BioPAXElementImpl (Paxtools Core (BioPAX object model, I/O API, implementation and extras) 4.3.1 API)

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

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement

Direct Known Subclasses:

L3ElementImpl
```
@Entity
public abstract class BioPAXElementImpl
extends Object
implements BioPAXElement
```
See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`FIELD_AVAILABILITY`
`static String`	`FIELD_COMMENT`
`static String`	`FIELD_DATASOURCE`
`static String`	`FIELD_ECNUMBER`
`static String`	`FIELD_KEYWORD`
`static String`	`FIELD_NAME`
`static String`	`FIELD_ORGANISM`
`static String`	`FIELD_PATHWAY`
`static String`	`FIELD_SEQUENCE`
`static String`	`FIELD_TERM`
`static String`	`FIELD_XREFDB`
`static String`	`FIELD_XREFID`
`static String`	`FILTER_BY_DATASOURCE`
`static String`	`FILTER_BY_ORGANISM`

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement
UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors
Constructor and Description

BioPAXElementImpl()

Constructors
Constructor and Description
`BioPAXElementImpl()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`equals(Object obj)` true if and only if the other obj has the same biopax type (same `BioPAXElement.getModelInterface()`, not a subclass) and same URI.
`int`	`equivalenceCode()` If two elements are equivalent, then their equivalence code should be the same.
`Map<String,Object>`	`getAnnotations()` A general-purpose map to optionally store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.
`String`	`getPk()` Gets Primary Key.
`String`	`getRDFId()` This method returns the full URI of the element (despite it is called RDFId).
`int`	`hashCode()` This method is consistent with the overridden `equals(Object)` method (biopax type and URI are what matters)
`boolean`	`isEquivalent(BioPAXElement element)` This method compares the given element for equivalency.
`protected boolean`	`semanticallyEquivalent(BioPAXElement element)`
`String`	`toString()`

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

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement
getModelInterface

- Field Detail
  - FIELD_AVAILABILITY
```
public static final String FIELD_AVAILABILITY
```
    See Also:
    
    Constant Field Values
  - FIELD_COMMENT
```
public static final String FIELD_COMMENT
```
    See Also:
    
    Constant Field Values
  - FIELD_KEYWORD
```
public static final String FIELD_KEYWORD
```
    See Also:
    
    Constant Field Values
  - FIELD_NAME
```
public static final String FIELD_NAME
```
    See Also:
    
    Constant Field Values
  - FIELD_TERM
```
public static final String FIELD_TERM
```
    See Also:
    
    Constant Field Values
  - FIELD_XREFDB
```
public static final String FIELD_XREFDB
```
    See Also:
    
    Constant Field Values
  - FIELD_XREFID
```
public static final String FIELD_XREFID
```
    See Also:
    
    Constant Field Values
  - FIELD_ECNUMBER
```
public static final String FIELD_ECNUMBER
```
    See Also:
    
    Constant Field Values
  - FIELD_SEQUENCE
```
public static final String FIELD_SEQUENCE
```
    See Also:
    
    Constant Field Values
  - FIELD_ORGANISM
```
public static final String FIELD_ORGANISM
```
    See Also:
    
    Constant Field Values
  - FIELD_DATASOURCE
```
public static final String FIELD_DATASOURCE
```
    See Also:
    
    Constant Field Values
  - FIELD_PATHWAY
```
public static final String FIELD_PATHWAY
```
    See Also:
    
    Constant Field Values
  - FILTER_BY_ORGANISM
```
public static final String FILTER_BY_ORGANISM
```
    See Also:
    
    Constant Field Values
  - FILTER_BY_DATASOURCE
```
public static final String FILTER_BY_DATASOURCE
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - BioPAXElementImpl
```
public BioPAXElementImpl()
```
- Method Detail
  - getPk
```
public String getPk()
```
    Gets Primary Key. This method may be useful within a persistence context (Hibernate). This is not part of Paxtools standard BioPAX API, it is implementation detail. Normally, one should always use getRDFId() to get BioPAX element's URI and use it in data analysis.
    
    Returns:
    
    primary key (for persistence)
  - isEquivalent
```
public boolean isEquivalent(BioPAXElement element)
```
    Description copied from interface: BioPAXElement
    This method compares the given element for equivalency. This is different from equals(), as BioPAX elements resolve equality based on RDF ID. Equivalent returns true if elements are equal or if
    - both elements implement the same model interface AND
    - both elements have equivalent key properties
    These key properties vary from class to class.
    Specified by:
    
    isEquivalent in interface BioPAXElement
    
    Parameters:
    
    element - to be compared for equivalency
    
    Returns:
    
    true if the element equals to this, or has equivalent critical properties.
  - semanticallyEquivalent
```
protected boolean semanticallyEquivalent(BioPAXElement element)
```
  - equivalenceCode
```
public int equivalenceCode()
```
    Description copied from interface: BioPAXElement
    
    If two elements are equivalent, then their equivalence code should be the same.
    
    Specified by:
    
    equivalenceCode in interface BioPAXElement
    
    Returns:
    
    an integer that is same across all equivalent entities.
  - getRDFId
```
public String getRDFId()
```
    Description copied from interface: BioPAXElement
    
    This method returns the full URI of the element (despite it is called RDFId). BioPAX data providers are responsible for generating globally unique and standard URIs for their BioPAX elements.
    
    Specified by:
    
    getRDFId in interface BioPAXElement
    
    Returns:
    
    the unique URI for this object.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - getAnnotations
```
public Map<String,Object> getAnnotations()
```
    Description copied from interface: BioPAXElement
    
    A general-purpose map to optionally store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.
    
    Specified by:
    
    getAnnotations in interface BioPAXElement
    
    Returns:
    
    additional (not BioPAX standard) annotations
  - equals
```
public boolean equals(Object obj)
```
    true if and only if the other obj has the same biopax type (same BioPAXElement.getModelInterface(), not a subclass) and same URI. Other properties are not considered.
    
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    This method is consistent with the overridden equals(Object) method (biopax type and URI are what matters)
    
    Overrides:
    
    hashCode in class Object

Class BioPAXElementImpl

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

Field Detail

FIELD_AVAILABILITY

FIELD_COMMENT

FIELD_KEYWORD

FIELD_NAME

FIELD_TERM

FIELD_XREFDB

FIELD_XREFID

FIELD_ECNUMBER

FIELD_SEQUENCE

FIELD_ORGANISM

FIELD_DATASOURCE

FIELD_PATHWAY

FILTER_BY_ORGANISM

FILTER_BY_DATASOURCE

Constructor Detail

BioPAXElementImpl

Method Detail

getPk

isEquivalent

semanticallyEquivalent

equivalenceCode

getRDFId

toString

getAnnotations

equals

hashCode