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

Example 6 with TransformGroup

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

the class RendererCache method createTransformGroup.

private static final TransformGroup createTransformGroup(Transform3D transform3D) {
    TransformGroup transformGroup;
    if (transform3D == null) {
        transformGroup = new TransformGroup();
    } else {
        transformGroup = new TransformGroup(transform3D);
    }
    transformGroup.setCapability(TransformGroup.ALLOW_TRANSFORM_READ);
    transformGroup.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE);
    transformGroup.setCapability(TransformGroup.ALLOW_CHILDREN_READ);
    return transformGroup;
}

Example 7 with TransformGroup

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

the class GraphicsEvents method systemTranslate.

private boolean systemTranslate() {
    TransformGroup tg = null;
    GraphicsCanvas.MouseMode mouseMode = graphics3D.getMouseMode();
    if ((mouseMode == GraphicsCanvas.MouseMode.SYSTEMBELOWMOUSE) && atom != null) {
        tg = (TransformGroup) pickResult.getNode(PickResult.TRANSFORM_GROUP);
    } else if (mouseMode == GraphicsCanvas.MouseMode.ACTIVESYSTEM) {
        if (mainPanel.getHierarchy().getActive() != null) {
            tg = mainPanel.getHierarchy().getActive().getTransformGroup();
        }
    }
    if ((tg != null) && (tg.getCapability(TransformGroup.ALLOW_TRANSFORM_READ)) && (tg.getCapability(TransformGroup.ALLOW_TRANSFORM_WRITE))) {
        systemTranslate.setTransformGroup(tg);
        postId(TRANSLATEPOST);
        return true;
    }
    return false;
}

Example 8 with TransformGroup

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

the class MainPanel method merge.

/**
 * Merge two or more selected FSystem Nodes into one FSystem node. There are
 * a few gotchas that need to be fixed
 *
 * @param nodesToMerge a {@link java.util.ArrayList} object.
 */
public void merge(ArrayList<MSNode> nodesToMerge) {
    ArrayList<MSNode> activeNodes = new ArrayList<MSNode>();
    for (MSNode node : nodesToMerge) {
        if (node != null && !(node instanceof MSRoot)) {
            activeNodes.add(node);
        }
    }
    if (activeNodes.size() <= 1) {
        return;
    }
    // Set up a structure to hold the new system
    FFXSystem active = hierarchy.getActive();
    File file = SystemFilter.version(hierarchy.getActive().getFile());
    FFXSystem system = new FFXSystem(file, "Merge Result", active.getProperties());
    system.setKeyFile(active.getKeyFile());
    system.setKeywords(KeyFilter.open(active.getKeyFile()));
    // Fill arrays with the atoms and bonds from the systems to be combined
    ArrayList<Atom> mergedAtoms = new ArrayList<Atom>();
    ArrayList<Bond> mergedBonds = new ArrayList<Bond>();
    ArrayList<FFXSystem> systems = new ArrayList<FFXSystem>();
    TransformGroup parentTransformGroup = null;
    FFXSystem parentSystem;
    Transform3D parentTransform3D = new Transform3D();
    Vector3d parentPosition = new Vector3d();
    Vector3d atomPosition = new Vector3d();
    // TINKER Atom Numbers start at 1
    int atomNum = 1;
    Vector3d zero = new Vector3d(0.0, 0.0, 0.0);
    for (MSNode m : activeNodes) {
        parentSystem = (FFXSystem) m.getMSNode(FFXSystem.class);
        if (parentSystem == null) {
            return;
        }
        if (!systems.contains(parentSystem)) {
            graphicsCanvas.updateSceneWait(parentSystem, false, true, RendererCache.ViewModel.WIREFRAME, false, null);
            systems.add(parentSystem);
        }
        // Move each atom into the global frame by applying the System
        // Transform to
        // relative atomic position
        parentTransformGroup = parentSystem.getOriginToRot();
        parentTransformGroup.getTransform(parentTransform3D);
        parentTransform3D.get(parentPosition);
        parentTransform3D.setTranslation(zero);
        // parentTransform3D.setScale(1.0d);
        ArrayList<Atom> atoms = m.getAtomList();
        ArrayList<ROLS> bonds = m.getBondList();
        for (Atom atom : atoms) {
            atom.removeFromParent();
            atom.setXyzIndex(atomNum++);
            mergedAtoms.add(atom);
            atom.getV3D(atomPosition);
            parentTransform3D.transform(atomPosition);
            atomPosition.add(parentPosition);
            atom.moveTo(atomPosition);
        }
        for (ROLS msm : bonds) {
            Bond bond = (Bond) msm;
            bond.removeFromParent();
            mergedBonds.add((Bond) msm);
        }
    }
    for (FFXSystem sys : systems) {
        close(sys);
    }
    MergeFilter mergeFilter = new MergeFilter(system, mergedAtoms, mergedBonds);
    UIFileOpener fileOpener = new UIFileOpener(mergeFilter, this);
    if (fileOpenerThreads > 0) {
        fileOpener.setNThreads(fileOpenerThreads);
    }
    Thread thread = new Thread(fileOpener);
    thread.start();
}

Example 9 with TransformGroup

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

the class GraphicsAxis method createAxisLabel.

