ur_rna.StructureEditor.models

Class Motif.Branch

java.lang.Object

ur_rna.StructureEditor.models.Motif.Branch

All Implemented Interfaces:

java.lang.Iterable<Nuc>, IMotif, INucGroup

Enclosing class:

Motif

public static class Motif.Branch
extends java.lang.Object
implements IMotif

Represents a complete helix (the "base" of the Branch) along with all helix and loop regions on one side of it. A more precise definition depends on whether or not the base helix is uni-molecular or bi-molecular (i.e. composed of one or two strands). For a uni-molecular base helix, the corresponding Branch is the same as the Domain defined by the 5'-most nucleotide in the base helix. (This differs from a Domain in general because a Domain need not include all nucleotides in a helix, while a Branch by definition does.) Specifically, a uni-molecular Branch with base helix 'H' is the union of getDomain(nuc) with getHelix(nuc) for any nucleotide 'nuc' in 'H'. For a bimolecular base helix the definition becomes more complicated, and the choice of which side of the helix to include becomes arbitrary, leading to two possible branches, both with the same base: 'N5' 'N3' |'H'| S1 5'.....GCAUG.....3' S2 (left).....CGUAC.....(right) Note: S2 can be aligned parallel or anti-parallel to S1 | | so "left" can be 5' for parallel or 3' for anti-parallel. 'N5P' 'N3P' B1 ---------> B2 <--------- Let 'H' be the base helix, 'S1' the strand with the lower index, and 'S2' the other strand. Let 'N5' be the 5'-most nucleotide on S1 that is in H and 'N3' the 3'-most nucleotide on 'S1' that is in 'H'. Let 'N5P' be the nucleotide paired with N5 and N3P the one paired with N3. Note that N5P and N3P are both on S2, but the alignment of S1 with respect to S1 could be anti-parallel (which places N3P closer to the 5' end of S2 than N5P) or parallel (in which case N5P is on 5' side of N3P). The two possible branches based at H are: B1: All nucleotides in H and all nucleotides on the 3' side of N3 on S1 and to the right* of N3P on S2. B2: All nucleotides in H and all nucleotides on the 5' side of N5 on S1 and to the left* of N5P on S2. * The terms "right" and "left" depend on the alignment of S2 with respect to S1: For S2-parallel: "right" means the 3' side whereas "left" means the 5' side. For S2-anti-parallel: the above definitions are reversed -- "right" means 5' and "left" means 3'.

Field Summary

Fields

Modifier and Type	Field and Description
private Motif.Helix	base
private boolean	isLowerBranch

Constructor Summary

Constructors

Constructor and Description
Branch()
Branch(Motif.Helix base, boolean isLowerBranch)
Branch(Nuc n) Creates a unimolecular branch that extends from the specified nucleotide to its pair.

Method Summary

Modifier and Type	Method and Description
Motif.Helix	getBaseHelix()
java.util.Collection<Nuc>	getBases() Get a set of all nucleotides included in the group.
static Motif.Branch	getBranch(Nuc nuc) Return the smallest branch that contains nuc or null if nuc is not contained in any branch (e.g.
boolean	isHybrid()
boolean	isParallel()
void	validate()

Methods inherited from class java.lang.Object

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

Methods inherited from interface ur_rna.StructureEditor.models.INucGroup

iterator, transformAll

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

base

private Motif.Helix base

isLowerBranch

private boolean isLowerBranch

Constructor Detail

Branch

public Branch()

Branch

public Branch(Motif.Helix base,
              boolean isLowerBranch)

Branch

public Branch(Nuc n)

Creates a unimolecular branch that extends from the specified nucleotide to its pair.

Parameters:

n - A nucleotide in the base helix of a unimolecular branch.

Method Detail

getBaseHelix

public Motif.Helix getBaseHelix()

getBases

public java.util.Collection<Nuc> getBases()

Get a set of all nucleotides included in the group.

Specified by:

getBases in interface INucGroup

Returns:

a Collection of nucleotides.

getBranch

public static Motif.Branch getBranch(Nuc nuc)

Return the smallest branch that contains nuc or null if nuc is not contained in any branch (e.g. if it is in a terminal loop or part of a multibranch loop segment.)

Parameters:

nuc -

isHybrid

public boolean isHybrid()

isParallel

public boolean isParallel()

validate

public void validate()