Examples of Matrix3f

com.jme.math.Matrix3f
com.jme3.math.Matrix3f
Matrix3f defines a 3x3 matrix. Matrix data is maintained internally and is accessible via the get and set methods. Convenience methods are used for matrix operations as well as generating a matrix from a given set of values. @author Mark Powell @author Joshua Slack
javax.vecmath.Matrix3f
net.rim.device.api.math.Matrix3f

Examples of javax.vecmath.Matrix3f

    float[] f;
    switch (x1.tok) {
    case Token.matrix3f:
      if (n < 0 || n > 2)
        return false;
      Matrix3f m = (Matrix3f) x1.value;
      switch (tok) {
      case Token.row:
        f = new float[3];
        m.getRow(n, f);
        return addX(f);
      case Token.col:
      default:
        f = new float[3];
        m.getColumn(n, f);
        return addX(f);
      }
    case Token.matrix4f:
      if (n < 0 || n > 2)
        return false;

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Examples of javax.vecmath.Matrix3f

            m[pt++] = x;
          }
        }
        if (isMatrix) {
          if (len == 3)
            return addX(new Matrix3f(m));
          return addX(new Matrix4f(m));
        }
      }
    }
    ScriptVariable[] a = new ScriptVariable[args.length];

View Full Code Here

Examples of javax.vecmath.Matrix3f

  private boolean operate() throws ScriptException {


    Token op = oStack[oPt--];
    Point3f pt;
    Point4f pt4;
    Matrix3f m;
    String s;
    float f;


    if (logMessages) {
      dumpStacks("operate: " + op);
    }


    // check for a[3][2] 
    if (isArrayItem && squareCount == 0 && equalCount == 1 && oPt < 0
        && (op.tok == Token.opEQ)) {
      return true;
    }


    ScriptVariable x2 = getX();
    if (x2 == Token.tokenArraySelector)
      return false;


    // unary:


    if (x2.tok == Token.varray || x2.tok == Token.matrix3f
        || x2.tok == Token.matrix4f)
      x2 = ScriptVariable.selectItem(x2);


    if (op.tok == Token.minusMinus || op.tok == Token.plusPlus) {
      if (!isSyntaxCheck && !x2.increment(incrementX))
        return false;
      wasX = true;
      putX(x2); // reverse getX()
      return true;
    }
    if (op.tok == Token.opNot) {
      if (isSyntaxCheck)
        return addX(true);
      switch (x2.tok) {
      case Token.point4f: // quaternion
        return addX((new Quaternion((Point4f) x2.value)).inv().toPoint4f());
      case Token.matrix3f:
        m = new Matrix3f((Matrix3f) x2.value);
        m.invert();
        return addX(m);
      case Token.matrix4f:
        Matrix4f m4 = new Matrix4f((Matrix4f) x2.value);
        m4.invert();
        return addX(m4);
      case Token.bitset:
        return addX(BitSetUtil.copyInvert(ScriptVariable.bsSelect(x2),
            (x2.value instanceof BondSet ? viewer.getBondCount() : viewer
                .getAtomCount())));
      default:
        return addX(!ScriptVariable.bValue(x2));
      }
    }
    int iv = op.intValue & ~Token.minmaxmask;
    if (op.tok == Token.propselector) {
      switch (iv) {
      case Token.length:
        if (!(x2.value instanceof BondSet))
          return addX(ScriptVariable.sizeOf(x2));
        break;
      case Token.size:
        return addX(ScriptVariable.sizeOf(x2));
      case Token.type:
        return addX(ScriptVariable.typeOf(x2));
      case Token.keys:
        if (x2.tok != Token.hash)
          return addX("");
        Object[] keys = ((Map) x2.value).keySet().toArray();
        Arrays.sort(keys);
        String[] ret = new String[keys.length];
        for (int i = 0; i < keys.length; i++)
          ret[i] = (String) keys[i];
        return addX(ret);
      case Token.lines:
        switch (x2.tok) {
        case Token.matrix3f:
        case Token.matrix4f:
          s = ScriptVariable.sValue(x2);
          s = TextFormat.simpleReplace(s.substring(1, s.length() - 1), "],[",
              "]\n[");
          break;
        case Token.string:
          s = (String) x2.value;
          break;
        default:
          s = ScriptVariable.sValue(x2);
        }
        s = TextFormat.simpleReplace(s, "\n\r", "\n").replace('\r', '\n');
        return addX(TextFormat.split(s, '\n'));
      case Token.color:
        switch (x2.tok) {
        case Token.string:
        case Token.varray:
          s = ScriptVariable.sValue(x2);
          pt = new Point3f();
          return addX(Graphics3D.colorPointFromString(s, pt));
        case Token.integer:
        case Token.decimal:
          return addX(viewer.getColorPointForPropertyValue(ScriptVariable
              .fValue(x2)));
        case Token.point3f:
          return addX(Escape.escapeColor(Graphics3D
              .colorPtToInt((Point3f) x2.value)));
        default:
          // handle bitset later
        }
        break;
      case Token.boundbox:
        return (isSyntaxCheck ? addX("x") : getBoundBox(x2));
      }
      if (isSyntaxCheck)
        return addX(ScriptVariable.sValue(x2));
      if (x2.tok == Token.string) {
        Object v = ScriptVariable
            .unescapePointOrBitsetAsVariable(ScriptVariable.sValue(x2));
        if (!(v instanceof ScriptVariable))
          return false;
        x2 = (ScriptVariable) v;
      }
      if (op.tok == x2.tok)
        x2 = getX();
      return getPointOrBitsetOperation(op, x2);
    }


