private void stepSimplicies3() {
if (count3 < complex.getSimplicies()[3].getSize()) {
Simplex simplex3 = (Simplex) complex.getSimplicies()[3].get(count3);
addTetrahedron(simplex3, Colors.yellow);
System.out.println(count3 + ": alpha3 = " + simplex3.getAlpha());
count3++;
}
}
public BranchGroup addTriangle(Simplex simplex, Color3f color) {
int[] p = simplex.getPoints();
BranchGroup bgTriangle = new BranchGroup();
bgTriangle.setCapability(BranchGroup.ALLOW_DETACH);
javax.vecmath.Point3d[] coords = new javax.vecmath.Point3d[6];
TriangleArray ta = new TriangleArray(6, TriangleArray.COORDINATES | TriangleArray.COLOR_3);
Point3d p0 = (Point3d) complex.getPoints().get(simplex.getPoints()[0]);
Point3d p1 = (Point3d) complex.getPoints().get(simplex.getPoints()[1]);
Point3d p2 = (Point3d) complex.getPoints().get(simplex.getPoints()[2]);
coords[0] = new javax.vecmath.Point3d(p0.getX(), p0.getY(), p0.getZ());
coords[1] = new javax.vecmath.Point3d(p1.getX(), p1.getY(), p1.getZ());
coords[2] = new javax.vecmath.Point3d(p2.getX(), p2.getY(), p2.getZ());
coords[3] = new javax.vecmath.Point3d(p0.getX(), p0.getY(), p0.getZ());
coords[4] = new javax.vecmath.Point3d(p2.getX(), p2.getY(), p2.getZ());
coords[5] = new javax.vecmath.Point3d(p1.getX(), p1.getY(), p1.getZ());
ta.setCoordinates(0, coords);
Color3f[] colors = new Color3f[6];
for (int i = 0; i < 3; i++) colors[i] = Colors.black;
for (int i = 3; i < 6; i++) colors[i] = Colors.yellow;
ta.setColors(0, colors);
Appearance ap = new Appearance();
ap.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ);
ap.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE);
ap.setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_READ);
ap.setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_WRITE);
ap.setLineAttributes(new LineAttributes(2, LineAttributes.PATTERN_SOLID, false));
ap.setMaterial(new Material());
ap.setTransparencyAttributes(
new TransparencyAttributes(TransparencyAttributes.SCREEN_DOOR, 0.5f));
Shape3D shape = new Shape3D(ta, ap);
shape.setCapability(Shape3D.ALLOW_APPEARANCE_READ);
shape.setCapability(Shape3D.ALLOW_APPEARANCE_WRITE);
simplex.setTriangle(shape);
// simplex.bgTriangle = bgTriangle;
TransformGroup tgTriangle = new TransformGroup();
tgTriangle.addChild(shape);
bgTriangle.addChild(tgTriangle);
spin.addChild(bgTriangle);
return bgTriangle;
}
private void stepSimplicies23() {
if ((count2 < complex.getSimplicies()[2].getSize())
&& (count3 < complex.getSimplicies()[3].getSize())) {
Simplex simplex2 = (Simplex) complex.getSimplicies()[2].get(count2);
Simplex simplex3 = (Simplex) complex.getSimplicies()[3].get(count3);
if (simplex3.getAlpha() < simplex2.getAlpha()) {
addTetrahedron(simplex3, Colors.yellow);
System.out.println(count3 + ": alpha3 = " + simplex3.getAlpha());
count3++;
} else {
System.out.println(count2 + ": alpha2 = " + simplex2.getAlpha());
addTriangle(simplex2, Colors.yellow);
count2++;
}
} else {
if (count2 < complex.getSimplicies()[2].getSize()) {
Simplex simplex2 = (Simplex) complex.getSimplicies()[2].get(count2);
System.out.println(count2 + ": alpha2 = " + simplex2.getAlpha());
addTriangle(simplex2, Colors.yellow);
count2++;
} else {
if (count3 < complex.getSimplicies()[3].getSize()) {
Simplex simplex3 = (Simplex) complex.getSimplicies()[3].get(count3);
addTetrahedron(simplex3, Colors.yellow);
System.out.println(count3 + ": alpha3 = " + simplex3.getAlpha());
count3++;
}
}
}
}
public void addSphere(Simplex simplex, double radius, Color3f color) {
geom3d.Point3d p = (Point3d) complex.getPoints().get(simplex.getPoints()[0]);
BranchGroup bgSphere = new BranchGroup();
bgSphere.setCapability(BranchGroup.ALLOW_DETACH);
Appearance ap = new Appearance();
ap.setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_READ);
ap.setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_WRITE);
ap.setColoringAttributes(new ColoringAttributes(color, ColoringAttributes.NICEST));
simplex.setSphere(new Sphere(new Float(radius), ap));
simplex.getSphere().getShape().setCapability(Shape3D.ALLOW_APPEARANCE_READ);
