Examples of javax.vecmath.Point3f

javax.vecmath.Point3f

      iToken = i;
    switch (tok) {
    case Token.lattice:
      if (checkOnly)
        return true;
      Point3f lattice = getPoint3f(iToken + 1, false);
      lattice.x = (int) lattice.x;
      lattice.y = (int) lattice.y;
      lattice.z = (int) lattice.z;
      propertyName = "lattice";
      propertyValue = lattice;

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     * bind "MOUSE-ACTION" actionName bind "MOUSE-ACTION" "script" range
     * [xyrange] [xyrange]
     */
    String mouseAction = stringParameter(1);
    String name = parameterAsString(2);
    Point3f range1 = null;
    Point3f range2 = null;
    if (tokAt(3) == Token.range) {
      range1 = xypParameter(4);
      range2 = xypParameter(++iToken);
      checkLast(iToken);
    } else {

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  public Point3f[] getFrameOffsets(BitSet bsAtoms) {
    if (bsAtoms == null)
      return null;
    Point3f[] offsets = new Point3f[modelCount];
    for (int i = 0; i < modelCount; i++)
      offsets[i] = new Point3f();
    int lastModel = 0;
    int n = 0;
    Point3f offset = offsets[0];
    boolean asTrajectory = (trajectorySteps != null && trajectorySteps.size() == modelCount);
    int m1 = (asTrajectory ? modelCount : 1);
    for (int m = 0; m < m1; m++) {
      if (asTrajectory)
        setTrajectory(m);
      for (int i = 0; i <= atomCount; i++) {
        if (i == atomCount || atoms[i].modelIndex != lastModel) {
          if (n > 0) {
            offset.scale(-1.0f / n);
            if (lastModel != 0)
              offset.sub(offsets[0]);
            n = 0;
          }
          if (i == atomCount)
            break;
          lastModel = atoms[i].modelIndex;
          offset = offsets[lastModel];
        }
        if (!bsAtoms.get(i))
          continue;
        offset.add(atoms[i]);
        n++;
      }
    }
    offsets[0].set(0, 0, 0);
    return offsets;

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   */
  public Point3f[] jvxlDecodeVertexData(String data, boolean asArray) throws Exception {
    int vertexCount = parseInt(XmlReader.getXmlAttrib(data, "count"));
    if (!asArray)
      Logger.info("Reading " + vertexCount + " vertices");
    Point3f min = xr.getXmlPoint(data, "min");
    Point3f range = xr.getXmlPoint(data, "max");
    range.sub(min);
    int colorFractionBase = jvxlData.colorFractionBase;
    int colorFractionRange = jvxlData.colorFractionRange;
    int ptCount = vertexCount * 3;
    Point3f[] vertices = (asArray ? new Point3f[vertexCount] : null);
    Point3f p = (asArray ? null : new Point3f());
    float fraction;
    String s = JvxlCoder.jvxlUncompressString(XmlReader.getXmlAttrib(data, "data"));
    if (s.length() == 0)
      s = xr.getXmlData("jvxlVertexData", data, false, false); 
    for (int i = 0, pt = -1; i < vertexCount; i++) {
      if (asArray)
        p = vertices[i] = new Point3f();
      fraction = JvxlCoder.jvxlFractionFromCharacter2(s.charAt(++pt), s.charAt(pt
          + ptCount), colorFractionBase, colorFractionRange);
      p.x = min.x + fraction * range.x;
      fraction = JvxlCoder.jvxlFractionFromCharacter2(s.charAt(++pt), s.charAt(pt
          + ptCount), colorFractionBase, colorFractionRange);

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  MapFileReader(SurfaceGenerator sg, BufferedReader br) {
    super(sg, br);
    isAngstroms = true;
    adjustment = sg.getParams().center;
    if (adjustment.x == Float.MAX_VALUE)
      adjustment = new Point3f();
  }

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     our z: volVector[2] = vector[mapc - 1]  (fast)
    
     This is because our x is the slowest running variable.
    */               
        
      vectors[0] = new Point3f(1, 0, 0);
    vectors[1] = new Point3f(0, 1, 0);
    vectors[2] = new Point3f(0, 0, 1);
    unitCell.toCartesian(vectors[0], false);
    unitCell.toCartesian(vectors[1], false);
    unitCell.toCartesian(vectors[2], false);


    Logger.info("Jmol unit cell vectors:");

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         Point3f pointB, Point3f pointC, Point3f ptRef, Vector3f vNorm, 
         Vector3f vAB, Vector3f vAC) {
    // for x = plane({atomno=1}, {atomno=2}, {atomno=3}, {atomno=4})
    float nd = getNormalThroughPoints(pointA, pointB, pointC, vNorm, vAB, vAC);
    if (ptRef != null) {
      Point3f pt0 = new Point3f(pointA);
      pt0.add(vNorm);
      float d = pt0.distance(ptRef);
      pt0.set(pointA);
      pt0.sub(vNorm);
      if (d > pt0.distance(ptRef)) {
        vNorm.scale(-1);
        nd = -nd;
      }
    }
    return nd;

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     * Iteration here gets the job done.
     * We now find the projections of the endpoints onto the axis
     * 
     */


    Point3f tempA = new Point3f(points[0]);
    projectOntoAxis(tempA, axisA, axisUnitVector, vectorProjection);
    axisA.set(tempA);
  }

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  public static float findAxis(Point3f[] points, int nPoints, Point3f axisA,
                        Vector3f axisUnitVector, Vector3f vectorProjection) {
    Vector3f sumXiYi = new Vector3f();
    Vector3f vTemp = new Vector3f();
    Point3f pt = new Point3f();
    Point3f ptProj = new Point3f();
    Vector3f a = new Vector3f(axisUnitVector);


    float sum_Xi2 = 0;
    float sum_Yi2 = 0;
    for (int i = nPoints; --i >= 0;) {
      pt.set(points[i]);
      ptProj.set(pt);
      projectOntoAxis(ptProj, axisA, axisUnitVector,
          vectorProjection);
      vTemp.sub(pt, ptProj);
      sum_Yi2 += vTemp.lengthSquared();
      vTemp.cross(vectorProjection, vTemp);

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  }


  public static Point3f[] getCenterAndPoints(List vPts) {
    int n = vPts.size();
    Point3f[] pts = new Point3f[n + 1];
    pts[0] = new Point3f();
    if (n > 0) {
      for (int i = 0; i < n; i++)
        pts[0].add(pts[i + 1] = (Point3f) vPts.get(i));
      pts[0].scale(1f / n);
    }

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