@SuppressWarnings("unchecked")
private TransformGroup createAxisLabel(String letter, Font3D font3d, Appearance ap, double x, double y, double z) {
    Text3D text = new Text3D(font3d, letter);
    text.setUserData(this);
    Transform3D t3D = new Transform3D();
    t3D.setTranslation(new Vector3d(x, y, z));
    TransformGroup tg = new TransformGroup(t3D);
    Shape3D text3d = new Shape3D(text, ap);
    text3d.setUserData(this);
    for (Enumeration<Geometry> e = text3d.getAllGeometries(); e.hasMoreElements(); ) {
        Geometry g = e.nextElement();
        g.setCapability(Geometry.ALLOW_INTERSECT);
    }
    text3d.setCapability(Shape3D.ENABLE_PICK_REPORTING);
    text3d.setCapability(Shape3D.ALLOW_GEOMETRY_READ);
    tg.addChild(text3d);
    return tg;
}

Example 10 with TransformGroup

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

the class MolecularAssembly method createScene.

/**
 * The MolecularAssembly BranchGroup has two TransformGroups between it and
 * the "base" node where geometry is attached. If the point between the two
 * transformations is where user rotation occurs. For example, if rotating
 * about the center of mass of the system, the RotToCOM transformation will
 * be an identity transformation (ie. none). If rotation is about some atom
 * or group of atoms within the system, then the RotToCOM transformation
 * will be a translation from that point to the COM.
 *
 * @param zero boolean
 * @return BranchGroup
 */
public BranchGroup createScene(boolean zero) {
    originToRotT3D = new Transform3D();
    originToRotV3D = new Vector3d();
    originToRot = new TransformGroup(originToRotT3D);
    branchGroup = new BranchGroup();
    rotToCOM = new TransformGroup();
    rotToCOMT3D = new Transform3D();
    rotToCOMV3D = new Vector3d();
    // Set capabilities needed for picking and moving the MolecularAssembly
    branchGroup.setCapability(BranchGroup.ALLOW_DETACH);
    originToRot.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE);
    originToRot.setCapability(TransformGroup.ALLOW_TRANSFORM_READ);
    originToRot.setCapability(TransformGroup.ENABLE_PICK_REPORTING);
    rotToCOM.setCapability(TransformGroup.ALLOW_TRANSFORM_READ);
    rotToCOM.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE);
    // Put the MolecularAssembly in the middle of the scene
    if (zero) {
        originToRotV3D.set(0.0, 0.0, 0.0);
        originToRotT3D.set(originToRotV3D);
        originToRot.setTransform(originToRotT3D);
    }
    wire = renderWire();
    switchGroup = new Switch(Switch.CHILD_NONE);
    switchGroup.setCapability(Switch.ALLOW_SWITCH_WRITE);
    base = new BranchGroup();
    base.setCapability(BranchGroup.ALLOW_CHILDREN_EXTEND);
    base.setCapability(BranchGroup.ALLOW_CHILDREN_WRITE);
    childNodes = new BranchGroup();
    childNodes.setCapability(BranchGroup.ALLOW_DETACH);
    childNodes.setCapability(BranchGroup.ALLOW_CHILDREN_EXTEND);
    childNodes.setCapability(BranchGroup.ALLOW_CHILDREN_WRITE);
    switchGroup.addChild(base);
    if (wire != null) {
        base.addChild(wire);
    }
    vrml = loadVRML();
    if (vrml != null) {
        vrmlTG = new TransformGroup();
        vrmlTd = new Transform3D();
        vrmlTG.setTransform(vrmlTd);
        vrmlTG.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE);
        vrmlTG.addChild(vrml);
        switchGroup.addChild(vrmlTG);
        setView(RendererCache.ViewModel.INVISIBLE, null);
    }
    switchGroup.setWhichChild(Switch.CHILD_ALL);
    rotToCOM.addChild(switchGroup);
    originToRot.addChild(rotToCOM);
    branchGroup.addChild(originToRot);
    branchGroup.compile();
    return branchGroup;
}