ur_rna.StructureEditor.models

Class Motif.Loop

java.lang.Object

ur_rna.StructureEditor.models.Motif.Segment

ur_rna.StructureEditor.models.Motif.Loop

All Implemented Interfaces:

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

Enclosing class:

Motif

public static class Motif.Loop
extends Motif.Segment
implements IMotif

A Loop represents a series of adjacent unpaired nucleotides. Loops can be categorized as follows:

Hairpin

A single-stranded region that connects one side of a helix to the other without any intervening helices. e.g.: A:B-C-D-E-F-(A) (Notation: X:Y represents a base-pair; X-Y represents a 3'-to-5' covalent bond between nucleotides X and Y. (A) means the same "A" nucleotide that appeared earlier in the sequence.)

Internal Loop

A single-stranded region that connects one side of a helix to the same side of another helix. (Same side means without any intervening helices. e.g.: A:B-C-D-E-F-G:H-[I-J-...]-(A) --There can be no intervening helices between H and A

Multibranch Loop

A series of single-stranded regions that connect multiple helices together. e.g.: A:B-C-D-E-F-G:H-I-J-K:L-M-N-(A)

Terminal Loop

A single-stranded regions that is only connected to a helix on one side. e.g.: A-B-C-D-E-F-G:H

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Motif.Loop.LoopType

Field Summary

Fields

Modifier and Type	Field and Description
private Motif.Loop.LoopType	type

Fields inherited from class ur_rna.StructureEditor.models.Motif.Segment

end, start

Constructor Summary

Constructors

Constructor and Description
Loop()
Loop(Nuc start, Nuc end)
Loop(Nuc start, Nuc end, Motif.Loop.LoopType type)

Method Summary

Modifier and Type	Method and Description
private static Motif.Loop.LoopType	calcLoopType(Motif.Loop l)
static java.util.List<Motif.Loop>	findAll(RnaScene scene) Find all distinct single-stranded regions in specified list of strands.
static Motif.Loop	getLoop(Nuc nuc) Return the single-stranded region (loop) that contains the given nuc or null if nuc is not in a loop (i.e.
static java.util.List<Bond>	getMultiBranchBasePairs(Nuc n)
static java.util.List<Bond>	getMultiBranchBasePairs(Nuc n, boolean includeExteriorLoop)
static java.util.List<Bond>	getMultiBranchBasePairs(Nuc n, boolean includeExteriorLoop, Bond.MultiLoopRole basePairRole) Retrieve a list of all bonds that are part of a multi-branch loop.
Motif.Loop.LoopType	getType()
java.lang.String	toString()

Methods inherited from class ur_rna.StructureEditor.models.Motif.Segment

getBases, getNuc3, getNuc5, getNucAt, orderNucs, size, swapNucs

Methods inherited from class java.lang.Object

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

Methods inherited from interface ur_rna.StructureEditor.models.INucGroup

getBases, iterator, transformAll

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

type

private Motif.Loop.LoopType type

Constructor Detail

Loop

public Loop()

Loop

public Loop(Nuc start,
            Nuc end)

Loop

public Loop(Nuc start,
            Nuc end,
            Motif.Loop.LoopType type)

Method Detail

calcLoopType

private static Motif.Loop.LoopType calcLoopType(Motif.Loop l)

findAll

public static java.util.List<Motif.Loop> findAll(RnaScene scene)

Find all distinct single-stranded regions in specified list of strands.

Returns:

a list of single-stranded regions (aka loops).

getLoop

public static Motif.Loop getLoop(Nuc nuc)

Return the single-stranded region (loop) that contains the given nuc or null if nuc is not in a loop (i.e. it paired)

getMultiBranchBasePairs

public static java.util.List<Bond> getMultiBranchBasePairs(Nuc n)

getMultiBranchBasePairs

public static java.util.List<Bond> getMultiBranchBasePairs(Nuc n,
                                                           boolean includeExteriorLoop)

getMultiBranchBasePairs

public static java.util.List<Bond> getMultiBranchBasePairs(Nuc n,
                                                           boolean includeExteriorLoop,
                                                           Bond.MultiLoopRole basePairRole)

Retrieve a list of all bonds that are part of a multi-branch loop. (i.e. the bases of all helices that extend from the multi-branch loop. The list is built by starting with n and traversing the strand in a forward direction, jumping across base-pairs until either n is reached again or the strand terminates. If the strand terminates before n is reached, the n nucleotide was NOT in a multi-branch loop, and NULL is returned.

Parameters:

n - Any nucleotide in the multi-branch loop. Note that if n is paired, it is technically possible for it to be simultaneously in two adjacent multi-branch loops (assuming it belongs to a "helix" containing only a single base-pair). For this reason, it is better to pass an unpaired nucleotide in for n, to avoid any ambiguity.

includeExteriorLoop - if false, null is returned if the given nucleotide is part of an exterior loop. Otherwise all the branches starting at or after n will be included in the returned list (but those BEFORE n will not be.)

basePairRole - Only applies when n is paired and the bases in either direction are unpaired (or paired to bases in different helices than n). (i.e. n is in a helix comprised of a single pair). This parameter imfluences how the basepair is interpreted -- as an exit or entrance pair.

Returns:

a list of bonds (if nStart was in fact in a multi-branch loop) or null otherwise.

getType

public Motif.Loop.LoopType getType()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object