edu.mssm.crover.domain2d
Class Domain2D_Annotation

java.lang.Object
  |
  +--edu.mssm.crover.representation.Annotation
        |
        +--edu.mssm.crover.domain2d.Domain2D_Annotation

All Implemented Interfaces:

BiologicalAnnotation, RootObject, java.io.Serializable

public class Domain2D_Annotation

extends Annotation

implements java.io.Serializable

This annotation describes the information needed for the rendering of a two dimensional protein diagram. Basically, this information is made of two parts.

The layout information describes the relative positions and orientations of the subunits on the page.

The rendering information encodes the choice for the rendering algorithm to be used for each subunit individually.

See Also:

Serialized Form

Nested Class Summary

class	Domain2D_Annotation.BadDomain2DRenderingClass
class	Domain2D_Annotation.BadLoopTemplateClass
class	Domain2D_Annotation.LayoutInfo Encapsultates the layout for one subunit (a Domain2D)
class	Domain2D_Annotation.RenderingInfo Encapsultates the rendering algorithm choice for one subunit (a Domain2D)

Field Summary

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

origin

Constructor Summary

Domain2D_Annotation()

Method Summary

void	addCterm(int start, int end) Convenience method to add a Cterminus representation to this diagram.
void	addHelix(int start, int end) Adds an helix representation to this diagram.
void	addHelix(int start, int end, java.awt.Point direction) Convenience method to add an helix representation to this diagram.
void	addLoop(int start, int end, java.awt.Point spacer) Convenience method to add a loop representation to this diagram.
void	addNterm(int start, int end) Convenience method to add an Nterminus representation to this diagram.
void	addStrand(int start, int end) Adds a strand representation to this diagram.
void	addStrand(int start, int end, java.awt.Point direction) Convenience method to add a strand representation to this diagram.
void	addSubunit(Domain2D_Annotation.LayoutInfo _li, Domain2D_Annotation.RenderingInfo _ri) Adds a subunit to this Diagram model.
boolean	describesResidue(int position) This annotation does not describe independant residues.
java.lang.String	getInfo() Returns a consise text that describes the nature of this annotation.
Domain2D_Annotation.LayoutInfo	getLayoutInfo(int index)
Domain2D_Annotation.RenderingInfo	getRenderingInfo(int index)
java.lang.String	getShortName()
int	getSubunitNumber()
Domain2D_Annotation.LayoutInfo[]	layoutInfo()
static void	main(java.lang.String[] args)
void	modifySubunit(int index, Domain2D_Annotation.LayoutInfo li)
void	modifySubunit(int index, Domain2D_Annotation.RenderingInfo li)
void	removeSubunit(int index) the following methods are for extension purpose only.
Domain2D_Annotation.RenderingInfo[]	renderingInfo()
java.lang.String	toString() translate the model to a String for debugging purpose.

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

Constructor Detail

Domain2D_Annotation

public Domain2D_Annotation()

Method Detail

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

describesResidue

public boolean describesResidue(int position)

This annotation does not describe independant residues. returns false.

Specified by:

describesResidue in interface BiologicalAnnotation

getShortName

public java.lang.String getShortName()

getSubunitNumber

public int getSubunitNumber()

renderingInfo

public Domain2D_Annotation.RenderingInfo[] renderingInfo()

layoutInfo

public Domain2D_Annotation.LayoutInfo[] layoutInfo()

getLayoutInfo

public Domain2D_Annotation.LayoutInfo getLayoutInfo(int index)

getRenderingInfo

public Domain2D_Annotation.RenderingInfo getRenderingInfo(int index)

addSubunit

public void addSubunit(Domain2D_Annotation.LayoutInfo _li,
                       Domain2D_Annotation.RenderingInfo _ri)

Adds a subunit to this Diagram model. The subunit is added to the end of the sequence.

addNterm

public void addNterm(int start,
                     int end)

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(int start,
                     int end)

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.

addHelix

public void addHelix(int start,
                     int end,
                     java.awt.Point direction)

Convenience method to add an helix 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.HelicalDomain is not found, an error is generated. In this case, it is likely that there is an installation problem as the HelicalDomain must be in the same package as this class.

addHelix

public void addHelix(int start,
                     int end)

Adds an helix representation to this diagram.

See Also:

addStrand(int start, int end,Point direction)

addLoop

public void addLoop(int start,
                    int end,
                    java.awt.Point spacer)

Convenience method to add a loop 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.FreeLoop is not found, an error is generated. In this case, it is likely that there is an installation problem as the HelicalDomain must be in the same package as this class.

addStrand

public void addStrand(int start,
                      int end,
                      java.awt.Point direction)

Convenience method to add a strand 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.HelicalDomain is not found, an error is generated. In this case, it is likely that there is an installation problem as the HelicalDomain must be in the same package as this class.

addStrand

public void addStrand(int start,
                      int end)

Adds a strand representation to this diagram.

See Also:

#addStrand(int start, int end,Point2D direction)

removeSubunit

public void removeSubunit(int index)

the following methods are for extension purpose only.

modifySubunit

public void modifySubunit(int index,
                          Domain2D_Annotation.LayoutInfo li)

modifySubunit

public void modifySubunit(int index,
                          Domain2D_Annotation.RenderingInfo li)

toString

public java.lang.String toString()

translate the model to a String for debugging purpose.

Overrides:

toString in class Annotation

main

public static void main(java.lang.String[] args)