ur_rna.StructureEditor.models

Class Strand

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<Nuc>

ur_rna.StructureEditor.models.Strand

All Implemented Interfaces:

java.lang.Iterable<Nuc>, java.util.Collection<Nuc>, java.util.List<Nuc>, INucGroup

public class Strand
extends java.util.AbstractList<Nuc>
implements INucGroup

A Strand represents a single RNA strand. An RNA drawing could potentially contain multiple strands, and the strands can each contain inter-molecular connections (e.g. base pairs) to other strands.

Field Summary

Fields

Modifier and Type	Field and Description
(package private) int	index
(package private) int	offset
protected StrandList	owner
private RnaScene	scene
(package private) int	size
protected java.util.List<Nuc>	source

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor and Description
Strand(RnaScene scene, StrandList owner, int index, java.util.List<Nuc> nucs, int offset, int size)

Method Summary

Modifier and Type	Method and Description
Nuc	add()
void	add(int index, Nuc element)
Nuc	add(java.lang.String symbol)
java.util.List<Nuc>	addAll(java.lang.CharSequence sequence)
boolean	addAll(java.util.Collection<? extends Nuc> c)
java.util.List<Nuc>	addAll(int index, java.lang.CharSequence sequence)
boolean	addAll(int index, java.util.Collection<? extends Nuc> c)
java.util.List<Nuc>	addPlaceholders(int count)
java.util.List<Nuc>	addPlaceholders(int index, int count)
void	clear()
Nuc	first()
Nuc	get(int index)
java.util.Collection<Nuc>	getBases() Implements INucGroup.getBases()
(package private) int	getEnd() Get the scene index of the last nucleotide in this strand plus one.
int	getIndex() Get the index of this strand in the list of RnaScene strands.
Nuc	getNext(Nuc nuc)
Nuc	getNext(Nuc nuc, int steps)
Nuc	getNextInScene(Nuc nuc, int steps, boolean loopToBeginning) Returns the next nucleotide after the specified one, regardless of whether it is in this strand or another one.
Nuc	getPrev(Nuc nuc)
RnaScene	getScene()
int	getSceneEnd() Get the index (relative to all nucleotides in the scene) immediately AFTER last nucleotide in this Strand
int	getSceneStart() Get the index (relative to all nucleotides in the scene) of the first nucleotide in this Strand
java.util.Iterator<Nuc>	iterator() Returns an iterator over all Nucletotides in the group.
Nuc	last()
java.util.ListIterator<Nuc>	listIterator(int startIndex)
protected java.lang.String	outOfBoundsMsg(int index)
protected void	rangeCheck(int index)
protected void	rangeCheckForAdd(int index)
Nuc	remove(int index)
boolean	removeAll(java.util.Collection<?> c)
boolean	retainAll(java.util.Collection<?> c)
int	sceneToStrandIndex(int nucIndexInScene)
Nuc	set(int index, Nuc element)
(package private) void	setEnd(int end)
int	size()
int	strandToSceneIndex(int nucIndexInStrand)
private java.lang.UnsupportedOperationException	unsupported()

Methods inherited from class java.util.AbstractList

add, equals, hashCode, indexOf, lastIndexOf, listIterator, removeRange, subList

Methods inherited from class java.util.AbstractCollection

contains, containsAll, isEmpty, remove, toArray, toArray, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ur_rna.StructureEditor.models.INucGroup

transformAll

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface java.util.List

contains, containsAll, isEmpty, remove, replaceAll, sort, spliterator, toArray, toArray

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Field Detail

index

int index

offset

int offset

owner

protected final StrandList owner

scene

private RnaScene scene

size

int size

source

protected final java.util.List<Nuc> source

Constructor Detail

Strand

Strand(RnaScene scene,
       StrandList owner,
       int index,
       java.util.List<Nuc> nucs,
       int offset,
       int size)

Method Detail

add

public Nuc add()

add

public void add(int index,
                Nuc element)

Specified by:

add in interface java.util.List<Nuc>

Overrides:

add in class java.util.AbstractList<Nuc>

add

public Nuc add(java.lang.String symbol)

addAll

public java.util.List<Nuc> addAll(java.lang.CharSequence sequence)

addAll

public boolean addAll(java.util.Collection<? extends Nuc> c)

Specified by:

addAll in interface java.util.Collection<Nuc>

Specified by:

addAll in interface java.util.List<Nuc>

Overrides:

addAll in class java.util.AbstractCollection<Nuc>

addAll

public java.util.List<Nuc> addAll(int index,
                                  java.lang.CharSequence sequence)

addAll

public boolean addAll(int index,
                      java.util.Collection<? extends Nuc> c)

