ur_rna.StructureEditor.models

Class Motif.Segment

java.lang.Object

ur_rna.StructureEditor.models.Motif.Segment

All Implemented Interfaces:

java.lang.Iterable<Nuc>, INucGroup

Direct Known Subclasses:

Motif.Domain, Motif.Loop

Enclosing class:

Motif

public static class Motif.Segment
extends java.lang.Object
implements INucGroup

Represents a contiguous section of an RNA strand. Note that in a Segment, the Nucs 'start' and 'end' are not necessarily in order (5' to 3' respectively) (However for derived types, such as a Loop or Branch, start is always the 5'-most Nuc and end is always the 3'-most Nuc.)

Field Summary

Fields

Modifier and Type	Field and Description
Nuc	end The end of the segment (the 3' side)
Nuc	start The start of the segment (the 5' side)

Constructor Summary

Constructors

Constructor and Description
Segment()
Segment(Nuc start, int length)
Segment(Nuc start, Nuc end)
Segment(Strand s, int start, int end)

Method Summary

Modifier and Type	Method and Description
java.util.Collection<Nuc>	getBases() Get a set of all nucleotides included in the group.
Nuc	getNuc3()
Nuc	getNuc5()
Nuc	getNucAt(int pos)
void	orderNucs()
int	size() Get the number of nucleotides in the loop.
void	swapNucs()

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

end

public Nuc end

The end of the segment (the 3' side)

start

public Nuc start

The start of the segment (the 5' side)

Constructor Detail

Segment

public Segment()

Segment

public Segment(Nuc start,
               int length)

Segment

public Segment(Nuc start,
               Nuc end)

Segment

public Segment(Strand s,
               int start,
               int end)

Method Detail

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.

getNuc3

public Nuc getNuc3()

getNuc5

public Nuc getNuc5()

getNucAt

public Nuc getNucAt(int pos)

orderNucs

public void orderNucs()

size

public int size()

Get the number of nucleotides in the loop.

swapNucs

public void swapNucs()