DrawSettings

java.lang.Object
- ur_rna.StructureEditor.models.DrawSettings

All Implemented Interfaces:

java.lang.Cloneable
```
public final class DrawSettings
extends java.lang.Object
implements java.lang.Cloneable
```
Container for settings related to drawing RNA scenes. The fields in this class are saved and loaded along with program settings, but fields marked as transient are NOT saved or loaded.

Field Summary

Fields
Modifier and Type	Field and Description
`java.awt.Color`	`backboneColor`
`java.awt.Stroke`	`backboneStroke`
`float`	`backboneWidth`
`java.awt.Color`	`bondColor`
`java.awt.Color`	`bondColorPseudo`
`float`	`bondLength`
`java.awt.Stroke`	`bondStroke`
`java.awt.Stroke`	`bondStrokePseudo`
`float`	`bondWidth`
`double`	`circularStartAngle`
`private NucStyle`	`defaultStyle`
`boolean`	`drawBackboneCurved`
`boolean`	`drawBackboneInHelix`
`boolean`	`drawBackboneInLoops`
`boolean`	`drawBondsInHelix`
`boolean`	`drawNumbers`
`boolean`	`drawNumbersAtHelix`
`int`	`drawNumbersInterval`
`java.awt.Stroke`	`editBondStroke`
`java.awt.Color`	`hint`
`java.awt.Color`	`hintEmphasis`
`float`	`loopSpacing` Spacing between nucs in a loop or hairpin.
`java.awt.Color`	`nucFillColor`
`java.awt.Color`	`nucFocusColor`
`java.awt.Font`	`nucFont`
`java.awt.Color`	`nucHitColor`
`java.awt.Color`	`nucOutlineColor`
`java.awt.Stroke`	`nucOutlineSelStroke`
`java.awt.Stroke`	`nucOutlineStroke`
`float`	`nucOutlineWidth`
`float`	`nucRadius`
`java.awt.Color`	`nucSelColor`
`float`	`nucSpacing` Spacing between nucs in a helix.
`java.awt.Color`	`nucTextColor`
`float`	`numberDistance`
`java.awt.Font`	`numberFont`
`java.awt.Color`	`numberLineColor`
`float`	`numberLineMargin`
`java.awt.Stroke`	`numberLineStroke`
`float`	`numberLineWidth`
`float`	`pseudoBondWidth`
`java.awt.Color`	`sceneBgColor`
`java.awt.Color`	`selBandFillColor`
`java.awt.Color`	`selBandLineColor`
`java.awt.Stroke`	`selBandOutline`

Constructor Summary

Constructors
Constructor and Description

DrawSettings()

