edu.mssm.crover.representation
Class Spacer_Annotation

java.lang.Object
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  +--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.