simplex.getSphere().getShape().setCapability(Shape3D.ALLOW_APPEARANCE_WRITE);
Transform3D tr = new Transform3D();
tr.setTranslation(new javax.vecmath.Vector3d(p.getX(), p.getY(), p.getZ()));
TransformGroup tgSphere = new TransformGroup(tr);
tgSphere.addChild(simplex.getSphere());
bgSphere.addChild(tgSphere);
spin.addChild(bgSphere);
}
public BranchGroup addTetrahedron(Simplex simplex, Color3f color) {
BranchGroup bgTetrahedron = new BranchGroup();
bgTetrahedron.setCapability(BranchGroup.ALLOW_DETACH);
javax.vecmath.Point3d[] coords = new javax.vecmath.Point3d[12];
LineArray la = new LineArray(12, LineArray.COORDINATES | LineArray.COLOR_3);
Point3d p0 = (Point3d) complex.getPoints().get(simplex.getPoints()[0]);
Point3d p1 = (Point3d) complex.getPoints().get(simplex.getPoints()[1]);
Point3d p2 = (Point3d) complex.getPoints().get(simplex.getPoints()[2]);
Point3d p3 = (Point3d) complex.getPoints().get(simplex.getPoints()[3]);
coords[0] = coords[2] = coords[4] = new javax.vecmath.Point3d(p0.getX(), p0.getY(), p0.getZ());
coords[1] = coords[6] = coords[8] = new javax.vecmath.Point3d(p1.getX(), p1.getY(), p1.getZ());
coords[3] = coords[7] = coords[10] = new javax.vecmath.Point3d(p2.getX(), p2.getY(), p2.getZ());
coords[5] = coords[9] = coords[11] = new javax.vecmath.Point3d(p3.getX(), p3.getY(), p3.getZ());
la.setCoordinates(0, coords);
Color3f[] colors = new Color3f[12];
for (int i = 0; i < 12; i++) colors[i] = Colors.black;
la.setColors(0, colors);
javax.vecmath.Point3d[] coordsTr = new javax.vecmath.Point3d[24];
TriangleArray tr = new TriangleArray(24, TriangleArray.COORDINATES | TriangleArray.COLOR_3);
coordsTr[0] =
coordsTr[3] = coordsTr[6] = new javax.vecmath.Point3d(p0.getX(), p0.getY(), p0.getZ());
coordsTr[1] =
coordsTr[4] = coordsTr[9] = new javax.vecmath.Point3d(p1.getX(), p1.getY(), p1.getZ());
coordsTr[2] =
coordsTr[7] = coordsTr[10] = new javax.vecmath.Point3d(p2.getX(), p2.getY(), p2.getZ());
coordsTr[5] =
coordsTr[8] = coordsTr[11] = new javax.vecmath.Point3d(p3.getX(), p3.getY(), p3.getZ());
coordsTr[12] =
coordsTr[15] = coordsTr[18] = new javax.vecmath.Point3d(p0.getX(), p0.getY(), p0.getZ());
coordsTr[14] =
coordsTr[17] = coordsTr[21] = new javax.vecmath.Point3d(p1.getX(), p1.getY(), p1.getZ());
coordsTr[13] =
coordsTr[20] = coordsTr[23] = new javax.vecmath.Point3d(p2.getX(), p2.getY(), p2.getZ());
coordsTr[16] =
coordsTr[19] = coordsTr[22] = new javax.vecmath.Point3d(p3.getX(), p3.getY(), p3.getZ());
tr.setCoordinates(0, coordsTr);
Color3f[] colorsTr = new Color3f[24];
for (int i = 0; i < 24; i++) colorsTr[i] = Colors.green;
tr.setColors(0, colorsTr);
Appearance ap = new Appearance();
ap.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ);
ap.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE);
ap.setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_READ);
ap.setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_WRITE);
// ap.setCapability(Appearance.ALLOW_MATERIAL_READ);
// ap.setCapability(Appearance.ALLOW_MATERIAL_WRITE);
ap.setLineAttributes(new LineAttributes(2, LineAttributes.PATTERN_SOLID, false));
ap.setMaterial(new Material());
// ap.setTransparencyAttributes(new
// TransparencyAttributes(TransparencyAttributes.SCREEN_DOOR, 0.5f));
// LineArray la = cell.getLineArray();
Shape3D shape = new Shape3D(la, ap);
Shape3D shapeTr = new Shape3D(tr, ap);
shape.setCapability(Shape3D.ALLOW_APPEARANCE_READ);
shape.setCapability(Shape3D.ALLOW_APPEARANCE_WRITE);
simplex.setTetrahedron(shape);
// cell.setLineArray(la);
simplex.setTriangleArray(tr);
simplex.setBgTetrahedron(bgTetrahedron);
TransformGroup tgTetrahedron = new TransformGroup();
tgTetrahedron.addChild(shape);
tgTetrahedron.addChild(shapeTr);
bgTetrahedron.addChild(tgTetrahedron);
spin.addChild(bgTetrahedron);
return bgTetrahedron;
}
public void actionPerformed(ActionEvent actionEvent) {
String cmd = actionEvent.getActionCommand();
if ("Console"
.equals(
cmd)) { // opens a window to read the coordinates of a point that is added to the point
// set.
