Examples with Shape3D javax.media.j3d.Shape3D used on opensource projects

Example 1 with Shape3D

use of javax.media.j3d.Shape3D in project ffx by mjschnie.

the class GraphicsPicking method updateScene.

/**
 * {@inheritDoc}
 *
 * Called by Java3D when an atom is picked
 */
public void updateScene(int xpos, int ypos) {
    if (picking == false) {
        return;
    }
    // Determine what FNode was picked
    pickCanvas.setShapeLocation(xpos, ypos);
    PickResult result = pickCanvas.pickClosest();
    if (result != null) {
        SceneGraphPath sceneGraphPath = result.getSceneGraphPath();
        Node node = sceneGraphPath.getObject();
        if (!(node instanceof Shape3D)) {
            return;
        }
        Shape3D pickedShape3D = (Shape3D) node;
        Object userData = pickedShape3D.getUserData();
        if (userData instanceof MolecularAssembly) {
            FFXSystem sys = (FFXSystem) userData;
            if (result.numIntersections() > 0) {
                PickIntersection pickIntersection = result.getIntersection(0);
                int[] coords = pickIntersection.getPrimitiveCoordinateIndices();
                userData = sys.getAtomFromWireVertex(coords[0]);
            } else {
                return;
            }
        }
        if (userData instanceof Atom) {
            Atom a = (Atom) userData;
            // Check to see if the pickLevel has changed
            if (!(pickLevel == newPickLevel)) {
                pickLevel = newPickLevel;
                pickNumber = 0;
            }
            // Clear selections between measurements
            String pickLevelString = pickLevel.toString();
            boolean measure = pickLevelString.startsWith("MEASURE");
            if (!measure || count == 0) {
                for (Atom matom : atomCache) {
                    matom.setSelected(false);
                    matom.setColor(RendererCache.ColorModel.SELECT, null, null);
                }
                atomCache.clear();
                count = 0;
            }
            // If measuring, select the current atom and add it to the cache
            if (measure && !atomCache.contains(a)) {
                atomCache.add(0, a);
                a.setSelected(true);
                a.setColor(RendererCache.ColorModel.PICK, null, null);
                count++;
                measure();
            }
            if (!measure) {
                // This allows iteration through the atom's terms
                if (a == previousAtom) {
                    pickNumber++;
                } else {
                    previousAtom = a;
                    pickNumber = 0;
                }
                MSNode currentPick = null;
                switch(pickLevel) {
                    case PICKATOM:
                        currentPick = a;
                        break;
                    case PICKBOND:
                    case PICKANGLE:
                    case PICKDIHEDRAL:
                        ArrayList terms = null;
                        if (pickLevel == PickLevel.PICKBOND) {
                            terms = a.getBonds();
                        } else if (pickLevel == PickLevel.PICKANGLE) {
                            terms = a.getAngles();
                        } else if (pickLevel == PickLevel.PICKDIHEDRAL) {
                            terms = a.getTorsions();
                        }
                        if (terms == null) {
                            return;
                        }
                        int num = terms.size();
                        if (pickNumber >= num) {
                            pickNumber = 0;
                        }
                        currentPick = (BondedTerm) terms.get(pickNumber);
                        break;
                    case PICKRESIDUE:
                    case PICKPOLYMER:
                    case PICKMOLECULE:
                    case PICKSYSTEM:
                        MSNode dataNode = null;
                        if (pickLevel == PickLevel.PICKRESIDUE) {
                            dataNode = (MSNode) a.getMSNode(Residue.class);
                        } else if (pickLevel == PickLevel.PICKPOLYMER) {
                            dataNode = (MSNode) a.getMSNode(Polymer.class);
                        } else if (pickLevel == PickLevel.PICKSYSTEM) {
                            dataNode = (MSNode) a.getMSNode(MolecularAssembly.class);
                        } else if (pickLevel == PickLevel.PICKMOLECULE) {
                            dataNode = (MSNode) a.getMSNode(Molecule.class);
                            if (dataNode == null) {
                                dataNode = (MSNode) a.getMSNode(Polymer.class);
                            }
                        }
                        currentPick = dataNode;
                        break;
                    case MEASUREANGLE:
                    case MEASUREDIHEDRAL:
                    case MEASUREDISTANCE:
                        break;
                }
                // Add the selected node to the Tree View
                if (currentPick != null) {
                    if (controlButton) {
                        mainPanel.getHierarchy().toggleSelection(currentPick);
                    } else if (currentPick != previousPick) {
                        mainPanel.getHierarchy().onlySelection(currentPick);
                    }
                    // Color the Current Pick by Picking Color
                    mainPanel.getGraphics3D().updateScene(currentPick, false, false, null, true, RendererCache.ColorModel.PICK);
                }
                // Remove picking color from the previousPick
                if (previousPick != null && previousPick != currentPick) {
                    previousPick.setColor(RendererCache.ColorModel.REVERT, null, null);
                }
                previousPick = currentPick;
            }
        }
    }
}

Example 2 with Shape3D

use of javax.media.j3d.Shape3D in project ffx by mjschnie.

the class MolecularAssembly method createBox.

