-Clazz.declarePackage ("javajs.util");
-Clazz.load (["javajs.util.V3"], "javajs.util.Measure", ["java.lang.Float", "javajs.api.Interface", "javajs.util.Lst", "$.P3", "$.P4", "$.Quat"], function () {
-c$ = Clazz.declareType (javajs.util, "Measure");
-c$.computeAngle = Clazz.defineMethod (c$, "computeAngle",
-function (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees) {
-vectorBA.sub2 (pointA, pointB);
-vectorBC.sub2 (pointC, pointB);
-var angle = vectorBA.angle (vectorBC);
-return (asDegrees ? angle / 0.017453292 : angle);
-}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,~B");
-c$.computeAngleABC = Clazz.defineMethod (c$, "computeAngleABC",
-function (pointA, pointB, pointC, asDegrees) {
-var vectorBA = new javajs.util.V3 ();
-var vectorBC = new javajs.util.V3 ();
-return javajs.util.Measure.computeAngle (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees);
-}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,~B");
-c$.computeTorsion = Clazz.defineMethod (c$, "computeTorsion",
-function (p1, p2, p3, p4, asDegrees) {
-var ijx = p1.x - p2.x;
-var ijy = p1.y - p2.y;
-var ijz = p1.z - p2.z;
-var kjx = p3.x - p2.x;
-var kjy = p3.y - p2.y;
-var kjz = p3.z - p2.z;
-var klx = p3.x - p4.x;
-var kly = p3.y - p4.y;
-var klz = p3.z - p4.z;
-var ax = ijy * kjz - ijz * kjy;
-var ay = ijz * kjx - ijx * kjz;
-var az = ijx * kjy - ijy * kjx;
-var cx = kjy * klz - kjz * kly;
-var cy = kjz * klx - kjx * klz;
-var cz = kjx * kly - kjy * klx;
-var ai2 = 1 / (ax * ax + ay * ay + az * az);
-var ci2 = 1 / (cx * cx + cy * cy + cz * cz);
-var ai = Math.sqrt (ai2);
-var ci = Math.sqrt (ci2);
-var denom = ai * ci;
-var cross = ax * cx + ay * cy + az * cz;
-var cosang = cross * denom;
-if (cosang > 1) {
-cosang = 1;
-}if (cosang < -1) {
-cosang = -1;
-}var torsion = Math.acos (cosang);
-var dot = ijx * cx + ijy * cy + ijz * cz;
-var absDot = Math.abs (dot);
-torsion = (dot / absDot > 0) ? torsion : -torsion;
-return (asDegrees ? torsion / 0.017453292 : torsion);
-}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,~B");
-c$.computeHelicalAxis = Clazz.defineMethod (c$, "computeHelicalAxis",
-function (a, b, dq) {
-var vab = new javajs.util.V3 ();
-vab.sub2 (b, a);
-var theta = dq.getTheta ();
-var n = dq.getNormal ();
-var v_dot_n = vab.dot (n);
-if (Math.abs (v_dot_n) < 0.0001) v_dot_n = 0;
-var va_prime_d = new javajs.util.V3 ();
-va_prime_d.cross (vab, n);
-if (va_prime_d.dot (va_prime_d) != 0) va_prime_d.normalize ();
-var vda = new javajs.util.V3 ();
-var vcb = javajs.util.V3.newV (n);
-if (v_dot_n == 0) v_dot_n = 1.4E-45;
-vcb.scale (v_dot_n);
-vda.sub2 (vcb, vab);
-vda.scale (0.5);
-va_prime_d.scale (theta == 0 ? 0 : (vda.length () / Math.tan (theta / 2 / 180 * 3.141592653589793)));
-var r = javajs.util.V3.newV (va_prime_d);
-if (theta != 0) r.add (vda);
-var pt_a_prime = javajs.util.P3.newP (a);
-pt_a_prime.sub (r);
-if (v_dot_n != 1.4E-45) n.scale (v_dot_n);
-var pt_b_prime = javajs.util.P3.newP (pt_a_prime);
-pt_b_prime.add (n);
-theta = javajs.util.Measure.computeTorsion (a, pt_a_prime, pt_b_prime, b, true);
-if (Float.isNaN (theta) || r.length () < 0.0001) theta = dq.getThetaDirectedV (n);
-var residuesPerTurn = Math.abs (theta == 0 ? 0 : 360 / theta);
-var pitch = Math.abs (v_dot_n == 1.4E-45 ? 0 : n.length () * (theta == 0 ? 1 : 360 / theta));
-return Clazz.newArray (-1, [pt_a_prime, n, r, javajs.util.P3.new3 (theta, pitch, residuesPerTurn), pt_b_prime]);
-}, "javajs.util.P3,javajs.util.P3,javajs.util.Quat");
-c$.getPlaneThroughPoints = Clazz.defineMethod (c$, "getPlaneThroughPoints",
-function (pointA, pointB, pointC, vNorm, vAB, plane) {
-var w = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB);
-plane.set4 (vNorm.x, vNorm.y, vNorm.z, w);
-return plane;
-}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,javajs.util.P4");
-c$.getPlaneThroughPoint = Clazz.defineMethod (c$, "getPlaneThroughPoint",
-function (pt, normal, plane) {
-plane.set4 (normal.x, normal.y, normal.z, -normal.dot (pt));
-}, "javajs.util.T3,javajs.util.V3,javajs.util.P4");
-c$.distanceToPlane = Clazz.defineMethod (c$, "distanceToPlane",
