org.biopax.paxtools.impl
Class BioPAXElementImpl

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

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, BioPAXElement

Direct Known Subclasses:

L3ElementImpl

@Entity
public abstract class BioPAXElementImpl
extends java.lang.Object
implements BioPAXElement

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

static java.lang.String	SEARCH_FIELD_AVAILABILITY
static java.lang.String	SEARCH_FIELD_COMMENT
static java.lang.String	SEARCH_FIELD_EC_NUMBER
static java.lang.String	SEARCH_FIELD_KEYWORD
static java.lang.String	SEARCH_FIELD_NAME
static java.lang.String	SEARCH_FIELD_SEQUENCE
static java.lang.String	SEARCH_FIELD_TERM
static java.lang.String	SEARCH_FIELD_XREF_DB
static java.lang.String	SEARCH_FIELD_XREF_ID
static java.lang.String	SEARCH_INDEX_NAME

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

BioPAXElementImpl()

BioPAXElementImpl(java.lang.String uri)

Method Summary

int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
java.util.Map<java.lang.String,java.lang.Object>	getAnnotations() A general-purpose map to optionallly store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.
java.lang.Long	getProxyId() Deprecated.
java.lang.String	getRDFId() This method returns the RDF Id of the element.
java.lang.Integer	getVersion()
boolean	isEquivalent(BioPAXElement element) This method compares the given element for equivalency.
protected boolean	semanticallyEquivalent(BioPAXElement element)
protected void	setProxyId(java.lang.Long value)
protected void	setRDFId(java.lang.String id)
protected void	setVersion(java.lang.Integer version)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

getModelInterface

Field Detail

SEARCH_FIELD_KEYWORD

public static final java.lang.String SEARCH_FIELD_KEYWORD

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Constant Field Values

SEARCH_FIELD_NAME

public static final java.lang.String SEARCH_FIELD_NAME

See Also:

Constant Field Values

SEARCH_FIELD_TERM

public static final java.lang.String SEARCH_FIELD_TERM

See Also:

Constant Field Values

SEARCH_FIELD_EC_NUMBER

public static final java.lang.String SEARCH_FIELD_EC_NUMBER

See Also:

Constant Field Values

SEARCH_FIELD_SEQUENCE

public static final java.lang.String SEARCH_FIELD_SEQUENCE

See Also:

Constant Field Values

SEARCH_FIELD_XREF_DB

public static final java.lang.String SEARCH_FIELD_XREF_DB

See Also:

Constant Field Values

SEARCH_FIELD_XREF_ID

public static final java.lang.String SEARCH_FIELD_XREF_ID

See Also:

Constant Field Values

SEARCH_FIELD_AVAILABILITY

public static final java.lang.String SEARCH_FIELD_AVAILABILITY

See Also:

Constant Field Values

SEARCH_FIELD_COMMENT

public static final java.lang.String SEARCH_FIELD_COMMENT

See Also:

Constant Field Values

SEARCH_INDEX_NAME

public static final java.lang.String SEARCH_INDEX_NAME

See Also:

Constant Field Values

Constructor Detail

BioPAXElementImpl

public BioPAXElementImpl()

BioPAXElementImpl

public BioPAXElementImpl(java.lang.String uri)

Method Detail

getProxyId

public java.lang.Long getProxyId()

Deprecated.

setProxyId

protected void setProxyId(java.lang.Long value)

getVersion

public java.lang.Integer getVersion()

setVersion

protected void setVersion(java.lang.Integer version)

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

@DocumentId
public java.lang.String getRDFId()

Description copied from interface: BioPAXElement

This method returns the RDF Id of the element. All data providers are responsible for generating unique ids.

Specified by:

getRDFId in interface BioPAXElement

Returns:

the unique rdf Id for this object.

setRDFId

protected void setRDFId(java.lang.String id)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getAnnotations

public java.util.Map<java.lang.String,java.lang.Object> getAnnotations()

Description copied from interface: BioPAXElement

A general-purpose map to optionallly store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.

Specified by:

getAnnotations in interface BioPAXElement

Returns: