edu.mssm.crover.representation
Class Spacer_Annotation

java.lang.Object
  |
  +--edu.mssm.crover.representation.Annotation
        |
        +--edu.mssm.crover.representation.Spacer_Annotation
All Implemented Interfaces:
BiologicalAnnotation, RootObject, java.io.Serializable

public class Spacer_Annotation
extends Annotation

Annotates N and C term spacers for use in drawing RbDg diagrams.

Author:
luce
See Also:
Serialized Form

Field Summary
 
Fields inherited from class edu.mssm.crover.representation.Annotation
origin
 
Constructor Summary
Spacer_Annotation()
           
 
Method Summary
 void addCterm(Domain2D_Annotation d2da, int start, int end, int x_spacer, int y_spacer)
          Convenience method to add a Cterminus representation to this diagram.
 void addNterm(Domain2D_Annotation d2da, int start, int end, int x_spacer, int y_spacer)
          Convenience method to add an Nterminus representation to this diagram.
 boolean describesResidue(int position)
          Don't need this method for this class.
 int getCtermx()
           
 int getCtermy()
           
 java.lang.String getInfo()
          Returns a consise text that describes the nature of this annotation.
 int getNtermx()
           
 int getNtermy()
           
 void setCtermx(int x)
           
 void setCtermy(int y)
           
 void setNtermx(int x)
          Methods to get and set the Nterm and Cterm spacer variables.
 void setNtermy(int y)
           
 
Methods inherited from class edu.mssm.crover.representation.Annotation
getOrigin, setOrigin, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Spacer_Annotation

public Spacer_Annotation()
Method Detail

setNtermx

public void setNtermx(int x)
Methods to get and set the Nterm and Cterm spacer variables.


setNtermy

public void setNtermy(int y)

setCtermx

public void setCtermx(int x)

setCtermy

public void setCtermy(int y)

getNtermx

public int getNtermx()

getNtermy

public int getNtermy()

getCtermx

public int getCtermx()

getCtermy

public int getCtermy()

addNterm

public void addNterm(Domain2D_Annotation d2da,
                     int start,
                     int end,
                     int x_spacer,
                     int y_spacer)
Convenience method to add an Nterminus representation to this diagram.
Please note that this method, for convenience, does not raise any exception. In case of failure, for instance if the class domain2d.ExtremityDomain is not found, an error is generated. In this case, it is likely that there is an installation problem as the ExtremityDomain must be in the same package as this class.


addCterm

public void addCterm(Domain2D_Annotation d2da,
                     int start,
                     int end,
                     int x_spacer,
                     int y_spacer)
Convenience method to add a Cterminus representation to this diagram.
Please note that this method, for convenience, does not raise any exception. In case of failure, for instance if the class domain2d.ExtremityDomain is not found, an error is generated. In this case, it is likely that there is an installation problem as the ExtremityDomain must be in the same package as this class. The C terminus spacer is rotated by an angle. This angle is determined according to the exitDirection of the previous subunit (eD). This is consistent with the way Cterm determines its direction from its predecessor SSR exitDirection. When eD == (0,1) no rotation is applied to the spacer.


getInfo

public java.lang.String getInfo()
Description copied from interface: BiologicalAnnotation
Returns a consise text that describes the nature of this annotation. This text is constant over several instances of the same class.

Specified by:
getInfo in interface BiologicalAnnotation
Specified by:
getInfo in class Annotation
Returns:
"spacer".

describesResidue

public boolean describesResidue(int position)
Don't need this method for this class. Return a default of false.



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