-function (plane, pt) {
-return (plane == null ? NaN : (plane.dot (pt) + plane.w) / Math.sqrt (plane.dot (plane)));
-}, "javajs.util.P4,javajs.util.T3");
-c$.directedDistanceToPlane = Clazz.defineMethod (c$, "directedDistanceToPlane",
-function (pt, plane, ptref) {
-var f = plane.dot (pt) + plane.w;
-var f1 = plane.dot (ptref) + plane.w;
-return Math.signum (f1) * f / Math.sqrt (plane.dot (plane));
-}, "javajs.util.P3,javajs.util.P4,javajs.util.P3");
-c$.distanceToPlaneD = Clazz.defineMethod (c$, "distanceToPlaneD",
-function (plane, d, pt) {
-return (plane == null ? NaN : (plane.dot (pt) + plane.w) / d);
-}, "javajs.util.P4,~N,javajs.util.P3");
-c$.distanceToPlaneV = Clazz.defineMethod (c$, "distanceToPlaneV",
-function (norm, w, pt) {
-return (norm == null ? NaN : (norm.dot (pt) + w) / Math.sqrt (norm.dot (norm)));
-}, "javajs.util.V3,~N,javajs.util.P3");
-c$.calcNormalizedNormal = Clazz.defineMethod (c$, "calcNormalizedNormal",
-function (pointA, pointB, pointC, vNormNorm, vAB) {
-vAB.sub2 (pointB, pointA);
-vNormNorm.sub2 (pointC, pointA);
-vNormNorm.cross (vAB, vNormNorm);
-vNormNorm.normalize ();
-}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3");
-c$.getDirectedNormalThroughPoints = Clazz.defineMethod (c$, "getDirectedNormalThroughPoints",
-function (pointA, pointB, pointC, ptRef, vNorm, vAB) {
-var nd = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB);
-if (ptRef != null) {
-var pt0 = javajs.util.P3.newP (pointA);
-pt0.add (vNorm);
-var d = pt0.distance (ptRef);
-pt0.sub2 (pointA, vNorm);
-if (d > pt0.distance (ptRef)) {
-vNorm.scale (-1);
-nd = -nd;
-}}return nd;
-}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3");
-c$.getNormalThroughPoints = Clazz.defineMethod (c$, "getNormalThroughPoints",
-function (pointA, pointB, pointC, vNorm, vTemp) {
-javajs.util.Measure.calcNormalizedNormal (pointA, pointB, pointC, vNorm, vTemp);
-vTemp.setT (pointA);
-return -vTemp.dot (vNorm);
-}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3");
-c$.getPlaneProjection = Clazz.defineMethod (c$, "getPlaneProjection",
-function (pt, plane, ptProj, vNorm) {
-var dist = javajs.util.Measure.distanceToPlane (plane, pt);
-vNorm.set (plane.x, plane.y, plane.z);
-vNorm.normalize ();
-vNorm.scale (-dist);
-ptProj.add2 (pt, vNorm);
-}, "javajs.util.P3,javajs.util.P4,javajs.util.P3,javajs.util.V3");
-c$.getNormalToLine = Clazz.defineMethod (c$, "getNormalToLine",
-function (pointA, pointB, vNormNorm) {
-vNormNorm.sub2 (pointA, pointB);
-vNormNorm.cross (vNormNorm, javajs.util.Measure.axisY);
-vNormNorm.normalize ();
-if (Float.isNaN (vNormNorm.x)) vNormNorm.set (1, 0, 0);
-}, "javajs.util.P3,javajs.util.P3,javajs.util.V3");
-c$.getBisectingPlane = Clazz.defineMethod (c$, "getBisectingPlane",
-function (pointA, vAB, ptTemp, vTemp, plane) {
-ptTemp.scaleAdd2 (0.5, vAB, pointA);
-vTemp.setT (vAB);
-vTemp.normalize ();
-javajs.util.Measure.getPlaneThroughPoint (ptTemp, vTemp, plane);
-}, "javajs.util.P3,javajs.util.V3,javajs.util.T3,javajs.util.V3,javajs.util.P4");
-c$.projectOntoAxis = Clazz.defineMethod (c$, "projectOntoAxis",
-function (point, axisA, axisUnitVector, vectorProjection) {
-vectorProjection.sub2 (point, axisA);
-var projectedLength = vectorProjection.dot (axisUnitVector);
-point.scaleAdd2 (projectedLength, axisUnitVector, axisA);
-vectorProjection.sub2 (point, axisA);
-}, "javajs.util.P3,javajs.util.P3,javajs.util.V3,javajs.util.V3");
-c$.calcBestAxisThroughPoints = Clazz.defineMethod (c$, "calcBestAxisThroughPoints",
-function (points, axisA, axisUnitVector, vectorProjection, nTriesMax) {
-var nPoints = points.length;
-axisA.setT (points[0]);
-axisUnitVector.sub2 (points[nPoints - 1], axisA);
-axisUnitVector.normalize ();
-javajs.util.Measure.calcAveragePointN (points, nPoints, axisA);
-var nTries = 0;
-while (nTries++ < nTriesMax && javajs.util.Measure.findAxis (points, nPoints, axisA, axisUnitVector, vectorProjection) > 0.001) {
-}
-var tempA = javajs.util.P3.newP (points[0]);
-javajs.util.Measure.projectOntoAxis (tempA, axisA, axisUnitVector, vectorProjection);
-axisA.setT (tempA);
