public void renderRopeSegment(short colix, short[] mads, int i, int monomerCount, Monomer[] monomers, Point3i[] leadMidpointScreens, bool[] isSpecials)
{
int iPrev1 = i - 1;
if (iPrev1 < 0)
iPrev1 = 0;
int iNext1 = i + 1;
if (iNext1 > monomerCount)
iNext1 = monomerCount;
int iNext2 = i + 2;
if (iNext2 > monomerCount)
iNext2 = monomerCount;
int madThis, madBeg, madEnd;
madThis = madBeg = madEnd = mads[i];
if (isSpecials != null)
{
if (!isSpecials[iPrev1])
madBeg = (mads[iPrev1] + madThis) / 2;
if (!isSpecials[iNext1])
madEnd = (mads[iNext1] + madThis) / 2;
}
int diameterBeg = leadMidpointScreens[i].z;//viewer.scaleToScreen(leadMidpointScreens[i].z, madBeg);
int diameterEnd = leadMidpointScreens[iNext1].z;//viewer.scaleToScreen(leadMidpointScreens[iNext1].z, madEnd);
int diameterMid = monomers[i].LeadAtom.ScreenZ;//viewer.scaleToScreen(monomers[i].LeadAtom.ScreenZ, madThis);
g3d.fillHermite(colix, monomers[i].Nucleic?4:7, diameterBeg, diameterMid, diameterEnd, leadMidpointScreens[iPrev1], leadMidpointScreens[i], leadMidpointScreens[iNext1], leadMidpointScreens[iNext2]);
}
public virtual Point3i[] calcScreens(Point3f[] centers, Vector3f[] vectors, short[] mads, float offsetFraction)
{
// this basically does object->screen transformation??
Point3i[] screens = new Point3i[centers.Length];// viewer.allocTempScreens(centers.Length);
if (offsetFraction == 0)
{
for (int i = centers.Length; --i >= 0; )
screens[i] = new Point3i((int)centers[i].x, (int)centers[i].y, (int)centers[i].z);
//viewer.transformPoint(centers[i], screens[i]);
}
else
{
offsetFraction /= 1000;
for (int i = centers.Length; --i >= 0; )
{
pointT.set_Renamed(vectors[i]);
float scale = mads[i] * offsetFraction;
pointT.scaleAdd(scale, centers[i]);
//if (float.IsNaN(pointT.x))
//{
// System.Console.Out.WriteLine(" vectors[" + i + "]=" + vectors[i] + " centers[" + i + "]=" + centers[i] + " mads[" + i + "]=" + mads[i] + " scale=" + scale + " --> " + pointT);
//}
//viewer.transformPoint(pointT, screens[i]);
screens[i] = new Point3i((int)pointT.x, (int)pointT.y, (int)pointT.z);
}
}
return screens;
}
public virtual void calc1Screen(Point3f center, Vector3f vector, short mad, float offsetFraction, Point3i screen)
{
pointT.set_Renamed(vector);
float scale = mad * offsetFraction;
pointT.scaleAdd(scale, center);
//viewer.transformPoint(pointT, screen);
}
private void InitBlock()
{
ring6Screens[5] = new Point3i();
for (int i = 5; --i >= 0; )
{
ring5Screens[i] = new Point3i();
ring6Screens[i] = new Point3i();
}
}
public Point3i[] calcScreenLeadMidpoints(int monomerCount, Point3f[] leadMidpoints)
{
int count = monomerCount + 1;
Point3i[] leadMidpointScreens = new Point3i[count];// null;// viewer.allocTempScreens(count);
for (int i = count; --i >= 0; )
{
leadMidpointScreens[i] = new Point3i((int)leadMidpoints[i].x, (int)leadMidpoints[i].y, (int)leadMidpoints[i].z);
