ur_rna.StructureEditor.services.drawing

Class NucLayout

java.lang.Object

ur_rna.StructureEditor.services.drawing.NucLayout

public class NucLayout
extends java.lang.Object

Performs nucleotide layouts of various types.

Field Summary

Fields

Modifier and Type	Field and Description
private DrawSettings	drawSettings

Constructor Summary

Constructors

Constructor and Description
NucLayout()
NucLayout(DrawSettings drawSettings)

Method Summary

Modifier and Type	Method and Description
private void	backendRedrawRadial(RnaScene scene, RNA rna, int structureNumber)
Ellipses.Circle	calcLoopBestFitCircle(Motif.Loop m)
Ellipses.Circle	calcMultiLoopBestFitCircle(Motif.MultiLoop m)
float	calcOptimalMultiLoopRadius(Motif.MultiLoop m)
static java.awt.geom.QuadCurve2D	getCircularBond(Bond b)
static java.awt.geom.Arc2D	getLinearBond(Bond b)
private static int	iceil(double number)
void	redrawCircular(RnaScene scene)
void	redrawHelix(Motif.Helix h)
void	redrawLinear(RnaScene scene)
void	redrawLoop(Motif.Loop m)
void	redrawMultiLoop(Motif.MultiLoop m, SceneController controller)
void	redrawRadial(RnaScene scene)
void	redrawRadial(RnaSceneGroup group)
void	setDrawSettings(DrawSettings drawSettings)

Methods inherited from class java.lang.Object

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

Field Detail

drawSettings

private DrawSettings drawSettings

Constructor Detail

NucLayout

public NucLayout()

NucLayout

public NucLayout(DrawSettings drawSettings)

Method Detail

backendRedrawRadial

private void backendRedrawRadial(RnaScene scene,
                                 RNA rna,
                                 int structureNumber)

calcLoopBestFitCircle

public Ellipses.Circle calcLoopBestFitCircle(Motif.Loop m)

calcMultiLoopBestFitCircle

public Ellipses.Circle calcMultiLoopBestFitCircle(Motif.MultiLoop m)

calcOptimalMultiLoopRadius

public float calcOptimalMultiLoopRadius(Motif.MultiLoop m)

getCircularBond

public static java.awt.geom.QuadCurve2D getCircularBond(Bond b)

getLinearBond

public static java.awt.geom.Arc2D getLinearBond(Bond b)

iceil

private static int iceil(double number)

redrawCircular

public void redrawCircular(RnaScene scene)

redrawHelix

public void redrawHelix(Motif.Helix h)

redrawLinear

public void redrawLinear(RnaScene scene)

redrawLoop

public void redrawLoop(Motif.Loop m)

redrawMultiLoop

public void redrawMultiLoop(Motif.MultiLoop m,
                            SceneController controller)

redrawRadial

public void redrawRadial(RnaScene scene)
                  throws RnaBackendException

Throws:

RnaBackendException

redrawRadial

public void redrawRadial(RnaSceneGroup group)
                  throws RnaBackendException

Throws:

RnaBackendException

setDrawSettings

public void setDrawSettings(DrawSettings drawSettings)