Package org.jmol.renderbio
Class BioShapeRenderer
java.lang.Object
org.jmol.render.ShapeRenderer
org.jmol.renderbio.BioShapeRenderer
- Direct Known Subclasses:
BackboneRenderer
,StrandsRenderer
- Author:
- Alexander Rose, Bob Hanson
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Field Summary
FieldsModifier and TypeFieldDescription(package private) float
(package private) BioShape
protected javajs.util.BS
protected boolean
(package private) short
protected short[]
protected short[]
protected javajs.util.P3[]
protected javajs.util.P3[]
(package private) int
(package private) int
(package private) int
private boolean
(package private) int
(package private) int
(package private) int
(package private) int
private boolean
private boolean
(package private) int
protected boolean
private boolean
(package private) boolean
protected boolean
protected boolean
private boolean
protected int[]
(package private) short
(package private) short
(package private) short
protected short[]
(package private) BioMeshRenderer
protected int
protected Monomer[]
private boolean
private final javajs.util.P3
private javajs.util.BS
private boolean
protected javajs.util.P3[]
protected javajs.util.P3[]
private final javajs.util.P3
private final javajs.util.P3
private final javajs.util.P3
private final javajs.util.P3
private float
protected STR[]
protected javajs.util.V3[]
protected boolean
Fields inherited from class org.jmol.render.ShapeRenderer
colix, exportType, g3d, isExport, mad, ms, myVisibilityFlag, shape, shapeID, tm, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate void
calc1Screen
(javajs.util.P3 center, javajs.util.V3 vector, short mad, float offset_1000, javajs.util.P3 screen) protected void
protected javajs.util.P3[]
calcScreens
(float offsetFraction, short[] mads) calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)protected void
drawSegmentAB
(Atom atomA, Atom atomB, short colixA, short colixB, float max) private void
protected short
getLeadColix
(int i) protected short
getLeadColixBack
(int i) private boolean
initializePolymer
(BioShape bioShape) protected boolean
render()
protected abstract void
renderBioShape
(BioShape bioShape) protected void
renderHermiteArrowHead
(int i) protected void
renderHermiteConic
(int i, boolean thisTypeOnly, int tension) protected void
renderHermiteCylinder
(javajs.util.P3[] screens, int i) protected void
renderHermiteRibbon
(boolean doFill, int i, boolean thisTypeOnly) private void
protected boolean
setBioColix
(short colix) protected boolean
setColix
(short colix) private void
private boolean
setMads
(int i, boolean thisTypeOnly) set diameters for a bioshape(package private) void
setNeighbors
(int i) private void
Methods inherited from class org.jmol.render.ShapeRenderer
initRenderer, isVisibleForMe, renderShape, setup, setViewerG3dShapeID
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Field Details
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invalidateMesh
private boolean invalidateMesh -
invalidateSheets
private boolean invalidateSheets -
isTraceAlpha
private boolean isTraceAlpha -
ribbonBorder
private boolean ribbonBorder -
haveControlPointScreens
private boolean haveControlPointScreens -
aspectRatio
float aspectRatio -
hermiteLevel
int hermiteLevel -
sheetSmoothing
private float sheetSmoothing -
cartoonsFancy
protected boolean cartoonsFancy -
monomerCount
protected int monomerCount -
monomers
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isNucleic
protected boolean isNucleic -
isPhosphorusOnly
protected boolean isPhosphorusOnly -
isCarbohydrate
protected boolean isCarbohydrate -
bsVisible
protected javajs.util.BS bsVisible -
ribbonTopScreens
protected javajs.util.P3[] ribbonTopScreens -
ribbonBottomScreens
protected javajs.util.P3[] ribbonBottomScreens -
controlPoints
protected javajs.util.P3[] controlPoints -
controlPointScreens
protected javajs.util.P3[] controlPointScreens -
leadAtomIndices
protected int[] leadAtomIndices -
wingVectors
protected javajs.util.V3[] wingVectors -
mads
protected short[] mads -
colixes
protected short[] colixes -
colixesBack
protected short[] colixesBack -
structureTypes
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isHighRes
boolean isHighRes -
wireframeOnly
protected boolean wireframeOnly -
needTranslucent
private boolean needTranslucent -
meshRenderer
BioMeshRenderer meshRenderer -
bioShape
BioShape bioShape -
pointT
private final javajs.util.P3 pointT -
iPrev
int iPrev -
iNext
int iNext -
iNext2
int iNext2 -
iNext3
int iNext3 -
diameterBeg
int diameterBeg -
diameterMid
int diameterMid -
diameterEnd
int diameterEnd -
madBeg
short madBeg -
madMid
short madMid -
madEnd
short madEnd -
colixBack
short colixBack -
reversed
private javajs.util.BS reversed -
isCyclic
private boolean isCyclic -
screenArrowTop
private final javajs.util.P3 screenArrowTop -
screenArrowTopPrev
private final javajs.util.P3 screenArrowTopPrev -
screenArrowBot
private final javajs.util.P3 screenArrowBot -
screenArrowBotPrev
private final javajs.util.P3 screenArrowBotPrev
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Constructor Details
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BioShapeRenderer
BioShapeRenderer()
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Method Details
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renderBioShape
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render
protected boolean render()- Specified by:
render
in classShapeRenderer
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setGlobals
private void setGlobals() -
renderShapes
private void renderShapes() -
setBioColix
protected boolean setBioColix(short colix) -
freeTempArrays
private void freeTempArrays() -
initializePolymer
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setStructureTypes
private void setStructureTypes() -
calcScreenControlPoints
protected void calcScreenControlPoints() -
calcScreens
protected javajs.util.P3[] calcScreens(float offsetFraction, short[] mads) calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)- Parameters:
offsetFraction
-mads
-- Returns:
- Point3i array THAT MUST BE LATER FREED
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calc1Screen
private void calc1Screen(javajs.util.P3 center, javajs.util.V3 vector, short mad, float offset_1000, javajs.util.P3 screen) -
getLeadColix
protected short getLeadColix(int i) -
getLeadColixBack
protected short getLeadColixBack(int i) -
setNeighbors
void setNeighbors(int i) -
setColix
protected boolean setColix(short colix) -
setMads
private boolean setMads(int i, boolean thisTypeOnly) set diameters for a bioshape- Parameters:
i
-thisTypeOnly
- true for Cartoon but not MeshRibbon- Returns:
- true if a mesh is needed
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renderHermiteCylinder
protected void renderHermiteCylinder(javajs.util.P3[] screens, int i) -
renderHermiteConic
protected void renderHermiteConic(int i, boolean thisTypeOnly, int tension) -
renderHermiteRibbon
protected void renderHermiteRibbon(boolean doFill, int i, boolean thisTypeOnly) - Parameters:
doFill
-i
-thisTypeOnly
- true for Cartoon but not MeshRibbon
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renderHermiteArrowHead
protected void renderHermiteArrowHead(int i) -
drawSegmentAB
-