public interface Model extends Serializable
Modifier and Type | Method and Description |
---|---|
void |
add(BioPAXElement aBioPAXElement)
This method add the given onject to this model.
|
<T extends BioPAXElement> |
addNew(Class<T> aClass,
String id)
This method creates a new object using the model's factory, adds it
to the model and returns it.
|
boolean |
contains(BioPAXElement aBioPAXElement)
This method returns true if the parameter is contained within
this model.
|
boolean |
containsID(String id)
This method checks for the biopax element with the given id,
returns true if the object with the given id exists.
|
BioPAXElement |
getByID(String id)
This method returns the biopax element with the given id,
returns null if the object with the given id does not exist
in this model.
|
BioPAXLevel |
getLevel()
This method returns the level of the objects that are
contained within this model.
|
Map<String,String> |
getNameSpacePrefixMap()
This method returns a map of name space prefixes.
|
Set<BioPAXElement> |
getObjects()
This method returns a set of objects in the model.
|
<T extends BioPAXElement> |
getObjects(Class<T> filterBy)
This method returns a set of objects in the model of the given class.
|
String |
getXmlBase()
Gets the model's xml:base (URI prefix/namespace), which
normally the majority of the BioPAX object's absolute URIs
in the model begin with.
|
boolean |
isAddDependencies()
When addDependencies is false, the model will not check for the dependent
objects of a newly added object.
|
void |
merge(Model source)
Merges the source model into this one.
|
void |
remove(BioPAXElement aBioPAXElement)
This method removes the given BioPAX Element from the model.
|
void |
repair()
Attempts to repair the model,
i.e., make it self-consistent, integral.
|
void |
replace(BioPAXElement existing,
BioPAXElement replacement)
Replaces existing BioPAX element with another one,
of the same or possibly equivalent type,
and updates all the affected references to it (object properties).
|
void |
setAddDependencies(boolean value)
When set to false, the model will not check for the dependent
objects of a newly added object.
|
void |
setFactory(BioPAXFactory factory)
This method sets the factory this model will use for creating
BioPAX objects.
|
void |
setXmlBase(String base)
Sets the xml:base to use when exporting a BioPAX model.
|
void add(BioPAXElement aBioPAXElement)
IllegalBioPAXArgumentException
aBioPAXElement
- to be added<T extends BioPAXElement> T addNew(Class<T> aClass, String id)
T
- a BioPAX typeaClass
- the BioPAX model interface classid
- of the new objectboolean contains(BioPAXElement aBioPAXElement)
containsID(String)
is 'true'
(using the URI of the parameter) if, e.g.,
model contains another object with the same URI.aBioPAXElement
- to be checkedcontainsID(String)
BioPAXElement getByID(String id)
id
- of the object to be retrieved.boolean containsID(String id)
id
- of the object to be retrieved.Map<String,String> getNameSpacePrefixMap()
Set<BioPAXElement> getObjects()
<T extends BioPAXElement> Set<T> getObjects(Class<T> filterBy)
T
- a BioPAX typefilterBy
- class to be used as a filter.void remove(BioPAXElement aBioPAXElement)
aBioPAXElement
- to be removed.void setFactory(BioPAXFactory factory)
addNew(Class, String)
method
uses this factory.factory
- this model will use for creating
BioPAX objects.BioPAXLevel getLevel()
void setAddDependencies(boolean value)
value
- defining the dependency adding behaviourboolean isAddDependencies()
void merge(Model source)
source
- a model to mergevoid replace(BioPAXElement existing, BioPAXElement replacement)
existing
- object to be replacedreplacement
- the replacement BioPAX objectvoid repair()
void setXmlBase(String base)
base
- a URI prefix or null.String getXmlBase()
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