ur_rna.StructureEditor.models

Class RnaScene

java.lang.Object

ur_rna.StructureEditor.models.RnaScene

All Implemented Interfaces:

java.lang.Cloneable

public class RnaScene
extends java.lang.Object
implements java.lang.Cloneable

Encompases all the information needed to an RNA "scene" which can include one or more strands of RNA in a specific 2D layout.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	drawFlipped Whether this nucleotides were drawn flipped (Clockwise) or normal (Counter-Clockwise)
SceneDrawMode	drawMode
History<HistoryState>	history
private java.util.List<Nuc>	nucs
StrandList	strands
java.lang.String	title

Constructor Summary

Constructors

Constructor and Description
RnaScene()

Method Summary

Modifier and Type	Method and Description
Bond	addBond(Bond.BondInfo bond)
private Bond	addBond(Bond b)
Bond	addBond(int nuc1, int nuc2, BondType type)
Bond	addBond(Nuc nuc1, Nuc nuc2)
Bond	addBond(Nuc nuc1, Nuc nuc2, BondType type)
Strand	addStrand()
java.util.List<Nuc>	allNucs() Returns a read-only list of all nucleotides.
void	breakBond(Bond b)
void	breakBonds(int... nucIndices)
int[]	buildStrandIndex(int start, int gapBetweenStrands) Creates a lookup-index where element[I] is the starting nuclotide index of the nucleotide belonging to strand[I].
void	clearBonds()
void	colorize(SceneColorizer c)
void	copyBonds(RnaScene copyFrom)
void	divideStrand(Nuc n)
Strand	firstStrand()
java.util.List<Bond>	getBonds()
java.util.List<Bond>	getBonds(boolean includePseudo)
java.util.List<Bond>	getBonds(java.lang.Iterable<Nuc> region, boolean includePseudo) Get all bonds associated with nucleotides in the specified region, which can be a Strand or a Motif etc.
Motif.Branch	getBranch(Nuc nuc)
Motif.Domain	getDomain(Nuc nuc)
java.util.List<Motif.Helix>	getHelices() Returns the list of helices in the RNA scene
Motif.Helix	getHelix(Nuc nuc)
Motif.Loop	getLoop(Nuc nuc)
java.util.List<Motif.Loop>	getLoops()
java.util.List<Motif.MultiLoop>	getMultiLoops(int minimumBranches, boolean includeExterior)
Nuc	getNuc(int index)
int	getNucCount()
RnaSceneState	getState()
Strand	getStrand(int strandIndex)
Strand	getStrand(int strandIndex, boolean createIfNotExisting)
boolean	hasBonds()
void	identifyPseudoknots()
void	joinStrands(Strand s1, Strand s2)
void	loadState(RnaSceneState state)
Nuc	nucAtSceneIndex(int index)
void	removeNucs(Nuc[] nucs)
Strand	secondStrand()

Methods inherited from class java.lang.Object

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

Field Detail

drawFlipped

public boolean drawFlipped

Whether this nucleotides were drawn flipped (Clockwise) or normal (Counter-Clockwise)

drawMode

public SceneDrawMode drawMode

history

public History<HistoryState> history

nucs

private java.util.List<Nuc> nucs

strands

public StrandList strands

title

public java.lang.String title

Constructor Detail

RnaScene

public RnaScene()

Method Detail

addBond

public Bond addBond(Bond.BondInfo bond)

addBond

private Bond addBond(Bond b)

addBond

public Bond addBond(int nuc1,
                    int nuc2,
                    BondType type)

addBond

public Bond addBond(Nuc nuc1,
                    Nuc nuc2)

addBond

public Bond addBond(Nuc nuc1,
                    Nuc nuc2,
                    BondType type)

addStrand

public Strand addStrand()

allNucs

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

Returns a read-only list of all nucleotides.

breakBond

public void breakBond(Bond b)

breakBonds

public void breakBonds(int... nucIndices)

buildStrandIndex

public int[] buildStrandIndex(int start,
                              int gapBetweenStrands)

Creates a lookup-index where element[I] is the starting nuclotide index of the nucleotide belonging to strand[I]. For example: 3 strands with size 10, 5, and 8: buildStrandIndex(0, 0) => int[] { 0, 10, 15 } .. i.e. nucs: { S1{0-9}, S2{10-14}, S3{15-22} } buildStrandIndex(0, 3) => int[] { 0, 13, 21 } .. i.e. nucs: { S1{0-9}, S2{13-17}, S3{21-28} } buildStrandIndex(1, 3) => int[] { 1, 14, 22 } .. i.e. nucs: { S1{1-10}, S2{14-18}, S3{22-29} }

Parameters:

start - The desired index of the first nucleotide in the first strand.

gapBetweenStrands - The number of index positions to skip between strands (i.e. if inter-molecular linkers need to be inserted)

Returns:

An integer array with each element[I] equal to the overall position of the first nucleotide in strand[I]

clearBonds

public void clearBonds()

colorize

public void colorize(SceneColorizer c)

copyBonds

public void copyBonds(RnaScene copyFrom)

divideStrand

public void divideStrand(Nuc n)

firstStrand

public Strand firstStrand()

getBonds

public java.util.List<Bond> getBonds()

getBonds

public java.util.List<Bond> getBonds(boolean includePseudo)

getBonds

public java.util.List<Bond> getBonds(java.lang.Iterable<Nuc> region,
                                     boolean includePseudo)

Get all bonds associated with nucleotides in the specified region, which can be a Strand or a Motif etc.

getBranch

public Motif.Branch getBranch(Nuc nuc)

getDomain

public Motif.Domain getDomain(Nuc nuc)

getHelices

public java.util.List<Motif.Helix> getHelices()

Returns the list of helices in the RNA scene

getHelix

public Motif.Helix getHelix(Nuc nuc)

getLoop

public Motif.Loop getLoop(Nuc nuc)

getLoops

public java.util.List<Motif.Loop> getLoops()

getMultiLoops

public java.util.List<Motif.MultiLoop> getMultiLoops(int minimumBranches,
                                                     boolean includeExterior)

getNuc

public Nuc getNuc(int index)

getNucCount

public int getNucCount()

getState

public RnaSceneState getState()

getStrand

public Strand getStrand(int strandIndex)

getStrand

public Strand getStrand(int strandIndex,
                        boolean createIfNotExisting)

hasBonds

public boolean hasBonds()

identifyPseudoknots

public void identifyPseudoknots()

joinStrands

public void joinStrands(Strand s1,
                        Strand s2)

loadState

public void loadState(RnaSceneState state)

nucAtSceneIndex

public Nuc nucAtSceneIndex(int index)

removeNucs

public void removeNucs(Nuc[] nucs)

secondStrand

public Strand secondStrand()