Class BioShapeRenderer

    • Field Detail

      • 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
      • 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 Detail

      • BioShapeRenderer

        BioShapeRenderer()
    • Method Detail

      • renderBioShape

        protected abstract void renderBioShape​(BioShape bioShape)
      • 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)