ur_rna.StructureEditor.models

Class Motif.MultiLoop

java.lang.Object

ur_rna.StructureEditor.models.Motif.MultiLoop

All Implemented Interfaces:

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

Enclosing class:

Motif

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

Field Summary

Fields

Modifier and Type	Field and Description
private Bond[]	branchBonds
java.util.List<java.lang.Object>	elements
private int	loopNucs
private Motif.Loop[]	loops

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	MultiLoop()
	MultiLoop(java.util.List<Bond> bonds, boolean preSorted)
	MultiLoop(Nuc loopNuc)

Method Summary

Modifier and Type	Method and Description
int	countLoops()
protected static void	findAll(java.util.List<Motif.MultiLoop> list, Bond trunkBond, int minimumBranches)
static java.util.List<Motif.MultiLoop>	findAll(RnaScene scene, int minimumBranches, boolean includeExteriorLoop)
java.util.Collection<Nuc>	getBases() Get a set of all nucleotides included in the group.
java.util.List<Bond>	getBonds()
static Motif.MultiLoop	getFor(Nuc nuc, int minimumBranches, boolean includeExterior)
java.util.List<Motif.Loop>	getLoops()
Nuc	getN3() Get the "ending" base -- i.e.
Nuc	getN5() Get the "starting" base -- i.e.
Bond	getTrunk()
int	helixCount()
protected void	init(java.util.List<Bond> bonds, boolean preSorted)
int	loopNucCount()
int	nucCount()
java.lang.String	toString()

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

iterator, transformAll

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

branchBonds

private Bond[] branchBonds

elements

public final java.util.List<java.lang.Object> elements

loopNucs

private int loopNucs

loops

private Motif.Loop[] loops

Constructor Detail

MultiLoop

protected MultiLoop()

MultiLoop

public MultiLoop(java.util.List<Bond> bonds,
                 boolean preSorted)

MultiLoop

public MultiLoop(Nuc loopNuc)

Method Detail

countLoops

public int countLoops()

findAll

protected static void findAll(java.util.List<Motif.MultiLoop> list,
                              Bond trunkBond,
                              int minimumBranches)

findAll

public static java.util.List<Motif.MultiLoop> findAll(RnaScene scene,
                                                      int minimumBranches,
                                                      boolean includeExteriorLoop)

getBases

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

Description copied from interface: INucGroup

Get a set of all nucleotides included in the group.

Specified by:

getBases in interface INucGroup

Returns:

a Collection of nucleotides.

getBonds

public java.util.List<Bond> getBonds()

getFor

public static Motif.MultiLoop getFor(Nuc nuc,
                                     int minimumBranches,
                                     boolean includeExterior)

getLoops

public java.util.List<Motif.Loop> getLoops()

getN3

public Nuc getN3()

Get the "ending" base -- i.e. the 3'-most base (the base with the highest scene-index)

getN5

public Nuc getN5()

Get the "starting" base -- i.e. the 5'-most base (the base with the lowest scene-index)

getTrunk

public Bond getTrunk()

helixCount

public int helixCount()

init

protected void init(java.util.List<Bond> bonds,
                    boolean preSorted)

loopNucCount

public int loopNucCount()

nucCount

public int nucCount()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object