ModelImpl (Paxtools Core (BioPAX object model, I/O API, implementation and extras) 5.1.0 API)

java.lang.Object
- org.biopax.paxtools.impl.ModelImpl

All Implemented Interfaces:

Serializable, Model
```
public class ModelImpl
extends Object
implements Model
```
This is the default implementation of the Model. Use a factory to create a model.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field and Description

protected Map<String,BioPAXElement> idMap

Fields
Modifier and Type	Field and Description
`protected Map<String,BioPAXElement>`	`idMap`

Constructor Summary

Constructors
Modifier Constructor and Description

protected ModelImpl()

ModelImpl(BioPAXFactory factory)

protected ModelImpl(BioPAXLevel level)

Constructors
Modifier	Constructor and Description
`protected`	`ModelImpl()`
	`ModelImpl(BioPAXFactory factory)`
`protected`	`ModelImpl(BioPAXLevel level)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`add(BioPAXElement aBioPAXElement)` This method adds the given object to this model.
`<T extends BioPAXElement> T`	`addNew(Class<T> c, 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 given element is the same object ("==") as the object stored in the model usually (for self-consistent models) but not necessarily under the element's ID.
`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.
`String`	`getName()` URI of this BioPAX 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> Set<T>`	`getObjects(Class<T> filterBy)` This method returns a set of objects in the model of the given class.
`String`	`getUri()` URI of this BioPAX Model.
`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)` This is default implementation that uses the id-based merging (`SimpleMerger.merge(Model, Model...)`) NOTE: some applications, such as those dealing with persistence/transactions or advanced BioPAX alignment/comparison algorithms (like the Patch), may have to implement and use a more specific method instead.
`void`	`remove(BioPAXElement aBioPAXElement)` This method removes the given BioPAX Element from the model.
`void`	`repair()` This implementation "repairs" the model without unnecessarily copying objects: - recursively adds lost "children" (not null object property values for which `Model.contains(BioPAXElement)` returns False) - updates object properties (should refer to model's elements)
`void`	`replace(BioPAXElement existing, BioPAXElement replacement)` It does not automatically replace or clean up the old element's object properties, therefore, some child elements may become "dangling" if they were used by the replaced element only.
`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`	`setName(String modelName)`
`void`	`setUri(String modelUri)`
`void`	`setXmlBase(String base)` Sets the xml:base to use when exporting a BioPAX model.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - idMap
```
protected final Map<String,BioPAXElement> idMap
```
- Constructor Detail
  - ModelImpl
```
protected ModelImpl()
```
  - ModelImpl
```
protected ModelImpl(BioPAXLevel level)
```
  - ModelImpl
```
public ModelImpl(BioPAXFactory factory)
```
- Method Detail
  - containsID
```
public boolean containsID(String id)
```
    Description copied from interface: Model
    
    This method checks for the biopax element with the given id, returns true if the object with the given id exists. in this model.
    
    Specified by:
    
    containsID in interface Model
    
    Parameters:
    
    id - of the object to be retrieved.
    
    Returns:
    
    biopax element with the given id.
  - getByID
```
public BioPAXElement getByID(String id)
```
    Description copied from interface: Model
    
    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.
    
    Specified by:
    
    getByID in interface Model
    
    Parameters:
    
    id - of the object to be retrieved.
    
    Returns:
    
    biopax element with the given id.
  - getNameSpacePrefixMap
```
public Map<String,String> getNameSpacePrefixMap()
```
    Description copied from interface: Model
    
    This method returns a map of name space prefixes. This map can be modified.
    
    Specified by:
    
    getNameSpacePrefixMap in interface Model
    
    Returns:
    
    a map, mapping prefixes to full namespaces.
  - setFactory
```
public void setFactory(BioPAXFactory factory)
```
    Description copied from interface: Model
    
    This method sets the factory this model will use for creating BioPAX objects. For example Model.addNew(Class, String) method uses this factory.
    
    Specified by:
    
    setFactory in interface Model
    
    Parameters:
    
    factory - this model will use for creating BioPAX objects.
  - getObjects
```
public Set<BioPAXElement> getObjects()
```
    Description copied from interface: Model
    
    This method returns a set of objects in the model. Contents of this set can not be modified.
    
    Specified by:
    
    getObjects in interface Model
    
    Returns:
    
    an unmodifiable set of objects.
  - getObjects
```
public <T extends BioPAXElement> Set<T> getObjects(Class<T> filterBy)
```
    Description copied from interface: Model
    
    This method returns a set of objects in the model of the given class. Contents of this set should not be modified.
    
    Specified by:
    
    getObjects in interface Model
    
    Type Parameters:
    
    T - a BioPAX type
    
    Parameters:
    
    filterBy - class to be used as a filter.
    
    Returns:
    
    an unmodifiable set of objects of the given class.
  - remove
```
public void remove(BioPAXElement aBioPAXElement)
```
    Description copied from interface: Model
    
    This method removes the given BioPAX Element from the model. Other objects in the model can still point to this object. It is user's responsibility to properly excise these properties.
    
    Specified by:
    
    remove in interface Model
    
    Parameters:
    
    aBioPAXElement - to be removed.
  - addNew
```
public <T extends BioPAXElement> T addNew(Class<T> c,
                                          String id)
```
    Description copied from interface: Model
    
    This method creates a new object using the model's factory, adds it to the model and returns it.
    
