// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.potential.bonded;
  
  import java.io.Serial;
  import java.util.ArrayList;
  import java.util.Collections;
  import java.util.Enumeration;
  import java.util.List;
  import java.util.Objects;
  import javax.swing.tree.DefaultMutableTreeNode;
  import javax.swing.tree.TreeNode;
  import org.jogamp.java3d.BranchGroup;
  import org.jogamp.java3d.Canvas3D;
  import org.jogamp.java3d.J3DGraphics2D;
  import org.jogamp.java3d.Material;
  import org.jogamp.java3d.Node;
  import org.jogamp.vecmath.Color3f;
  
  /**
   * The MSNode class forms the basic unit that all data classes extend.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  @SuppressWarnings("CloneableImplementsClone")
  public class MSNode extends DefaultMutableTreeNode implements ROLS {
  
    @Serial
    private static final long serialVersionUID = 1L;
  
    /** The multiscale level of this node. */
    private final int MultiScaleLevel;
    /** True if this node is selected. */
    protected boolean selected = false;
    /** The name of this node. */
    private String name;
    /** Total mass of this node and its children. */
    private double totalMass;
  
    /** Default MSNode Constructor */
    public MSNode() {
      name = "";
      MultiScaleLevel = ROLS.MaxLengthScale;
    }
  
    /**
     * Constructs a MSNode with the name n.
     *
     * @param n a {@link java.lang.String} object.
     */
    public MSNode(String n) {
      name = n;
      MultiScaleLevel = ROLS.MaxLengthScale;
    }
  
    /**
     * Constructor for MSNode.
     *
     * @param n a {@link java.lang.String} object.
     * @param multiScaleLevel The multiscale level of this node.
     */
    public MSNode(String n, int multiScaleLevel) {
      this.name = n;
     this.MultiScaleLevel = multiScaleLevel;
   }
 
   /**
    * If <code>this</code> MSNode or any MSNode below it <code>equals</code> the argument, that MSNode
    * is returned.
    *
    * @param msNode a {@link ffx.potential.bonded.MSNode} object.
    * @return a {@link ffx.potential.bonded.MSNode} object.
    */
   public MSNode contains(MSNode msNode) {
     @SuppressWarnings("unchecked")
     Enumeration<TreeNode> e = depthFirstEnumeration();
     List<TreeNode> list = Collections.list(e);
     for (TreeNode node : list) {
       if (node.equals(msNode)) {
         return (MSNode) node;
       }
     }
     return null;
   }
 
   /**
    * destroy
    *
    * @return a boolean.
    */
   public boolean destroy() {
     if (getParent() != null) {
       removeFromParent();
     }
     name = null;
     selected = false;
     return true;
   }
 
   /** {@inheritDoc} */
   @Override
   public void drawLabel(Canvas3D graphics, J3DGraphics2D g2d, Node node) {
     if (!isSelected()) {
       return;
     }
     for (Enumeration<TreeNode> e = children(); e.hasMoreElements(); ) {
       MSNode dataNode = (MSNode) e.nextElement();
       dataNode.drawLabel(graphics, g2d, node);
     }
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>MSNode equality := same class and same name. Consider replacing with a
    * Comparator&lt;MSNode&gt; for cases where non-reference equality is desired.
    */
   @Override
   public boolean equals(Object o) {
     if (this == o) {
       return true;
     }
     if (o == null || getClass() != o.getClass()) {
       return false;
     }
     MSNode msNode = (MSNode) o;
     return Objects.equals(name, msNode.getName());
   }
 
   /**
    * Returns a List of all Angles below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<Angle> getAngleList() {
     return getList(Angle.class);
   }
 
   /**
    * Returns a List of all AngleTorsions below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<AngleTorsion> getAngleTorsionList() {
     return getList(AngleTorsion.class);
   }
 
   /**
    * Returns a List of all Atoms below the present MSNode.
    *
    * @return a new {@link java.util.List} object.
    */
   public List<Atom> getAtomList() {
     List<Atom> atomList = getList(Atom.class);
     Collections.sort(atomList);
     return atomList;
   }
 
   /**
    * getAtomList.
    *
    * @param originalOrder a boolean.
    * @return a {@link java.util.List} object.
    */
   public List<Atom> getAtomList(boolean originalOrder) {
     // As of now, for generic MSNode objects, atoms remain in their original
     // order. It is presently only a concern for MultiResidue.
     return getAtomList();
   }
 
   /**
    * Returns a List of all Bonds below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<Bond> getBondList() {
     return getList(Bond.class);
   }
 