//viewer.transformPoint(leadMidpoints[i], leadMidpointScreens[i]);
//g3d.fillSphereCentered(Graphics3D.CYAN, 15, leadMidpointScreens[i]);
g3d.fillSphereCentered(0, 15, leadMidpointScreens[i]);
}
return leadMidpointScreens;
}
public NuHermite3D(NuGraphics3D g3d)
{
this.g3d = g3d;
for (int i = 16; --i >= 0; )
{
pLeft[i] = new Point3i();
pRight[i] = new Point3i();
pTopLeft[i] = new Point3f();
pTopRight[i] = new Point3f();
pBotLeft[i] = new Point3f();
pBotRight[i] = new Point3f();
}
triStripBuffer = new List<List<Vector3>>();
}
public virtual Point3i[] calcScreens(Point3f[] centers, Vector3f[] vectors, short[] mads, float offsetFraction)
{
int count = centers.Length;
Point3i[] screens = new Point3i[count];// null;// viewer.allocTempScreens(count);
if (offsetFraction == 0)
{
for (int i = count; --i >= 0; )
screens[i] = new Point3i((int)centers[i].x, (int)centers[i].y, (int)centers[i].z);
// viewer.transformPoint(centers[i], screens[i]);
}
else
{
for (int i = count; --i >= 0; )
{
pointT.set_Renamed(vectors[i]);
//boolean isSpecial = isSpecials[i];
short mad = mads[i];
/*
if (isSpecial && !lastWasSpecial)
mad *= 2;
*/
/*
short mad = isSpecial || i == 0 ? mads[i] : mads[i - 1];
if (i + 1 < count && isSpecial) {
if (isSpecial && ! isSpecials[i + 1])
mad = mads[i];
}
*/
float scale = mad * offsetFraction;
pointT.scaleAdd(scale, centers[i]);
screens[i] = new Point3i((int)pointT.x, (int)pointT.y, (int)pointT.z);
//viewer.transformPoint(pointT, screens[i]);
}
}
return screens;
}
public virtual void render2Strand(int monomerCount, Monomer[] monomers, short[] mads, short[] colixes, Point3i[] ribbonTopScreens, Point3i[] ribbonBottomScreens)
{
for (int i = monomerCount; --i >= 0; )
if (mads[i] > 0)
render2StrandSegment(monomerCount, monomers[i], colixes[i], mads, ribbonTopScreens, ribbonBottomScreens, i);
}
public virtual void render2StrandSegment(int monomerCount, Monomer monomer, short colix, short[] mads, Point3i[] ribbonTopScreens, Point3i[] ribbonBottomScreens, int i)
{
int iLast = monomerCount;
int iPrev = i - 1;
if (iPrev < 0)
iPrev = 0;
int iNext = i + 1;
if (iNext > iLast)
iNext = iLast;
int iNext2 = i + 2;
if (iNext2 > iLast)
iNext2 = iLast;
//colix = Graphics3D.inheritColix(colix, monomer.LeadAtom.colixAtom);
g3d.drawHermite(true, ribbonBorder, colix, isNucleic?4:7, ribbonTopScreens[iPrev], ribbonTopScreens[i], ribbonTopScreens[iNext], ribbonTopScreens[iNext2], ribbonBottomScreens[iPrev], ribbonBottomScreens[i], ribbonBottomScreens[iNext], ribbonBottomScreens[iNext2]);
}
public void fillTriangle(short colix, Point3i screenA, Point3i screenB, Point3i screenC)
{
fillTriangle(screenA, screenB, screenC);
}
public void render2(bool fill, bool border, short colix, int tension,
//top strand segment
Point3i p0, Point3i p1, Point3i p2, Point3i p3,