-}, "~A,javajs.util.P3,javajs.util.V3,javajs.util.V3,~N");
-c$.findAxis = Clazz.defineMethod (c$, "findAxis",
-function (points, nPoints, axisA, axisUnitVector, vectorProjection) {
-var sumXiYi = new javajs.util.V3 ();
-var vTemp = new javajs.util.V3 ();
-var pt = new javajs.util.P3 ();
-var ptProj = new javajs.util.P3 ();
-var a = javajs.util.V3.newV (axisUnitVector);
-var sum_Xi2 = 0;
-for (var i = nPoints; --i >= 0; ) {
-pt.setT (points[i]);
-ptProj.setT (pt);
-javajs.util.Measure.projectOntoAxis (ptProj, axisA, axisUnitVector, vectorProjection);
-vTemp.sub2 (pt, ptProj);
-vTemp.cross (vectorProjection, vTemp);
-sumXiYi.add (vTemp);
-sum_Xi2 += vectorProjection.lengthSquared ();
-}
-var m = javajs.util.V3.newV (sumXiYi);
-m.scale (1 / sum_Xi2);
-vTemp.cross (m, axisUnitVector);
-axisUnitVector.add (vTemp);
-axisUnitVector.normalize ();
-vTemp.sub2 (axisUnitVector, a);
-return vTemp.length ();
-}, "~A,~N,javajs.util.P3,javajs.util.V3,javajs.util.V3");
-c$.calcAveragePoint = Clazz.defineMethod (c$, "calcAveragePoint",
-function (pointA, pointB, pointC) {
-pointC.set ((pointA.x + pointB.x) / 2, (pointA.y + pointB.y) / 2, (pointA.z + pointB.z) / 2);
-}, "javajs.util.P3,javajs.util.P3,javajs.util.P3");
-c$.calcAveragePointN = Clazz.defineMethod (c$, "calcAveragePointN",
-function (points, nPoints, averagePoint) {
-averagePoint.setT (points[0]);
-for (var i = 1; i < nPoints; i++) averagePoint.add (points[i]);
-
-averagePoint.scale (1 / nPoints);
-}, "~A,~N,javajs.util.P3");
-c$.transformPoints = Clazz.defineMethod (c$, "transformPoints",
-function (vPts, m4, center) {
-var v = new javajs.util.Lst ();
-for (var i = 0; i < vPts.size (); i++) {
-var pt = javajs.util.P3.newP (vPts.get (i));
-pt.sub (center);
-m4.rotTrans (pt);
-pt.add (center);
-v.addLast (pt);
-}
-return v;
-}, "javajs.util.Lst,javajs.util.M4,javajs.util.P3");
-c$.isInTetrahedron = Clazz.defineMethod (c$, "isInTetrahedron",
-function (pt, ptA, ptB, ptC, ptD, plane, vTemp, vTemp2, fullyEnclosed) {
-var b = (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptC, ptD, ptA, vTemp, vTemp2, plane), pt) >= 0);
-if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptD, ptB, vTemp, vTemp2, plane), pt) >= 0)) return false;
-if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptB, ptD, ptC, vTemp, vTemp2, plane), pt) >= 0)) return false;
-var d = javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptB, ptC, vTemp, vTemp2, plane), pt);
-if (fullyEnclosed) return (b == (d >= 0));
-var d1 = javajs.util.Measure.distanceToPlane (plane, ptD);
-return d1 * d <= 0 || Math.abs (d1) > Math.abs (d);
-}, "javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P4,javajs.util.V3,javajs.util.V3,~B");
-c$.getIntersectionPP = Clazz.defineMethod (c$, "getIntersectionPP",
-function (plane1, plane2) {
-var a1 = plane1.x;
-var b1 = plane1.y;
-var c1 = plane1.z;
-var d1 = plane1.w;
-var a2 = plane2.x;
-var b2 = plane2.y;
-var c2 = plane2.z;
-var d2 = plane2.w;
-var norm1 = javajs.util.V3.new3 (a1, b1, c1);
-var norm2 = javajs.util.V3.new3 (a2, b2, c2);
-var nxn = new javajs.util.V3 ();
-nxn.cross (norm1, norm2);
-var ax = Math.abs (nxn.x);
-var ay = Math.abs (nxn.y);
-var az = Math.abs (nxn.z);
-var x;
-var y;
-var z;
-var diff;
-var type = (ax > ay ? (ax > az ? 1 : 3) : ay > az ? 2 : 3);
-switch (type) {
-case 1:
-x = 0;
-diff = (b1 * c2 - b2 * c1);
-if (Math.abs (diff) < 0.01) return null;
-y = (c1 * d2 - c2 * d1) / diff;
-z = (b2 * d1 - d2 * b1) / diff;
-break;
-case 2:
-diff = (a1 * c2 - a2 * c1);
-if (Math.abs (diff) < 0.01) return null;
-x = (c1 * d2 - c2 * d1) / diff;
-y = 0;
-z = (a2 * d1 - d2 * a1) / diff;
-break;
-case 3:
-default:
-diff = (a1 * b2 - a2 * b1);
-if (Math.abs (diff) < 0.01) return null;
-x = (b1 * d2 - b2 * d1) / diff;
-y = (a2 * d1 - d2 * a1) / diff;
-z = 0;
-}
-var list = new javajs.util.Lst ();
-list.addLast (javajs.util.P3.new3 (x, y, z));
-nxn.normalize ();
-list.addLast (nxn);
-return list;
-}, "javajs.util.P4,javajs.util.P4");
-c$.getIntersection = Clazz.defineMethod (c$, "getIntersection",
-function (pt1, v, plane, ptRet, tempNorm, vTemp) {
