Class BioShapeRenderer

java.lang.Object
org.jmol.render.ShapeRenderer
org.jmol.renderbio.BioShapeRenderer
Direct Known Subclasses:
BackboneRenderer, StrandsRenderer

abstract class BioShapeRenderer extends ShapeRenderer
Author:
Alexander Rose, Bob Hanson
  • Field Details

    • 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

      protected Monomer[] monomers
    • 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

      protected STR[] structureTypes
    • 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
  • Constructor Details

    • BioShapeRenderer

      BioShapeRenderer()
  • Method Details

    • renderBioShape

      protected abstract void renderBioShape(BioShape bioShape)
    • render

      protected boolean render()
      Specified by:
      render in class ShapeRenderer
    • setGlobals

      private void setGlobals()
    • renderShapes

      private void renderShapes()
    • setBioColix

      protected boolean setBioColix(short colix)
    • freeTempArrays

      private void freeTempArrays()
    • initializePolymer

      private boolean initializePolymer(BioShape bioShape)
    • 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
    • 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
    • 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
    • renderHermiteArrowHead

      protected void renderHermiteArrowHead(int i)
    • drawSegmentAB

      protected void drawSegmentAB(Atom atomA, Atom atomB, short colixA, short colixB, float max)