    // binary:
    ScriptVariable x1 = getX();
    if (isSyntaxCheck) {
      if (op == Token.tokenAndFALSE || op == Token.tokenOrTRUE)
        isSyntaxCheck = false;
      return addX(new ScriptVariable(x1));
    }
    switch (op.tok) {
    case Token.opAND:
    case Token.opAnd:
      switch (x1.tok) {
      case Token.bitset:
        BitSet bs = ScriptVariable.bsSelect(x1);
        switch (x2.tok) {
        case Token.bitset:
          bs = BitSetUtil.copy(bs);
          bs.and(ScriptVariable.bsSelect(x2));
          return addX(bs);
        case Token.integer:
          int x = ScriptVariable.iValue(x2);
          return (addX(x < 0 ? false : bs.get(x)));
        }
        break;
      }
      return addX(ScriptVariable.bValue(x1) && ScriptVariable.bValue(x2));
    case Token.opOr:
      switch (x1.tok) {
      case Token.bitset:
        BitSet bs = BitSetUtil.copy(ScriptVariable.bsSelect(x1));
        switch (x2.tok) {
        case Token.bitset:
          bs.or(ScriptVariable.bsSelect(x2));
          return addX(bs);
        case Token.integer:
          int x = ScriptVariable.iValue(x2);
          if (x < 0) 
            break;
          bs.set(x);
          return addX(bs);
        case Token.varray:
          List sv = (ArrayList) x2.value;
          for (int i = sv.size(); --i >= 0;)
            bs.set(ScriptVariable.iValue((ScriptVariable) sv.get(i)));
          return addX(bs);
        }
        break;
      case Token.varray:
        return addX(ScriptVariable.concatList(x1, x2, false));
      }
      return addX(ScriptVariable.bValue(x1) || ScriptVariable.bValue(x2));
    case Token.opXor:
      if (x1.tok == Token.bitset && x2.tok == Token.bitset) {
        BitSet bs = BitSetUtil.copy(ScriptVariable.bsSelect(x1));
        bs.xor(ScriptVariable.bsSelect(x2));
        return addX(bs);
      }
      boolean a = ScriptVariable.bValue(x1);
      boolean b = ScriptVariable.bValue(x2);
      return addX(a && !b || b && !a);
    case Token.opToggle:
      if (x1.tok != Token.bitset || x2.tok != Token.bitset)
        return false;
      return addX(BitSetUtil.toggleInPlace(BitSetUtil.copy(ScriptVariable
          .bsSelect(x1)), ScriptVariable.bsSelect(x2)));
    case Token.opLE:
      return addX(ScriptVariable.fValue(x1) <= ScriptVariable.fValue(x2));
    case Token.opGE:
      return addX(ScriptVariable.fValue(x1) >= ScriptVariable.fValue(x2));
    case Token.opGT:
      return addX(ScriptVariable.fValue(x1) > ScriptVariable.fValue(x2));
    case Token.opLT:
      return addX(ScriptVariable.fValue(x1) < ScriptVariable.fValue(x2));
    case Token.opEQ:
      return addX(ScriptVariable.areEqual(x1, x2));
    case Token.opNE:
      if (x1.tok == Token.string && x2.tok == Token.string)
        return addX(!(ScriptVariable.sValue(x1).equalsIgnoreCase(ScriptVariable
            .sValue(x2))));
      if (x1.tok == Token.point3f && x2.tok == Token.point3f)
        return addX(((Point3f) x1.value).distance((Point3f) x2.value) >= 0.000001);
      if (x1.tok == Token.point4f && x2.tok == Token.point4f)
        return addX(((Point4f) x1.value).distance((Point4f) x2.value) >= 0.000001);
      {
        float f1 = ScriptVariable.fValue(x1);
        float f2 = ScriptVariable.fValue(x2);