-javajs.util.Measure.getPlaneProjection (pt1, plane, ptRet, tempNorm);
-tempNorm.set (plane.x, plane.y, plane.z);
-tempNorm.normalize ();
-if (v == null) v = javajs.util.V3.newV (tempNorm);
-var l_dot_n = v.dot (tempNorm);
-if (Math.abs (l_dot_n) < 0.01) return null;
-vTemp.sub2 (ptRet, pt1);
-ptRet.scaleAdd2 (vTemp.dot (tempNorm) / l_dot_n, v, pt1);
-return ptRet;
-}, "javajs.util.P3,javajs.util.V3,javajs.util.P4,javajs.util.P3,javajs.util.V3,javajs.util.V3");
-c$.calculateQuaternionRotation = Clazz.defineMethod (c$, "calculateQuaternionRotation",
-function (centerAndPoints, retStddev) {
-retStddev[1] = NaN;
-var q = new javajs.util.Quat ();
-if (centerAndPoints[0].length == 1 || centerAndPoints[0].length != centerAndPoints[1].length) return q;
-var n = centerAndPoints[0].length - 1;
-if (n < 2) return q;
-var Sxx = 0;
-var Sxy = 0;
-var Sxz = 0;
-var Syx = 0;
-var Syy = 0;
-var Syz = 0;
-var Szx = 0;
-var Szy = 0;
-var Szz = 0;
-var ptA = new javajs.util.P3 ();
-var ptB = new javajs.util.P3 ();
-for (var i = n + 1; --i >= 1; ) {
-var aij = centerAndPoints[0][i];
-var bij = centerAndPoints[1][i];
-ptA.sub2 (aij, centerAndPoints[0][0]);
-ptB.sub2 (bij, centerAndPoints[0][1]);
-Sxx += ptA.x * ptB.x;
-Sxy += ptA.x * ptB.y;
-Sxz += ptA.x * ptB.z;
-Syx += ptA.y * ptB.x;
-Syy += ptA.y * ptB.y;
-Syz += ptA.y * ptB.z;
-Szx += ptA.z * ptB.x;
-Szy += ptA.z * ptB.y;
-Szz += ptA.z * ptB.z;
-}
-retStddev[0] = javajs.util.Measure.getRmsd (centerAndPoints, q);
-var N = Clazz.newDoubleArray (4, 4, 0);
-N[0][0] = Sxx + Syy + Szz;
-N[0][1] = N[1][0] = Syz - Szy;
-N[0][2] = N[2][0] = Szx - Sxz;
-N[0][3] = N[3][0] = Sxy - Syx;
-N[1][1] = Sxx - Syy - Szz;
-N[1][2] = N[2][1] = Sxy + Syx;
-N[1][3] = N[3][1] = Szx + Sxz;
-N[2][2] = -Sxx + Syy - Szz;
-N[2][3] = N[3][2] = Syz + Szy;
-N[3][3] = -Sxx - Syy + Szz;
-var v = (javajs.api.Interface.getInterface ("javajs.util.Eigen")).setM (N).getEigenvectorsFloatTransposed ()[3];
-q = javajs.util.Quat.newP4 (javajs.util.P4.new4 (v[1], v[2], v[3], v[0]));
-retStddev[1] = javajs.util.Measure.getRmsd (centerAndPoints, q);
-return q;
-}, "~A,~A");
-c$.getTransformMatrix4 = Clazz.defineMethod (c$, "getTransformMatrix4",
-function (ptsA, ptsB, m, centerA) {
-var cptsA = javajs.util.Measure.getCenterAndPoints (ptsA);
-var cptsB = javajs.util.Measure.getCenterAndPoints (ptsB);
-var retStddev = Clazz.newFloatArray (2, 0);
-var q = javajs.util.Measure.calculateQuaternionRotation ( Clazz.newArray (-1, [cptsA, cptsB]), retStddev);
-var r = q.getMatrix ();
-if (centerA == null) r.rotate (cptsA[0]);
- else centerA.setT (cptsA[0]);
-var t = javajs.util.V3.newVsub (cptsB[0], cptsA[0]);
-m.setMV (r, t);
-return retStddev[1];
-}, "javajs.util.Lst,javajs.util.Lst,javajs.util.M4,javajs.util.P3");
-c$.getCenterAndPoints = Clazz.defineMethod (c$, "getCenterAndPoints",
-function (vPts) {
-var n = vPts.size ();
-var pts = new Array (n + 1);
-pts[0] = new javajs.util.P3 ();
-if (n > 0) {
-for (var i = 0; i < n; i++) {
-pts[0].add (pts[i + 1] = vPts.get (i));
-}
-pts[0].scale (1 / n);
-}return pts;
-}, "javajs.util.Lst");
-c$.getRmsd = Clazz.defineMethod (c$, "getRmsd",
-function (centerAndPoints, q) {
-var sum2 = 0;
-var ptsA = centerAndPoints[0];
-var ptsB = centerAndPoints[1];
-var cA = ptsA[0];
-var cB = ptsB[0];
-var n = ptsA.length - 1;
-var ptAnew = new javajs.util.P3 ();
-for (var i = n + 1; --i >= 1; ) {
-ptAnew.sub2 (ptsA[i], cA);
-q.transform2 (ptAnew, ptAnew).add (cB);
-sum2 += ptAnew.distanceSquared (ptsB[i]);
-}
-return Math.sqrt (sum2 / n);
-}, "~A,javajs.util.Quat");
-Clazz.defineStatics (c$,
-"radiansPerDegree", (0.017453292519943295));
-c$.axisY = c$.prototype.axisY = javajs.util.V3.new3 (0, 1, 0);
-});
+Clazz.declarePackage ("javajs.util");\r
+Clazz.load (["javajs.util.V3"], "javajs.util.Measure", ["java.lang.Float", "javajs.api.Interface", "javajs.util.Lst", "$.P3", "$.P4", "$.Quat"], function () {\r
+c$ = Clazz.declareType (javajs.util, "Measure");\r
+c$.computeAngle = Clazz.defineMethod (c$, "computeAngle", \r
+function (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees) {\r
+vectorBA.sub2 (pointA, pointB);\r
