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 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 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)

• 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)