//bottom strand segment
Point3i p4, Point3i p5, Point3i p6, Point3i p7)
{
if (!fill)
{
render2x(fill, colix, tension, p0, p1, p2, p3, p4, p5, p6, p7);
return;
}
/*
System.out.println("------------render2-------------");
System.out.println("p1=" + p1 + " p2=" + p2 + "\np3=" + p3 + " p4=" + p4);
*/
int x1 = p1.x, y1 = p1.y, z1 = p1.z;
int x2 = p2.x, y2 = p2.y, z2 = p2.z;
int xT1 = ((x2 - p0.x) * tension) / 8;
int yT1 = ((y2 - p0.y) * tension) / 8;
int zT1 = ((z2 - p0.z) * tension) / 8;
int xT2 = ((p3.x - x1) * tension) / 8;
int yT2 = ((p3.y - y1) * tension) / 8;
int zT2 = ((p3.z - z1) * tension) / 8;
set(pTopLeft[0], p1);
set(pTopRight[0], p2);
int x5 = p5.x, y5 = p5.y, z5 = p5.z;
int x6 = p6.x, y6 = p6.y, z6 = p6.z;
int xT5 = ((x6 - p4.x) * tension) / 8;
int yT5 = ((y6 - p4.y) * tension) / 8;
int zT5 = ((z6 - p4.z) * tension) / 8;
int xT6 = ((p7.x - x5) * tension) / 8;
int yT6 = ((p7.y - y5) * tension) / 8;
int zT6 = ((p7.z - z5) * tension) / 8;
set(pBotLeft[0], p5);
set(pBotRight[0], p6);
sLeft[0] = 0;
sRight[0] = 1;
needToFill[0] = true;
sp = 0;
do
{
Point3f a = pTopLeft[sp];
Point3f b = pTopRight[sp];
double dxTop = b.x - a.x;
double dxTop2 = dxTop * dxTop;
if (dxTop2 < 10)
{
double dyTop = b.y - a.y;
double dyTop2 = dyTop * dyTop;
if (dyTop2 < 10)
{
Point3f c = pBotLeft[sp];
Point3f d = pBotRight[sp];
double dxBot = d.x - c.x;
double dxBot2 = dxBot * dxBot;
if (dxBot2 < 8)
{
double dyBot = d.y - c.y;
double dyBot2 = dyBot * dyBot;
if (dyBot2 < 8)
{
if (border)
{
g3d.fillSphereCentered(colix, 3, a);
g3d.fillSphereCentered(colix, 3, c);
}
if (needToFill[sp])
{
//g3d.fillQuadrilateral(colix, a, b, d, c);
// see if fits on end of any existing
bool appended = false;
for (int strip = 0; strip < triStripBuffer.Count; strip++)
{
int end2Idx = triStripBuffer[strip].Count - 2;
if (triStripBuffer[strip][end2Idx].X == b.x &&
triStripBuffer[strip][end2Idx].Y == b.y &&
triStripBuffer[strip][end2Idx].Z == b.z &&
triStripBuffer[strip][end2Idx + 1].X == d.x &&
triStripBuffer[strip][end2Idx + 1].Y == d.y &&
triStripBuffer[strip][end2Idx + 1].Z == d.z)
{
// append to end
triStripBuffer[strip].Add(new Vector3(a.x, a.y, a.z));
triStripBuffer[strip].Add(new Vector3(c.x, c.y, c.z));
appended = true;
}
}
if (!appended)
{
List<Vector3> strip = new List<Vector3>();
triStripBuffer.Add(strip);
strip.Add(new Vector3(b.x, b.y, b.z));
strip.Add(new Vector3(d.x, d.y, d.z));
strip.Add(new Vector3(a.x, a.y, a.z));
strip.Add(new Vector3(c.x, c.y, c.z));
}
needToFill[sp] = false;
}
if (dxTop2 + dyTop2 < 2 &&
dxBot2 + dyBot2 < 2)
{
--sp;
continue;
}
}
}
}
}
double s = (sLeft[sp] + sRight[sp]) / 2;
double s2 = s * s;
double s3 = s2 * s;
double h1 = 2 * s3 - 3 * s2 + 1;
double h2 = -2 * s3 + 3 * s2;
double h3 = s3 - 2 * s2 + s;
double h4 = s3 - s2;
int spNext = sp + 1;