new InputPanelPointApplet(this);
} else if ("Select_Point"
.equals(cmd)) { // opens a window with the list of points. One is to be selected.
new SelectPointPanelApplet(this);
} else if ("Select_Cell"
.equals(cmd)) { // opens a window with the list of cells. One is to be selected.
// new SelectCellPanelApplet(this);
} else if ("Random Point".equals(cmd)) { // adds random point to the point set
/* com.artchase.geom3d.Point3d pointToAdd = new com.artchase.geom3d.Point3d(randGen);
int size = getCells().getVertices().getSize();
Vertex v = new Vertex(pointToAdd, size);
getCells().getVertices().insert(v);
addSphere(v, 0.02f, Colors.red);
getCells().setNrVertices(size+1);
*/ } else if ("Selected_Point_Move".equals(cmd)) {
// new SelectedPointMovePanel(this);
} else if ("Selected_Cell_Adjacent".equals(cmd)) {
/* if (selectedCell != null) {
System.out.println("selectedCell is not null");
if (selectedAdjCell != null) {
System.out.println("adjacentCellShown is TRUE");
selectedAdjCell.changeAppearance(1, LineAttributes.PATTERN_SOLID, Colors.yellow);
selectedAdjCell = null;
}
System.out.println("adjacentCellShown is FALSE");
if (cells.getNrCells() > 0) {
System.out.println("Number of cells is " + cells.getNrCells());
int nrIter = 0;
do {
nrIter++;
selectedAdjCellIndex = (++selectedAdjCellIndex)%4;
System.out.println("selectedAdjCellIndex = " + selectedAdjCellIndex);
selectedAdjCell = selectedCell.getAdjCell(selectedAdjCellIndex);
} while (selectedAdjCell.isInfiniteCell() && (nrIter < 4));
if (!selectedAdjCell.isInfiniteCell()) { // adjacent cell found
System.out.println("i am here displaying cell " + selectedAdjCellIndex);
selectedAdjCell.changeAppearance(5, LineAttributes.PATTERN_SOLID, Colors.magenta);
} else selectedAdjCell = null; // all adjacent cells are infinite
}
}
*/ } else if ("Selected_Cell_Circumcircle".equals(cmd)) {
/* if (circumCircleShown) {
circumCircleBranchGroup.detach();
circumCircleShown = false;
}
else {
com.artchase.geom3d.Point3d[] points = selectedCell.getPoints();
Sphere3d sphere = new Sphere3d(points[0],points[1],points[2],points[3]);
com.artchase.geom3d.Point3d center = sphere.getCenter();
circumCircleBranchGroup = addSphere(center, sphere.getRadius(), Colors.green);
circumCircleShown = true;
}
*/ } else if ("Random".equals(cmd)) {
complex.clear();
spin.removeAllChildren();
setNrSpannedVerticesField(0);
setNrEdgesField(0);
setNrFacesField(0);
setNrCellsField(0);
// Open window to get the number of random points to be generated.