        return addX(Float.isNaN(f1) || Float.isNaN(f2)
            || Math.abs(f1 - f2) >= 0.000001);
      }
    case Token.plus:
      switch (x1.tok) {
      default:
        return addX(ScriptVariable.fValue(x1) + ScriptVariable.fValue(x2));
      case Token.varray:
        return addX(ScriptVariable.concatList(x1, x2, true));
      case Token.integer:
        switch (x2.tok) {
        case Token.string:
          if ((s = (ScriptVariable.sValue(x2)).trim()).indexOf(".") < 0
              && s.indexOf("+") <= 0 && s.lastIndexOf("-") <= 0)
            return addX(x1.intValue + ScriptVariable.iValue(x2));
          break;
        case Token.decimal:
          return addX(x1.intValue + ScriptVariable.fValue(x2));
        default:
          return addX(x1.intValue + ScriptVariable.iValue(x2));
        }
      case Token.string:
        return addX(new ScriptVariable(Token.string, ScriptVariable.sValue(x1)
            + ScriptVariable.sValue(x2)));
      case Token.point4f:
        Quaternion q1 = new Quaternion((Point4f) x1.value);
        switch (x2.tok) {
        default:
          return addX(q1.add(ScriptVariable.fValue(x2)).toPoint4f());
        case Token.point4f:
          return addX(q1.mul(new Quaternion((Point4f) x2.value)).toPoint4f());
        }
      case Token.point3f:
        pt = new Point3f((Point3f) x1.value);
        switch (x2.tok) {
        case Token.point3f:
          pt.add((Point3f) x2.value);
          return addX(pt);
        case Token.point4f:
          // extract {xyz}
          pt4 = (Point4f) x2.value;
          pt.add(new Point3f(pt4.x, pt4.y, pt4.z));
          return addX(pt);
        default:
          f = ScriptVariable.fValue(x2);
          return addX(new Point3f(pt.x + f, pt.y + f, pt.z + f));
        }
      case Token.matrix3f:
        switch (x2.tok) {
        default:
          return addX(ScriptVariable.fValue(x1) + ScriptVariable.fValue(x2));
        case Token.matrix3f:
          m = new Matrix3f((Matrix3f) x1.value);
          m.add((Matrix3f) x2.value);
          return addX(m);
        case Token.point3f:
          return addX(getMatrix4f((Matrix3f) x1.value, (Point3f) x2.value));
        }
      }
    case Token.minus:
      if (x1.tok == Token.integer) {
        if (x2.tok == Token.string) {
          if ((s = (ScriptVariable.sValue(x2)).trim()).indexOf(".") < 0
              && s.indexOf("+") <= 0 && s.lastIndexOf("-") <= 0)
            return addX(x1.intValue - ScriptVariable.iValue(x2));
        } else if (x2.tok != Token.decimal)
          return addX(x1.intValue - ScriptVariable.iValue(x2));
      }
      if (x1.tok == Token.string && x2.tok == Token.integer) {
        if ((s = (ScriptVariable.sValue(x1)).trim()).indexOf(".") < 0
            && s.indexOf("+") <= 0 && s.lastIndexOf("-") <= 0)
          return addX(ScriptVariable.iValue(x1) - x2.intValue);
      }
      switch (x1.tok) {
      default:
        return addX(ScriptVariable.fValue(x1) - ScriptVariable.fValue(x2));
      case Token.hash:
        Map ht = new Hashtable((Map) x1.value);
        ht.remove(ScriptVariable.sValue(x2));
        return addX(ScriptVariable.getVariable(ht));
      case Token.matrix3f:
        switch (x2.tok) {
        default:
