ur_rna.StructureEditor.models

Class Motif

java.lang.Object

ur_rna.StructureEditor.models.Motif

public abstract class Motif
extends java.lang.Object

Represents a structural element (motif) of an RNA structure -- e.g. a base, pair, bulge, loop, helix, hairpin, domain, etc.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Motif.Branch Represents a complete helix (the "base" of the Branch) along with all helix and loop regions on one side of it.
static class	Motif.Domain Represents a segment of an RNA strand that extends from a nucleotide to its pair.
static class	Motif.Helix A helix represents a series of adjacent nucleotides which are all paired to a another series of adjacent nucleotides on the same RNA strand or a different RNA strand.
private static class	Motif.IntervalStack
static class	Motif.Loop A Loop represents a series of adjacent unpaired nucleotides.
static class	Motif.MultiLoop
static class	Motif.Segment Represents a contiguous section of an RNA strand.

Constructor Summary

Constructors

Constructor and Description
Motif()

Method Summary

Modifier and Type	Method and Description
static java.util.Set<Bond>	findNonCrossingBonds(java.util.Collection<Bond> bonds)
static java.util.Set<Bond>	findNonCrossingBonds(java.util.Collection<Bond> bonds, java.util.Collection<Bond> crossing)
static java.util.Set<Bond>	findNonCrossingBonds(RnaScene scene)
static java.util.Set<Bond>	findPseudoKnots(RnaScene scene)
static boolean	hasPseudoKnots(RnaScene scene, boolean ignoreMarkedPseudoBonds)

Methods inherited from class java.lang.Object

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

Constructor Detail

Motif

public Motif()

Method Detail

findNonCrossingBonds

public static java.util.Set<Bond> findNonCrossingBonds(java.util.Collection<Bond> bonds)

findNonCrossingBonds

public static java.util.Set<Bond> findNonCrossingBonds(java.util.Collection<Bond> bonds,
                                                       java.util.Collection<Bond> crossing)

findNonCrossingBonds

public static java.util.Set<Bond> findNonCrossingBonds(RnaScene scene)

findPseudoKnots

public static java.util.Set<Bond> findPseudoKnots(RnaScene scene)

hasPseudoKnots

public static boolean hasPseudoKnots(RnaScene scene,
                                     boolean ignoreMarkedPseudoBonds)