Point3f pMidTop = pTopRight[spNext];
pMidTop.x = (float)(h1 * x1 + h2 * x2 + h3 * xT1 + h4 * xT2);
pMidTop.y = (float)(h1 * y1 + h2 * y2 + h3 * yT1 + h4 * yT2);
pMidTop.z = (float)(h1 * z1 + h2 * z2 + h3 * zT1 + h4 * zT2);
Point3f pMidBot = pBotRight[spNext];
pMidBot.x = (float)(h1 * x5 + h2 * x6 + h3 * xT5 + h4 * xT6);
pMidBot.y = (float)(h1 * y5 + h2 * y6 + h3 * yT5 + h4 * yT6);
pMidBot.z = (float)(h1 * z5 + h2 * z6 + h3 * zT5 + h4 * zT6);
pTopRight[spNext] = pTopRight[sp];
pTopRight[sp] = pMidTop;
pBotRight[spNext] = pBotRight[sp];
pBotRight[sp] = pMidBot;
sRight[spNext] = sRight[sp];
sRight[sp] = (float)s;
needToFill[spNext] = needToFill[sp];
pTopLeft[spNext].set_Renamed(pMidTop);
pBotLeft[spNext].set_Renamed(pMidBot);
sLeft[spNext] = (float)s;
++sp;
} while (sp >= 0);
}
public void render(bool tFill, short colix, int tension,
int diameterBeg, int diameterMid, int diameterEnd,
Point3i p0, Point3i p1, Point3i p2, Point3i p3)
{
int x1 = p1.x, y1 = p1.y, z1 = p1.z;
int x2 = p2.x, y2 = p2.y, z2 = p2.z;
int xT1 = ((x2 - p0.x) * tension) / 8;
int yT1 = ((y2 - p0.y) * tension) / 8;
int zT1 = ((z2 - p0.z) * tension) / 8;
int xT2 = ((p3.x - x1) * tension) / 8;
int yT2 = ((p3.y - y1) * tension) / 8;
int zT2 = ((p3.z - z1) * tension) / 8;
sLeft[0] = 0;
pLeft[0].set_Renamed(p1);
sRight[0] = 1;
pRight[0].set_Renamed(p2);
sp = 0;
int dDiameterFirstHalf = 0;
int dDiameterSecondHalf = 0;
if (tFill)
{
dDiameterFirstHalf = 2 * (diameterMid - diameterBeg);
dDiameterSecondHalf = 2 * (diameterEnd - diameterMid);
}
else
g3d.setColix(colix);
do
{
Point3i a = pLeft[sp];
Point3i b = pRight[sp];
int dx = b.x - a.x;
if (dx >= -1 && dx <= 1)
{
int dy = b.y - a.y;
if (dy >= -1 && dy <= 1)
{
// mth 2003 10 13
// I tried drawing short cylinder segments here,
// but drawing spheres was faster
float _s = sLeft[sp];
if (tFill)
{
int d =(_s < 0.5f
? diameterBeg + (int)(dDiameterFirstHalf * _s)
: diameterMid + (int)(dDiameterSecondHalf * (_s - 0.5f)));
g3d.fillSphereCentered(colix, d, a);
}
//else
// g3d.plotPixelClipped(a);
}
--sp;
continue;
}
double s = (sLeft[sp] + sRight[sp]) / 2;
double s2 = s * s;
double s3 = s2 * s;
double h1 = 2 * s3 - 3 * s2 + 1;
double h2 = -2 * s3 + 3 * s2;
double h3 = s3 - 2 * s2 + s;
double h4 = s3 - s2;
Point3i pMid = pRight[sp + 1];
pMid.x = (int)(h1 * x1 + h2 * x2 + h3 * xT1 + h4 * xT2);
pMid.y = (int)(h1 * y1 + h2 * y2 + h3 * yT1 + h4 * yT2);
pMid.z = (int)(h1 * z1 + h2 * z2 + h3 * zT1 + h4 * zT2);
pRight[sp + 1] = pRight[sp];
sRight[sp + 1] = sRight[sp];
pRight[sp] = pMid;
sRight[sp] = (float)s;
++sp;
pLeft[sp].set_Renamed(pMid);
sLeft[sp] = (float)s;
}
while (sp >= 0);
}
public void drawLine(Point3i pointA, Point3i pointB)
{
currentSceneBuffer.lines.Add(new Vector3(pointA.x, pointA.y, pointA.z));
currentSceneBuffer.lines.Add(new Vector3(pointB.x, pointB.y, pointB.z));
}
