ur_rna.StructureEditor.models

Class StrandList

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<Strand>

ur_rna.StructureEditor.models.StrandList

All Implemented Interfaces:

java.lang.Iterable<Strand>, java.util.Collection<Strand>, java.util.List<Strand>

public class StrandList
extends java.util.AbstractList<Strand>

A list of Strand that coordinates strand divisions etc to ensure the segmentation of nucleotides is consistent.

Field Summary

Fields

Modifier and Type	Field and Description
private int	lowestUpdateNucIndex
(package private) static int	NO_REINDEX
private java.util.List<Nuc>	nucs
(package private) java.util.List<Strand>	others
private java.util.List<Nuc>	readOnlyNucs
(package private) Strand	s1
(package private) Strand	s2
private RnaScene	scene
(package private) int	size
private int	suppressUpdateCounter

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor and Description
StrandList(RnaScene scene, java.util.List<Nuc> nucs)

Method Summary

Modifier and Type	Method and Description
Strand	add()
Strand	add(int insertAtIndex)
void	add(int index, Strand element) Deprecated.
boolean	add(Strand strand) Deprecated.
boolean	addAll(java.util.Collection<? extends Strand> c) Deprecated.
boolean	addAll(int index, java.util.Collection<? extends Strand> c) Deprecated.
java.util.List<Nuc>	allNucs() Returns a read-only list of all nucleotides.
void	clear() Deprecated.
boolean	contains(java.lang.Object o)
void	divideStrand(int strandIndex, int nucIndexInStrand) Divides one strand into two separate strands.
void	divideStrand(Strand strand, int nucIndexInStrand) Divides one strand into two separate strands.
Strand	first()
Strand	get(int index)
RnaScene	getScene()
int	indexOf(java.lang.Object o)
boolean	isEmpty()
void	joinStrands(Strand s1, Strand s2)
Strand	last()
int	lastIndexOf(java.lang.Object o)
private Strand	newStrand(int index)
private Strand	newStrand(int index, int offset, int size)
private java.lang.UnsupportedOperationException	noChangeError()
private java.util.List<Strand>	others()
private java.lang.String	outOfBoundsMsg(int index)
private void	rangeCheck(int index)
private void	reIndexNucs(int start)
Strand	remove(int index) Deprecated.
boolean	remove(java.lang.Object o) Deprecated.
boolean	removeAll(java.util.Collection<?> c) Deprecated.
Strand	removeDirect(int index)
void	resumeUpdate()
void	resumeUpdate(boolean performUpdate)
boolean	retainAll(java.util.Collection<?> c) Deprecated.
Strand	second()
Strand	set(int index, Strand element) Deprecated.
int	size()
void	suspendUpdate()
java.lang.Object[]	toArray()
void	updateStrands(int updateNucIndex)

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, removeRange, subList

Methods inherited from class java.util.AbstractCollection

containsAll, toArray, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.List

containsAll, replaceAll, sort, spliterator, toArray

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Field Detail

lowestUpdateNucIndex

private int lowestUpdateNucIndex

NO_REINDEX

static final int NO_REINDEX

See Also:

Constant Field Values

nucs

private java.util.List<Nuc> nucs

others

java.util.List<Strand> others

readOnlyNucs

private java.util.List<Nuc> readOnlyNucs

s1

Strand s1

s2

Strand s2

scene

private final RnaScene scene

size

int size

suppressUpdateCounter

private int suppressUpdateCounter

Constructor Detail

StrandList

public StrandList(RnaScene scene,
                  java.util.List<Nuc> nucs)

Method Detail

add

public Strand add()

add

public Strand add(int insertAtIndex)

add

@Deprecated
public void add(int index,
                             Strand element)

Deprecated.

Specified by:

add in interface java.util.List<Strand>

Overrides:

add in class java.util.AbstractList<Strand>

add

@Deprecated
public boolean add(Strand strand)

Deprecated.

Specified by:

add in interface java.util.Collection<Strand>

Specified by:

add in interface java.util.List<Strand>

Overrides:

add in class java.util.AbstractList<Strand>

addAll

@Deprecated
public boolean addAll(java.util.Collection<? extends Strand> c)

Deprecated.

Specified by:

addAll in interface java.util.Collection<Strand>

Specified by:

addAll in interface java.util.List<Strand>

Overrides:

addAll in class java.util.AbstractCollection<Strand>

addAll

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

Deprecated.

