Package org.jmol.renderbio
Class BioShapeRenderer
- java.lang.Object
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- org.jmol.render.ShapeRenderer
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- org.jmol.renderbio.BioShapeRenderer
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- Direct Known Subclasses:
BackboneRenderer
,StrandsRenderer
abstract class BioShapeRenderer extends ShapeRenderer
- Author:
- Alexander Rose, Bob Hanson
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Field Summary
Fields Modifier and Type Field Description (package private) float
aspectRatio
(package private) BioShape
bioShape
protected BS
bsVisible
protected boolean
cartoonsFancy
(package private) short
colixBack
protected short[]
colixes
protected short[]
colixesBack
protected javajs.util.P3[]
controlPoints
protected javajs.util.P3[]
controlPointScreens
(package private) int
diameterBeg
(package private) int
diameterEnd
(package private) int
diameterMid
private boolean
haveControlPointScreens
(package private) int
hermiteLevel
(package private) int
iNext
(package private) int
iNext2
(package private) int
iNext3
private boolean
invalidateMesh
private boolean
invalidateSheets
(package private) int
iPrev
protected boolean
isCarbohydrate
private boolean
isCyclic
(package private) boolean
isHighRes
protected boolean
isNucleic
protected boolean
isPhosphorusOnly
private boolean
isTraceAlpha
protected int[]
leadAtomIndices
(package private) short
madBeg
(package private) short
madEnd
(package private) short
madMid
protected short[]
mads
(package private) BioMeshRenderer
meshRenderer
protected int
monomerCount
protected Monomer[]
monomers
private boolean
needTranslucent
private javajs.util.P3
pointT
private BS
reversed
private boolean
ribbonBorder
protected javajs.util.P3[]
ribbonBottomScreens
protected javajs.util.P3[]
ribbonTopScreens
private javajs.util.P3
screenArrowBot
private javajs.util.P3
screenArrowBotPrev
private javajs.util.P3
screenArrowTop
private javajs.util.P3
screenArrowTopPrev
private float
sheetSmoothing
protected STR[]
structureTypes
protected javajs.util.V3[]
wingVectors
protected boolean
wireframeOnly
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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 Constructor Description BioShapeRenderer()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description private void
calc1Screen(javajs.util.P3 center, javajs.util.V3 vector, short mad, float offset_1000, javajs.util.P3 screen)
protected void
calcScreenControlPoints()
protected javajs.util.P3[]
calcScreens(float offsetFraction, short[] mads)
calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)private void
freeTempArrays()
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
renderShapes()
protected boolean
setBioColix(short colix)
protected boolean
setColix(short colix)
private void
setGlobals()
private boolean
setMads(int i, boolean thisTypeOnly)
set diameters for a bioshape(package private) void
setNeighbors(int i)
private void
setStructureTypes()
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Methods inherited from class org.jmol.render.ShapeRenderer
initRenderer, isVisibleForMe, renderShape, setup, setViewerG3dShapeID
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Field Detail
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invalidateMesh
private boolean invalidateMesh
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invalidateSheets
private boolean invalidateSheets
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isTraceAlpha
private boolean isTraceAlpha
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ribbonBorder
private boolean ribbonBorder
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haveControlPointScreens
private boolean haveControlPointScreens
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aspectRatio
float aspectRatio
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hermiteLevel
int hermiteLevel
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sheetSmoothing
private float sheetSmoothing
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cartoonsFancy
protected boolean cartoonsFancy
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monomerCount
protected int monomerCount
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monomers
protected Monomer[] monomers
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isNucleic
protected boolean isNucleic
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isPhosphorusOnly
protected boolean isPhosphorusOnly
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isCarbohydrate
protected boolean isCarbohydrate
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bsVisible
protected BS bsVisible
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ribbonTopScreens
protected javajs.util.P3[] ribbonTopScreens
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ribbonBottomScreens
protected javajs.util.P3[] ribbonBottomScreens
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controlPoints
protected javajs.util.P3[] controlPoints
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controlPointScreens
protected javajs.util.P3[] controlPointScreens
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leadAtomIndices
protected int[] leadAtomIndices
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wingVectors
protected javajs.util.V3[] wingVectors
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mads
protected short[] mads
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colixes
protected short[] colixes
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colixesBack
protected short[] colixesBack
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structureTypes
protected STR[] structureTypes
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isHighRes
boolean isHighRes
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wireframeOnly
protected boolean wireframeOnly
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needTranslucent
private boolean needTranslucent
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meshRenderer
BioMeshRenderer meshRenderer
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bioShape
BioShape bioShape
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pointT
private final javajs.util.P3 pointT
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iPrev
int iPrev
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iNext
int iNext
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iNext2
int iNext2
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iNext3
int iNext3
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diameterBeg
int diameterBeg
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diameterMid
int diameterMid
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diameterEnd
int diameterEnd
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madBeg
short madBeg
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madMid
short madMid
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madEnd
short madEnd
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colixBack
short colixBack
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reversed
private BS reversed
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isCyclic
private boolean isCyclic
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screenArrowTop
private final javajs.util.P3 screenArrowTop
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screenArrowTopPrev
private final javajs.util.P3 screenArrowTopPrev
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screenArrowBot
private final javajs.util.P3 screenArrowBot
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screenArrowBotPrev
private final javajs.util.P3 screenArrowBotPrev
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Method Detail
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renderBioShape
protected abstract void renderBioShape(BioShape bioShape)
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render
protected boolean render()
- Specified by:
render
in classShapeRenderer
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setGlobals
private void setGlobals()
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renderShapes
private void renderShapes()
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setBioColix
protected boolean setBioColix(short colix)
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freeTempArrays
private void freeTempArrays()
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initializePolymer
private boolean initializePolymer(BioShape bioShape)
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setStructureTypes
private void setStructureTypes()
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calcScreenControlPoints
protected void calcScreenControlPoints()
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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)
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getLeadColix
protected short getLeadColix(int i)
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getLeadColixBack
protected short getLeadColixBack(int i)
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setNeighbors
void setNeighbors(int i)
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setColix
protected boolean setColix(short colix)
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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)
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renderHermiteConic
protected void renderHermiteConic(int i, boolean thisTypeOnly, int tension)
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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)
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