edu.mssm.crover.representation
Class Domain_Annotation

java.lang.Object
  |
  +--edu.mssm.crover.representation.Annotation
        |
        +--edu.mssm.crover.representation.Domain_Annotation

All Implemented Interfaces:

BiologicalAnnotation, RootObject, java.io.Serializable

Direct Known Subclasses:

TM_Annotation

public class Domain_Annotation

extends Annotation

implements java.io.Serializable

Annotates protein domains. A domain made of several part of a sequence which are not contiguous in sequence is represented by several domain annotations attached to the sequence.

Author:

Fabien Campagne

See Also:

Serialized Form

Field Summary

protected java.lang.Integer	end
protected java.lang.Integer	start

Fields inherited from class edu.mssm.crover.representation.Annotation

origin

Constructor Summary

Domain_Annotation(BiologicalOrigin origin, java.lang.String type_of)
Constructs a domain annotation of a given type, with a specific origin.

Domain_Annotation(java.lang.String type_of)
Constructs a domain annotation of a given type, with an unspecified origin.

Method Summary

boolean	describesResidue(int position) Is this position part of this domain ?
java.lang.Integer	getEndResidue() Get the end residue of the domain described by this annotation.
java.lang.String	getInfo() This annotation describes a protein domain ("domain").
java.lang.Integer	getStartResidue() Get the first residue of the domain described by this annotation.
java.lang.String	getTypeOf() Get the type of this domain as a descriptive text.
void	setEndResidue(java.lang.Integer res) Get the end residue of the domain described by this annotation.
void	setStartResidue(java.lang.Integer res) Set the first residue of the domain described by this annotation.
java.lang.String	toString()

Methods inherited from class edu.mssm.crover.representation.Annotation

getOrigin, setOrigin

Methods inherited from class java.lang.Object

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

Field Detail

start

protected java.lang.Integer start

end

protected java.lang.Integer end

Constructor Detail

Domain_Annotation

public Domain_Annotation(java.lang.String type_of)

Constructs a domain annotation of a given type, with an unspecified origin. (It is not know where this domain information comes from.)

Domain_Annotation

public Domain_Annotation(BiologicalOrigin origin,
                         java.lang.String type_of)

Constructs a domain annotation of a given type, with a specific origin.

Method Detail

getTypeOf

public java.lang.String getTypeOf()

Get the type of this domain as a descriptive text.

getInfo

public java.lang.String getInfo()

This annotation describes a protein domain ("domain").

Specified by:

getInfo in interface BiologicalAnnotation

Specified by:

getInfo in class Annotation

getStartResidue

public java.lang.Integer getStartResidue()

Get the first residue of the domain described by this annotation.

setStartResidue

public void setStartResidue(java.lang.Integer res)

Set the first residue of the domain described by this annotation.

getEndResidue

public java.lang.Integer getEndResidue()

Get the end residue of the domain described by this annotation.

setEndResidue

public void setEndResidue(java.lang.Integer res)

Get the end residue of the domain described by this annotation.

toString

public java.lang.String toString()

Overrides:

toString in class Annotation

describesResidue

public boolean describesResidue(int position)

Is this position part of this domain ?

Specified by:

describesResidue in interface BiologicalAnnotation

Returns:

True when the position is such that position>=start and position <=end.