Specified by:

addAll in interface java.util.List<Strand>

Overrides:

addAll in class java.util.AbstractList<Strand>

allNucs

public java.util.List<Nuc> allNucs()

Returns a read-only list of all nucleotides.

clear

@Deprecated
public void clear()

Deprecated.

Specified by:

clear in interface java.util.Collection<Strand>

Specified by:

clear in interface java.util.List<Strand>

Overrides:

clear in class java.util.AbstractList<Strand>

contains

public boolean contains(java.lang.Object o)

Specified by:

contains in interface java.util.Collection<Strand>

Specified by:

contains in interface java.util.List<Strand>

Overrides:

contains in class java.util.AbstractCollection<Strand>

divideStrand

public void divideStrand(int strandIndex,
                         int nucIndexInStrand)

Divides one strand into two separate strands. The division occurs immediately before nucIndexInStrand, so after the division, the Nuc at nucIndexInStrand-1 will be the last Nuc in Strand, while the Nuc previously at nucIndexInStrand will be the first Nuc in the newly created subsequent strand.

divideStrand

public void divideStrand(Strand strand,
                         int nucIndexInStrand)

Divides one strand into two separate strands. The division occurs immediately before nucIndexInStrand, so after the division, the Nuc at nucIndexInStrand-1 will be the last Nuc in Strand, while the Nuc previously at nucIndexInStrand will be the first Nuc in the newly created subsequent strand.

first

public Strand first()

get

public Strand get(int index)

Specified by:

get in interface java.util.List<Strand>

Specified by:

get in class java.util.AbstractList<Strand>

getScene

public RnaScene getScene()

indexOf

public int indexOf(java.lang.Object o)

Specified by:

indexOf in interface java.util.List<Strand>

Overrides:

indexOf in class java.util.AbstractList<Strand>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface java.util.Collection<Strand>

Specified by:

isEmpty in interface java.util.List<Strand>

Overrides:

isEmpty in class java.util.AbstractCollection<Strand>

joinStrands

public void joinStrands(Strand s1,
                        Strand s2)

last

public Strand last()

lastIndexOf

public int lastIndexOf(java.lang.Object o)

Specified by:

lastIndexOf in interface java.util.List<Strand>

Overrides:

lastIndexOf in class java.util.AbstractList<Strand>

newStrand

private Strand newStrand(int index)

newStrand

private Strand newStrand(int index,
                         int offset,
                         int size)

noChangeError

private java.lang.UnsupportedOperationException noChangeError()

others

private java.util.List<Strand> others()

outOfBoundsMsg

private java.lang.String outOfBoundsMsg(int index)

rangeCheck

private void rangeCheck(int index)

reIndexNucs

private void reIndexNucs(int start)

remove

@Deprecated
public Strand remove(int index)

Deprecated.

Specified by:

remove in interface java.util.List<Strand>

Overrides:

remove in class java.util.AbstractList<Strand>

remove

@Deprecated
public boolean remove(java.lang.Object o)

Deprecated.

Specified by:

remove in interface java.util.Collection<Strand>

Specified by:

remove in interface java.util.List<Strand>

Overrides:

remove in class java.util.AbstractCollection<Strand>

removeAll

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

Deprecated.

Specified by:

removeAll in interface java.util.Collection<Strand>

Specified by:

removeAll in interface java.util.List<Strand>

Overrides:

removeAll in class java.util.AbstractCollection<Strand>

removeDirect

public Strand removeDirect(int index)

resumeUpdate

public void resumeUpdate()

resumeUpdate

public void resumeUpdate(boolean performUpdate)

retainAll

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

Deprecated.

Specified by:

retainAll in interface java.util.Collection<Strand>

Specified by:

retainAll in interface java.util.List<Strand>

Overrides:

retainAll in class java.util.AbstractCollection<Strand>

second

public Strand second()

set

@Deprecated
public Strand set(int index,
                               Strand element)

Deprecated.

Specified by:

set in interface java.util.List<Strand>

Overrides:

set in class java.util.AbstractList<Strand>

size

public int size()

Specified by:

size in interface java.util.Collection<Strand>

Specified by:

size in interface java.util.List<Strand>

Specified by:

size in class java.util.AbstractCollection<Strand>

suspendUpdate

public void suspendUpdate()

toArray

public java.lang.Object[] toArray()

Specified by:

toArray in interface java.util.Collection<Strand>

Specified by:

toArray in interface java.util.List<Strand>

Overrides:

toArray in class java.util.AbstractCollection<Strand>

updateStrands

public void updateStrands(int updateNucIndex)