI" />
     ...
     </rdf:Bag>
   </RELATION_ELEMENT>
   ...
 </rdf:Description>
 
```
    In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.
    The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace 'http://biomodels.net/model-qualifiers' (for model qualifiers) or 'http://biomodels.net/biology-qualifiers' (for biological qualifier). Callers will typically use getQualifierType() to find out the type of qualifier relevant to this particular CVTerm object, then if it is a model qualifier, use the present method to determine the specific qualifier.
    Annotations with model qualifiers express a relationship between an annotation resource and the modeling concept represented by a given object in the model. The diagram below illustrates the relationship in this case:
    
    The set of known model qualifiers is, at the time of this libSBML release, the following:
    Any other BioModels.net qualifier found in the model is considered unknown by libSBML and reported as BQM_UNKNOWN.
    Returns:
    the model qualifier type of this object or BQM_UNKNOWN (the default).
  - getNumResources
```
public long getNumResources()
```
    Returns the number of resources for this CVTerm object.
    
    The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
```
 <rdf:Description rdf:about="#meta id">
   HISTORY
   <RELATION_ELEMENT>
     <rdf:Bag>
     <rdf:li rdf:resource="resource URI" />
     ...
     </rdf:Bag>
   </RELATION_ELEMENT>
   ...
 </rdf:Description>
 
```
    In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.
    The fragment above illustrates that there can be more than one resource referenced by a given relationship annotation (i.e., the resource URI values associated with a particular RELATION_ELEMENT). The present method returns a count of the resources stored in this CVTerm object.
    Returns:
    the number of resources in the set of XMLAttributes of this CVTerm.
    See Also:
    CVTerm.getResources(), CVTerm.getResourceURI(long n)
  - getQualifierType
```
public int getQualifierType()
```
    Returns the qualifier type of this CVTerm object.
    
    The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
```
 <rdf:Description rdf:about="#meta id">
   HISTORY
   <RELATION_ELEMENT>
     <rdf:Bag>
     <rdf:li rdf:resource="resource URI" />
     ...
     </rdf:Bag>
   </RELATION_ELEMENT>
   ...
 </rdf:Description>
 
```
    In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.
    The placeholder RELATION_ELEMENT refers to a BioModels.net qualifier element name. This is an element in either the XML namespace 'http://biomodels.net/model-qualifiers' (for model qualifiers) or 'http://biomodels.net/biology-qualifiers' (for biological qualifier). The present method returns a code identifying which one of these two relationship namespaces is being used any other qualifier in libSBML is considered unknown (as far as the CVTerm class is concerned). Consequently, this method will return one of the following values:
    The specific relationship of this CVTerm to the enclosing SBML object can be determined using the CVTerm methods such as getModelQualifierType() and getBiologicalQualifierType(). Callers will typically want to use the present method to find out which one of the other two methods to call to find out the specific relationship.
    Returns:
    the qualifier type of this object or UNKNOWN_QUALIFIER (the default).
    See Also:
    CVTerm.getResources(), CVTerm.getModelQualifierType(), CVTerm.getBiologicalQualifierType()
  - getResources
```
public XMLAttributes getResources()
```
    Returns the resource references for this CVTerm object.
    
    The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
```
 <rdf:Description rdf:about="#meta id">
   HISTORY
   <RELATION_ELEMENT>
     <rdf:Bag>
     <rdf:li rdf:resource="resource URI" />
     ...
     </rdf:Bag>
   </RELATION_ELEMENT>
   ...
 </rdf:Description>
 
```
    In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.
    The resource URI values shown in the template above are stored internally in CVTerm objects using an XMLAttributes object. Each attribute stored inside the XMLAttributes will have the same name (specifically, "rdf:resource") but a different value, and the value will be a resource URI shown in the XML template above.
    A valid CVTerm entity must always have at least one resource and a value for the relationship qualifier.
    Returns:
    the XMLAttributes that store the resources of this CVTerm.
    See Also:
    CVTerm.getQualifierType(), CVTerm.addResource(String resource), CVTerm.getResourceURI(long n)
  - getResourceURI
```
public java.lang.String getResourceURI(long n)
```
    Returns the value of the nth resource for this CVTerm object.
    
    The RDF element used in the SBML format for referring to external entities is <rdf:Description>, with a <rdf:Bag> element inside of it containing one or more <rdf:li> elements. The following template illustrates the structure:
```
 <rdf:Description rdf:about="#meta id">
   HISTORY
   <RELATION_ELEMENT>
     <rdf:Bag>
     <rdf:li rdf:resource="resource URI" />
     ...
     </rdf:Bag>
   </RELATION_ELEMENT>
   ...
