org.biojava.nbio.structure.symmetry.internal

Class ResidueGroup

java.lang.Object

org.biojava.nbio.structure.symmetry.internal.ResidueGroup

public class ResidueGroup
extends Object

A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.

This class provides an interface for comparing and combining them to refine self-Alignments into consistent MultipleAlignments of repeats.

Since:

4.2.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
ResidueGroup(Set<Integer> component) Create a ResidueGroup object from a maximally connected component.

Method Summary

Modifier and Type	Method and Description
void	combineWith(List<List<Integer>> alignRes) Combine the ResidueGroup with the alignment block.
boolean	isCompatible(ResidueGroup other) Determine if two Residuegroups (maximally connected components of the alignment Graph) are compatible, based in the following criterion: Two maximally connected components of the self-alignment Graph are compatible if they can be combined in a consistent multiple alignment of repeats, i.e.there exists one residue in c1 between each sorted pair of residues in c2.
int	order() The order of symmetry of the group is the number of connected residues.

Methods inherited from class java.lang.Object

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

Constructor Detail

ResidueGroup

public ResidueGroup(Set<Integer> component)

Create a ResidueGroup object from a maximally connected component.

Parameters:

component - set of residues connected

Method Detail

order

public int order()

The order of symmetry of the group is the number of connected residues.

Returns:

size of residues List

isCompatible

public boolean isCompatible(ResidueGroup other)

Determine if two Residuegroups (maximally connected components of the alignment Graph) are compatible, based in the following criterion:

 Two maximally connected components of the self-alignment Graph are
 compatible if they can be combined in a consistent multiple alignment
 of repeats, i.e.there exists one residue in c1 between each sorted
 pair of residues in c2.
 

Compatibility is an intransitive relation, which means that for three ResidueGroups {A,B,C}, if A is compatible with B and B is compatible with C, then A is not necessarily compatible with C.

Parameters:

c2 - second maximally connected component

Returns:

true if compatible, false otherwise

combineWith

public void combineWith(List<List<Integer>> alignRes)

Combine the ResidueGroup with the alignment block.

Parameters:

alignRes - the alignment block, will be modified.