    Specified by:
    
    addNew in interface Model
    
    Type Parameters:
    
    T - a BioPAX type
    
    Parameters:
    
    c - the BioPAX model interface class
    
    id - of the new object
    
    Returns:
    
    newly created object
  - contains
```
public boolean contains(BioPAXElement aBioPAXElement)
```
    This method returns true if given element is the same object ("==") as the object stored in the model usually (for self-consistent models) but not necessarily under the element's ID.
    
    Specified by:
    
    contains in interface Model
    
    Parameters:
    
    aBioPAXElement - BioPAX object (individual)
    
    Returns:
    
    true/false - whether this model contains the object or not
    
    See Also:
    
    Model.containsID(String)
  - getUri
```
public String getUri()
```
    Description copied from interface: Model
    
    URI of this BioPAX Model. This can be used in many ways to refer to this model when: - logging; - merging several models; - converting to or from another data format, such as GMT (GSEA); - saving to or reading from RDF/XML file (e.g., save/read a special Provenance object)
    
    Specified by:
    
    getUri in interface Model
    
    Returns:
    
    model's uri
  - setUri
```
public void setUri(String modelUri)
```
    Specified by:
    
    setUri in interface Model
  - getName
```
public String getName()
```
    Description copied from interface: Model
    
    URI of this BioPAX Model. This can be used in many ways; see Model.getUri().
    
    Specified by:
    
    getName in interface Model
    
    Returns:
    
    model's name
  - setName
```
public void setName(String modelName)
```
    Specified by:
    
    setName in interface Model
  - add
```
public void add(BioPAXElement aBioPAXElement)
```
    Description copied from interface: Model
    
    This method adds the given object to this model. If the object points to other objects that are not in the model, it is user's responsibility to add them into the model as well. If an object with the same id already exists, it will throw an IllegalBioPAXArgumentException
    
    Specified by:
    
    add in interface Model
    
    Parameters:
    
    aBioPAXElement - to be added
  - getLevel
```
public BioPAXLevel getLevel()
```
    Description copied from interface: Model
    
    This method returns the level of the objects that are contained within this model.
    
    Specified by:
    
    getLevel in interface Model
    
    Returns:
    
    level of the objects within this model.
  - setAddDependencies
```
public void setAddDependencies(boolean value)
```
    Description copied from interface: Model
    
    When set to false, the model will not check for the dependent objects of a newly added object. When true it will traverse and add all dependent objects that are not already in the model. This feature is currently experimental.
    
    Specified by:
    
    setAddDependencies in interface Model
    
    Parameters:
    
    value - defining the dependency adding behaviour
  - isAddDependencies
```
public boolean isAddDependencies()
```
    Description copied from interface: Model
    
    When addDependencies is false, the model will not check for the dependent objects of a newly added object. When true it will traverse and add all dependent objects that are not already in the model. This feature is currently experimental.
    
    Specified by:
    
    isAddDependencies in interface Model
    
    Returns:
    
    whether adding dependencies.
  - replace
```
public void replace(BioPAXElement existing,
                    BioPAXElement replacement)
```
    It does not automatically replace or clean up the old element's object properties, therefore, some child elements may become "dangling" if they were used by the replaced element only. Can also clear object properties (- replace with null).
    
    Specified by:
    
    replace in interface Model
    
    Parameters:
    
    existing - object to be replaced
    
    replacement - the replacement BioPAX object
  - merge
```
public void merge(Model source)
```
    This is default implementation that uses the id-based merging (SimpleMerger.merge(Model, Model...)) NOTE: some applications, such as those dealing with persistence/transactions or advanced BioPAX alignment/comparison algorithms (like the Patch), may have to implement and use a more specific method instead.
    
    Specified by:
    
    merge in interface Model
    
    Parameters:
    
    source - a model to merge
    
    See Also:
    
    SimpleMerger, Model.merge(Model)
  - repair
```
public void repair()
```
    This implementation "repairs" the model without unnecessarily copying objects: - recursively adds lost "children" (not null object property values for which Model.contains(BioPAXElement) returns False) - updates object properties (should refer to model's elements)
    
    Specified by:
    
    repair in interface Model
  - setXmlBase
```
public void setXmlBase(String base)
```
    Description copied from interface: Model
    
    Sets the xml:base to use when exporting a BioPAX model. Usually, is is a data-provider's URI prefix, e.g., xml:base="http://www.pantherdb.org/pathways/biopax#" Setting this to null makes the exporter print using absolute URIs (and rdf:about) instead of relative ones (and rdf:ID).
    
    Specified by:
    
    setXmlBase in interface Model
    
    Parameters:
    
    base - a URI prefix or null.
  - getXmlBase
```
public String getXmlBase()
```
    Description copied from interface: Model
    
    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. Note: it's not required that all the BioPAX objects in the model have the same URI prefix/namespace; e.g., there are can be (and perfectly legal) objects that use other URI bases, such as http://identifiers.org/, http://purl.org/, etc. (- usually these are well-known standard xml bases, or these result from merging several BioPAX models of different data providers into one model.)
    
    Specified by:
    
    getXmlBase in interface Model
    
    Returns:
    
    xml:base value

Class ModelImpl

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

idMap

Constructor Detail

ModelImpl

ModelImpl

ModelImpl

Method Detail

containsID

getByID

getNameSpacePrefixMap

setFactory

getObjects

getObjects

remove

addNew

contains

getUri

setUri

getName

setName

add

getLevel

setAddDependencies

isAddDependencies

replace

merge

repair

setXmlBase

getXmlBase