Constructors
Constructor and Description
`DrawSettings()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`float`	`calcBondLength()`
`float`	`calcOptimalLoopDistance(int nucCount, int endSpacers)` Calculate the optimal circumference for a circle containing the given number of nucleotides.
`float`	`calcOptimalLoopDistance(Nuc n1, Nuc n2, int endSpacers)` Calculate the optimal circumference for a circle containing nucs in the given region.
`float`	`calcOptimalNuc2NucDistance(int nucCount)`
`float`	`calcOptimalNuc2NucDistance(Nuc n1, Nuc n2)` Calculate the optimal distance between nuc midpoints.
`float`	`calcOptimalOuterDistance(int nucCount, int endSpacers)`
`float`	`calcOptimalOuterDistance(Nuc n1, Nuc n2, int endSpacers)` Calculate the optimal distance from the outside of one nuc to the outside of another.
`DrawSettings`	`copy()`
`void`	`fillStyle(Nuc n, NucStyle fillProperties)`
`NucStyle`	`getStyle(Nuc n)`
`float`	`nucDiameter()`
`float`	`nucleotideRadius(Nuc nuc)`
`void`	`onSettingsChanged()` Call this to update dependent settings whenever settings have been changed.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - backboneColor
```
public java.awt.Color backboneColor
```
  - backboneStroke
```
public transient java.awt.Stroke backboneStroke
```
  - backboneWidth
```
public float backboneWidth
```
  - bondColor
```
public java.awt.Color bondColor
```
  - bondColorPseudo
```
public java.awt.Color bondColorPseudo
```
  - bondLength
```
public transient float bondLength
```
  - bondStroke
```
public transient java.awt.Stroke bondStroke
```
  - bondStrokePseudo
```
public transient java.awt.Stroke bondStrokePseudo
```
  - bondWidth
```
public float bondWidth
```
  - circularStartAngle
```
public double circularStartAngle
```
  - defaultStyle
```
private transient NucStyle defaultStyle
```
  - drawBackboneCurved
```
public boolean drawBackboneCurved
```
  - drawBackboneInHelix
```
public boolean drawBackboneInHelix
```
  - drawBackboneInLoops
```
public boolean drawBackboneInLoops
```
  - drawBondsInHelix
```
public boolean drawBondsInHelix
```
  - drawNumbers
```
public boolean drawNumbers
```
  - drawNumbersAtHelix
```
public boolean drawNumbersAtHelix
```
  - drawNumbersInterval
```
public int drawNumbersInterval
```
  - editBondStroke
```
public transient java.awt.Stroke editBondStroke
```
  - hint
```
public java.awt.Color hint
```
  - hintEmphasis
```
public java.awt.Color hintEmphasis
```
  - loopSpacing
```
public float loopSpacing
```
    Spacing between nucs in a loop or hairpin. Does not include radius, which must be added in to calculate full point-to-point distance. See calcOptimalLoopDistance(Nuc, Nuc, int) for details.
  - nucFillColor
```
public java.awt.Color nucFillColor
```
  - nucFocusColor
```
public java.awt.Color nucFocusColor
```
  - nucFont
```
public java.awt.Font nucFont
```
  - nucHitColor
```
public java.awt.Color nucHitColor
```
  - nucOutlineColor
```
public java.awt.Color nucOutlineColor
```
  - nucOutlineSelStroke
```
public transient java.awt.Stroke nucOutlineSelStroke
```
  - nucOutlineStroke
```
public transient java.awt.Stroke nucOutlineStroke
```
  - nucOutlineWidth
```
public float nucOutlineWidth
```
  - nucRadius
```
public float nucRadius
```
  - nucSelColor
```
public java.awt.Color nucSelColor
```
  - nucSpacing
```
public float nucSpacing
```
    Spacing between nucs in a helix. Does not include radius, which must be added in to calculate full point-to-point distance. See calcOptimalNuc2NucDistance(Nuc, Nuc) for details.
  - nucTextColor
```
public java.awt.Color nucTextColor
```
  - numberDistance
```
public float numberDistance
```
  - numberFont
```
public java.awt.Font numberFont
```
  - numberLineColor
```
public java.awt.Color numberLineColor
```
  - numberLineMargin
```
public float numberLineMargin
```
  - numberLineStroke
```
public transient java.awt.Stroke numberLineStroke
```
  - numberLineWidth
```
public float numberLineWidth
```
  - pseudoBondWidth
```
public float pseudoBondWidth
```
  - sceneBgColor
```
public java.awt.Color sceneBgColor
```
  - selBandFillColor
```
public java.awt.Color selBandFillColor
```
  - selBandLineColor
```
public java.awt.Color selBandLineColor
```
  - selBandOutline
```
public transient java.awt.Stroke selBandOutline
```
- Constructor Detail
  - DrawSettings
```
public DrawSettings()
```
- Method Detail
  - calcBondLength
```
public float calcBondLength()
```
  - calcOptimalLoopDistance
```
public float calcOptimalLoopDistance(int nucCount,
                                     int endSpacers)
```
    Calculate the optimal circumference for a circle containing the given number of nucleotides.
    
    Parameters:
    
    nucCount - the number of nucleotides in the circle
    
    endSpacers - the number of spacers required on the outside of the terminal nucs (n1=first and n2=last) 0 means no space before the center of n1 or the after the center of n2 (e.g. the arc-length of a hairpin loop from the center of n1 to the center of n2) 1 means a single spacer (e.g. connecting n1 to n2 in a circle) 2 means a spacer before n1 and after n2 (e.g. a spacer connecting n1 to a previous nuc and another connecting n2 to a subsequent nuc)
  - calcOptimalLoopDistance
```
public float calcOptimalLoopDistance(Nuc n1,
                                     Nuc n2,
                                     int endSpacers)
```
    Calculate the optimal circumference for a circle containing nucs in the given region.
    