+vectorBC.sub2 (pointC, pointB);\r
+var angle = vectorBA.angle (vectorBC);\r
+return (asDegrees ? angle / 0.017453292 : angle);\r
+}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,~B");\r
+c$.computeAngleABC = Clazz.defineMethod (c$, "computeAngleABC", \r
+function (pointA, pointB, pointC, asDegrees) {\r
+var vectorBA = new javajs.util.V3 ();\r
+var vectorBC = new javajs.util.V3 ();\r
+return javajs.util.Measure.computeAngle (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees);\r
+}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,~B");\r
+c$.computeTorsion = Clazz.defineMethod (c$, "computeTorsion", \r
+function (p1, p2, p3, p4, asDegrees) {\r
+var ijx = p1.x - p2.x;\r
+var ijy = p1.y - p2.y;\r
+var ijz = p1.z - p2.z;\r
+var kjx = p3.x - p2.x;\r
+var kjy = p3.y - p2.y;\r
+var kjz = p3.z - p2.z;\r
+var klx = p3.x - p4.x;\r
+var kly = p3.y - p4.y;\r
+var klz = p3.z - p4.z;\r
+var ax = ijy * kjz - ijz * kjy;\r
+var ay = ijz * kjx - ijx * kjz;\r
+var az = ijx * kjy - ijy * kjx;\r
+var cx = kjy * klz - kjz * kly;\r
+var cy = kjz * klx - kjx * klz;\r
+var cz = kjx * kly - kjy * klx;\r
+var ai2 = 1 / (ax * ax + ay * ay + az * az);\r
+var ci2 = 1 / (cx * cx + cy * cy + cz * cz);\r
+var ai = Math.sqrt (ai2);\r
+var ci = Math.sqrt (ci2);\r
+var denom = ai * ci;\r
+var cross = ax * cx + ay * cy + az * cz;\r
+var cosang = cross * denom;\r
+if (cosang > 1) {\r
+cosang = 1;\r
+}if (cosang < -1) {\r
+cosang = -1;\r
+}var torsion = Math.acos (cosang);\r
+var dot = ijx * cx + ijy * cy + ijz * cz;\r
+var absDot = Math.abs (dot);\r
+torsion = (dot / absDot > 0) ? torsion : -torsion;\r
+return (asDegrees ? torsion / 0.017453292 : torsion);\r
+}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,~B");\r
+c$.computeHelicalAxis = Clazz.defineMethod (c$, "computeHelicalAxis", \r
+function (a, b, dq) {\r
+var vab = new javajs.util.V3 ();\r
+vab.sub2 (b, a);\r
+var theta = dq.getTheta ();\r
+var n = dq.getNormal ();\r
+var v_dot_n = vab.dot (n);\r
+if (Math.abs (v_dot_n) < 0.0001) v_dot_n = 0;\r
+var va_prime_d = new javajs.util.V3 ();\r
+va_prime_d.cross (vab, n);\r
+if (va_prime_d.dot (va_prime_d) != 0) va_prime_d.normalize ();\r
+var vda = new javajs.util.V3 ();\r
+var vcb = javajs.util.V3.newV (n);\r
+if (v_dot_n == 0) v_dot_n = 1.4E-45;\r
+vcb.scale (v_dot_n);\r
+vda.sub2 (vcb, vab);\r
+vda.scale (0.5);\r
+va_prime_d.scale (theta == 0 ? 0 : (vda.length () / Math.tan (theta / 2 / 180 * 3.141592653589793)));\r
+var r = javajs.util.V3.newV (va_prime_d);\r
+if (theta != 0) r.add (vda);\r
+var pt_a_prime = javajs.util.P3.newP (a);\r
+pt_a_prime.sub (r);\r
+if (v_dot_n != 1.4E-45) n.scale (v_dot_n);\r
+var pt_b_prime = javajs.util.P3.newP (pt_a_prime);\r
+pt_b_prime.add (n);\r
+theta = javajs.util.Measure.computeTorsion (a, pt_a_prime, pt_b_prime, b, true);\r
+if (Float.isNaN (theta) || r.length () < 0.0001) theta = dq.getThetaDirectedV (n);\r
+var residuesPerTurn = Math.abs (theta == 0 ? 0 : 360 / theta);\r
+var pitch = Math.abs (v_dot_n == 1.4E-45 ? 0 : n.length () * (theta == 0 ? 1 : 360 / theta));\r
+return Clazz.newArray (-1, [pt_a_prime, n, r, javajs.util.P3.new3 (theta, pitch, residuesPerTurn), pt_b_prime]);\r
+}, "javajs.util.P3,javajs.util.P3,javajs.util.Quat");\r
+c$.getPlaneThroughPoints = Clazz.defineMethod (c$, "getPlaneThroughPoints", \r
+function (pointA, pointB, pointC, vNorm, vAB, plane) {\r
+var w = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB);\r
+plane.set4 (vNorm.x, vNorm.y, vNorm.z, w);\r
+return plane;\r
+}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,javajs.util.P4");\r
+c$.getPlaneThroughPoint = Clazz.defineMethod (c$, "getPlaneThroughPoint", \r
+function (pt, normal, plane) {\r
+plane.set4 (normal.x, normal.y, normal.z, -normal.dot (pt));\r
+}, "javajs.util.T3,javajs.util.V3,javajs.util.P4");\r
+c$.distanceToPlane = Clazz.defineMethod (c$, "distanceToPlane", \r
+function (plane, pt) {\r
+return (plane == null ? NaN : (plane.dot (pt) + plane.w) / Math.sqrt (plane.dot (plane)));\r
+}, "javajs.util.P4,javajs.util.T3");\r
+c$.directedDistanceToPlane = Clazz.defineMethod (c$, "directedDistanceToPlane", \r