          return addX(ScriptVariable.fValue(x1) - ScriptVariable.fValue(x2));
        case Token.matrix3f:
          m = new Matrix3f((Matrix3f) x1.value);
          m.sub((Matrix3f) x2.value);
          return addX(m);
        }
      case Token.matrix4f:
        switch (x2.tok) {
        default:
          return addX(ScriptVariable.fValue(x1) - ScriptVariable.fValue(x2));
        case Token.matrix4f:
          Matrix4f m4 = new Matrix4f((Matrix4f) x1.value);
          m4.sub((Matrix4f) x2.value);
          return addX(m4);
        }
      case Token.point3f:
        pt = new Point3f((Point3f) x1.value);
        switch (x2.tok) {
        default:
          f = ScriptVariable.fValue(x2);
          return addX(new Point3f(pt.x - f, pt.y - f, pt.z - f));
        case Token.point3f:
          pt.sub((Point3f) x2.value);
          return addX(pt);
        case Token.point4f:
          // extract {xyz}
          pt4 = (Point4f) x2.value;
          pt.sub(new Point3f(pt4.x, pt4.y, pt4.z));
          return addX(pt);
        }
      case Token.point4f:
        Quaternion q1 = new Quaternion((Point4f) x1.value);
        switch (x2.tok) {
        default:
          return addX(q1.add(-ScriptVariable.fValue(x2)).toPoint4f());
        case Token.point4f:
          Quaternion q2 = new Quaternion((Point4f) x2.value);
          return addX(q2.mul(q1.inv()).toPoint4f());
        }
      }
    case Token.unaryMinus:
      switch (x2.tok) {
      default:
        return addX(-ScriptVariable.fValue(x2));
      case Token.integer:
        return addX(-ScriptVariable.iValue(x2));
      case Token.point3f:
        pt = new Point3f((Point3f) x2.value);
        pt.scale(-1f);
        return addX(pt);
      case Token.point4f:
        pt4 = new Point4f((Point4f) x2.value);
        pt4.scale(-1f);
        return addX(pt4);
      case Token.matrix3f:
        m = new Matrix3f((Matrix3f) x2.value);
        m.transpose();
        return addX(m);
      case Token.matrix4f:
        Matrix4f m4 = new Matrix4f((Matrix4f) x2.value);
        m4.transpose();
        return addX(m4);
      case Token.bitset:
        return addX(BitSetUtil.copyInvert(ScriptVariable.bsSelect(x2),
            (x2.value instanceof BondSet ? viewer.getBondCount() : viewer
                .getAtomCount())));
      }
    case Token.times:
      if (x1.tok == Token.integer && x2.tok != Token.decimal)
        return addX(x1.intValue * ScriptVariable.iValue(x2));
      pt = (x1.tok == Token.matrix3f ? ptValue(x2, false)
          : x2.tok == Token.matrix3f ? ptValue(x1, false) : null);
      pt4 = (x1.tok == Token.matrix4f ? planeValue(x2)
          : x2.tok == Token.matrix4f ? planeValue(x1) : null);
      // checking here to make sure arrays remain arrays and
      // points remain points with matrix operations.
      // we check x2, because x1 could be many things.
      switch (x2.tok) {
      case Token.matrix3f:
        if (pt != null) {
          // pt * m
          Matrix3f m3b = new Matrix3f((Matrix3f) x2.value);
          m3b.transpose();
          m3b.transform(pt);
          if (x1.tok == Token.varray)
            return addX(ScriptVariable.getVariable(new float[] { pt.x, pt.y,
                pt.z }));
          return addX(pt);
        }
        if (pt4 != null) {
