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.


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.