/* Copyright (C) 2006-2007  Egon Willighagen <egonw@users.sf.net>
 *
 * 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.interfaces;

import java.util.Collection;
import java.util.Map;

/**
 * A Strand is an AtomContainer which stores additional strand specific
 * informations for a group of Atoms.
 *
 * @cdk.module  interfaces
 * @cdk.githash
 * @cdk.created 2004-12-20
 * @author Martin Eklund &lt;martin.eklund@farmbio.uu.se&gt;
 */
public interface IStrand extends IAtomContainer {

    /**
     * Retrieve the strand name.
     *
     * @return The name of the Strand object
     * @see    #setStrandName(String)
     */
    public String getStrandName();

    /**
     * Retrieve the strand type.
     *
     * @return The type of the Strand object
     * @see    #setStrandType(String)
     */
    public String getStrandType();

    /**
     * Set the name of the Strand object.
     *
     * @param cStrandName  The new name for this strand
     * @see                #getStrandName()
     */
    public void setStrandName(String cStrandName);

    /**
     * Set the type of the Strand object.
     *
     * @param cStrandType  The new type for this strand
     * @see                #getStrandType()
     */
    public void setStrandType(String 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);

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

    /**
     * Return the number of monomers present in the Strand.
     *
     * @return number of monomers
     */
    public int getMonomerCount();

    /**
     * Retrieve 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
     */
    public IMonomer getMonomer(String 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.
     */
    public Collection<String> getMonomerNames();

    /**
     * Removes a particular monomer, specified by its name.
     *
     * @param name The name of the monomer to remove
     */
    public void removeMonomer(String name);

    /**
     * Returns the monomers in this strand.
     *
     * @return Map containing the monomers in the strand.
     */
    public Map<String, IMonomer> getMonomers();

    /**
     *{@inheritDoc}
     */
    @Override
    public IStrand clone() throws CloneNotSupportedException;
}