          // q * m --> q
          return addX(((new Quaternion(pt4)).mul(new Quaternion(
              (Matrix3f) x2.value))));
        }
        break;
      case Token.matrix4f:
        // pt4 * m4
        // [a b c d] * m4
        if (pt4 != null) {
          Matrix4f m4b = new Matrix4f((Matrix4f) x2.value);
          m4b.transpose();
          m4b.transform(pt4);
          if (x1.tok == Token.varray)
            return addX(ScriptVariable.getVariable(new float[] { pt4.x, pt4.y,
                pt4.z, pt4.w }));
          return addX(pt4);
        }
        break;
      }
      switch (x1.tok) {
      default:
        return addX(ScriptVariable.fValue(x1) * ScriptVariable.fValue(x2));
      case Token.matrix3f:
        Matrix3f m3 = (Matrix3f) x1.value;
        if (pt != null) {
          m3.transform(pt);
          if (x2.tok == Token.varray)
            return addX(ScriptVariable.getVariable(new float[] { pt.x, pt.y,
                pt.z }));
          return addX(pt);
        }
        switch (x2.tok) {
        case Token.matrix3f:
          m = new Matrix3f((Matrix3f) x2.value);
          m.mul(m3, m);
          return addX(m);
        case Token.point4f:
          // m * q
          return addX((new Quaternion(m3)).mul(
              new Quaternion((Point4f) x2.value)).getMatrix());
        default:
          f = ScriptVariable.fValue(x2);
          AxisAngle4f aa = new AxisAngle4f();
          aa.set(m3);
          aa.angle *= f;
          Matrix3f m2 = new Matrix3f();
          m2.set(aa);
          return addX(m2);
        }
      case Token.matrix4f:
        Matrix4f m4 = (Matrix4f) x1.value;
        if (pt != null) {
          m4.transform(pt);
          if (x2.tok == Token.varray)
            return addX(ScriptVariable.getVariable(new float[] { pt.x, pt.y,
                pt.z }));
          return addX(pt);
        }
        if (pt4 != null) {
          m4.transform(pt4);
          if (x2.tok == Token.varray)
            return addX(ScriptVariable.getVariable(new float[] { pt4.x, pt4.y,
                pt4.z, pt4.w }));
          return addX(pt4);
        }
        switch (x2.tok) {
        case Token.matrix4f:
          Matrix4f m4b = new Matrix4f((Matrix4f) x2.value);
          m4b.mul(m4, m4b);
          return addX(m4b);
        default:
          return addX("NaN");
        }
      case Token.point3f:
        pt = new Point3f((Point3f) x1.value);
        switch (x2.tok) {
        case Token.point3f:
          Point3f pt2 = ((Point3f) x2.value);
          return addX(pt.x * pt2.x + pt.y * pt2.y + pt.z * pt2.z);
        default:
          f = ScriptVariable.fValue(x2);
          return addX(new Point3f(pt.x * f, pt.y * f, pt.z * f));
        }
      case Token.point4f:
        switch (x2.tok) {
        case Token.point4f:
          // quaternion multiplication
          // note that Point4f is {x,y,z,w} so we use that for
          // quaternion notation as well here.
          return addX((new Quaternion((Point4f) x1.value)).mul(new Quaternion(
              (Point4f) x2.value)));
        }
        return addX(new Quaternion((Point4f) x1.value).mul(
            ScriptVariable.fValue(x2)).toPoint4f());
      }
    case Token.percent:
      // more than just modulus


