/* Copyright (C) 2004-2007  Martin Eklund <martin.eklund@farmbio.uu.se>
 *
 * Contact: cdk-devel@lists.sourceforge.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 *
 * This program 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 Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.silent;

import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IMonomer;
import org.openscience.cdk.interfaces.IStrand;

import java.util.Collection;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.Map;

/**
 * A Strand is an AtomContainer which stores additional strand specific
 * informations for a group of Atoms.
 *
 * @cdk.module  silent
 * @cdk.githash
 * @cdk.created 2004-12-20
 * @author Martin Eklund &lt;martin.eklund@farmbio.uu.se&gt;
 * @author Ola Spjuth &lt;ola.spjuth@farmbio.uu.se&gt;
 */
public class Strand extends AtomContainer implements java.io.Serializable, IStrand {

    /**
     * Determines if a de-serialized object is compatible with this class.
     *
     * This value must only be changed if and only if the new version
     * of this class is incompatible with the old version. See Sun docs
     * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
     * /serialization/spec/version.doc.html>details</a>.
     */
    private static final long     serialVersionUID = 4200943086350928356L;

    /** The list of all Monomers in the Strand.*/
    private Map<String, IMonomer> monomers;
    /** The name of this strand (e.g. A, B). */
    private String                strandName;
    /** The type of this strand (e.g. PEPTIDE, DNA, RNA). */
    private String                strandType;

    /**
     * Constructs a new Strand.
     */
    public Strand() {
        super();
        // Stand stuff
        monomers = new Hashtable<String, IMonomer>();
        Monomer oMonomer = new Monomer();
        oMonomer.setMonomerName("");
        oMonomer.setMonomerType("UNKNOWN");
        monomers.put("", oMonomer);
        strandName = "";
    }

    /**
     * Retrieves the strand name.
     *
     * @return The name of the Strand object
     * @see #setStrandName
     */
    @Override
    public String getStrandName() {
        return strandName;
    }

    /**
     * Retrieves the strand type.
     *
     * @return The type of the Strand object
     * @see #setStrandType
     */
    @Override
    public String getStrandType() {
        return strandType;
    }

    /**
     * Sets the name of the Strand object.
     *
     * @param cStrandName  The new name for this strand
     * @see #getStrandName
     */
    @Override
    public void setStrandName(String cStrandName) {
        strandName = cStrandName;
    }

    /**
     * Sets the type of the Strand object.
     *
     * @param cStrandType  The new type for this strand
     * @see #getStrandType
     */
    @Override
    public void setStrandType(String cStrandType) {
        strandType = cStrandType;
    }

    /**
     *
     * Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the
     * atom gets added to a Monomer of type UNKNOWN in a Strand of type UNKNOWN.
     *
     * @param oAtom  The atom to add
     *
     */
    @Override
    public void addAtom(IAtom oAtom) {
        addAtom(oAtom, getMonomer(""));
    }

    /**
     *
     * Adds the atom oAtom to a specific Monomer.
     *
     * @param oAtom  The atom to add
     * @param oMonomer  The monomer the atom belongs to
     *
     */
    @Override
    public void addAtom(IAtom oAtom, IMonomer oMonomer) {

        int atomCount = super.getAtomCount();

        // Add atom to AtomContainer
        super.addAtom(oAtom);

        if (atomCount != super.getAtomCount()) { // ok, super did not yet contain the atom

            if (oMonomer == null) {
                oMonomer = getMonomer("");
            }

            oMonomer.addAtom(oAtom);
            if (!monomers.containsKey(oMonomer.getMonomerName())) {
                monomers.put(oMonomer.getMonomerName(), oMonomer);
            }
        }
    }

    /**
     *
     * Returns the number of monomers present in the Strand.
     *
     * @return number of monomers
     *
     */
    @Override
    public int getMonomerCount() {
        return monomers.size() - 1;
    }

    /**
     *
     * Retrieves a Monomer object by specifying its name.
     *
     * @param cName  The name of the monomer to look for
     * @return The Monomer object which was asked for
     *
     */
    @Override
    public IMonomer getMonomer(String cName) {
        return (Monomer) monomers.get(cName);
    }

    /**
     * Returns a collection of the names of all <code>Monomer</code>s in this
     * polymer.
     *
     * @return a <code>Collection</code> of all the monomer names.
     */
    @Override
    public Collection<String> getMonomerNames() {
        return monomers.keySet();
    }

    /**
     *
     * Adds a <code>Monomer</code> to this <code>Strand</code>. All atoms and
     * bonds in the Monomer are added. NB: The <code>Monomer</code> will *not*
     * "automatically" be connected to the <code>Strand</code>. That has to be
     * done "manually" (as the "connection point" is not known).
     * @param monomer
     */
    /*
     * public void addMonomer(Monomer monomer) { if (!
     * monomers.contains(monomer.getMonomerName())) {
     * monomers.put(monomer.getMonomerName(), monomer); } }
     */

    /**
     * Removes a particular monomer, specified by its name.
     *
     * @param name The name of the monomer to remove
     */
    @Override
    public void removeMonomer(String name) {
        if (monomers.containsKey(name)) {
            Monomer monomer = (Monomer) monomers.get(name);
            this.remove(monomer);
            monomers.remove(name);
        }
    }

    /**
     * Returns a hashtable containing the monomers in the strand.
     *
     * @return hashtable containing the monomers in the strand.
     */
    @Override
    public Map<String, IMonomer> getMonomers() {
        return monomers;
    }

    @Override
    public String toString() {
        StringBuffer stringContent = new StringBuffer(32);
        stringContent.append("Strand(");
        stringContent.append(this.hashCode());
        if (getStrandName() != null) {
            stringContent.append(", N:").append(getStrandName());
        }
        if (getStrandType() != null) {
            stringContent.append(", T:").append(getStrandType()).append(", ");
        }
        stringContent.append(super.toString());
        stringContent.append(')');
        return stringContent.toString();
    }

    @Override
    public IStrand clone() throws CloneNotSupportedException {
        Strand clone = (Strand) super.clone();
        clone.monomers.clear();
        for (Iterator<String> iter = clone.getMonomerNames().iterator(); iter.hasNext();) {
            Monomer monomerClone = (Monomer) (clone.getMonomer(iter.next().toString()).clone());
            Iterator<IAtom> atoms = monomerClone.atoms().iterator();
            while (atoms.hasNext()) {
                clone.addAtom(atoms.next(), monomerClone);
            }
        }
        return clone;
    }
}