    Parameters:
    
    n1 - the nucleotide at the start of the region (inclusive)
    
    n2 - the nucleotide at the end of the region (inclusive)
    
    endSpacers - the number of spacers required on the outside of the region. 0 means no space before the center of n1 or the after the center of n2 (e.g. the arc-length of a hairpin loop from the center of n1 to the center of n2) 1 means a single spacer (e.g. connecting n1 to n2 in a circle) 2 means a spacer before n1 and after n2 (e.g. a spacer connecting n1 to a previous nuc and another connecting n2 to a subsequent nuc)
  - calcOptimalNuc2NucDistance
```
public float calcOptimalNuc2NucDistance(int nucCount)
```
  - calcOptimalNuc2NucDistance
```
public float calcOptimalNuc2NucDistance(Nuc n1,
                                        Nuc n2)
```
    Calculate the optimal distance between nuc midpoints. Does not include any extra space on the outside ends of the nucs. e.g. For 2 adjacent nucs: N1)-(N2 (two radii + 1 spacer) e.g. For 3 consecutive nucs: N1)-(N2)-(N3 (4 radii + 2 spacers) Let N be ABS(n1.index-n2.index), then distance = N*(2*radius+spacer) See calcOptimalOuterDistance(Nuc, Nuc, int) for a calculation that includes the end-to-end distance when the outer ends are included.
  - calcOptimalOuterDistance
```
public float calcOptimalOuterDistance(int nucCount,
                                      int endSpacers)
```
  - calcOptimalOuterDistance
```
public float calcOptimalOuterDistance(Nuc n1,
                                      Nuc n2,
                                      int endSpacers)
```
    Calculate the optimal distance from the outside of one nuc to the outside of another. This always includes the outer radii and can optionally include 0, 1 or 2 outside spacers. e.g. For 2 adjacent nucs, endSpacers==0: (N1)-(N2) (4 radii + 1 total spacer) e.g. For 2 adjacent nucs, endSpacers==1: -(N1)-(N2) (4 radii + 2 total spacers) e.g. For 2 adjacent nucs, endSpacers==2: -(N1)-(N2)- (4 radii + 3 total spacers) e.g. For 3 consecutive nucs, endSpacers==0: (N1)-(N2)-(N3) (6 radii + 2 total spacers) e.g. For 3 consecutive nucs, endSpacers==1: -(N1)-(N2)-(N3) (6 radii + 3 total spacers) e.g. For 3 consecutive nucs, endSpacers==2: -(N1)-(N2)-(N3)- (6 radii + 4 total spacers)
  - copy
```
public DrawSettings copy()
```
  - fillStyle
```
public void fillStyle(Nuc n,
                      NucStyle fillProperties)
```
  - getStyle
```
public NucStyle getStyle(Nuc n)
```
  - nucDiameter
```
public float nucDiameter()
```
  - nucleotideRadius
```
public float nucleotideRadius(Nuc nuc)
```
  - onSettingsChanged
```
public void onSettingsChanged()
```
    Call this to update dependent settings whenever settings have been changed. E.g. bondStroke needs to be re-created whenever bondWidth is changed.

Class DrawSettings

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

backboneColor

backboneStroke

backboneWidth

bondColor

bondColorPseudo

bondLength

bondStroke

bondStrokePseudo

bondWidth

circularStartAngle

defaultStyle

drawBackboneCurved

drawBackboneInHelix

drawBackboneInLoops

drawBondsInHelix

drawNumbers

drawNumbersAtHelix

drawNumbersInterval

editBondStroke

hint

hintEmphasis

loopSpacing

nucFillColor

nucFocusColor

nucFont

nucHitColor

nucOutlineColor

nucOutlineSelStroke

nucOutlineStroke

nucOutlineWidth

nucRadius

nucSelColor

nucSpacing

nucTextColor

numberDistance

numberFont

numberLineColor

numberLineMargin

numberLineStroke

numberLineWidth

pseudoBondWidth

sceneBgColor

selBandFillColor

selBandLineColor

selBandOutline

Constructor Detail

DrawSettings

Method Detail

calcBondLength

calcOptimalLoopDistance

calcOptimalLoopDistance

calcOptimalNuc2NucDistance

calcOptimalNuc2NucDistance

calcOptimalOuterDistance

calcOptimalOuterDistance

copy

fillStyle

getStyle

nucDiameter

nucleotideRadius

onSettingsChanged