   /** {@inheritDoc} */
   @Override
   public double[] getCenter(boolean w) {
     double[] Rc = {0, 0, 0};
     double sum = 0, mass = 1;
     List<Atom> atomList = getAtomList();
     for (Atom a : atomList) {
       if (w) {
         mass = a.getMass();
         sum += mass;
       }
       Rc[0] += mass * a.getX();
       Rc[1] += mass * a.getY();
       Rc[2] += mass * a.getZ();
     }
     if (!w) {
       sum = atomList.size();
     }
     for (int i = 0; i < 3; i++) {
       Rc[i] /= sum;
     }
     return Rc;
   }
 
   /**
    * Returns a List of the MSNode's Children (instead of using an Enumeration).
    *
    * @return a {@link java.util.List} object.
    */
   public List<MSNode> getChildList() {
     List<MSNode> l = new ArrayList<>();
     Enumeration<TreeNode> e = children();
     while (e.hasMoreElements()) {
       l.add((MSNode) e.nextElement());
     }
     return l;
   }
 
   /**
    * getExtent
    *
    * @return a double.
    */
   public double getExtent() {
     double extent = 0.0;
     for (Enumeration<TreeNode> e = children(); e.hasMoreElements(); ) {
       MSNode node = (MSNode) e.nextElement();
       double temp = node.getExtent();
       if (temp > extent) {
         extent = temp;
       }
     }
     return extent;
   }
 
   /**
    * Returns a List of all ImproperTorsions below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<ImproperTorsion> getImproperTorsionList() {
     return getList(ImproperTorsion.class);
   }
 
   /** {@inheritDoc} */
   public <T extends TreeNode> List<T> getList(Class<T> c) {
     return getList(c, new ArrayList<>());
   }
 
   /** {@inheritDoc} */
   @Override
   public <T extends TreeNode> List<T> getList(Class<T> c, List<T> nodes) {
     if (c.isInstance(this)) {
       nodes.add(c.cast(this));
     }
     if (isLeaf() || !canBeChild(c)) {
       return nodes;
     }
     for (Enumeration<TreeNode> e = children(); e.hasMoreElements(); ) {
       MSNode node = (MSNode) e.nextElement();
       node.getList(c, nodes);
     }
     return nodes;
   }
 
   /** {@inheritDoc} */
   @Override
   public <T extends TreeNode> long getMSCount(Class<T> c, long count) {
     if (c.isInstance(this)) {
       count++;
     }
     if (!canBeChild(c)) {
       return count;
     }
     for (Enumeration<TreeNode> e = children(); e.hasMoreElements(); ) {
       MSNode node = (MSNode) e.nextElement();
       count += node.getMSCount(c, count);
     }
     return count;
   }
 
   /** {@inheritDoc} */
   @Override
   public <T extends TreeNode> T getMSNode(Class<T> c) {
     TreeNode[] nodes = getPath();
     for (TreeNode n : nodes) {
       if (c.isInstance(n)) {
         return c.cast(n);
       }
     }
     return null;
   }
 
   /** {@inheritDoc} */
   @Override
   public double getMW() {
     double weight = 0.0;
     for (Atom atom : getAtomList()) {
       weight += atom.getMass();
     }
     return weight;
   }
 
   /**
    * Returns the name of this MSNode.
    *
    * @return a {@link java.lang.String} object.
    */
   public String getName() {
     return name;
   }
 
   /**
    * Sets the name of this NodeObject to n.
    *
    * @param n a {@link java.lang.String} object.
    */
   public void setName(String n) {
     name = n;
   }
 
   /**
    * Returns a List of all Out-of-Plane Bends below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<OutOfPlaneBend> getOutOfPlaneBendList() {
     return getList(OutOfPlaneBend.class);
   }
 
   /**
    * Returns a List of all Pi-Orbital Torsions below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<PiOrbitalTorsion> getPiOrbitalTorsionList() {
     return getList(PiOrbitalTorsion.class);
   }
 
   /**
    * Returns a List of all Stretch-Bends below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<StretchBend> getStretchBendList() {
     return getList(StretchBend.class);
   }
 
   /**
    * Returns a List of all StretchTorsions below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<StretchTorsion> getStretchTorsionList() {
     return getList(StretchTorsion.class);
   }
 
   /**
    * Returns a List of all Torsions below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<Torsion> getTorsionList() {
     return getList(Torsion.class);
   }
 
   /**
    * Returns a List of all Torsion-Torsions below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<TorsionTorsion> getTorsionTorsionList() {
     return getList(TorsionTorsion.class);
   }
 
