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Public Member Functions | Protected Member Functions | Protected Attributes | Package Attributes | Private Member Functions | Private Attributes | Static Private Attributes

org::jmol::shapebio::BioShapeRenderer Class Reference

Inheritance diagram for org::jmol::shapebio::BioShapeRenderer:
Inheritance graph
Collaboration diagram for org::jmol::shapebio::BioShapeRenderer:
Collaboration graph

List of all members.

Public Member Functions

void render (JmolRendererInterface g3d, ModelSet modelSet, Shape shape)
boolean render1 (Mesh mesh)
final void setViewerG3dShapeID (Viewer viewer, JmolRendererInterface g3d, int shapeID)

Protected Member Functions

void calcScreenControlPoints ()
void calcScreenControlPoints (Point3f[] points)
Point3i[] calcScreens (float offsetFraction)
void drawLine (int iA, int iB, boolean fill, Point3f vA, Point3f vB, Point3i sA, Point3i sB)
void exportSurface ()
short getLeadColix (int i)
void initRenderer ()
boolean isHelix (int i)
boolean isPolygonDisplayable (int i)
void render ()
void render2 (boolean generateSet)
abstract void renderBioShape (BioShape bioShape)
void renderCone (int i, Point3f pointBegin, Point3f pointEnd, Point3f screenPtBegin, Point3f screenPtEnd)
void renderHermiteArrowHead (int i)
void renderHermiteConic (int i, boolean thisTypeOnly)
void renderHermiteCylinder (Point3i[] screens, int i)
void renderHermiteRibbon (boolean doFill, int i, boolean thisTypeOnly)
void renderPoints ()
void renderTriangles (boolean fill, boolean iShowTriangles, boolean generateSet)

Protected Attributes

boolean antialias
BitSet bsFaces = new BitSet()
BitSet bsVisible = new BitSet()
short colix
short[] colixes
Point3f[] controlPoints
Point3i[] controlPointScreens
int diameter
int exportType
boolean frontOnly
JmolRendererInterface g3d
float imageFontScaling
boolean isCarbohydrate
boolean isNucleic
boolean isTranslucent
Point3f latticeOffset = new Point3f()
int[] leadAtomIndices
short mad
short madBeg
short madEnd
short madMid
short[] mads
Mesh mesh
ModelSet modelSet
int monomerCount
Monomer[] monomers
int myVisibilityFlag
short[] normixes
final Point3f pt1f = new Point3f()
final Point3i pt1i = new Point3i()
final Point3f pt2f = new Point3f()
final Point3i pt2i = new Point3i()
final Point3i pt3i = new Point3i()
Point3i[] ribbonBottomScreens
Point3i[] ribbonTopScreens
float scalePixelsPerMicron
Point3i[] screens
Shape shape
int shapeID
byte[] structureTypes
Point4f thePlane
Vector3f[] transformedVectors
int vertexCount
Point3f[] vertices
Viewer viewer
float width
Vector3f[] wingVectors

Package Attributes

int diameterEnd
int diameterMid
boolean doCap1
int iNext
int iNext2
int iNext3

Private Member Functions

void calc1Screen (Point3f center, Vector3f vector, short mad, float offset_1000, Point3i screen)
boolean checkDiameter (int d)
boolean createMeshCylinder (int i, int madBeg, int madMid, int madEnd, int aspectRatio)
void freeTempArrays ()
boolean initializePolymer (BioShape bioShape)
boolean setMads (int i, boolean thisTypeOnly)
void setNeighbors (int i)
void setStructureTypes ()

Private Attributes

final AxisAngle4f aa = new AxisAngle4f()
int aspectRatio
Point3f[] controlHermites
int diameterBeg
boolean doCap0
boolean haveControlPointScreens
int hermiteLevel
boolean invalidateMesh
boolean invalidateSheets
int iPrev
boolean isHighRes
boolean isTraceAlpha
final Matrix3f mat = new Matrix3f()
Mesh[] meshes
boolean[] meshReady
Vector3f norm = new Vector3f()
final Point3f pointT = new Point3f()
final Point3f pt = new Point3f()
final Point3f pt1 = new Point3f()
final Point3f ptNext = new Point3f()
final Point3f ptPrev = new Point3f()
Point3f[] radiusHermites
boolean ribbonBorder = false
final Point3i screenArrowBot = new Point3i()
final Point3i screenArrowBotPrev = new Point3i()
final Point3i screenArrowTop = new Point3i()
final Point3i screenArrowTopPrev = new Point3i()
float sheetSmoothing
final Vector3f wing = new Vector3f()
final Vector3f wing0 = new Vector3f()
final Vector3f wing1 = new Vector3f()
Vector3f[] wingHermites
final Vector3f wingT = new Vector3f()
final Vector3f Z = new Vector3f(0.1345f, 0.5426f, 0.3675f)

Static Private Attributes

static final int ABSOLUTE_MIN_MESH_SIZE = 3
static final int MIN_MESH_RENDER_SIZE = 8

Detailed Description

Definition at line 47 of file BioShapeRenderer.java.

The documentation for this class was generated from the following file:

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