 </rdf:Description>
 
```
    In the template above, the placeholder meta id stands for the element's meta identifier, which is a field available on all SBML components derived from the SBase base object class. The dotted portions are optional, and the ellipses ... are placeholders for zero or more elements of the same form as the immediately preceding element.
    The fragment above illustrates that there can be more than one resource referenced by a given relationship annotation (i.e., the resource URI values associated with a particular RELATION_ELEMENT). LibSBML stores all resource URIs in a single CVTerm object for a given relationship. Callers can use getNumResources() to find out how many resources are stored in this CVTerm object, then call this method to retrieve the nth resource URI.
    Parameters:
    n - the index of the resource to query
    
    Returns:
    string representing the value of the nth resource in the set of XMLAttributes of this CVTerm.
    See Also:
    CVTerm.getNumResources(), CVTerm.getQualifierType()
  - hashCode
```
public int hashCode()
```
    Returns a hashcode for this CVTerm object.
    
    Overrides:
    
    hashCode in class java.lang.Object
    
    Returns:
    a hash code usable by Java methods that need them.
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Predicate returning true if all the required elements for this CVTerm object have been set.
    "Note:"
    The required attributes for a CVTerm are:
    
    a qualifier type, which can be either a model qualifier or a biological qualifier
    at least one resource
  - removeResource
```
public int removeResource(java.lang.String resource)
```
    Removes a resource URI from the set of resources stored in this CVTerm object.
    Parameters:
    resource - a string representing the resource URI to remove e.g., 'http://www.geneontology.org/#GO:0005892'.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    See Also:
    CVTerm.addResource(String resource)
  - setBiologicalQualifierType
```
public int setBiologicalQualifierType(int type)
```
    Sets the biology qualifier type of this CVTerm object.
    Parameters:
    type - the biology qualifier type.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    See Also:
    CVTerm.getQualifierType(), CVTerm.setQualifierType(int type)
    "Note:"
    
    If the Qualifier Type of this object is not BIOLOGICAL_QUALIFIER, then the biology qualifier type will default to BQB_UNKNOWN.
  - setBiologicalQualifierType
```
public int setBiologicalQualifierType(java.lang.String qualifier)
```
    Sets the biology qualifier type code of this CVTerm object.
    Parameters:
    qualifier - the string representing a biology qualifier
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    See Also:
    CVTerm.getQualifierType(), CVTerm.setQualifierType(int type)
    "Note:"
    
    If the Qualifier Type of this object is not BIOLOGICAL_QUALIFIER, then the biology qualifier type code value will default to BQB_UNKNOWN.
  - setModelQualifierType
```
public int setModelQualifierType(int type)
```
    Sets the model qualifier type of this CVTerm object.
    Parameters:
    type - the model qualifier type
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    See Also:
    CVTerm.getQualifierType(), CVTerm.setQualifierType(int type)
    "Note:"
    
    If the Qualifier Type of this object is not MODEL_QUALIFIER, then the ModelQualifierType_t value will default to BQM_UNKNOWN.
  - setModelQualifierType
```
public int setModelQualifierType(java.lang.String qualifier)
```
    Sets the model qualifier type code value of this CVTerm object.
    Parameters:
    qualifier - the string representing a model qualifier
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    See Also:
    CVTerm.getQualifierType(), CVTerm.setQualifierType(int type)
    "Note:"
    
    If the Qualifier Type of this object is not MODEL_QUALIFIER, then the ModelQualifierType_t value will default to BQM_UNKNOWN.
  - setQualifierType
```
public int setQualifierType(int type)
```
    Sets the qualifier code of this CVTerm object.
    Parameters:
    type - the qualifier type. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    See Also:
    CVTerm.getQualifierType()

Class CVTerm

Components of an SBML annotation

The parts of a `CVTerm`

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

CVTerm

CVTerm

CVTerm

CVTerm

Method Detail

addResource

cloneObject

delete

equals

getBiologicalQualifierType

getModelQualifierType

getNumResources

getQualifierType

getResources

getResourceURI

hashCode

hasRequiredAttributes

removeResource

setBiologicalQualifierType

setBiologicalQualifierType

setModelQualifierType

setModelQualifierType

setQualifierType

Class CVTerm

Components of an SBML annotation

The parts of a CVTerm

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

CVTerm

CVTerm

CVTerm

CVTerm

Method Detail

addResource

cloneObject

delete

equals

getBiologicalQualifierType

getModelQualifierType

getNumResources

getQualifierType

getResources

getResourceURI

hashCode

hasRequiredAttributes

removeResource

setBiologicalQualifierType

setBiologicalQualifierType

setModelQualifierType

setModelQualifierType

setQualifierType

The parts of a `CVTerm`