org.jmol.shapebio
Class BioShapeRenderer
java.lang.Object
org.jmol.shape.ShapeRenderer
org.jmol.shape.MeshRenderer
org.jmol.shapebio.BioShapeRenderer
- Direct Known Subclasses:
- BackboneRenderer, RocketsRenderer, StrandsRenderer, TraceRenderer
abstract class BioShapeRenderer
- extends MeshRenderer
Fields inherited from class org.jmol.shape.MeshRenderer |
antialias, bsPolygons, diameter, frontOnly, imageFontScaling, isTranslucent, latticeOffset, mesh, normixes, pt1f, pt1i, pt2f, pt2i, pt3i, scalePixelsPerMicron, screens, thePlane, transformedVectors, vertexCount, vertices, width |
Fields inherited from class org.jmol.shape.ShapeRenderer |
colix, exportType, g3d, mad, madBeg, madEnd, madMid, modelSet, myVisibilityFlag, shape, shapeID, viewer |
Method Summary |
private void |
calc1Screen(Point3f center,
Vector3f vector,
short mad,
float offset_1000,
Point3i screen)
|
protected void |
calcScreenControlPoints()
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protected void |
calcScreenControlPoints(Point3f[] points)
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protected Point3i[] |
calcScreens(float offsetFraction)
calculate screen points based on control points and wing positions
(cartoon, strand, meshRibbon, and ribbon) |
private boolean |
checkDiameter(int d)
|
private boolean |
createMeshCylinder(int i,
int madBeg,
int madMid,
int madEnd,
int aspectRatio)
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private void |
freeTempArrays()
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protected short |
getLeadColix(int i)
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private boolean |
initializePolymer(BioShape bioShape)
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protected boolean |
isHelix(int i)
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protected void |
render()
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protected abstract void |
renderBioShape(BioShape bioShape)
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protected void |
renderCone(int i,
Point3f pointBegin,
Point3f pointEnd,
Point3f screenPtBegin,
Point3f screenPtEnd)
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protected void |
renderHermiteArrowHead(int i)
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protected void |
renderHermiteConic(int i,
boolean thisTypeOnly)
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protected void |
renderHermiteCylinder(Point3i[] screens,
int i)
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protected void |
renderHermiteRibbon(boolean doFill,
int i,
boolean thisTypeOnly)
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private boolean |
setMads(int i,
boolean thisTypeOnly)
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private void |
setNeighbors(int i)
|
private void |
setStructureTypes()
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
invalidateMesh
private boolean invalidateMesh
invalidateSheets
private boolean invalidateSheets
isHighRes
private boolean isHighRes
isTraceAlpha
private boolean isTraceAlpha
ribbonBorder
private boolean ribbonBorder
haveControlPointScreens
private boolean haveControlPointScreens
aspectRatio
private int aspectRatio
hermiteLevel
private int hermiteLevel
sheetSmoothing
private float sheetSmoothing
meshes
private Mesh[] meshes
meshReady
private boolean[] meshReady
monomerCount
protected int monomerCount
monomers
protected Monomer[] monomers
isNucleic
protected boolean isNucleic
isCarbohydrate
protected boolean isCarbohydrate
bsVisible
protected BitSet bsVisible
ribbonTopScreens
protected Point3i[] ribbonTopScreens
ribbonBottomScreens
protected Point3i[] ribbonBottomScreens
controlPoints
protected Point3f[] controlPoints
controlPointScreens
protected Point3i[] controlPointScreens
leadAtomIndices
protected int[] leadAtomIndices
wingVectors
protected Vector3f[] wingVectors
mads
protected short[] mads
colixes
protected short[] colixes
structureTypes
protected byte[] structureTypes
pointT
private final Point3f pointT
iPrev
private int iPrev
iNext
private int iNext
iNext2
private int iNext2
iNext3
private int iNext3
diameterBeg
private int diameterBeg
diameterMid
private int diameterMid
diameterEnd
private int diameterEnd
doCap0
private boolean doCap0
doCap1
private boolean doCap1
screenArrowTop
private final Point3i screenArrowTop
screenArrowTopPrev
private final Point3i screenArrowTopPrev
screenArrowBot
private final Point3i screenArrowBot
screenArrowBotPrev
private final Point3i screenArrowBotPrev
ABSOLUTE_MIN_MESH_SIZE
private static final int ABSOLUTE_MIN_MESH_SIZE
- See Also:
- Constant Field Values
MIN_MESH_RENDER_SIZE
private static final int MIN_MESH_RENDER_SIZE
- See Also:
- Constant Field Values
controlHermites
private Point3f[] controlHermites
wingHermites
private Vector3f[] wingHermites
radiusHermites
private Point3f[] radiusHermites
norm
private Vector3f norm
Z
private final Vector3f Z
wing
private final Vector3f wing
wing0
private final Vector3f wing0
wing1
private final Vector3f wing1
wingT
private final Vector3f wingT
aa
private final AxisAngle4f aa
pt
private final Point3f pt
pt1
private final Point3f pt1
ptPrev
private final Point3f ptPrev
ptNext
private final Point3f ptNext
mat
private final Matrix3f mat
BioShapeRenderer
BioShapeRenderer()
renderBioShape
protected abstract void renderBioShape(BioShape bioShape)
render
protected void render()
- Overrides:
render
in class MeshRenderer
freeTempArrays
private void freeTempArrays()
initializePolymer
private boolean initializePolymer(BioShape bioShape)
setStructureTypes
private void setStructureTypes()
isHelix
protected boolean isHelix(int i)
calcScreenControlPoints
protected void calcScreenControlPoints()
calcScreenControlPoints
protected void calcScreenControlPoints(Point3f[] points)
calcScreens
protected Point3i[] calcScreens(float offsetFraction)
- calculate screen points based on control points and wing positions
(cartoon, strand, meshRibbon, and ribbon)
- Parameters:
offsetFraction
-
- Returns:
- Point3i array THAT MUST BE LATER FREED
calc1Screen
private void calc1Screen(Point3f center,
Vector3f vector,
short mad,
float offset_1000,
Point3i screen)
getLeadColix
protected short getLeadColix(int i)
setNeighbors
private void setNeighbors(int i)
renderHermiteCylinder
protected void renderHermiteCylinder(Point3i[] screens,
int i)
setMads
private boolean setMads(int i,
boolean thisTypeOnly)
checkDiameter
private boolean checkDiameter(int d)
renderHermiteConic
protected void renderHermiteConic(int i,
boolean thisTypeOnly)
renderHermiteRibbon
protected void renderHermiteRibbon(boolean doFill,
int i,
boolean thisTypeOnly)
renderHermiteArrowHead
protected void renderHermiteArrowHead(int i)
renderCone
protected void renderCone(int i,
Point3f pointBegin,
Point3f pointEnd,
Point3f screenPtBegin,
Point3f screenPtEnd)
createMeshCylinder
private boolean createMeshCylinder(int i,
int madBeg,
int madMid,
int madEnd,
int aspectRatio)