      // float % n round to n digits; n = 0 does "nice" rounding
      // String % -n trim to width n; left justify
      // String % n trim to width n; right justify
      // Point3f % n ah... sets to multiple of unit cell!
      // bitset % n
      // Point3f * Point3f does dot product
      // Point3f / Point3f divides by magnitude
      // float * Point3f gets m agnitude
      // Point4f % n returns q0, q1, q2, q3, or theta
      // Point4f % Point4f
      s = null;
      int n = ScriptVariable.iValue(x2);
      switch (x1.tok) {
      case Token.on:
      case Token.off:
      case Token.integer:
      default:
        if (n == 0)
          return addX(0);
        return addX(ScriptVariable.iValue(x1) % n);
      case Token.decimal:
        f = ScriptVariable.fValue(x1);
        // neg is scientific notation
        if (n == 0)
          return addX((int) (f + 0.5f * (f < 0 ? -1 : 1)));
        s = TextFormat.formatDecimal(f, n);
        return addX(s);
      case Token.string:
        s = (String) x1.value;
        if (n == 0)
          return addX(TextFormat.trim(s, "\n\t "));
        if (n == 9999)
          return addX(s.toUpperCase());
        if (n == -9999)
          return addX(s.toLowerCase());
        if (n > 0)
          return addX(TextFormat.format(s, n, n, false, false));
        return addX(TextFormat.format(s, -n, n - 1, true, false));
      case Token.varray:
        String[] list = ScriptVariable.listValue(x1);
        for (int i = 0; i < list.length; i++) {
          if (n == 0)
            list[i] = list[i].trim();
          else if (n > 0)
            list[i] = TextFormat.format(list[i], n, n, true, false);
          else
            list[i] = TextFormat.format(s, -n, n, false, false);
        }
        return addX(list);
      case Token.point3f:
        pt = new Point3f((Point3f) x1.value);
        viewer.toUnitCell(pt, new Point3f(n, n, n));
        return addX(pt);
      case Token.point4f:
        pt4 = (Point4f) x1.value;
        if (x2.tok == Token.point3f)
          return addX((new Quaternion(pt4)).transform((Point3f) x2.value));
        if (x2.tok == Token.point4f) {
          Point4f v4 = new Point4f((Point4f) x2.value);
          (new Quaternion(pt4)).getThetaDirected(v4);
          return addX(v4);
        }
        switch (n) {
        // q%0 w
        // q%1 x
        // q%2 y
        // q%3 z
        // q%4 normal
        // q%-1 vector(1)
        // q%-2 theta
        // q%-3 Matrix column 0
        // q%-4 Matrix column 1
        // q%-5 Matrix column 2
        // q%-6 AxisAngle format
        // q%-9 Matrix format
        case 0:
          return addX(pt4.w);
        case 1:
          return addX(pt4.x);
        case 2:
          return addX(pt4.y);
        case 3:
          return addX(pt4.z);
        case 4:
          return addX((new Quaternion(pt4)).getNormal());
        case -1:
          return addX(new Quaternion(pt4).getVector(-1));
        case -2:
          return addX((new Quaternion(pt4)).getTheta());
        case -3:
          return addX((new Quaternion(pt4)).getVector(0));
        case -4:
          return addX((new Quaternion(pt4)).getVector(1));
        case -5:
          return addX((new Quaternion(pt4)).getVector(2));
        case -6:
          AxisAngle4f ax = (new Quaternion(pt4)).toAxisAngle4f();
          return addX(new Point4f(ax.x, ax.y, ax.z,
              (float) (ax.angle * 180 / Math.PI)));
        case -9:
          return addX((new Quaternion(pt4)).getMatrix());
        default:
          return addX(pt4);
        }
      case Token.matrix4f:
        Matrix4f m4 = (Matrix4f) x1.value;
        switch (n) {
        case 1:
          Matrix3f m3 = new Matrix3f();
          m4.get(m3);
          return addX(m3);
        case 2:
          Vector3f v3 = new Vector3f();
          m4.get(v3);