+function (pt, plane, ptref) {\r
+var f = plane.dot (pt) + plane.w;\r
+var f1 = plane.dot (ptref) + plane.w;\r
+return Math.signum (f1) * f / Math.sqrt (plane.dot (plane));\r
+}, "javajs.util.P3,javajs.util.P4,javajs.util.P3");\r
+c$.distanceToPlaneD = Clazz.defineMethod (c$, "distanceToPlaneD", \r
+function (plane, d, pt) {\r
+return (plane == null ? NaN : (plane.dot (pt) + plane.w) / d);\r
+}, "javajs.util.P4,~N,javajs.util.P3");\r
+c$.distanceToPlaneV = Clazz.defineMethod (c$, "distanceToPlaneV", \r
+function (norm, w, pt) {\r
+return (norm == null ? NaN : (norm.dot (pt) + w) / Math.sqrt (norm.dot (norm)));\r
+}, "javajs.util.V3,~N,javajs.util.P3");\r
+c$.calcNormalizedNormal = Clazz.defineMethod (c$, "calcNormalizedNormal", \r
+function (pointA, pointB, pointC, vNormNorm, vAB) {\r
+vAB.sub2 (pointB, pointA);\r
+vNormNorm.sub2 (pointC, pointA);\r
+vNormNorm.cross (vAB, vNormNorm);\r
+vNormNorm.normalize ();\r
+}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3");\r
+c$.getDirectedNormalThroughPoints = Clazz.defineMethod (c$, "getDirectedNormalThroughPoints", \r
+function (pointA, pointB, pointC, ptRef, vNorm, vAB) {\r
+var nd = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB);\r
+if (ptRef != null) {\r
+var pt0 = javajs.util.P3.newP (pointA);\r
+pt0.add (vNorm);\r
+var d = pt0.distance (ptRef);\r
+pt0.sub2 (pointA, vNorm);\r
+if (d > pt0.distance (ptRef)) {\r
+vNorm.scale (-1);\r
+nd = -nd;\r
+}}return nd;\r
+}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3");\r
+c$.getNormalThroughPoints = Clazz.defineMethod (c$, "getNormalThroughPoints", \r
+function (pointA, pointB, pointC, vNorm, vTemp) {\r
+javajs.util.Measure.calcNormalizedNormal (pointA, pointB, pointC, vNorm, vTemp);\r
+vTemp.setT (pointA);\r
+return -vTemp.dot (vNorm);\r
+}, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3");\r
+c$.getPlaneProjection = Clazz.defineMethod (c$, "getPlaneProjection", \r
+function (pt, plane, ptProj, vNorm) {\r
+var dist = javajs.util.Measure.distanceToPlane (plane, pt);\r
+vNorm.set (plane.x, plane.y, plane.z);\r
+vNorm.normalize ();\r
+vNorm.scale (-dist);\r
+ptProj.add2 (pt, vNorm);\r
+}, "javajs.util.P3,javajs.util.P4,javajs.util.P3,javajs.util.V3");\r
+c$.getNormalToLine = Clazz.defineMethod (c$, "getNormalToLine", \r
+function (pointA, pointB, vNormNorm) {\r
+vNormNorm.sub2 (pointA, pointB);\r
+vNormNorm.cross (vNormNorm, javajs.util.Measure.axisY);\r
+vNormNorm.normalize ();\r
+if (Float.isNaN (vNormNorm.x)) vNormNorm.set (1, 0, 0);\r
+}, "javajs.util.P3,javajs.util.P3,javajs.util.V3");\r
+c$.getBisectingPlane = Clazz.defineMethod (c$, "getBisectingPlane", \r
+function (pointA, vAB, ptTemp, vTemp, plane) {\r
+ptTemp.scaleAdd2 (0.5, vAB, pointA);\r
+vTemp.setT (vAB);\r
+vTemp.normalize ();\r
+javajs.util.Measure.getPlaneThroughPoint (ptTemp, vTemp, plane);\r
+}, "javajs.util.P3,javajs.util.V3,javajs.util.T3,javajs.util.V3,javajs.util.P4");\r
+c$.projectOntoAxis = Clazz.defineMethod (c$, "projectOntoAxis", \r
+function (point, axisA, axisUnitVector, vectorProjection) {\r
+vectorProjection.sub2 (point, axisA);\r
+var projectedLength = vectorProjection.dot (axisUnitVector);\r
+point.scaleAdd2 (projectedLength, axisUnitVector, axisA);\r
+vectorProjection.sub2 (point, axisA);\r
+}, "javajs.util.P3,javajs.util.P3,javajs.util.V3,javajs.util.V3");\r
+c$.calcBestAxisThroughPoints = Clazz.defineMethod (c$, "calcBestAxisThroughPoints", \r
+function (points, axisA, axisUnitVector, vectorProjection, nTriesMax) {\r
+var nPoints = points.length;\r
+axisA.setT (points[0]);\r
+axisUnitVector.sub2 (points[nPoints - 1], axisA);\r
+axisUnitVector.normalize ();\r
+javajs.util.Measure.calcAveragePointN (points, nPoints, axisA);\r
+var nTries = 0;\r
+while (nTries++ < nTriesMax && javajs.util.Measure.findAxis (points, nPoints, axisA, axisUnitVector, vectorProjection) > 0.001) {\r
+}\r
+var tempA = javajs.util.P3.newP (points[0]);\r
+javajs.util.Measure.projectOntoAxis (tempA, axisA, axisUnitVector, vectorProjection);\r
+axisA.setT (tempA);\r
+}, "~A,javajs.util.P3,javajs.util.V3,javajs.util.V3,~N");\r
