edu.mssm.crover.domain2d
Class Domain2D_ABuilder

java.lang.Object
  |
  +--edu.mssm.crover.domain2d.Domain2D_ABuilder

public class Domain2D_ABuilder

extends java.lang.Object

Builds a Domain2D_Annotation from a Domain_Annotation. This class is responsible for chopping the sequence into domains that Domain2D_Annotation recognizes and associating appropriate rendering engines with them. Domain2D_ABuilder: the A stands for Annotation. The default layout is for membrane proteins.

Nested Class Summary

class

Domain2D_ABuilder.UnsupportedSubunitType

Constructor Summary

Domain2D_ABuilder()

Method Summary

Domain2D_Annotation	build(BiologicalSequence seq, SecondaryStructure_Annotation ssa) Builds a Domain2D_Annotation for the sequence seq.
static TM_Annotation	findTM(BiologicalAnnotations ba, int index) Returns the TM_Annotation that containts index residue.
static void	main(java.lang.String[] args) Performs various tests of this class behaviour.
void	otherAnnotations(BiologicalAnnotations anns) Passes the builder other annotations that may be used to adjust the spacers.
protected boolean	sameTM(int start, int end) Returns true when the start and end residue are part of the same TM domain annotation.
void	setNtermDirection(java.awt.geom.Point2D start) Sets the exitDirection of the Nterm domain.

Methods inherited from class java.lang.Object

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

Constructor Detail

Domain2D_ABuilder

public Domain2D_ABuilder()

Method Detail

otherAnnotations

public void otherAnnotations(BiologicalAnnotations anns)

Passes the builder other annotations that may be used to adjust the spacers. These annotations include TM_Annotations that describe a range of residue to be considered together in a row without breaking the flow of the subunits in their middle.

build

public Domain2D_Annotation build(BiologicalSequence seq,
                                 SecondaryStructure_Annotation ssa)
                          throws Domain2D_ABuilder.UnsupportedSubunitType

Builds a Domain2D_Annotation for the sequence seq. Uses the SecondaryStructure_Annotation ssa for that purpose:

adds an ExtremityDomain that range from the first residue of the sequence to the first residue of the first subunit described in the Domain_Annotation.

adds a helix, or beta strand for each subunit of this kind found in the Domain_Annotation.

follow by a loop or an ExtremityDomain and repeat from the previous step, until the end of the sequence is reached.

Domain2D_ABuilder.UnsupportedSubunitType

sameTM

protected boolean sameTM(int start,
                         int end)

Returns true when the start and end residue are part of the same TM domain annotation. Returns false otherwise or when no annotations are available for the sequence (no call to otherAnnotations has been made).

setNtermDirection

public void setNtermDirection(java.awt.geom.Point2D start)

Sets the exitDirection of the Nterm domain. Allows to control if the Nterm appear intra-cellular or extracellular. (0,1) will make it extracellular, (0,-1) intracellular. Other values can result in funny layouts...

findTM

public static TM_Annotation findTM(BiologicalAnnotations ba,
                                   int index)

Returns the TM_Annotation that containts index residue.

Returns:

null if not found or the TM_Annotation

main

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

Performs various tests of this class behaviour.