View Full Code Here

Examples of javax.vecmath.Matrix3f

      a = directLatticeVectors[0];
      b = directLatticeVectors[1];
    } else {
      if (primitiveToCryst == null)
        return true;
      Matrix3f mp = new Matrix3f();
      mp.setColumn(0, directLatticeVectors[0]);
      mp.setColumn(1, directLatticeVectors[1]);
      mp.setColumn(2, directLatticeVectors[2]);
      mp.mul(primitiveToCryst);
      a = new Vector3f();
      b = new Vector3f();
      mp.getColumn(0, a);
      mp.getColumn(1, b);
    }
    matUnitCellOrientation = Quaternion.getQuaternionFrame(new Point3f(), a, b)
        .getMatrix();
    Logger.info("oriented unit cell is in model "
        + atomSetCollection.getAtomSetCount());

View Full Code Here

Examples of javax.vecmath.Matrix3f

   */


  private void readTransformationMatrix() throws Exception {
    float[] f = new float[9];
    fillFloatArray(f, null, 0);
    primitiveToCryst = new Matrix3f(f);
  }

View Full Code Here

Examples of javax.vecmath.Matrix3f

          m4, null, !isSmiles);
      if (Float.isNaN(stddev))
        error(ERROR_invalidArgument);
      Vector3f translation = new Vector3f();
      m4.get(translation);
      Matrix3f m3 = new Matrix3f();
      m4.get(m3);
      q = new Quaternion(m3);
    } else {
      // atoms
      if (bsAtoms1 == null) {

View Full Code Here

Examples of javax.vecmath.Matrix3f

    List ptsA = null;
    Point3f[] points = new Point3f[2];
    Vector3f rotAxis = new Vector3f(0, 1, 0);
    Vector3f translation = null;
    Matrix4f m4 = null;
    Matrix3f m3 = null;
    int direction = 1;
    int tok;
    Quaternion q = null;
    boolean helicalPath = false;
    List ptsB = null;
    BitSet bsCompare = null;
    Point3f invPoint = null;
    Point4f invPlane = null;
    boolean axesOrientationRasmol = viewer.getAxesOrientationRasmol();
    for (int i = 1; i < statementLength; ++i) {
      switch (tok = getToken(i).tok) {
      case Token.bitset:
      case Token.expressionBegin:
      case Token.leftbrace:
      case Token.point3f:
      case Token.dollarsign:
        if (tok == Token.bitset || tok == Token.expressionBegin) {
          if (translation != null || q != null || nPoints == 2) {
            bsAtoms = atomExpression(i);
            ptsB = null;
            isSelected = true;
            break;
          }
        }
        haveRotation = true;
        if (nPoints == 2)
          nPoints = 0;
        // {X, Y, Z}
        // $drawObject[n]
        Point3f pt1 = centerParameter(i, viewer.getCurrentModelIndex());
        if (!isSyntaxCheck && tok == Token.dollarsign
            && tokAt(i + 2) != Token.leftsquare) {
          // rotation about an axis such as $line1
          isMolecular = true;
          rotAxis = getDrawObjectAxis(objectNameParameter(++i), viewer
              .getCurrentModelIndex());
        }
        points[nPoints++] = pt1;
        break;
      case Token.spin:
        isSpin = true;
        continue;
      case Token.internal:
      case Token.molecular:
        isMolecular = true;
        continue;
      case Token.selected:
        isSelected = true;
        break;
      case Token.comma:
        continue;
      case Token.integer:
      case Token.decimal:
        if (endDegrees == Float.MAX_VALUE) {
          endDegrees = floatParameter(i);
        } else {
          degreesPerSecond = floatParameter(i);
          isSpin = (degreesPerSecond != 0);
        }
        continue;
      case Token.minus:
        direction = -1;
        continue;
      case Token.x:
        haveRotation = true;
        rotAxis.set(direction, 0, 0);
        continue;
      case Token.y:
        haveRotation = true;
        rotAxis.set(0, (axesOrientationRasmol && !isMolecular ? -direction
            : direction), 0);
        continue;
      case Token.z:
        haveRotation = true;
        rotAxis.set(0, 0, direction);
        continue;


        // 11.6 options


      case Token.point4f:
      case Token.quaternion:
        if (tok == Token.quaternion)
          i++;
        haveRotation = true;
        q = getQuaternionParameter(i);
        rotAxis.set(q.getNormal());
        endDegrees = q.getTheta();
        break;
      case Token.axisangle:
        haveRotation = true;
        if (isPoint3f(++i)) {
          rotAxis.set(centerParameter(i));
          break;
        }
        Point4f p4 = getPoint4f(i);
        rotAxis.set(p4.x, p4.y, p4.z);
        endDegrees = p4.w;
        q = new Quaternion(rotAxis, endDegrees);
        break;
      case Token.branch:
        haveRotation = true;
        int iAtom1 = atomExpression(++i).nextSetBit(0);
        int iAtom2 = atomExpression(++iToken).nextSetBit(0);
        if (iAtom1 < 0 || iAtom2 < 0)
          return;
        bsAtoms = viewer.getBranchBitSet(iAtom2, iAtom1);
        isSelected = true;
        isMolecular = true;
        points[0] = viewer.getAtomPoint3f(iAtom1);
        points[1] = viewer.getAtomPoint3f(iAtom2);
        nPoints = 2;
        break;