+c$.findAxis = Clazz.defineMethod (c$, "findAxis", \r
+function (points, nPoints, axisA, axisUnitVector, vectorProjection) {\r
+var sumXiYi = new javajs.util.V3 ();\r
+var vTemp = new javajs.util.V3 ();\r
+var pt = new javajs.util.P3 ();\r
+var ptProj = new javajs.util.P3 ();\r
+var a = javajs.util.V3.newV (axisUnitVector);\r
+var sum_Xi2 = 0;\r
+for (var i = nPoints; --i >= 0; ) {\r
+pt.setT (points[i]);\r
+ptProj.setT (pt);\r
+javajs.util.Measure.projectOntoAxis (ptProj, axisA, axisUnitVector, vectorProjection);\r
+vTemp.sub2 (pt, ptProj);\r
+vTemp.cross (vectorProjection, vTemp);\r
+sumXiYi.add (vTemp);\r
+sum_Xi2 += vectorProjection.lengthSquared ();\r
+}\r
+var m = javajs.util.V3.newV (sumXiYi);\r
+m.scale (1 / sum_Xi2);\r
+vTemp.cross (m, axisUnitVector);\r
+axisUnitVector.add (vTemp);\r
+axisUnitVector.normalize ();\r
+vTemp.sub2 (axisUnitVector, a);\r
+return vTemp.length ();\r
+}, "~A,~N,javajs.util.P3,javajs.util.V3,javajs.util.V3");\r
+c$.calcAveragePoint = Clazz.defineMethod (c$, "calcAveragePoint", \r
+function (pointA, pointB, pointC) {\r
+pointC.set ((pointA.x + pointB.x) / 2, (pointA.y + pointB.y) / 2, (pointA.z + pointB.z) / 2);\r
+}, "javajs.util.P3,javajs.util.P3,javajs.util.P3");\r
+c$.calcAveragePointN = Clazz.defineMethod (c$, "calcAveragePointN", \r
+function (points, nPoints, averagePoint) {\r
+averagePoint.setT (points[0]);\r
+for (var i = 1; i < nPoints; i++) averagePoint.add (points[i]);\r
+\r
+averagePoint.scale (1 / nPoints);\r
+}, "~A,~N,javajs.util.P3");\r
+c$.transformPoints = Clazz.defineMethod (c$, "transformPoints", \r
+function (vPts, m4, center) {\r
+var v = new javajs.util.Lst ();\r
+for (var i = 0; i < vPts.size (); i++) {\r
+var pt = javajs.util.P3.newP (vPts.get (i));\r
+pt.sub (center);\r
+m4.rotTrans (pt);\r
+pt.add (center);\r
+v.addLast (pt);\r
+}\r
+return v;\r
+}, "javajs.util.Lst,javajs.util.M4,javajs.util.P3");\r
+c$.isInTetrahedron = Clazz.defineMethod (c$, "isInTetrahedron", \r
+function (pt, ptA, ptB, ptC, ptD, plane, vTemp, vTemp2, fullyEnclosed) {\r
+var b = (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptC, ptD, ptA, vTemp, vTemp2, plane), pt) >= 0);\r
+if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptD, ptB, vTemp, vTemp2, plane), pt) >= 0)) return false;\r
+if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptB, ptD, ptC, vTemp, vTemp2, plane), pt) >= 0)) return false;\r
+var d = javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptB, ptC, vTemp, vTemp2, plane), pt);\r
+if (fullyEnclosed) return (b == (d >= 0));\r
+var d1 = javajs.util.Measure.distanceToPlane (plane, ptD);\r
+return d1 * d <= 0 || Math.abs (d1) > Math.abs (d);\r
+}, "javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P4,javajs.util.V3,javajs.util.V3,~B");\r
+c$.getIntersectionPP = Clazz.defineMethod (c$, "getIntersectionPP", \r
+function (plane1, plane2) {\r
+var a1 = plane1.x;\r
+var b1 = plane1.y;\r
+var c1 = plane1.z;\r
+var d1 = plane1.w;\r
+var a2 = plane2.x;\r
+var b2 = plane2.y;\r
+var c2 = plane2.z;\r
+var d2 = plane2.w;\r
+var norm1 = javajs.util.V3.new3 (a1, b1, c1);\r
+var norm2 = javajs.util.V3.new3 (a2, b2, c2);\r
+var nxn = new javajs.util.V3 ();\r
+nxn.cross (norm1, norm2);\r
+var ax = Math.abs (nxn.x);\r
+var ay = Math.abs (nxn.y);\r
+var az = Math.abs (nxn.z);\r
+var x;\r
+var y;\r
+var z;\r
+var diff;\r
+var type = (ax > ay ? (ax > az ? 1 : 3) : ay > az ? 2 : 3);\r
+switch (type) {\r
+case 1:\r
+x = 0;\r
+diff = (b1 * c2 - b2 * c1);\r
+if (Math.abs (diff) < 0.01) return null;\r
+y = (c1 * d2 - c2 * d1) / diff;\r
+z = (b2 * d1 - d2 * b1) / diff;\r
+break;\r
+case 2:\r
+diff = (a1 * c2 - a2 * c1);\r
+if (Math.abs (diff) < 0.01) return null;\r
+x = (c1 * d2 - c2 * d1) / diff;\r
+y = 0;\r
+z = (a2 * d1 - d2 * a1) / diff;\r
+break;\r
+case 3:\r
+default:\r
+diff = (a1 * b2 - a2 * b1);\r
+if (Math.abs (diff) < 0.01) return null;\r
+x = (b1 * d2 - b2 * d1) / diff;\r
+y = (a2 * d1 - d2 * a1) / diff;\r
+z = 0;\r
+}\r
+var list = new javajs.util.Lst ();\r
+list.addLast (javajs.util.P3.new3 (x, y, z));\r
+nxn.normalize ();\r
+list.addLast (nxn);\r
+return list;\r
