Package org.biopax.paxtools.impl.level3

Class BindingFeatureImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.EntityFeatureImpl

org.biopax.paxtools.impl.level3.BindingFeatureImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, BindingFeature, EntityFeature, Level3Element, Observable, UtilityClass

Direct Known Subclasses:

CovalentBindingFeatureImpl

public class BindingFeatureImpl
extends EntityFeatureImpl
implements BindingFeature

See Also:

• Serialized Form

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor	Description
BindingFeatureImpl()

Method Summary

Modifier and Type	Method	Description
int	equivalenceCode()	If two elements are equivalent, then their equivalence code should be the same.
BindingFeature	getBindsTo()	A binding feature represents a "half" of the bond between two entities.
Boolean	getIntraMolecular()	IntraMolecular flag is true iff this binding feature represents a bond within the same molecule, for example a disulfide bond within the same molecule.
Class<? extends BindingFeature>	getModelInterface()	This method returns the actual model interface that a class implements.
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setBindsTo(BindingFeature bindsTo)	This method will set the paired binding feature that binds to this feature.
void	setIntraMolecular(Boolean intramolecular)	IntraMolecular flag is true iff this binding feature represents a bond within the same molecule, for example a disulfide bond within the same molecule.

Methods inherited from class org.biopax.paxtools.impl.level3.EntityFeatureImpl

addEvidence, addMemberFeature, atEquivalentLocation, getEntityFeatureOf, getEvidence, getFeatureLocation, getFeatureLocationType, getFeatureOf, getMemberFeature, getMemberFeatureOf, getNotFeatureOf, locationCode, removeEvidence, removeMemberFeature, setEntityFeatureOf, setFeatureLocation, setFeatureLocationType

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, getAnnotations, getUri, hashCode, isEquivalent, 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

getAnnotations, getUri, isEquivalent

Methods inherited from interface org.biopax.paxtools.model.level3.EntityFeature

addMemberFeature, atEquivalentLocation, getEntityFeatureOf, getFeatureLocation, getFeatureLocationType, getFeatureOf, getMemberFeature, getMemberFeatureOf, getNotFeatureOf, removeMemberFeature, setFeatureLocation, setFeatureLocationType

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Constructor Details

BindingFeatureImpl

public BindingFeatureImpl()

Method Details

getModelInterface

public Class<? extends BindingFeature> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Overrides:

getModelInterface in class EntityFeatureImpl

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getBindsTo

public BindingFeature getBindsTo()

Description copied from interface: BindingFeature

A binding feature represents a "half" of the bond between two entities. This property points to another binding feature which represents the other half. The bond can be covalent or non-covalent.

Specified by:

getBindsTo in interface BindingFeature

Returns:

paired binding feature.

setBindsTo

public void setBindsTo(BindingFeature bindsTo)

This method will set the paired binding feature that binds to this feature. This method will preserve the symmetric bidirectional semantics. If not-null old feature's bindsTo will be set to null and if not null new feature's binds to will set to this

Specified by:

setBindsTo in interface BindingFeature

Parameters:

bindsTo - paired binding feature.

getIntraMolecular

public Boolean getIntraMolecular()

Description copied from interface: BindingFeature

IntraMolecular flag is true iff this binding feature represents a bond within the same molecule, for example a disulfide bond within the same molecule. A true value true implies that this.isEntityFeatureOf() == this.getBindsTo.isEntityFeatureOf() although the inverse is not true e.g a chain of actin proteins.

Specified by:

getIntraMolecular in interface BindingFeature

Returns:

true iff this binding feature represents a bond within the same molecule.

setIntraMolecular

public void setIntraMolecular(Boolean intramolecular)

Description copied from interface: BindingFeature

IntraMolecular flag is true iff this binding feature represents a bond within the same molecule, for example a disulfide bond within the same molecule. A true value implies that this.isEntityFeatureOf() == this.getBindsTo.isEntityFeatureOf() although the inverse is not true e.g a chain of actin proteins.

Specified by:

setIntraMolecular in interface BindingFeature

Parameters:

intramolecular - whether if this binding feature represents a bond within the same molecule.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class EntityFeatureImpl

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

Overrides:

equivalenceCode in class EntityFeatureImpl

Returns:

an integer that is same across all equivalent entities.