ur_rna.StructureEditor.models

Class Nuc

java.lang.Object

ur_rna.StructureEditor.models.Nuc

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable<Nuc>, java.lang.Iterable<Nuc>, INucGroup

public class Nuc
extends java.lang.Object
implements java.lang.Cloneable, INucGroup, java.lang.Comparable<Nuc>

Represents a single nucleotide.

Field Summary

Fields

Modifier and Type	Field and Description
(package private) int	indexInScene Stores the index of the nucleotide within the full scene.
java.awt.geom.Point2D.Float	location
int	number
(package private) Bond	pair
(package private) Strand	strand
NucStyle	style
java.lang.String	symbol

Constructor Summary

Constructors

Constructor and Description
Nuc()
Nuc(java.lang.String symbol)
Nuc(java.lang.String symbol, float x, float y)

Method Summary

Modifier and Type	Method and Description
Nuc	clone()
static int	compare(Nuc lhs, Nuc rhs) Compares based on index in scene.
int	compareTo(Nuc other) Compares based on index in scene.
java.util.Set<Nuc>	getBases() Implementation of INucGroup.getBases()
Motif.Branch	getBranch()
Motif.Domain	getDomain()
Motif.Helix	getHelix()
Motif.Loop	getLoop()
Motif.MultiLoop	getMultiLoop(int minimumBranches, boolean includeExterior)
Nuc	getNext()
Nuc	getNext(int steps)
Bond	getPairBond()
Nuc	getPaired()
Nuc	getPaired(boolean includePseudo)
Nuc	getPrev()
RnaScene	getScene()
Strand	getStrand()
int	getStrandIndex()
int	indexInScene() Gets the overall index of this nucleotide, including all nucleotides in previous strands.
int	indexInScene(int[] strandIndexes) Gets the overall index of this nucleotide, given the starting indices for each strand as specified in strandIndexes For example: strandIndexes = int[] { 1, 20, 100 } for a Nuc with index=0 in the first strand, indexInScene would return 1.
int	indexInStrand()
boolean	isPaired()
boolean	isPaired(boolean includePseudo)
Nuc	nextInScene()
Nuc	nextInScene(int steps, boolean loopToBeginning)
NucStyle	style() Returns the style for this nucleotide, creating a new one if necessary.
java.lang.String	toString() Returns a string representation of the object.
java.lang.String	toString(java.lang.String format)
void	transform(java.awt.geom.AffineTransform tr)
void	transformAll(java.awt.geom.AffineTransform tr) Implementation of INucGroup.transformAll(AffineTransform)
void	translate(float dx, float dy)

Methods inherited from class java.lang.Object

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

Methods inherited from interface ur_rna.StructureEditor.models.INucGroup

iterator

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

indexInScene

transient int indexInScene

Stores the index of the nucleotide within the full scene.

location

public java.awt.geom.Point2D.Float location

number

public int number

pair

Bond pair

strand

transient Strand strand

style

public NucStyle style

symbol

public java.lang.String symbol

Constructor Detail

Nuc

public Nuc()

Nuc

public Nuc(java.lang.String symbol)

Nuc

public Nuc(java.lang.String symbol,
           float x,
           float y)

Method Detail

clone

public Nuc clone()

Overrides:

clone in class java.lang.Object

compare

public static int compare(Nuc lhs,
                          Nuc rhs)

Compares based on index in scene. Returns -1 if lhs comes before rhs, 0 if they are at the same index, or 1 if lhs comes after rhs.

compareTo

public int compareTo(Nuc other)

Compares based on index in scene. Returns -1 if this Nuc comes before other, 0 if they are at the same index, or 1 if this Nuc comes after other.

Specified by:

compareTo in interface java.lang.Comparable<Nuc>

getBases

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

Implementation of INucGroup.getBases()

Specified by:

getBases in interface INucGroup

Returns:

a Collection of nucleotides.

getBranch

public Motif.Branch getBranch()

getDomain

public Motif.Domain getDomain()

getHelix

public Motif.Helix getHelix()

getLoop

public Motif.Loop getLoop()

getMultiLoop

public Motif.MultiLoop getMultiLoop(int minimumBranches,
                                    boolean includeExterior)

getNext

public Nuc getNext()

Returns:

The next nucleotide in this strand, or null if this is the last (3') nucleotide.

getNext

public Nuc getNext(int steps)

Returns:

The nucleotide in this strand that is the specified number of nucleotides (steps) away from this one. A negative number of steps will return nucleotides before this one in the strand, while a positive number will return nucleotides after this one.

getPairBond

public Bond getPairBond()

getPaired

public Nuc getPaired()

getPaired

public Nuc getPaired(boolean includePseudo)

getPrev

public Nuc getPrev()

Returns:

The previous nucleotide in this strand, or null if this is the first (5') nucleotide.

getScene

public RnaScene getScene()

getStrand

public Strand getStrand()

getStrandIndex

public int getStrandIndex()

indexInScene

public int indexInScene()

Gets the overall index of this nucleotide, including all nucleotides in previous strands.

indexInScene

public int indexInScene(int[] strandIndexes)

Gets the overall index of this nucleotide, given the starting indices for each strand as specified in strandIndexes For example: strandIndexes = int[] { 1, 20, 100 } for a Nuc with index=0 in the first strand, indexInScene would return 1. for a Nuc with index=5 in the second strand, indexInScene would return 25. for a Nuc with index=2 in the third strand, indexInScene would return 102.

indexInStrand

public int indexInStrand()

isPaired

public boolean isPaired()

isPaired

public boolean isPaired(boolean includePseudo)

nextInScene

public Nuc nextInScene()

nextInScene

public Nuc nextInScene(int steps,
                       boolean loopToBeginning)

style

@NotNull
public NucStyle style()

Returns the style for this nucleotide, creating a new one if necessary.

toString

public java.lang.String toString()

Returns a string representation of the object. In general, the toString method returns a string that "textually represents" this object. The result should be a concise but informative representation that is easy for a person to read. It is recommended that all subclasses override this method.

The toString method for class Object returns a string consisting of the name of the class of which the object is an instance, the at-sign character `@', and the unsigned hexadecimal representation of the hash code of the object. In other words, this method returns a string equal to the value of:

 getClass().getName() + '@' + Integer.toHexString(hashCode())
 

Overrides:

toString in class java.lang.Object

Returns:

a string representation of the object.

toString

public java.lang.String toString(java.lang.String format)

transform

public void transform(java.awt.geom.AffineTransform tr)

transformAll

public void transformAll(java.awt.geom.AffineTransform tr)

Implementation of INucGroup.transformAll(AffineTransform)

Specified by:

transformAll in interface INucGroup

translate

public void translate(float dx,
                      float dy)