static void set(Point3f p3f, Point3i p3i)
{
p3f.x = p3i.x;
p3f.y = p3i.y;
p3f.z = p3i.z;
}
public void fillTriangle(Point3i screenA, Point3i screenB, Point3i screenC)
{
currentSceneBuffer.triangles.Add(new Vector3(screenA.x, screenA.y, screenA.z));
currentSceneBuffer.triangles.Add(new Vector3(screenB.x, screenB.y, screenB.z));
currentSceneBuffer.triangles.Add(new Vector3(screenC.x, screenC.y, screenC.z));
}
public void transformPoints(Point3f[] pointsAngstroms, Point3i[] pointsScreens)
{
//transformManager.transformPoints(pointsAngstroms.length, pointsAngstroms, pointsScreens);
}
public void transformPoint(Point3f pointAngstroms, Vector3f vibrationVector, Point3i pointScreen)
{
//transformManager.transformPoint(pointAngstroms, vibrationVector, pointScreen);
}
public void drawHermite(bool fill, bool border, short colix, int tension,
Point3i s0, Point3i s1, Point3i s2, Point3i s3,
Point3i s4, Point3i s5, Point3i s6, Point3i s7)
{
hermite3d.render2(fill, border, colix, tension, s0, s1, s2, s3, s4, s5, s6, s7);
}
public void fillHermite(short colix, int tension, int diameterBeg, int diameterMid, int diameterEnd, Point3i s0, Point3i s1, Point3i s2, Point3i s3)
{
hermite3d.render(true, colix, tension, diameterBeg, diameterMid, diameterEnd, s0, s1, s2, s3);
}
public void transformPoint(Point3f pointAngstroms, Point3i pointScreen)
{
//transformManager.transformPoint(pointAngstroms, pointScreen);
}
void render2x(bool fill, short colix, int tension,
//top strand segment
Point3i p0, Point3i p1, Point3i p2, Point3i p3,
//bottom strand segment
Point3i p4, Point3i p5, Point3i p6, Point3i p7)
{
Point3i[] endPoints = { p2, p1, p6, p5 };
// stores all points for top+bottom strands of 1 segment
List<Point3i> points = new List<Point3i>(10);
int whichPoint = 0;
int numTopStrandPoints = 2; //first and last points automatically included
float numPointsPerSegment = 5.0f;//use 5 for mesh
// could make it so you can set this from script command
if (fill)
numPointsPerSegment = 10.0f;
float interval = (1.0f / numPointsPerSegment);
float currentInt = 0.0f;
int x1 = p1.x, y1 = p1.y, z1 = p1.z;
int x2 = p2.x, y2 = p2.y, z2 = p2.z;
int xT1 = ((x2 - p0.x) * tension) / 8;
int yT1 = ((y2 - p0.y) * tension) / 8;
int zT1 = ((z2 - p0.z) * tension) / 8;
int xT2 = ((p3.x - x1) * tension) / 8;
int yT2 = ((p3.y - y1) * tension) / 8;
int zT2 = ((p3.z - z1) * tension) / 8;
sLeft[0] = 0;
pLeft[0].set_Renamed(p1);
sRight[0] = 1;
pRight[0].set_Renamed(p2);
sp = 0;
g3d.setColix(colix); // set colix here for entire routine
for (int strands = 2; strands > 0; strands--)
{
if (strands == 1)
{
x1 = p5.x; y1 = p5.y; z1 = p5.z;
x2 = p6.x; y2 = p6.y; z2 = p6.z;
xT1 = ( (x2 - p4.x) * tension) / 8;
yT1 = ( (y2 - p4.y) * tension) / 8;
zT1 = ( (z2 - p4.z) * tension) / 8;
xT2 = ( (p7.x - x1) * tension) / 8;