+}, "javajs.util.P4,javajs.util.P4");\r
+c$.getIntersection = Clazz.defineMethod (c$, "getIntersection", \r
+function (pt1, v, plane, ptRet, tempNorm, vTemp) {\r
+javajs.util.Measure.getPlaneProjection (pt1, plane, ptRet, tempNorm);\r
+tempNorm.set (plane.x, plane.y, plane.z);\r
+tempNorm.normalize ();\r
+if (v == null) v = javajs.util.V3.newV (tempNorm);\r
+var l_dot_n = v.dot (tempNorm);\r
+if (Math.abs (l_dot_n) < 0.01) return null;\r
+vTemp.sub2 (ptRet, pt1);\r
+ptRet.scaleAdd2 (vTemp.dot (tempNorm) / l_dot_n, v, pt1);\r
+return ptRet;\r
+}, "javajs.util.P3,javajs.util.V3,javajs.util.P4,javajs.util.P3,javajs.util.V3,javajs.util.V3");\r
+c$.calculateQuaternionRotation = Clazz.defineMethod (c$, "calculateQuaternionRotation", \r
+function (centerAndPoints, retStddev) {\r
+retStddev[1] = NaN;\r
+var q = new javajs.util.Quat ();\r
+if (centerAndPoints[0].length == 1 || centerAndPoints[0].length != centerAndPoints[1].length) return q;\r
+var n = centerAndPoints[0].length - 1;\r
+if (n < 2) return q;\r
+var Sxx = 0;\r
+var Sxy = 0;\r
+var Sxz = 0;\r
+var Syx = 0;\r
+var Syy = 0;\r
+var Syz = 0;\r
+var Szx = 0;\r
+var Szy = 0;\r
+var Szz = 0;\r
+var ptA = new javajs.util.P3 ();\r
+var ptB = new javajs.util.P3 ();\r
+for (var i = n + 1; --i >= 1; ) {\r
+var aij = centerAndPoints[0][i];\r
+var bij = centerAndPoints[1][i];\r
+ptA.sub2 (aij, centerAndPoints[0][0]);\r
+ptB.sub2 (bij, centerAndPoints[0][1]);\r
+Sxx += ptA.x * ptB.x;\r
+Sxy += ptA.x * ptB.y;\r
+Sxz += ptA.x * ptB.z;\r
+Syx += ptA.y * ptB.x;\r
+Syy += ptA.y * ptB.y;\r
+Syz += ptA.y * ptB.z;\r
+Szx += ptA.z * ptB.x;\r
+Szy += ptA.z * ptB.y;\r
+Szz += ptA.z * ptB.z;\r
+}\r
+retStddev[0] = javajs.util.Measure.getRmsd (centerAndPoints, q);\r
+var N = Clazz.newDoubleArray (4, 4, 0);\r
+N[0][0] = Sxx + Syy + Szz;\r
+N[0][1] = N[1][0] = Syz - Szy;\r
+N[0][2] = N[2][0] = Szx - Sxz;\r
+N[0][3] = N[3][0] = Sxy - Syx;\r
+N[1][1] = Sxx - Syy - Szz;\r
+N[1][2] = N[2][1] = Sxy + Syx;\r
+N[1][3] = N[3][1] = Szx + Sxz;\r
+N[2][2] = -Sxx + Syy - Szz;\r
+N[2][3] = N[3][2] = Syz + Szy;\r
+N[3][3] = -Sxx - Syy + Szz;\r
+var v = (javajs.api.Interface.getInterface ("javajs.util.Eigen")).setM (N).getEigenvectorsFloatTransposed ()[3];\r
+q = javajs.util.Quat.newP4 (javajs.util.P4.new4 (v[1], v[2], v[3], v[0]));\r
+retStddev[1] = javajs.util.Measure.getRmsd (centerAndPoints, q);\r
+return q;\r
+}, "~A,~A");\r
+c$.getTransformMatrix4 = Clazz.defineMethod (c$, "getTransformMatrix4", \r
+function (ptsA, ptsB, m, centerA) {\r
+var cptsA = javajs.util.Measure.getCenterAndPoints (ptsA);\r
+var cptsB = javajs.util.Measure.getCenterAndPoints (ptsB);\r
+var retStddev = Clazz.newFloatArray (2, 0);\r
+var q = javajs.util.Measure.calculateQuaternionRotation ( Clazz.newArray (-1, [cptsA, cptsB]), retStddev);\r
+var r = q.getMatrix ();\r
+if (centerA == null) r.rotate (cptsA[0]);\r
+ else centerA.setT (cptsA[0]);\r
+var t = javajs.util.V3.newVsub (cptsB[0], cptsA[0]);\r
+m.setMV (r, t);\r
+return retStddev[1];\r
+}, "javajs.util.Lst,javajs.util.Lst,javajs.util.M4,javajs.util.P3");\r
+c$.getCenterAndPoints = Clazz.defineMethod (c$, "getCenterAndPoints", \r
+function (vPts) {\r
+var n = vPts.size ();\r
+var pts = new Array (n + 1);\r
+pts[0] = new javajs.util.P3 ();\r
+if (n > 0) {\r
+for (var i = 0; i < n; i++) {\r
+pts[0].add (pts[i + 1] = vPts.get (i));\r
+}\r
+pts[0].scale (1 / n);\r
+}return pts;\r
+}, "javajs.util.Lst");\r
+c$.getRmsd = Clazz.defineMethod (c$, "getRmsd", \r
+function (centerAndPoints, q) {\r
+var sum2 = 0;\r
+var ptsA = centerAndPoints[0];\r
+var ptsB = centerAndPoints[1];\r
+var cA = ptsA[0];\r
+var cB = ptsB[0];\r
+var n = ptsA.length - 1;\r
+var ptAnew = new javajs.util.P3 ();\r
+for (var i = n + 1; --i >= 1; ) {\r
+ptAnew.sub2 (ptsA[i], cA);\r
+q.transform2 (ptAnew, ptAnew).add (cB);\r
+sum2 += ptAnew.distanceSquared (ptsB[i]);\r
+}\r
+return Math.sqrt (sum2 / n);\r
+}, "~A,javajs.util.Quat");\r
+Clazz.defineStatics (c$,\r
+"radiansPerDegree", (0.017453292519943295));\r
+c$.axisY = c$.prototype.axisY = javajs.util.V3.new3 (0, 1, 0);\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff