Package org.jmol.shapesurface

Class IsosurfaceMesh

java.lang.Object
org.jmol.util.MeshSurface
org.jmol.shape.Mesh
org.jmol.shapesurface.IsosurfaceMesh
public class IsosurfaceMesh extends Mesh

  • Field Details

    • jvxlData

      public JvxlData jvxlData

    • vertexIncrement

      public int vertexIncrement

    • firstRealVertex

      public int firstRealVertex

    • dataType

      public int dataType

    • hasGridPoints

      public boolean hasGridPoints

    • colorEncoder

      public ColorEncoder colorEncoder

  • Method Details

    • getResolution

      public float getResolution()
      Overrides:
      getResolution in class MeshSurface

    • setTranslucent

      public void setTranslucent(boolean isTranslucent, float iLevel)
      Overrides:
      setTranslucent in class Mesh

    • setMerged

      public void setMerged(boolean TF)

    • sumVertexNormals

      protected void sumVertexNormals(T3[] vertices, V3[] vectorSums)
      Overrides:
      sumVertexNormals in class Mesh

    • getContours

      public Lst<Object>[] getContours()
      create a set of contour data. Each contour is a Vector containing: 0 Integer number of polygons (length of BitSet) 1 BitSet of critical triangles 2 Float value 3 int[] [colorArgb] 4 StringXBuilder containing encoded data for each segment: char type ('3', '6', '5') indicating which two edges of the triangle are connected: '3' 0x011 AB-BC '5' 0x101 AB-CA '6' 0x110 BC-CA char fraction along first edge (jvxlFractionToCharacter) char fraction along second edge (jvxlFractionToCharacter) 5- stream of pairs of points for rendering
      Returns:
      contour vector set

    • getPmeshData

      public Object getPmeshData(boolean isBinary)

    • getPLYData

      public Object getPLYData(boolean isBinary)

    • setContourVector

      public static void setContourVector(Lst<Object> v, int nPolygons, BS bsContour, float value, short colix, int color, SB fData)

    • addContourPoints

      public static void addContourPoints(Lst<Object> v, BS bsContour, int i, SB fData, T3[] vertices, float[] vertexValues, int iA, int iB, int iC, float value)

    • setDiscreteColixes

      public void setDiscreteColixes(float[] values, short[] colixes)

    • reinitializeLightingAndColor

      public void reinitializeLightingAndColor(Viewer vwr)

    • getBoundingBox

      public P3[] getBoundingBox()
      Overrides:
      getBoundingBox in class Mesh

    • setBoundingBox

      public void setBoundingBox(P3[] pts)
      Overrides:
      setBoundingBox in class MeshSurface
      Parameters:
      pts -

    • merge

      protected void merge(MeshData m)

    • getUnitCell

      public SymmetryInterface getUnitCell()
      Overrides:
      getUnitCell in class Mesh
      Returns:
      unitcell

    • getMinDistance2ForVertexGrouping

      protected float getMinDistance2ForVertexGrouping()
      Overrides:
      getMinDistance2ForVertexGrouping in class Mesh

    • getVisibleVertexBitSet

      public BS getVisibleVertexBitSet()
      Overrides:
      getVisibleVertexBitSet in class Mesh

    • updateCoordinates

      public void updateCoordinates(M4 m, BS bs)
      bs will be null if this is a set from the new isosurface MOVE [mat4] command
      Parameters:
      m -
      bs -

    • getInfo

      public Object getInfo(boolean isAll)
      Overrides:
      getInfo in class Mesh

    • getValidValues

      public float[] getValidValues(BS bs)

    • getValidVertices

      public T3[] getValidVertices(BS bs)

    • copyVertexColorMap

      public Map<String,BS> copyVertexColorMap()