Field Detail

• jvxlData

  public JvxlData jvxlData

• vertexIncrement

  public int vertexIncrement

• firstRealVertex

  public int firstRealVertex

• dataType

  public int dataType

• hasGridPoints

  public boolean hasGridPoints

• calculatedArea

  java.lang.Object calculatedArea

• calculatedVolume

  java.lang.Object calculatedVolume

• info

  java.lang.Object info

• assocGridPointMap

  private java.util.Map<java.lang.Integer,​java.lang.Integer> assocGridPointMap

• assocGridPointNormals

  private java.util.Map<java.lang.Integer,​javajs.util.V3> assocGridPointNormals

• mergeAssociatedNormalCount

  private int mergeAssociatedNormalCount

• centers

  javajs.util.P3[] centers

• contourValues

  float[] contourValues

• contourColixes

  short[] contourColixes

• colorEncoder

  public ColorEncoder colorEncoder

• bsVdw

  BS bsVdw

• colorPhased

  public boolean colorPhased

Constructor Detail

• IsosurfaceMesh

  IsosurfaceMesh​(Viewer vwr,
                 java.lang.String thisID,
                 short colix,
                 int index)

  Parameters:

  vwr -

  thisID -

  colix -

  index -

Method Detail

• getResolution

  public float getResolution()

  Overrides:

  getResolution in class MeshSurface

• clearType

  void clearType​(java.lang.String meshType,
                 boolean iAddGridPoints)

• allocVertexColixes

  void allocVertexColixes()

• addVertexCopy

  int addVertexCopy​(javajs.util.T3 vertex,
                    float value,
                    int assocVertex,
                    boolean associateNormals,
                    boolean asCopy)

• setTranslucent

  public void setTranslucent​(boolean isTranslucent,
                             float iLevel)

  Overrides:

  setTranslucent in class Mesh

• setMerged

  public void setMerged​(boolean TF)

• sumVertexNormals

  protected void sumVertexNormals​(javajs.util.T3[] vertices,
                                  javajs.util.V3[] vectorSums)

  Overrides:

  sumVertexNormals in class Mesh

• getCenters

  javajs.util.P3[] getCenters()

• getContours

  public javajs.util.Lst<java.lang.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

• get3dContour

  private static void get3dContour​(IsosurfaceMesh m,
                                   javajs.util.Lst<java.lang.Object> v,
                                   float value,
                                   short colix)

• setContourVector

  public static void setContourVector​(javajs.util.Lst<java.lang.Object> v,
                                      int nPolygons,
                                      BS bsContour,
                                      float value,
                                      short colix,
                                      int color,
                                      javajs.util.SB fData)

• addContourPoints

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

• checkPt

  private static float checkPt​(float[] vertexValues,
                               int i,
                               int j,
                               float v)

  two values -- v1, and v2, which need not be ordered v1 < v2. v == v1 --> 0 v == v2 --> 1 v1 < v < v2 --> f in (0,1) v2 < v < v1 --> f in (0,1) i.e. (v1 < v) == (v < v2) We check AB, then (usually) BC, then (sometimes) CA. What if two end points are identical values? So, for example, if v = 1.0 and: A 1.0 0.5 1.0 1.0 / \ / \ / \ / \ / \ / \ / \ / \ / \ / \ C-----B 1.0--0.5 1.0--1.0 0.5--1.0 1.0---1.0 case I case II case III case IV case I: AB[0] and BC[1], type == 3 --> CA not tested. case II: AB[1] and CA[0]; f1 == 1.0 --> BC not tested. case III: AB[0] and BC[0], type == 3 --> CA not tested. case IV: AB[0] and BC[0], type == 3 --> CA not tested. what if v = 0.5? case I: AB[1]; BC not tested --> type == 1, invalid. case II: AB[0]; type == 1, f1 == 0.0 --> CA not tested. case III: BC[1]; f2 == 1.0 --> CA not tested.

  Parameters:

  vertexValues -

  i -

  j -

  v -

  Returns:

  fraction along the edge or NaN

• getContourPoint

  private static javajs.util.P3 getContourPoint​(javajs.util.T3[] vertices,
                                                int i,
                                                int j,
                                                float f)

• setDiscreteColixes

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

• getContourList

  java.util.Map<java.lang.String,​java.lang.Object> getContourList​(Viewer vwr)

  Parameters:

  vwr -

  Returns:

  a Hashtable containing "values" and "colors"

• deleteContours

  void deleteContours()

• setVertexColorMap

  void setVertexColorMap()

• setVertexColixesForAtoms

  void setVertexColixesForAtoms​(Viewer vwr,
                                short[] colixes,
                                int[] atomMap,
                                BS bs)

• colorVertices

  void colorVertices​(short colix,
                     BS bs,
                     boolean isAtoms)

  color a specific set of vertices a specific color

  Parameters:

  colix -

  bs -

  isAtoms -

• checkAllocColixes

  void checkAllocColixes()

• addColorToMap

  private static void addColorToMap​(java.util.Map<java.lang.String,​BS> colorMap,
                                    java.lang.String color,
                                    BS bs)

  adds a set of specifically-colored vertices to the map, ensuring that no vertex is in two maps.

  Parameters:

  colorMap -

  color -

  bs -

• setJvxlColorMap

  void setJvxlColorMap​(boolean isAll)

  set up the jvxlData fields needed for either just the header (isAll = false) or the full file (isAll = true)

  Parameters:

  isAll -

• setColorCommand

  void setColorCommand()

  just sets the color command for this isosurface.

• setColorsFromJvxlData

  boolean setColorsFromJvxlData​(int colorRgb)

  from Isosurface.notifySurfaceGenerationCompleted() starting with Jmol 12.1.50, JVXL files contain color, translucency, color scheme information, and vertex color mappings (as from COLOR ISOSURFACE {hydrophobic} WHITE), returning these settings when the JVXL file is opened.

  Parameters:

  colorRgb -

  Returns:

  true if still need color handling

• setJvxlDataRendering

  void setJvxlDataRendering()

• remapColors

  void remapColors​(Viewer vwr,
                   ColorEncoder ce,
                   float translucentLevel)

  remaps colors based on a new color scheme or translucency level

  Parameters:

  vwr -

  ce -

  translucentLevel -

• reinitializeLightingAndColor

  public void reinitializeLightingAndColor​(Viewer vwr)

• getBoundingBox

  public javajs.util.P3[] getBoundingBox()

  Overrides:

  getBoundingBox in class Mesh

• setBoundingBox

  public void setBoundingBox​(javajs.util.P3[] pts)

  Overrides:

  setBoundingBox in class MeshSurface

• merge

  protected void merge​(MeshData m)

• mergePolygons

  private static int mergePolygons​(MeshSurface m,
                                   int ipt,
                                   int vertexCount,
                                   int[][] newPolygons)

• getUnitCell

  public SymmetryInterface getUnitCell()

  Overrides:

  getUnitCell in class Mesh

  Returns:

  unitcell

• fixLattice

  void fixLattice()

• getMinDistance2ForVertexGrouping

  protected float getMinDistance2ForVertexGrouping()

  Overrides:

  getMinDistance2ForVertexGrouping in class Mesh

• getVisibleVertexBitSet

  public BS getVisibleVertexBitSet()

  Overrides:

  getVisibleVertexBitSet in class Mesh

• updateCoordinates

  public void updateCoordinates​(javajs.util.M4 m,
                                BS bs)

  bs will be null if this is a set from the new isosurface MOVE [mat4] command

  Parameters:

  m -

  bs -

• getDataRange

  float[] getDataRange()