public class ResidueGroup
extends java.lang.Object
This class provides an interface for comparing and combining them to refine self-Alignments into consistent MultipleAlignments of repeats.
Constructor and Description |
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ResidueGroup(java.util.Set<java.lang.Integer> component)
Create a ResidueGroup object from a maximally connected component.
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Modifier and Type | Method and Description |
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void |
combineWith(java.util.List<java.util.List<java.lang.Integer>> alignRes)
Combine the ResidueGroup with the alignment block.
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boolean |
isCompatible(ResidueGroup other)
Determine if two Residuegroups (maximally connected components of the
alignment Graph) are compatible, based in the following criterion:
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int |
order()
The order of symmetry of the group is the number of connected residues.
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public ResidueGroup(java.util.Set<java.lang.Integer> component)
component
- set of residues connectedpublic int order()
public boolean isCompatible(ResidueGroup other)
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.
c2
- second maximally connected componentpublic void combineWith(java.util.List<java.util.List<java.lang.Integer>> alignRes)
alignRes
- the alignment block, will be modified.