      // 12.0 options


      case Token.translate:
        translation = new Vector3f(centerParameter(++i));
        isMolecular = isSelected = true;
        break;
      case Token.helix:
        // screw motion, for quaternion-based operations
        helicalPath = true;
        continue;
      case Token.symop:
        int symop = intParameter(++i);
        if (isSyntaxCheck)
          continue;
        Hashtable info = viewer.getSpaceGroupInfo(null);
        Object[] op = (info == null ? null : (Object[]) info.get("operations"));
        if (symop == 0 || op == null || op.length < Math.abs(symop))
          error(ERROR_invalidArgument);
        op = (Object[]) op[Math.abs(symop) - 1];
        translation = (Vector3f) op[5];
        invPoint = (Point3f) op[6];
        points[0] = (Point3f) op[7];
        if (op[8] != null)
          rotAxis = (Vector3f) op[8];
        endDegrees = ((Integer) op[9]).intValue();
        if (symop < 0) {
          endDegrees = -endDegrees;
          if (translation != null)
            translation.scale(-1);
        }
        if (endDegrees == 0 && points[0] != null) {
          // glide plane
          invPlane = Measure.getPlaneThroughPoint(points[0], rotAxis);
        }
        q = new Quaternion(rotAxis, endDegrees);
        nPoints = (points[0] == null ? 0 : 1);
        isMolecular = true;
        haveRotation = true;
        isSelected = true;
        continue;
      case Token.compare:
      case Token.matrix4f:
      case Token.matrix3f:
        haveRotation = true;
        if (tok == Token.compare) {
          bsCompare = atomExpression(++i);
          ptsA = viewer.getAtomPointVector(bsCompare);
          if (ptsA == null)
            error(ERROR_invalidArgument, i);
          i = iToken;
          ptsB = getPointVector(getToken(++i), i);
          if (ptsB == null || ptsA.size() != ptsB.size())
            error(ERROR_invalidArgument, i);
          m4 = new Matrix4f();
          points[0] = new Point3f();
          nPoints = 1;
          float stddev = (isSyntaxCheck ? 0 : Measure.getTransformMatrix4(ptsA,
              ptsB, m4, points[0]));
          // if the standard deviation is very small, we leave ptsB
          // because it will be used to set the absolute final positions
          if (stddev > 0.001)
            ptsB = null;
        } else if (tok == Token.matrix4f) {
          m4 = (Matrix4f) theToken.value;
        }
        m3 = new Matrix3f();
        if (m4 != null) {
          translation = new Vector3f();
          m4.get(translation);
          m4.get(m3);
        } else {

View Full Code Here

Examples of javax.vecmath.Matrix3f

    Vector3f z = new Vector3f(0, 0, 1);
    ecc.add(z);
    ecc.normalize();
    if (Float.isNaN(ecc.x)) // was exactly {0 0 -1} -- just rotate about x
      ecc.set(1, 0, 0);
    eccentricityMatrix = new Matrix3f();
    eccentricityMatrix.setIdentity();
    eccentricityMatrix.set(new AxisAngle4f(ecc, (float) Math.PI));
    eccentricityMatrixInverse = new Matrix3f();
    eccentricityMatrixInverse.invert(eccentricityMatrix);
    isEccentric = isAnisotropic = true;
    eccentricityScale = c;
    eccentricityRatio = fab_c;
    if (fab_c > 1)

View Full Code Here

Examples of javax.vecmath.Matrix3f

      }
    }
    if (!Float.isNaN(Parser.parseFloat(str, next)))
      return strMatrix; // overflow
    if (nPoints == 9)
      return new Matrix3f(points);
    if (nPoints == 16)
      return new Matrix4f(points);
    return strMatrix;
  }

View Full Code Here

Examples of javax.vecmath.Matrix3f

      sb.append(']');
      return packageJSON(infoType, sb);
    }
    if (info instanceof Matrix3f) {
      float[] x = new float[3];
      Matrix3f m3 = (Matrix3f) info;
      sb.append('[');
      for (int i = 0; i < 3; i++) {
        if (i > 0)
          sb.append(',');
        m3.getRow(i, x);
        sb.append(toJSON(null, x));
      }
      sb.append(']');
      return packageJSON(infoType, sb);
    }

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