Specified by:

addAll in interface java.util.List<Nuc>

Overrides:

addAll in class java.util.AbstractList<Nuc>

addPlaceholders

public java.util.List<Nuc> addPlaceholders(int count)

addPlaceholders

public java.util.List<Nuc> addPlaceholders(int index,
                                           int count)

clear

public void clear()

Specified by:

clear in interface java.util.Collection<Nuc>

Specified by:

clear in interface java.util.List<Nuc>

Overrides:

clear in class java.util.AbstractList<Nuc>

first

public Nuc first()

get

public Nuc get(int index)

Specified by:

get in interface java.util.List<Nuc>

Specified by:

get in class java.util.AbstractList<Nuc>

getBases

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

Implements INucGroup.getBases()

Specified by:

getBases in interface INucGroup

Returns:

a Collection of nucleotides.

getEnd

int getEnd()

Get the scene index of the last nucleotide in this strand plus one. I.e. the index just beyond this strand: offset+size

getIndex

public int getIndex()

Get the index of this strand in the list of RnaScene strands.

getNext

public Nuc getNext(Nuc nuc)

getNext

public Nuc getNext(Nuc nuc,
                   int steps)

getNextInScene

public Nuc getNextInScene(Nuc nuc,
                          int steps,
                          boolean loopToBeginning)

Returns the next nucleotide after the specified one, regardless of whether it is in this strand or another one. If the resulting index is greater than the number of nucleotides, null will be returned, unless loopToBeginning is true, in which case the scene is considered to be a circuit and numbering continues at the beginning (i.e. the next Nuc after the last Nuc is the first Nuc etc).

getPrev

public Nuc getPrev(Nuc nuc)

getScene

public RnaScene getScene()

getSceneEnd

public int getSceneEnd()

Get the index (relative to all nucleotides in the scene) immediately AFTER last nucleotide in this Strand

getSceneStart

public int getSceneStart()

Get the index (relative to all nucleotides in the scene) of the first nucleotide in this Strand

iterator

public java.util.Iterator<Nuc> iterator()

Description copied from interface: INucGroup

Returns an iterator over all Nucletotides in the group.

Specified by:

iterator in interface java.lang.Iterable<Nuc>

Specified by:

iterator in interface java.util.Collection<Nuc>

Specified by:

iterator in interface java.util.List<Nuc>

Specified by:

iterator in interface INucGroup

Overrides:

iterator in class java.util.AbstractList<Nuc>

Returns:

an Iterator.

last

public Nuc last()

listIterator

public java.util.ListIterator<Nuc> listIterator(int startIndex)

Specified by:

listIterator in interface java.util.List<Nuc>

Overrides:

listIterator in class java.util.AbstractList<Nuc>

outOfBoundsMsg

protected java.lang.String outOfBoundsMsg(int index)

rangeCheck

protected void rangeCheck(int index)

rangeCheckForAdd

protected void rangeCheckForAdd(int index)

remove

public Nuc remove(int index)

Specified by:

remove in interface java.util.List<Nuc>

Overrides:

remove in class java.util.AbstractList<Nuc>

removeAll

public boolean removeAll(java.util.Collection<?> c)

Specified by:

removeAll in interface java.util.Collection<Nuc>

Specified by:

removeAll in interface java.util.List<Nuc>

Overrides:

removeAll in class java.util.AbstractCollection<Nuc>

retainAll

public boolean retainAll(java.util.Collection<?> c)

Specified by:

retainAll in interface java.util.Collection<Nuc>

Specified by:

retainAll in interface java.util.List<Nuc>

Overrides:

retainAll in class java.util.AbstractCollection<Nuc>

sceneToStrandIndex

public int sceneToStrandIndex(int nucIndexInScene)

set

public Nuc set(int index,
               Nuc element)

Specified by:

set in interface java.util.List<Nuc>

Overrides:

set in class java.util.AbstractList<Nuc>

setEnd

void setEnd(int end)

size

public int size()

Specified by:

size in interface java.util.Collection<Nuc>

Specified by:

size in interface java.util.List<Nuc>

Specified by:

size in class java.util.AbstractCollection<Nuc>

strandToSceneIndex

public int strandToSceneIndex(int nucIndexInStrand)

unsupported

private java.lang.UnsupportedOperationException unsupported()