   /**
    * Returns the total mass of all atoms in the MolecularAssembly, calculating the mass if it has not
    * already been done, defaulting to simple addition.
    *
    * @return Total mass of atoms in system.
    */
   public double getTotalMass() {
     if (totalMass == 0.0) {
       return getTotalMass(true, false);
     }
     return totalMass;
   }
 
   /**
    * Returns a List of all Urey-Bradleys below the present MSNode.
    *
    * @return a {@link java.util.List} object.
    */
   public List<UreyBradley> getUreyBradleyList() {
     return getList(UreyBradley.class);
   }
 
   /** {@inheritDoc} */
   @Override
   public int hashCode() {
     return Objects.hash(name);
   }
 
   /**
    * isSelected
    *
    * @return a boolean.
    */
   public boolean isSelected() {
     return selected;
   }
 
   /**
    * Setter for the field <code>selected</code>.
    *
    * @param b a boolean.
    */
   public void setSelected(boolean b) {
     selected = b;
     for (Enumeration<TreeNode> e = children(); e.hasMoreElements(); ) {
       MSNode node = (MSNode) e.nextElement();
       node.setSelected(b);
     }
   }
 
   /** Prints the MSNode's name */
   public void print() {
     System.out.println(name);
   }
 
   /**
    * removeChild.
    *
    * @param child a {@link ffx.potential.bonded.MSNode} object.
    */
   public void removeChild(MSNode child) {
     if (child != null && child.getParent() == this) {
       remove(child);
     }
   }
 
   /** {@inheritDoc} */
   @Override
   public void setColor(RendererCache.ColorModel colorModel, Color3f color, Material mat) {
     for (Enumeration<TreeNode> e = children(); e.hasMoreElements(); ) {
       MSNode node = (MSNode) e.nextElement();
       node.setColor(colorModel, color, mat);
     }
   }
 
   /** {@inheritDoc} */
   @Override
   public void setView(RendererCache.ViewModel viewModel, List<BranchGroup> newShapes) {
     for (Enumeration<TreeNode> e = children(); e.hasMoreElements(); ) {
       MSNode node = (MSNode) e.nextElement();
       node.setView(viewModel, newShapes);
     }
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Overridden toString method returns the MSNode's name
    */
   @Override
   public String toString() {
     return name;
   }
 
   /** {@inheritDoc} */
   @Override
   public void update() {
     for (Enumeration<TreeNode> e = children(); e.hasMoreElements(); ) {
       MSNode node = (MSNode) e.nextElement();
       node.update();
     }
   }
 
   /**
    * Calculates the total mass of all atoms in the MolecularAssembly, using either a simple addition
    * or the Kahan summation algorithm. The simple algorithm is a standard loop to add up the masses.
    *
    * @param recalculate Force recalculation
    * @param useKahan Use Kahan or simple addition algorithms
    * @return Total mass of all atoms in system.
    */
   private double getTotalMass(boolean recalculate, boolean useKahan) {
     if (recalculate) {
       List<Atom> atoms = getAtomList();
       if (atoms.isEmpty()) {
         totalMass = 0.0;
       } else if (useKahan) {
         totalMass = kahanSumMasses(atoms);
       } else {
         totalMass = sumMasses(atoms);
       }
     }
     return totalMass;
   }
 
   /**
    * Iterative summation of atomic masses.
    *
    * @param atoms List of atoms.
    * @return Mass of atoms.
    */
   private double sumMasses(List<Atom> atoms) {
     double sumMasses = 0.0;
     for (Atom atom : atoms) {
       sumMasses += atom.getMass();
     }
     return sumMasses;
   }
 
   /**
    * Implements the Kahan algorithm to very accurately sum the masses of all the atoms provided,
    * minimizing rounding error.
    *
    * @param atoms Atoms to sum the mass of.
    * @return Total mass.
    */
   private double kahanSumMasses(List<Atom> atoms) {
     double sum = 0.0;
     double comp = 0.0; // Running compensation
     for (Atom atom : atoms) {
       double atomMass = atom.getMass() - comp;
       double temp = sum + atomMass;
       comp = (temp - sum) - atomMass;
       sum = temp;
     }
     return sum;
   }
 
   /**
    * Returns true if Class c can be below this Class in the Hierarchy
    *
    * @param c Class
    * @return boolean
    */
   private <T extends TreeNode> boolean canBeChild(Class<T> c) {
     try {
       int multiScaleLevel = c.getDeclaredField("MultiScaleLevel").getInt(null);
       if (multiScaleLevel >= this.MultiScaleLevel) {
         return false;
       }
     } catch (NoSuchFieldException
              | SecurityException
              | IllegalArgumentException
              | IllegalAccessException e) {
       return true;
     }
     return true;
   }
 }