/**
 * <p>
 * createBox</p>
 */
public void createBox() {
    int vertices = 8;
    LineArray la = new LineArray(4 * vertices, GeometryArray.COORDINATES | GeometryArray.COLOR_4 | GeometryArray.NORMALS);
    la.setCapability(LineArray.ALLOW_COORDINATE_WRITE);
    la.setCapability(LineArray.ALLOW_COORDINATE_READ);
    la.setCapability(LineArray.ALLOW_COLOR_WRITE);
    la.setCapability(LineArray.ALLOW_COUNT_READ);
    la.setCapability(LineArray.ALLOW_INTERSECT);
    la.setCapability(LineArray.ALLOW_FORMAT_READ);
    // Create a normal
    // for (ListIterator<MSNode> li = bondlist.listIterator(); li.hasNext(); ){
    // la.setCoordinate(i, a1);
    // la.setColor(i, col);
    // la.setNormal(i++, a1);
    // }
    ColoringAttributes cola = new ColoringAttributes(new Color3f(), ColoringAttributes.SHADE_GOURAUD);
    Appearance app = new Appearance();
    lineAttributes = new LineAttributes();
    lineAttributes.setLineWidth(RendererCache.bondwidth);
    lineAttributes.setCapability(LineAttributes.ALLOW_WIDTH_WRITE);
    lineAttributes.setLineAntialiasingEnable(true);
    app.setLineAttributes(lineAttributes);
    app.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ);
    app.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE);
    RenderingAttributes ra = new RenderingAttributes();
    ra.setAlphaTestValue(0.1f);
    ra.setAlphaTestFunction(RenderingAttributes.GREATER);
    ra.setDepthBufferEnable(true);
    ra.setDepthBufferWriteEnable(true);
    app.setRenderingAttributes(ra);
    app.setColoringAttributes(cola);
    Shape3D wireframe = new Shape3D(la, app);
    // PickTool.setCapabilities(wire, PickTool.INTERSECT_COORD);
    wireframe.setUserData(this);
    wireframe.setBounds(new BoundingSphere(new Point3d(0, 0, 0), 10.0));
    try {
        wireframe.setBoundsAutoCompute(false);
    } catch (Exception e) {
        e.printStackTrace();
    }
    wireframe.setCapability(Shape3D.ALLOW_GEOMETRY_READ);
    wireframe.setCapability(Shape3D.ALLOW_APPEARANCE_READ);
// return wire;
}

Example 3 with Shape3D

use of javax.media.j3d.Shape3D in project ffx by mjschnie.

the class MolecularAssembly method recurseVRML.

private void recurseVRML(Node node) {
    if (node instanceof Shape3D) {
        Shape3D s3d = (Shape3D) node;
        PickTool.setCapabilities(s3d, PickTool.INTERSECT_COORD);
        return;
    } else if (node instanceof SharedGroup) {
        SharedGroup sg = (SharedGroup) node;
        for (Enumeration<Node> e = sg.getAllChildren(); e.hasMoreElements(); ) {
            recurseVRML(e.nextElement());
        }
        return;
    } else if (node instanceof BranchGroup) {
        BranchGroup bg = (BranchGroup) node;
        for (Enumeration<Node> e = bg.getAllChildren(); e.hasMoreElements(); ) {
            recurseVRML(e.nextElement());
        }
        return;
    } else if (node instanceof TransformGroup) {
        TransformGroup vrmlTG1 = (TransformGroup) node;
        for (Enumeration<Node> e = vrmlTG1.getAllChildren(); e.hasMoreElements(); ) {
            node = e.nextElement();
            recurseVRML(node);
        }
        return;
    } else if (node instanceof Link) {
        Link link = (Link) node;
        recurseVRML(link.getSharedGroup());
        return;
    } else if (node instanceof Group) {
        Group group = (Group) node;
        for (Enumeration<Node> e = group.getAllChildren(); e.hasMoreElements(); ) {
            Node n = e.nextElement();
            recurseVRML(n);
        }
    }
}

Example 4 with Shape3D

use of javax.media.j3d.Shape3D in project ffx by mjschnie.

the class RendererCache method createCylinder.

/**
 * This method creates a Cylinder
 *
 * @param ap a {@link javax.media.j3d.Appearance} object.
 * @param res a int.
 * @return a {@link javax.media.j3d.Shape3D} object.
 */
protected static final Shape3D createCylinder(Appearance ap, int res) {
    if (res < 0) {
        res = 0;
    }
    if (res > 10) {
        res = 10;
    }
    final Shape3D cyl = new Shape3D();
    cyl.setAppearance(ap);
    cyl.addGeometry(getCylinderGeom(0, res));
    cyl.addGeometry(getCylinderGeom(1, res));
    cyl.addGeometry(getCylinderGeom(2, res));
    cyl.setCapability(Shape3D.ALLOW_GEOMETRY_READ);
    cyl.setCapability(Shape3D.ALLOW_GEOMETRY_WRITE);
    cyl.setCapability(Shape3D.ALLOW_APPEARANCE_WRITE);
    cyl.setCapability(Shape3D.ALLOW_APPEARANCE_READ);
    cyl.setCapability(Shape3D.ENABLE_PICK_REPORTING);
    cyl.setCapability(Shape3D.ALLOW_PICKABLE_WRITE);
    return cyl;
}

Example 5 with Shape3D

use of javax.media.j3d.Shape3D in project ffx by mjschnie.

the class RendererCache method coneFactory.

/**
 * <p>
 * coneFactory</p>
 *
 * @param ap a {@link javax.media.j3d.Appearance} object.
 * @param res a int.
 * @return a {@link javax.media.j3d.Shape3D} object.
 */
protected static Shape3D coneFactory(Appearance ap, int res) {
    if (res > 3) {
        res = 3;
    }
    Shape3D cone = new Shape3D();
    cone.setAppearance(ap);
    cone.setCapability(Shape3D.ALLOW_GEOMETRY_READ);
    cone.setCapability(Shape3D.ALLOW_GEOMETRY_WRITE);
    cone.setCapability(Shape3D.ALLOW_APPEARANCE_WRITE);
    cone.setCapability(Shape3D.ALLOW_PICKABLE_WRITE);
    cone.addGeometry(getConeGeom(0, res));
    cone.addGeometry(getConeGeom(1, res));
    return cone;
}