yT2 = ( (p7.y - y1) * tension) / 8;
zT2 = ( (p7.z - z1) * tension) / 8;
sLeft[0] = 0;
pLeft[0].set_Renamed(p5);
sRight[0] = 1;
pRight[0].set_Renamed(p6);
sp = 0;
}
points.Add(endPoints[whichPoint++]);
currentInt = interval;
do
{
Point3i a = pLeft[sp];
Point3i b = pRight[sp];
int dx = b.x - a.x;
int dy = b.y - a.y;
int dist2 = dx * dx + dy * dy;
if (dist2 <= 2)
{
// mth 2003 10 13
// I tried drawing short cylinder segments here,
// but drawing spheres was faster
float s = sLeft[sp];
g3d.fillSphereCentered(colix, 3, a);
//draw outside edges of mesh
if (s < 1.0f - currentInt)
{ //if first point over the interval
Point3i temp = new Point3i();
temp.set_Renamed(a);
points.Add(temp); //store it
currentInt += interval; // increase to next interval
if (strands == 2)
{
numTopStrandPoints++;
}
}
--sp;
}
else
{
double s = (sLeft[sp] + sRight[sp]) / 2;
double s2 = s * s;
double s3 = s2 * s;
double h1 = 2 * s3 - 3 * s2 + 1;
double h2 = -2 * s3 + 3 * s2;
double h3 = s3 - 2 * s2 + s;
double h4 = s3 - s2;
Point3i pMid = pRight[sp + 1];
pMid.x = (int)(h1 * x1 + h2 * x2 + h3 * xT1 + h4 * xT2);
pMid.y = (int)(h1 * y1 + h2 * y2 + h3 * yT1 + h4 * yT2);
pMid.z = (int)(h1 * z1 + h2 * z2 + h3 * zT1 + h4 * zT2);
pRight[sp + 1] = pRight[sp];
sRight[sp + 1] = sRight[sp];
pRight[sp] = pMid;
sRight[sp] = (float)s;
++sp;
pLeft[sp].set_Renamed(pMid);
sLeft[sp] = (float)s;
}
}
while (sp >= 0);
points.Add(endPoints[whichPoint++]);
} //end of for loop - processed top and bottom strands
int size = points.Count;
if (fill)
{ //RIBBONS
Point3i t1 = null;
Point3i b1 = null;
Point3i t2 = null;
Point3i b2 = null;
int top = 1;
Vector3[] strip = new Vector3[numTopStrandPoints * 2];
int stIdx = 0;
for (; top < numTopStrandPoints && (top + numTopStrandPoints) < size; top++)
{
t1 = points[top - 1];
b1 = points[numTopStrandPoints + (top - 1)];
strip[stIdx++] = new Vector3(t1.X, t1.y, t1.z);
strip[stIdx++] = new Vector3(b1.x, b1.y, b1.z);
}
if ((numTopStrandPoints * 2) != size)
{ //BUG(DC09_MAY_2004): not sure why but
//sometimes misses triangle at very start of segment
//temp fix - will inestigate furture
g3d.fillTriangle(p1, p5, t2);
g3d.fillTriangle(b2, t2, p5);
}
g3d.FillTriangleStrip(strip);
}
else
{ //MESH
for (int top = 0;
top < numTopStrandPoints && (top + numTopStrandPoints) < size; top++)
{
g3d.drawLine(points[top],
points[top + numTopStrandPoints]);
}
}
}
public void freeTempScreens(Point3i[] tempScreens)
{
//tempManager.freeTempScreens(tempScreens);
}
/// <summary>
/// fills a solid sphere
/// </summary>
/// <param name="colix">the color index</param>
/// <param name="diameter">pixel count</param>
/// <param name="center">javax.vecmath.Point3i defining the center</param>
public void fillSphereCentered(short colix, int diameter, Point3i center)
{
fillSphereCentered(colix, diameter, center.X, center.Y, center.Z);
}