new InputPanelRandomApplet(this);
} else if ("Clear".equals(cmd)) {
complex.clear();
spin.removeAllChildren();
setNrSpannedVerticesField(0);
setNrEdgesField(0);
setNrFacesField(0);
setNrCellsField(0);
selectedSimplex = null;
selectedAdjCell = null;
count2 = count3 = 0;
} else if ("Run".equals(cmd)) {
Simplex simplex;
if (!complex.getPoints().isEmpty() && complex.isEmpty()) {
simplex = complex.first3Simplex();
// addTriangle(simplex,Colors.yellow);
while (!complex.getStack().isEmpty()) complex.next4Simplex();
/* int size = complex.simplicies[3].getSize();
for (int i = 0; i < size; i++) {
simplex = (Simplex)complex.simplicies[3].get(i);
addTetrahedron(simplex,Colors.yellow);
}
*/ complex.computeAlphaValues();
SorterSelection sorter = new SorterSelection();
SortToolSimplexAlpha sortTool = new SortToolSimplexAlpha();
sorter.Sort(complex.getSimplicies()[1], sortTool, false);
sorter.Sort(complex.getSimplicies()[2], sortTool, false);
sorter.Sort(complex.getSimplicies()[3], sortTool, false);
complex.toConsole(complex.getSimplicies()[1]);
complex.toConsole(complex.getSimplicies()[2]);
complex.toConsole(complex.getSimplicies()[3]);
}
/* if (!complex.points.isEmpty()) {
while (!complex.stack.isEmpty()) complex.next4Simplex();
int size = complex.simplicies[3].getSize();
for (int i = 0; i < size; i++) {
simplex = (Simplex)complex.simplicies[3].get(i);
addTetrahedron(simplex,Colors.yellow);
}
}
*/ } else if ("Step".equals(cmd)) stepSimplicies3(); // stepSimplicies23 also available
else if ("Step1".equals(cmd)) {
if (complex.isEmpty()) {
Simplex simplex = complex.first3Simplex();
addTriangle(simplex, Colors.yellow);
}
Simplex simplex = complex.next4Simplex();
if (simplex != null) addTetrahedron(simplex, Colors.yellow);
} else if ("Save".equals(cmd)) {
try {
BufferedWriter bw = new BufferedWriter(new FileWriter("data"));
PrintWriter out = new PrintWriter(bw);
int size = complex.getPoints().getSize();
Point3d p;
for (int i = 0; i < size; i++) {
p = (Point3d) complex.getPoints().get(i);
out.print(p.getX() + " " + p.getY() + " " + p.getZ() + '\n');
}
out.close();
} catch (IOException e) {
System.out.println("IOException error!");
e.printStackTrace();
}
} else if ("Load".equals(cmd)) {
complex.clear();
spin.removeAllChildren();
geom3d.PointSet3d points = new PointSet3d("data");
int size = points.getSize();
Point3d point;
for (int i = 0; i < size; i++) {
point = (Point3d) points.get(i);
complex.getPoints().insert(point);
Simplex simplex = new Simplex(i);
complex.insert(simplex);
addSphere(simplex, 0.02f, Colors.red);
}
} else if ("PDB".equals(cmd)) {
complex.clear();
spin.removeAllChildren();
Protein protein = new Protein("1CR4", 0, true);
PointSet3d points = protein.getPointSet();
points.translate(points.getCentroid());
int size = points.getSize();
Point3d point;
for (int i = 0; i < size; i++) {
point = (Point3d) points.get(i);
complex.getPoints().insert(point);
Simplex simplex = new Simplex(i);
complex.insert(simplex);
addSphere(simplex, 0.02f, Colors.red);
}
// new InputPanelPDBApplet(this);
} else if ("Point".equals(cmd)) {
/* ap.setPolygonAttributes(new PolygonAttributes(PolygonAttributes.POLYGON_POINT, PolygonAttributes.CULL_BACK, 0));
ap.setPointAttributes(new PointAttributes(5, false)); }
else if ("Line".equals(cmd)) {
/* ap.setPolygonAttributes(new PolygonAttributes(PolygonAttributes.POLYGON_LINE, PolygonAttributes.CULL_BACK, 0));
ap.setLineAttributes(new LineAttributes(2, LineAttributes.PATTERN_DASH,false));
*/ } else if ("Polygon".equals(cmd)) {
// ap.setPolygonAttributes(new PolygonAttributes(PolygonAttributes.POLYGON_FILL,
// PolygonAttributes.CULL_BACK, 0));
} else if ("Gouraud".equals(cmd)) {
/* ColoringAttributes ca = new ColoringAttributes();
ca.setShadeModel(ColoringAttributes.SHADE_GOURAUD);
ap.setColoringAttributes(ca);
ap.setMaterial(null);
RenderingAttributes ra = new RenderingAttributes();
ra.setIgnoreVertexColors(false);
ap.setRenderingAttributes(ra);
*/ } else if ("Lighting".equals(cmd)) {
/* ap.setMaterial(new Material());
RenderingAttributes ra = new RenderingAttributes();
ra.setIgnoreVertexColors(true);
ap.setRenderingAttributes(ra);
*/ }
}
public ComplexViewer(Delaunay3d complex) {
super();
this.complex = complex;
complex.setViewer(this);
toProcess = new Stack();
}